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|
<html><head><title></title></head>
<body>
<a name="932498">
<h1>1.0 </a>Introduction</h1>
</a>
<a name="936795">
</a>PDBLib is a small </a>library of </a>file management routines useful for storing and retrieving binary data in a portable format. It is intended to supply a flexible means of managing </a>binary databases without the user having to be concerned with the machines on which they are written or read.<p>
</a>
<a name="932499">
The specific goals for this library are:<p>
</a>
<ul><a name="932502">
<li>The </a>data files are portable. Using only simple binary file transfers, these files may be passed to any machine supporting an implementation of this library and the data in them immediately read.
</a>
<a name="932507">
<li>The </a>library routines are portable. The library is written in </a>C which is the most standardized language which also enjoys a broad range of implementations. In fact, a C compiler is probably the easiest piece of software to find for any given machine.
</a>
<a name="932511">
<li>The library will support </a>call-by-reference or </a>call-by-value interfaces. In this way the library can be used from </a>FORTRAN (a call-by-reference language) or C (a call-by-value language) programs.
</a>
<a name="932516">
<li> ‘Arbitrary’ </a>data structures may be defined to the PDB system so that there is maximum flexibility and ease of use for application programming. C </a>structs or FORTRAN </a>common blocks may be written or read as a whole. </a>Record structured variables are thus supported.
</a>
<a name="932522">
<li>Data files may be generated for a particular machine type. By default when files are created they are written with the format of the machine that does so. However, they can be written in the format of a designated machine. Thus a more powerful machine can prepare files for a less powerful one.
</a>
<a name="932525">
<li>The library will be small so that machines with as little memory as about 512 Kbytes will be able to profitably use the PDB system.
</a>
<a name="932536">
The binary data format of the files is not machine independent, but it is </a>portable. For the sake of efficiency, the data in any file is expressed in terms of some data format, e.g.</a> IEEE format with 32 bit integers and floats. When PDB files are passed around on machines with the same data format, the data reads and writes involve no </a>conversions. Only when one of these files is read on a machine with a different data format are conversions performed on the data it contains.<p>
</a>
<a name="932549">
This document is divided into several sections. The next section gives an overview of the use of </a>PDBLib and describes some programming practices which are necessary to the successful use of the library. It is followed by a section summarizing the C interface routines in PDBLib and a section giving a more formal and complete description of the C interface with information about normal and error return values, functionality, and rationale. Next are similar sections for the </a>FORTRAN interface routines. Subsequent sections discuss PDBLib design philosophy, data structures, examples, and related documentation.<p>
</a>
</ul><a name="932558">
<h1>2.0 </a>Overview of PDBLib</h1>
</a>
<a name="932569">
The functional PDBLib interface was designed as a minimal extension of the standard C library binary I/O interface. The relevant </a>C library functions are </a>fopen, </a>fclose, </a>fwrite, and </a>fread. The extensions are driven mainly by some missing features in C. Because C doesn’t handle data types as types, PDBLib must be told the type of a variable when it is written to a file. Because C variables don’t know about their dimensions, PDBLib must be given the dimensions when a variable is written out. On the other hand, because PDBLib knows both type and </a>dimension information about file variables, PDBLib requires less information from the programmer when reads are done.<p>
</a>
<a name="932575">
Since C doesn’t have the needed type handling facilities, data structures must be described to PDBLib. Therefore, in addition to the basic </a>I/O functions mentioned above, there is a function in PDBLib to be used when a C data structure or a FORTRAN common block must be described in a file.<p>
</a>
<a name="932585">
Next, to give the user the most flexibility and efficiency regarding </a>data conversions, PDBLib has a function which lets the user specify the binary data format of the file. In this way, a file can be targeted for a particular machine type. A common use for this might be when a powerful machine produces some data which is going to be reprocessed on a less powerful machine. The more powerful machine which writes the file might target the file for the less powerful one so that the conversions are done by the faster machine and not the slower one.<p>
</a>
<a name="932591">
Finally, in some applications with structures, some members of a structure may be pointers, and the actual type to which a pointer points may be changed by a cast depending on some other member’s value. PDBLib supports the notion of a ‘</a>cast’ in that it can be told to ignore the type of a structure member and get the actual type from another member when it writes out the structure.<p>
</a>
<a name="932599">
Because all of the information about files and their contents is contained in PDBLib structures and </a>hash tables, the </a>C API (Application Program Interface) has no inquiry functions. Users can extract information directly from the </a>PDBfile structure and they can use the hash table lookup function, </a>SC_def_lookup, to get access to the </a>syment and </a>defstr structures which describe variables and types, respectively.<p>
</a>
<a name="932605">
The </a>FORTRAN API to PDBLib has many of the same functions as the C API plus several more inquiry functions. These functions are necessary because FORTRAN cannot easily work with structures.<p>
</a>
<a name="932619">
There are also routines to manage </a>data </a>attributes. An </a>attribute table will be created for a PDB file the first time </a>PD_def_attribute is called. The attribute table is kept in the </a>PDBfile structure. Variables can be added to PDB files solely for their attribute values. Attributes can be given to entire variables or any part of them. This works because the attribute table is a separate hash table, like the symbol table, which associates names with attribute values. It also is used to manage the attributes themselves. It is not exactly clear why one should use these attributes. Most of the utility of attributes is already inherent in the structures or records which can by built with PDBLib’s mechanism for defining derived types. Since the structure handling mechanisms are much more efficient, the reason for using attributes instead of structures should be very clear in the mind of the application programmer.<p>
</a>
<a name="934624">
<h2>2.1 </a></a>Compiling and Loading</h2>
</a>
<a name="934626">
To compile your C programs you must use<p>
</a>
<A NAME="934702"><PRE> #include <pdb.h>
</PRE><a name="934721">
in the source files which deal with the interpreter.<p>
</a>
<a name="934723">
To link your application you must use the following libraries in the order specified.<p>
</a>
<dl>
<a name="934729">
<dt>-lpdb -lpml -lscore [-lm ...]
</a>
<a name="935243">
Although this is expressed as if for a UNIX linker, the order would be the same for any system with a single pass linker. The items in [] are optional or system dependent.<p>
</a>
<a name="935318">
Each system has different naming conventions for its libraries and the reader is assumed to understand the appropriate naming conventions as well as knowing how to tell the linker to find the installed PACT libraries on each system that they use.<p>
</a>
</dl>
<a name="934623">
<h2>2.2 </a>Memory Management Considerations</h2>
</a>
<a name="932632">
PDBLib is capable of correctly handling data that is indirectly referenced through arbitrary levels of </a>pointers. In order to do this it is necessary to put an extra layer of memory management over the standard C library routines. The basic requirement is that given a pointer, one would like to know how many bytes of data it points to. The functions, </a>SC_alloc, </a>SC_realloc, </a>SC_strsave, </a>SC_free, and </a>SC_arrlen, built on top of the standard C library functions, </a>malloc and </a>free, provide this capability. For C programmers, </a>macros are provided which offer a nice and intuitive way of using these functions (they also provide an </a>abstraction barrier against the details of any memory management scheme). These functions and macros are documented in the </a>SCORE User’s Manual.<p>
</a>
<a name="932638">
A brief discussion of the procedure for </a>writing and </a>reading </a>indirectly referenced data follows. Although the discussion will use integers as an example, the ideas apply to all data types, primitive or derived.<p>
</a>
<a name="932640">
Consider the following:<p>
</a>
<a name="932435">
<dd> int a[10], *b;<P>
</a>
<a name="932646">
<dd> b = MAKE_N(int, 10);<P>
</a>
<a name="932661">
Both a and b are pointers to 10 integers (</a>macro </a>MAKE_N is used to allocate the necessary space). The difference as far as an application is concerned is that the space that a points to was set aside by the compiler at compile time (for all practical purposes) while the space the b points to is created at run time. There is no possibility, given the definition of the C language, of asking the pointer a how many bytes it points to. On the other hand, since b is dynamically allocated, an extra layer of memory management could be provided so that a function, </a>SC_arrlen, could be defined to return the number of bytes that a dynamically allocated space has. In particular,<p>
</a>
<a name="932662">
<dd> SC_arrlen(a) => -1 (indicating an error)<P>
</a>
<a name="932664">
<dd> SC_arrlen(b) => 10<P>
</a>
<a name="932666">
<dd> SC_arrlen(b+5) => -1 (indicating an error)<P>
</a>
<a name="932673">
These functions and macros can be found in </a>SCORE. The general utility of something like </a>SC_arrlen made it desirable to put it in the lowest possible level library. This could be used for example, to implement some </a>dynamic </a>array </a>bound checking.<p>
</a>
<a name="932679">
PDBLib uses this idea to be able to trace down arbitrary layers of </a>indirection and obtain at each level the exact number of bytes to write out to a file. Of course, it also writes this information out so that the correct amount of space can be allocated by read operations as well as re-creating the correct </a>connectivity of </a>data structures.<p>
</a>
<a name="932691">
Great care must be taken that pointers to fixed arrays not be imbedded in a chain of indirects unless their dimension specifications are included either in the I/O request or the definition of a structure. This point cannot be over-emphasized! The extra memory management layer may fail to detect a </a>statically allocated array and return an erroneous byte count. This in turn will cause very obscure incorrect behavior (in the worst of circumstances) or a direct crash (the best outcome possible).<p>
</a>
<a name="932645">
Also, note that </a>subsets of </a>dynamically allocated arrays cannot know how many bytes they contain and hence care should be taken in their use. <p>
</a>
<a name="932697">
The example on the following page shows the different ways that </a>statically allocated arrays, </a>dynamically allocated arrays, </a>statically allocated </a>arrays of pointers, and </a>dynamically allocated arrays of pointers are handled by PDBLib. Note: The function </a>SC_strsave invokes the </a>MAKE_N </a>macro.<p>
</a>
<A NAME="932694"><PRE> /* define variables in pairs - one to write and one to read into */
</PRE><A NAME="932703"><PRE> PDBfile *strm;
</PRE><A NAME="932704"><PRE> char *a, *b;
</PRE><A NAME="932705"><PRE> char c[10], d[10];
</PRE><A NAME="932706"><PRE> char *e[3], *f[3];
</PRE><A NAME="932707"><PRE> char **s, **t;
</PRE><A NAME="932708"><PRE>
</PRE><A NAME="932709"><PRE> s = </a>MAKE_N(char *, 2);
</PRE><A NAME="932710"><PRE>
</PRE><A NAME="932711"><PRE> /* fill </a>statically and </a>dynamically allocated arrays */
</PRE><A NAME="932713"><PRE> strcpy(c, “bar”);
</PRE><A NAME="932546"><PRE> a = </a>SC_strsave(“foo”);
</PRE><A NAME="932714"><PRE>
</PRE><A NAME="932717"><PRE> /* fill </a>statically and </a>dynamically allocated arrays of pointers */
</PRE><A NAME="932720"><PRE> e[0] = SC_strsave(“Foo”);
</PRE><A NAME="932721"><PRE> e[1] = NULL;
</PRE><A NAME="932722"><PRE> e[2] = SC_strsave(“Bar”);
</PRE><A NAME="932712"><PRE> s[0] = SC_strsave(“Hello”);
</PRE><A NAME="932718"><PRE> s[1] = SC_strsave(“world”);
</PRE><A NAME="932723"><PRE>
</PRE><A NAME="932724"><PRE> /* write these variables out
</PRE><A NAME="932725"><PRE> * note the dimension specifications and the type
</PRE><A NAME="932726"><PRE> */
</PRE><A NAME="932727"><PRE> </a>PD_write(strm, “c(10)”, “char”, c);
</PRE><A NAME="932728"><PRE> PD_write(strm, “a”, “char *”, &a);
</PRE><A NAME="932729"><PRE> PD_write(strm, “e(3)”, “char *”, e);
</PRE><A NAME="932730"><PRE> PD_write(strm, “s”, “char **”, &s);
</PRE><A NAME="932731"><PRE>
</PRE><A NAME="932732"><PRE> /* read the file variables into fresh memory spaces
</PRE><A NAME="932733"><PRE> * note that the pointers to the pointers are passed in since the
</PRE><A NAME="932734"><PRE> * space is to be allocated and the value of the pointer here must
</PRE><A NAME="932735"><PRE> * be set to point to the new space
</PRE><A NAME="932736"><PRE> */
</PRE><A NAME="932737"><PRE> </a>PD_read(strm, “c”, d);
</PRE><A NAME="932738"><PRE> PD_read(strm, “a”, &b);
</PRE><A NAME="932739"><PRE> PD_read(strm, “e”, f);
</PRE><A NAME="932740"><PRE> PD_read(strm, “s”, &t);
</PRE><a name="933055">
<h2>2.3 PDB Syntax</h2>
</a>
<a name="933058">
This section contains discussion of some PDB concepts that are used elsewhere in this manual.<p>
</a>
<a name="934301">
In the following discussion and elsewhere in the manual a BNF style notation is used. In such places the following constructs are used:<p>
</a>
<dl>
<a name="934302">
<dt>| or
</a>
<a name="934311">
<dt>[] items between the brackets are optional
</a>
<a name="934303">
<dt>[]* zero or more instances of the items between the brackets
</a>
<a name="934309">
<dt>[]+ one or more instances of the items between the brackets
</a>
<a name="934310">
<dt>“x” literal x
</a>
<a name="933464">
Since a data entry can be of a structured type, in general, a data entry is a tree. A part of the data tree is specified by a path to that part. A path specification is of the form:<p>
</a>
<a name="933060">
<dt>path := node_spec | path.node_spec
</a>
<a name="933061">
<dt>node_spec := name[“[“ index_expr “]”]* | name[“(“ index_expr “)”]*
</a>
<a name="933926">
<dt>name := entry-name | member-name
</a>
<a name="933062">
The last node specified is referred to as the terminal node.<p>
</a>
<a name="933056">
<p>
</a>
</dl>
<a name="932745">
<h2>2.4 </a>PDBLib </a>Rules</h2>
</a>
<a name="932749">
There are a few crucial rules to be followed with PDBLib. If they are not obeyed, PDBLib may crash or the results desired will not occur.<p>
</a>
<A NAME="932755">The following </a>reserved characters are not allowed in variable names or </a>defstr </a>member
names: ‘</a>.’, ‘</a>(‘, ‘</a>)’, ‘</a>[‘, and ‘</a>]’. They are reserved by the grammar of the </a>data description
language which follows some C and some FORTRAN conventions.
<BR><A NAME="933265">In each read and write operation, the type of the argument corresponding to the variable
to be written or read must be a pointer to an object of the type specified for the entry.
For example,
<BR><A NAME="932759"><PRE> int *a, *b;
</PRE><A NAME="932762"><PRE> .
</PRE><A NAME="932763"><PRE> .
</PRE><A NAME="932765"><PRE> </a>PD_write(strm, “a”, “integer *”, &a);
</PRE><A NAME="932767"><PRE> </a>PD_read(strm, “a”, &b);
</PRE><A NAME="932768"><PRE> .
</PRE><A NAME="932770"><PRE> .
</PRE><A NAME="932776">When using </a>pointers and </a>dynamically </a>allocated memory with PDBLib, use </a>SC_alloc,
</a>SC_realloc, </a>SC_strsave, </a>MAKE, </a>MAKE_N, </a>REMAKE, or </a>REMAKE_N to allocate
memory. These functions and macros are documented in the </a>SCORE User’s Manual.
<BR><A NAME="934312">When </a>reading or </a>writing part of a variable, especially a structured variable, the terminal
node must be of primitive type or a structure containing no indirections and whose
descendant members contain no indirections. Furthermore, the path to the desired part
must contain one array reference for each level of </a>indirection traversed. For example,
<BR><A NAME="932784"><PRE> char **s, c;
</PRE><A NAME="932785"><PRE>
</PRE><A NAME="932786"><PRE> /* fill s so that s[0] = “Hello” and s[1] = “World” */
</PRE><A NAME="932787"><PRE> .
</PRE><A NAME="932788"><PRE> .
</PRE><A NAME="932790"><PRE> </a>PD_write(strm, “s”, “char **”, &s);
</PRE><A NAME="932791"><PRE>
</PRE><A NAME="932792"><PRE> /* read the ‘o’ in “Hello” */
</PRE><A NAME="932793"><PRE> </a>PD_read(strm, “s[0][4]”, &c);
</PRE><A NAME="932794"><PRE>
</PRE><A NAME="932795"><PRE> /* read the ‘o’ in “World” */
</PRE><A NAME="932796"><PRE> PD_read(strm, “s[1][1]”, &c);
</PRE><A NAME="932780"><PRE> .
</PRE><A NAME="932797"><PRE> .
</PRE><a name="932799">
<h1>3.0 </a>Summary of the </a>C </a>API</h1>
</a>
<a name="932821">
There is a hierarchy of routines in PDBLib from high to low level. The high level routines form the API while the lower level routines are modularized to perform the actual work. It should be noted that the lower level routines are sufficiently well modularized so as to make it possible to build entirely different API’s for PDBLib. <p>
</a>
<a name="932588">
The </a>high level PDBLib routines have a strict </a>naming convention. All high level routines begin with ‘</a>PD_’. Some routines have several related forms. These are referred to as families of functions. For example the PD_write family.<p>
</a>
<a name="932477">
Most of these routines put an </a>error message into a global variable called </a>PD_err. The error messages include the name of the routine in which they are made thus eliminating the need for error codes which must be cross referenced with some other document. In this way application programs can check for error conditions themselves and decide in what manner to use the PDBLib error messages instead of having error messages printed by the system routines. Error messages are not stacked and must be processed by the application before any other PDBLib calls are made in order to avoid potential overwrites. See the descriptions of individual routines for more information about error handling and messages. <p>
</a>
<a name="933585">
Programs written in C must include a </a>header which makes certain declarations and definitions needed to use the library. Much in the same spirit as one includes </a>stdio.h to use </a>printf and others, include </a>pdb.h as follows:<p>
</a>
<A NAME="932478"><PRE> </a>#</a>include “pdb.h”
</PRE><a name="932702">
The file </a>pdb.h </a>#</a>include’s some other files which must either be in your directory space or pointed to in some manner which your compiler can recognize. The auxiliary #include files are </a>schash.c, </a>scstd.h, and </a>score.h. These files are a part of the </a>SCORE package which you must have to use PDBLib.<p>
</a>
<a name="932446">
<h2>3.1 Some Guidance in Using the C API to PDBLib</h2>
</a>
<a name="932447">
PDBLib offers a great deal of flexibility to its users. In some cases the flexibility results in a bewildering assortment of function calls from which the application developer must choose. This section is intended to offer some guidance and enable developers to home in on the functions they need to use.<p>
</a>
<a name="932448">
<h3>3.1.1 Opening, Creating and Closing PDB Files</h3>
</a>
<a name="932450">
These are the most fundamental operations involving PDBLib. The function </a>PD_open is used to either open an existing file or create a new one. </a>PD_close is used to close a PDB file so that it can be recognized by PDBLib for future operations.<p>
</a>
<a name="932451">
PDBLib allows applications to specify the binary format in which a newly created file will be written. </a>PD_target does this work. It is not necessary to invoke </a>PD_target before creating a new PDB file. In this case the binary format is that appropriate for the host system.<p>
</a>
<a name="932452">
During the run of an application code, PDBLib can complete the information in an open PDB file so that in the event of a code crash, the file will be a valid PDB file. This functionality is provided by </a>PD_flush.<p>
</a>
<a name="932453">
<h3>3.1.2 Writing Data to PDB Files</h3>
</a>
<a name="932456">
The following paragraphs describe a sequence of increasingly more elaborate output operations for PDB files. They are all compatible with one another so users can select the ones which match their needs best. The most straightforward operations are first.<p>
</a>
<a name="932457">
There are two forms for the most basic data writing operations. These have to do with how the application wants to handle the dimension specifications. The two functions are </a>PD_write and </a>PD_write_alt.<p>
</a>
<a name="932461">
PDBLib supports the notion of writing data of one type out into a file as another type. More precisely, an integer type of data can be written to a file in the format of any other integer type, and similarly for floating point types. The application must take all responsibility for ensuring the appropriateness of this type of conversion (e.g. underflows and overflows). The functions which support this are </a>PD_write_as and </a>PD_write_as_alt.<p>
</a>
<a name="932462">
PDBLib allows applications to append data to existing entries. This is handy in situations where the total amount of data is not known in advance, but a logical ordering of the data is apparent which matches the order in which data will be written. The functions which do this are the </a>PD_append family of functions.<p>
</a>
<a name="932463">
Finally, PDBLib allows applications to reserve space on disk and then let subsequent writes fill in that space with values. This is handy in instances where an application knows a logical structure for a data set but needs to write it out in smaller pieces and not necessarily in the order implied by its logical structure. The functions which let applications reserve space are </a>PD_defent and </a>PD_defent_alt. Reserved spaces may be written to with any of the </a>PD_write family of commands.<p>
</a>
<a name="932464">
<h3>3.1.3 Reading Data from PDB Files</h3>
</a>
<a name="932465">
Since data in a file has a definite size and shape, the reading operations in PDBLib are somewhat simpler than the writing operation. The </a>PD_read family of operations which is the counterpart of the </a>PD_write family does all of the work in reading data from files.<p>
</a>
<a name="932466">
<h3>3.1.4 Defining New Data Types</h3>
</a>
<a name="932490">
To aid application developers in using structured data PDBLib lets applications define new data types in a PDBfile. New data types may either be derived from other existing data types or they may be primitive (integer types, floating point types, or byte sequences). To define derived types applications should use </a>PD_defstr or </a>PD_defstr_alt. To define primitive types use </a>PD_defix, </a>PD_defloat, or </a>PD_defncv.<p>
</a>
<a name="933004">
Since PDBLib supports pointered data types, it is often the case that a pointer in a derived type may point to data of any kind. In C, casts are used to control this behavior. PDBLib permits a member of a struct which is of type “char *” specify the actual type of another pointered member. The function </a>PD_cast is used to set up this behavior.<p>
</a>
<a name="934414">
<h3>3.1.5 Defining Attributes</h3>
</a>
<a name="934652">
PDBLib supports a general mechanism for managing a class of data which is variously referred to as attributes or meta data. In a great many cases, the careful design of data structures obviates the need for this kind of data. Nevertheless, PDBLib supplies four functions to manage attributive data: </a>PD_def_attribute, </a>PD_rem_attribute, </a>PD_get_attribute, </a>PD_set_attribute.<p>
</a>
<a name="932444">
<h3>3.1.6 Using Pointers</h3>
</a>
<a name="936787">
The ability to use pointers with PDBLib is very powerful. It is unfortunate perhaps that it can also be a little bit tricky. Application developers should be aware of a key issue when using pointers with PDBLib. In general, when you want to write a data tree, you want to faithfully reproduce the connectivity of the tree. That means that if many pointers refer to the same chunk of memory then the file will exhibit that same pattern. To do this, PDBLib remembers the pointers that it has written and if handed a pointer that it has already written it does NOT write that memory into the file again. It instead makes note of the connection to an already existing region of disk. These same considerations apply to reading with the requisite changes in sense.<p>
</a>
<a name="936831">
The difference between files and memory is that data trees may be created, destroyed, and pointers recycled. For instance, an application may wish to allocate an array, write it as an indirect, change it contents in memory, and write it out again under another name. This is a very common pattern of usage. If PDBLib remembers the pointers, only the first write will put any data on disk. Now PDBLib has no way of knowing what the application wants. The control that applications have is to remove the list of pointers that PDBLib knows about. This accomplished with the PD_reset_ptr_list command.<p>
</a>
<a name="936838">
<h2>3.2 Terms </h2>
</a>
<a name="932687">
A few </a>definitions must be given first to keep the following summary concise. Some of these will be elaborated upon in the next section.<p>
</a>
<A NAME="932824">
<BR><A NAME="932831"></a>PDBfile: for the purposes of a program this is a collection of all the relevant information about one of these data files (in the actual coding it is a C struct). See the section on
Data Structures for more information.
<BR><A NAME="932470">
<BR><A NAME="932835"></a>ASCII: a string
<BR><A NAME="932471">
<BR><A NAME="932839"></a>TRUE: a value of 1 (defined by PDBLib)
<BR><A NAME="932472">
<BR><A NAME="932843"></a>FALSE: a value of 0 (defined by PDBLib)
<BR><A NAME="932473">
<BR><A NAME="933465"></a>VOID: any C data type
<BR><A NAME="933616">
<BR><A NAME="932474"></a>LAST: a pointer to 0 (declared and defined by PDBLib)
<BR><A NAME="932476">
<BR><A NAME="932853"></a>ENTRY: for the purposes of a program this is a collection of all the relevant information about a variable written to a PDB file (in the actual coding it is a C struct). See the
discussion of </a>syment in the section on Data Structures.
<BR><A NAME="932475">
<BR><A NAME="932825"> </a>DEFSTR: for the purposes of a program this is a collection of all the relevant information about a data type in a PDB file (in the actual coding it is a C struct). See the discussion of defstr in the section on Data Structures.
<BR><a name="932892">
<h2>3.3 </a>Function Summary</h2>
</a>
<a name="932904">
These routines form the </a>interface between C application programs and the PDBLib system.<p>
</a>
<A NAME="934994"><P><B></a>PD_append(file, name, var)
</B><BR><A NAME="934995"></a>Append the data pointed to by <em>var</em> to an existing entry under <em>name</em> in PDB file <em>file</em>.
<BR><dl>
<a name="935016">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="935017">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file and any dimension information,<P>
</a>
<a name="935020">
<dd><em>var</em>, a pointer to the location where the data is stored in memory.<P>
</a>
<a name="935021">
<dt>Output: TRUE if successful, and NULL otherwise.
</a>
<A NAME="935018"><P><B></a>PD_append_alt(file, name, var, nd, ind)
</B><BR><A NAME="935022"></a>Append the data pointed to by <em>var</em> to an existing entry <em>name</em> in PDB file <em>file</em>. In this
alternate to </a>PD_append dimension information is provided in arguments nd and ind.
<BR><a name="935024">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="935025">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="935027">
<dd><em>var</em>, a pointer to the location where the data is stored in memory.<P>
</a>
<a name="935028">
<dd><em>nd</em>, an integer containing the number of dimensions,<P>
</a>
<a name="935029">
<dd><em>ind</em>, an array of long integers containing (min, max, stride) triples for each dimension.<P>
</a>
<a name="935031">
<dt>Output: TRUE if successful, and NULL otherwise.
</a>
<A NAME="935032"><P><B></a>PD_append_as(file, name, intype, var)
</B><BR><A NAME="935033"></a>Append the data pointed to by <em>var</em> with type <em>intype</em> to an existing entry <em>name</em> in PDB
file <em>file</em>.
<BR><a name="935034">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="935035">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file and any dimension information,<P>
</a>
<a name="935036">
<dd><em>intype</em>, an ASCII string containing the type of the data pointed to by var,<P>
</a>
<a name="935039">
<dd><em>var</em>, a pointer to the location where the data is stored in memory.<P>
</a>
<a name="935040">
<dt>Output: TRUE if successful, and NULL otherwise.
</a>
<A NAME="935041"><P><B></a>PD_append_as_alt(file, name, intype, var, nd, ind)
</B><BR><A NAME="935042"></a>Append the data pointed to by <em>var</em> with type <em>intype</em> to the entry <em>name</em> in PDB file <em>file</em>. In
this alternate to </a>PD_append_as dimension information is provided in arguments nd
and ind.
<BR><a name="935044">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="935046">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="935047">
<dd><em>intype</em>, an ASCII string containing the type of the data pointed to by var,<P>
</a>
<a name="935049">
<dd><em>var</em>, a pointer to the location where the data is stored in memory.<P>
</a>
<a name="935055">
<dd><em>nd</em>, an integer containing the number of dimensions,<P>
</a>
<a name="935056">
<dd><em>ind</em>, an array of long integers containing (min, max, stride) triples for each dimension.<P>
</a>
<a name="935057">
<dt>Output: TRUE if successful, and NULL otherwise.
</a>
<A NAME="934665"><P><B></a>PD_cast(file, type, memb, contr)
</B><BR><A NAME="934673">This function tells PDBLib to </a>substitute the type specified by the ASCII string in the
member <em>contr</em> for the type of member, <em>memb</em>, in the structure, <em>type</em>.
<BR><a name="934678">
<dt>Input: <em>file,</em> a pointer to a PDBfile,
</a>
<a name="934680">
<dd><em> type</em>, an ASCII string containing the name of the data type in the PDB file,<P>
</a>
<a name="934682">
<dd><em> memb</em>, an ASCII string containing the name of the member of t<em>ype</em> whose type is to be replaced,<P>
</a>
<a name="934684">
<dd> contr, an ASCII string containing the name of the member of <em>type</em> whose ASCII string value is to replace the type of the member, <em>memb</em>.<P>
</a>
<a name="934686">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="935288"><P><B></a>PD_cd(file, dirname)
</B><BR><A NAME="935289"></a>Change the </a>current </a>directory in file file to dirname.
<BR><a name="935290">
<dt>Input: <em>file,</em> a pointer to a PDBfile,
</a>
<a name="935291">
<dd><em> dirname</em>, an ASCII string containing the path name of the directory to change to.<P>
</a>
<a name="935294">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="932927"><P><B></a>PD_close(file)
</B><BR><A NAME="932930"></a>Close the <em>file</em> <em>file</em>. This function is used to complete and close a PDB file.
<BR><a name="932931">
<dt>Input: <em>file</em>, a pointer to a PDBfile.
</a>
<a name="932932">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="932482"><P><B></a>PD_def_attribute(file, attr, type)
</B><BR><A NAME="932881"></a>Define an attribute named <em>attr</em> of type <em>type</em> in PDB file <em>file</em>.
<BR><a name="932884">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="932891">
<dd><em>attr</em>, an ASCII string containing the name of the attribute to be added to the PDB file </a>attribute table,<P>
</a>
<a name="933097">
<dd><em>type</em>, an ASCII string containing the type of the attribute.<P>
</a>
<a name="933102">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="932665"><P><B></a>PD_defent(file, name, outtype)
</B><BR><A NAME="932667"></a>Define an entry in the symbol table of the PDB file <em>file</em>. This function </a>reserves space on
disk but writes no data. The data can be written with later PDBLib calls.
<BR><a name="932668">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="932669">
<dd> name, an ASCII string containing the name of the variable and any dimensional information,<P>
</a>
<a name="932689">
<dd> outtype, an ASCII string specifying the type of data in the file.<P>
</a>
<a name="932690">
<dt>Output: a pointer to the syment for the entry, if successful, and NULL otherwise.
</a>
<A NAME="932592"><P><B></a>PD_defent_alt(file, name, outtype, nd, ind)
</B><BR><A NAME="932655"></a>Define an entry in the symbol table of the PDB file <em>file</em>. This function </a>reserves space on
disk but writes no data. The data can be written with later calls.
<BR><a name="932656">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="932657">
<dd> name, an ASCII string containing the name of the variable (no dimensional information can be supplied with the name),<P>
</a>
<a name="932658">
<dd> outtype, an ASCII string specifying the type of data in the file,<P>
</a>
<a name="932659">
<dd> nd, the number of dimensions of the entry,<P>
</a>
<a name="932660">
<dd> find, an array of long integers containing (min, max) index range pairs for each dimension.<P>
</a>
<a name="932663">
<dt>Output: a pointer to the syment for the entry, if successful, and NULL otherwise.
</a>
<A NAME="933112"><P><B></a>PD_defix(file, name, bytespitem, align, flg)
</B><BR><A NAME="933113"></a>Define a </a>primitive integral type (</a>fixed point type) in the PDB file <em>file</em>.
<BR><a name="933114">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="933124">
<dd> name, an ASCII string containing the name of the new data type,<P>
</a>
<a name="933125">
<dd> bytespitem, the number of bytes required for 1 item of the new type,<P>
</a>
<a name="933128">
<dd> align, the byte alignment for the type,<P>
</a>
<a name="933129">
<dd> flg, a flag indicating whether the byte ordering of the type is normal or reverse ordered (</a>NORMAL_ORDER or </a>REVERSE_ORDER).<P>
</a>
<a name="933117">
<dt>Output: a pointer to the defstr for the type, if successful, and NULL otherwise.
</a>
<A NAME="933119"><P><B></a>PD_defloat(file, name, bytespitem, align, ordr, expb, mantb, sbs, sbe, sbm, hmb,
bias)
</B><BR><A NAME="933120"></a>Define a new </a>floating point type to the PDB file <em>file</em>.
<BR><a name="933121">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="933132">
<dd> <em>name</em>, an ASCII string containing the name of the data type in the PDB file,<P>
</a>
<a name="933134">
<dd><em> bytespitem, the number of bytes required for an item of the new type,</em><P>
</a>
<a name="933136">
<dd> align, the byte alignment for this type,<P>
</a>
<a name="933137">
<dd> ordr, an array of bytespitem integers specifying the byte order,<P>
</a>
<a name="933138">
<dd> expb, the number of exponent bits,<P>
</a>
<a name="933140">
<dd> mantb, the number of mantissa bits,<P>
</a>
<a name="933141">
<dd> sbs, the position of the sign bit,<P>
</a>
<a name="933142">
<dd> sbe, the starting bit of the exponent,<P>
</a>
<a name="933143">
<dd> sbm, the starting bit of the mantissa,<P>
</a>
<a name="933144">
<dd> hmb, the value of the high order mantissa bit,<P>
</a>
<a name="933145">
<dd> bias, the bias of the exponent.<P>
</a>
<a name="933123">
<dt>Output: a pointer to the defstr for the type, if successful, and NULL otherwise.
</a>
<A NAME="933552"><P><B></a>PD_defncv(file, name, bytespitem, align)
</B><BR><A NAME="933553"></a>Define a </a>primitive type that will not undergo format conversion from platform to platform in the PDB file <em>file</em>.
<BR><a name="933556">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="933557">
<dd> name, an ASCII string containing the name of the new data type,<P>
</a>
<a name="933558">
<dd> bytespitem, the number of bytes required for 1 item of the new type,<P>
</a>
<a name="933560">
<dd> align, the byte alignment for the type.<P>
</a>
<a name="933561">
<dt>Output: a pointer to the defstr for the type, if successful, and NULL otherwise.
</a>
<A NAME="933332"><P><B></a>PD_defstr(file, name, mem1, ..., memn, LAST)
</B><BR><A NAME="933847"></a>Define a </a>data structure called <em>name</em> with members <em>mem</em>1, ..., <em>mem</em>n. LAST <em>must</em> terminate the list of members. This uses a C-like syntax for the member definition and <em>name</em>
is used in subsequent writes to refer to this type of data structure.
<BR><a name="933908">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="933928">
<dd> <em>name</em>, an ASCII string containing the name of the data structure type in the PDB file,<P>
</a>
<a name="933961">
<dd><em>memi</em>, an ASCII string representing the declaration of a member of a data structure.<P>
</a>
<a name="933974">
<dt>Output: a pointer to the defstr for the data structure, if successful, and NULL otherwise.
</a>
<A NAME="932936"><P><B></a>PD_defstr_alt(file, name, nmemb, memb)
</B><BR><A NAME="932942"></a>Define a </a>data structure called <em>name</em> with members specified by memb.. This uses a C-
like syntax for the member definition and <em>name</em> is used in subsequent writes to refer to
this type of data structure.
<BR><a name="932943">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="932947">
<dd><em>name</em>, an ASCII string containing the name of the data structure type in the PDB file,<P>
</a>
<a name="934021">
<dd><em>nmemb</em>, an integer number of members in the data structure and the length of memb,<P>
</a>
<a name="932949">
<dd><em>memb</em>, an array of ASCII string representing the declarations of the members of a data structure.<P>
</a>
<a name="932951">
<dt>Output: a pointer to the defstr for the data structure, if successful, and NULL otherwise.
</a>
<A NAME="932621"><P><B></a>PD_family(file, flag)
</B><BR><A NAME="934719">If the <em>file,</em> <em>file</em>, has exceeded its size limit, open and return a new member of the </a>file
family. If flag is TRUE close the old file.
<BR><a name="934768">
<dt>Input: <em>file</em>, a pointer to a PDBfile.
</a>
<a name="937456">
<dd>flag, an integer flag.<P>
</a>
<a name="937477">
<dt>Output: a pointer to a PDBfile.
</a>
<A NAME="937434"><P><B></a>PD_flush(file)
</B><BR><A NAME="937436"></a>Flush the <em>file</em> <em>file</em>. This function is used to write the descriptive information of a PDB
file to disk.
<BR><a name="934296">
<dt>Input: <em>file</em>, a pointer to a PDBfile.
</a>
<a name="934297">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="933103"><P><B></a>PD_get_attribute(file, var, attr)
</B><BR><A NAME="933107">Get the value of the <em>attr</em> attribute of variable <em>var</em> in PDB file <em>file</em>. Variables only have
values for attributes which are explicitly given.
<BR><a name="933110">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="933111">
<dd><em>var</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="933115">
<dd><em>attr</em>, an ASCII string containing the name of the attribute in the PDB file attribute table.<P>
</a>
<a name="933116">
<dt>Output: a pointer to the attribute value, if successful, and NULL otherwise.
</a>
<A NAME="937491"><P><B><strong></a>PD_get_max_file_size(file)
</strong></B><BR><a name="937492">
<dt>Get the current maximum size for PDB file <em>file</em>.
</a>
<a name="937493">
<dt>Input: <em>file</em>, a pointer to a <strong>PDBfile</strong>.
</a>
<a name="937494">
<dt>Output: Return the integer value of the current maximum file size.
</a>
<A NAME="932761"><P><B></a>PD_get_mode(file)
</B><BR><A NAME="932769"></a>Get the current mode of PDB file<em> file</em>: 2 (append - ’a’), 3 (open - ’r’), 4 (create - ’w’).
<BR><a name="932798">
<dt>Input: <em>file</em>, a pointer to a PDBfile.
</a>
<a name="933127">
<dt>Output: Return the integer value of the current mode.
</a>
<A NAME="933266"><P><B></a>PD_get_offset(file)
</B><BR><A NAME="934191"></a>Get the current default offset for PDB file<em> file</em>.
<BR><a name="934192">
<dt>Input: <em>file</em>, a pointer to a PDBfile.
</a>
<a name="934193">
<dt>Output: Return the integer value of the default offset.
</a>
<A NAME="935292"><P><B></a>PD_ln(file, var, link)
</B><BR><A NAME="935293"></a>Create a </a>link to a variable in PDB file file.
<BR><a name="935296">
<dt>Input: <em>file,</em> a pointer to a PDBfile,
</a>
<a name="935299">
<dd><em> var</em>, an ASCII string containing the path name of the variable to link to,<P>
</a>
<a name="935297">
<dd><em> link</em>, an ASCII string containing the path name of the link.<P>
</a>
<a name="935298">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="934172"><P><B></a>PD_ls(file, path, type, num)
</B><BR><A NAME="935304"></a>Return a list of names of entries (variables and/or directories) in PDB file file that are of
a type type and that are in the </a>directory and match the variable name pattern specified
by path.
<BR><a name="935305">
<dt>Input: <em>file,</em> a pointer to a PDBfile,
</a>
<a name="935307">
<dd><em> path</em>, an ASCII string containing the path name of the directory to search and/or the variable name pattern to match,<P>
</a>
<a name="935308">
<dd><em> type</em>, an ASCII string containing the type of variables to return,<P>
</a>
<a name="935309">
<dd><em> num</em>, the number of entries returned.<P>
</a>
<a name="935311">
<dt>Output: a pointer to an array of pointers to entry names, if successful, and NULL otherwise.
</a>
<A NAME="935312"><P><B></a>PD_make_image(name, type, data, dx, dy, bpp, xmin, xmax, ymin, ymax, zmin,
zmax)
</B><BR><A NAME="932955">Create and initialize a PD_image data structure.
<BR><a name="932480">
<dt>Input: <em> name</em>, an ASCII string containing the name of the image,
</a>
<a name="934173">
<dd>type, an ASCII string containing the data type of the image elements (e.g. “char”, “float”, “complex”),<P>
</a>
<a name="934176">
<dd>data, pointer to array of image data of type type,<P>
</a>
<a name="934177">
<dd>dx, width of image,<P>
</a>
<a name="934178">
<dd>dy, height of image,<P>
</a>
<a name="934179">
<dd>bpp, bits per pixel of the image,<P>
</a>
<a name="934180">
<dd>xmin, minimum value of coordinate associated with image x direction,<P>
</a>
<a name="934181">
<dd>xmax, maximum value of coordinate associated with image x direction,<P>
</a>
<a name="934182">
<dd>ymin, minimum value of coordinate associated with image y direction,<P>
</a>
<a name="934183">
<dd>ymax, maximum value of coordinate associated with image y direction,<P>
</a>
<a name="932961">
<dd>zmin, minimum value of image data (for palette labelling),<P>
</a>
<a name="932965">
<dd><em>zmax</em>, maximum value of image data (for palette labelling).<P>
</a>
<a name="932967">
<dt>Output: a pointer to a PD_image.
</a>
<A NAME="935313"><P><B></a>PD_mkdir(file, dirname)
</B><BR><A NAME="935315"></a>Create a </a>directory dirname in PDB file file.
<BR><a name="935317">
<dt>Input: <em>file,</em> a pointer to a PDBfile,
</a>
<a name="933186">
<dd><em> dirname</em>, an ASCII string containing the new directory path name.<P>
</a>
<a name="935320">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="935319"><P><B>PD_open(filename, mode)
</B><BR><A NAME="934168"> </a>Open a PDB file on disk named <em>filename</em> in one of three modes: “</a>w” for </a>create, “</a>r” for
</a>read-only, or “a” for </a>append. This function is used to </a>create a new PDB file or to open
an existing PDB file for reading or for adding new entries.
<BR><a name="934169">
<dt>Input: <em> filename</em>, an ASCII string,
</a>
<a name="934170">
<dd><em>mode</em>, an ASCII string, either “w” for create, “r” for read, or “a” for append.<P>
</a>
<a name="934171">
<dt>Output: a pointer to a PDBfile, if successful, and NULL otherwise.
</a>
<A NAME="932972"><P><B></a>PD_put_image(file, image, index)
</B><BR><A NAME="932974"></a>Write image image to file file with index index.
<BR><a name="932975">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="932979">
<dd><em>image</em>, a pointer to the </a>image data structure to be written,<P>
</a>
<a name="932980">
<dd><em>index</em>, an unique integer ordinal index.<P>
</a>
<a name="932982">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="933159"><P><B></a>PD_put_mapping(file, mapping, index)
</B><BR><A NAME="933163"></a>Write mapping mapping to file file with index index.
<BR><a name="933164">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="933168">
<dd><em>mapping</em>, a pointer to the </a>mapping data structure to be written,<P>
</a>
<a name="933170">
<dd><em>index</em>, an unique integer ordinal index.<P>
</a>
<a name="933174">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="933179"><P><B></a>PD_put_set(file, set)
</B><BR><A NAME="933180"></a>Write set set to file file.
<BR><a name="933184">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="933188">
<dd><em>set</em>, a pointer to the </a>set data structure to be written.<P>
</a>
<a name="933190">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="935300"><P><B></a>PD_pwd(file)
</B><BR><A NAME="935301"></a>Return the </a>current </a>directory in PDB file file.
<BR><a name="935302">
<dt>Input: <em>file,</em> a pointer to a PDBfile.
</a>
<a name="935306">
<dt>Output a pointer to the path name of the current directory, if successful, and NULL otherwise.
</a>
<A NAME="934162"><P><B></a>PD_read(file, name, var)
</B><BR><A NAME="934163"></a>Read a variable <em>name</em> from PDB file <em>file</em> and put it in <em>var</em>.
<BR><a name="934164">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="934165">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="934166">
<dd><em>var</em>, a pointer to the location where the data is to be placed.<P>
</a>
<a name="934167">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="932506"><P><B></a>PD_read_alt(file, name, var, ind)
</B><BR><A NAME="932508"></a>Read part of a variable <em>name</em> from PDB file <em>file</em> and put it in <em>var</em>.
<BR><a name="932509">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="932510">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="932512">
<dd><em>var</em>, a pointer to the location where the data is to be placed.<P>
</a>
<a name="932513">
<dd><em>ind</em>, an array of integer triples specifying a start, stop, and step index for each dimension of the entry.<P>
</a>
<a name="932644">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="933100"><P><B></a>PD_read_as(file, name, type, var)
</B><BR><A NAME="933101"></a>Read a variable <em>name</em> from PDB file <em>file</em> and put it in <em>var</em> as data of type type.
<BR><a name="933104">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="933105">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="933109">
<dd><em>type</em>, an ASCII string containing the type of the data desired,<P>
</a>
<a name="933106">
<dd><em>var</em>, a pointer to the location where the data is to be placed.<P>
</a>
<a name="933108">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="932514"><P><B></a>PD_read_as_alt(file, name, type, var, ind)
</B><BR><A NAME="932515"></a>Read part of a variable <em>name</em> from PDB file <em>file</em> and put it in <em>var</em> as data of type type.
<BR><a name="932517">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="932518">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="932519">
<dd><em>type</em>, an ASCII string containing the type of the data desired,<P>
</a>
<a name="932520">
<dd><em>var</em>, a pointer to the location where the data is to be placed.<P>
</a>
<a name="932643">
<dd><em>ind</em>, an array of integer triples specifying a start, stop, and step index for each dimension of the entry.<P>
</a>
<a name="932647">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="933118"><P><B></a>PD_rel_image(image)
</B><BR><A NAME="933122">Release the space associated with a PD_image data structure.
<BR><a name="933126">
<dt>Input: <em>image, a pointer to a PD_image.</em>
</a>
<a name="933131">
<dt>Output: None.
</a>
<A NAME="936739"><P><B></a>PD_rem_attribute(file, attr)
</B><BR><A NAME="936793"></a>Remove an attribute named attr from the attribute table in PDB file <em>file</em>. All attribute
values are removed simultaneously with the attribute.
<BR><a name="936800">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="936818">
<dd><em>attr</em>, an ASCII string containing the name of the attribute in the PDB file attribute table.<P>
</a>
<a name="936819">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="934184"><P><B></a>PD_reset_ptr_list(file)
</B><BR><a name="934185">
Free the list of pointers which the PDB file <em>file</em> knows about. This includes both pointers in memory acquired during write operations and pointers in the file acquired during read operations.<p>
</a>
<a name="934187">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="934189">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="933133"><P><B></a>PD_set_attribute(file, var, attr, val)
</B><BR><A NAME="933135"></a>Set the value of an attribute attr of the <em>var</em> in PDB file <em>file</em> to <em>val</em>. Variables can be added
to PDB files solely for their attributes; that is, <em>var</em> need not be a variable in <em>file</em>.
<BR><a name="933139">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="933146">
<dd><em>var</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="933147">
<dd><em>attr</em>, an ASCII string containing the name of the attribute in the PDB file attribute table,<P>
</a>
<a name="933151">
<dd><em>val</em>, a pointer to the value of the attribute <em>attr</em> to be associated with <em>var</em>.<P>
</a>
<a name="933153">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="934194"><P><B></a>PD_set_max_file_size(file, v)
</B><BR><a name="937508">
<dt>Set the maximum size for PDB file <em>file</em>.
</a>
<a name="937531">
<dt>Input: <em>file</em>, a pointer to a PDBfile.
</a>
<a name="937536">
<dd><em>v</em>, an integer value for the maximum file size<P>
</a>
<a name="937532">
<dt>Output: Return the new integer value of the maximum file size.
</a>
<A NAME="937560"><P><B></a>PD_set_offset(file, v)
</B><BR><A NAME="937562"></a>Set the default offset for PDB file<em> file</em>.
<BR><a name="937563">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="934220">
<dd>v, an integer value for the default offset.<P>
</a>
<a name="934199">
<dt>Output: Return the new integer value of the default offset.
</a>
<A NAME="933025"><P><B></a>PD_target(std, align)
</B><BR><A NAME="933029">Set up the next PDB file as if written by a machine of type defined by the given
</a>data_standard and </a>data_alignment information. This <em>function must</em> be called before
the </a><em>PD_open</em> call which creates the file.
<BR><a name="933030">
<dt>Input: <em>std</em>, a pointer to a data_standard structure,
</a>
<a name="933033">
<dd><em>align</em>, a pointer to a data_alignment structure.<P>
</a>
<a name="933036">
<dt>Output: TRUE if successful, FALSE otherwise.
</a>
<A NAME="933548"><P><B></a>PD_typedef(file, oname, tname)
</B><BR><A NAME="933549"></a>Define an alias for an existing type in the specified file.
<BR><a name="933550">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="933551">
<dd> oname, an ASCII string containing the name of the old data type,<P>
</a>
<a name="933554">
<dd> tname, an ASCII string containing the name of the new data type.<P>
</a>
<a name="933555">
<dt>Output: a pointer to the defstr for the type, if successful, and NULL otherwise.
</a>
<A NAME="932481"><P><B></a>PD_write(file, name, type, var)
</B><BR><A NAME="933080"></a>Write the data pointed to by <em>var</em> under <em>name</em> and with <em>type</em> to PDB file <em>file</em>.
<BR><a name="933084">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="933088">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="933089">
<dd><em>type</em>, an ASCII string containing the type of the variable,<P>
</a>
<a name="933091">
<dd><em>var</em>, a pointer to the location where the data is stored in memory.<P>
</a>
<a name="933093">
<dt>Output: TRUE if successful, and NULL otherwise.
</a>
<A NAME="933315"><P><B></a>PD_write_alt(file, name, type, var, nd, ind)
</B><BR><A NAME="933316"></a>Write the data pointed to by <em>var</em> under <em>name</em> and with <em>type</em> to PDB file <em>file</em>. In this alternate to </a>PD_write </a>dimension information is provided in arguments nd and ind.
<BR><a name="933317">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="933318">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="933594">
<dd><em>type</em>, an ASCII string containing the type of the variable,<P>
</a>
<a name="933595">
<dd><em>var</em>, a pointer to the location where the data is stored in memory.<P>
</a>
<a name="933598">
<dd><em>nd</em>, an integer containing the number of dimensions,<P>
</a>
<a name="933599">
<dd><em>ind</em>, an array of long integers containing (min, max, stride) triples for each dimension.<P>
</a>
<a name="933596">
<dt>Output: TRUE if successful, and NULL otherwise.
</a>
<A NAME="933130"><P><B></a>PD_write_as(file, name, intype, outtype, var)
</B><BR><A NAME="933148"></a>Write the data pointed to by <em>var</em> under <em>name</em> and with <em>intype</em> to PDB file <em>file</em> as data of
outtype.
<BR><a name="933149">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="933150">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="933152">
<dd><em>intype</em>, an ASCII string containing the type of the variable,<P>
</a>
<a name="933154">
<dd><em>outtype</em>, an ASCII string containing the output type of the variable,<P>
</a>
<a name="933155">
<dd><em>var</em>, a pointer to the location where the data is stored in memory.<P>
</a>
<a name="933156">
<dt>Output: TRUE if successful, and NULL otherwise.
</a>
<A NAME="933600"><P><B></a>PD_write_as_alt(file, name, intype, outtype, var, nd, ind)
</B><BR><A NAME="933601"></a>Write the data pointed to by <em>var</em> under <em>name</em> and with <em>intype</em> to PDB file <em>file</em> as data of
outtype. In this alternate to </a>PD_write_as </a>dimension information is provided in arguments nd and ind.
<BR><a name="933602">
<dt>Input: <em>file</em>, a pointer to a PDBfile,
</a>
<a name="933603">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="933604">
<dd><em>intype</em>, an ASCII string containing the type of the variable,<P>
</a>
<a name="933606">
<dd><em>outtype</em>, an ASCII string containing the output type of the variable,<P>
</a>
<a name="933607">
<dd><em>var</em>, a pointer to the location where the data is stored in memory.<P>
</a>
<a name="933609">
<dd><em>nd</em>, an integer containing the number of dimensions,<P>
</a>
<a name="933610">
<dd><em>ind</em>, an array of long integers containing (min, max, stride) triples for each dimension.<P>
</a>
<a name="933608">
<dt>Output: TRUE if successful, and NULL otherwise.
</a>
</dl>
<a name="933564">
<h1>4.0 The </a>C </a>API</h1>
</a>
<a name="933568">
In this section a more </a>formal description of the C API for PDBLib is given including a more detailed account of their workings.<p>
</a>
<a name="933015">
<h2>4.1 PD_APPEND</h2>
</a>
<A NAME="933016"><PRE><B>
</B></PRE><A NAME="933018"><PRE><B>int </a>PD_append(PDBfile *file
</B></PRE><A NAME="933019"><PRE><B> char *name,
</B></PRE><A NAME="933021"><PRE><B> void *vr)
</B></PRE><a name="933059">
</a>Append data to an entry in the specified file. The type is assumed to be the same as for the original entry. The dimensions of the appended data are specified in name. They must match the original entry except for the most slowly varying one. The specification of the most slowly varying dimension must be one of the following:<p>
</a>
<dl>
<a name="934730">
<dt>min:max => new dimension is old_min:old_max+(max-min+1)
</a>
<a name="934732">
<dt> if min is the default_offset for the file
</a>
<a name="934733">
<dt> or
</a>
<a name="934735">
<dt>min:max => new dimension is old_min:max
</a>
<a name="935249">
<dt> if min is old_max+1
</a>
<a name="933065">
The rationale for this function is that some data sets are of unknown size until they are completely written. PDBLib permits any entry to reside in </a>discontiguous blocks of disk space. The library is responsible for reading and writing data correctly across these blocks.<p>
</a>
<a name="933066">
The shape or dimensional information of the entry is a part of the name string. In this respect </a>PD_append behaves just like </a>PD_write.<p>
</a>
<a name="933070">
Input to this function is: <em>file</em>, a pointer to a PDBfile, name, an ASCII string containing the name of the variable and any dimensional information, and vr, a pointer to the data to be appended.<p>
</a>
<a name="933071">
This function returns TRUE, if successful; otherwise, FALSE.<p>
</a>
<a name="933073">
See also </a>PD_append_alt, </a>PD_append_as, </a>PD_append_as_alt, </a>PD_defent, </a>PD_defent_alt, </a>PD_write, </a>PD_write_alt, </a>PD_write_as, </a>PD_write_as_alt.<p>
</a>
<a name="933074">
<p>
</a>
<A NAME="933639"><PRE><B>int </a>PD_append(PDBfile *file
</B></PRE><A NAME="933682"><PRE><B> char *name,
</B></PRE><A NAME="933684"><PRE><B> void *vr)
</B></PRE><A NAME="933198"><B>
</B><HR><A NAME="933199"><PRE> #include “pdb.h”
</PRE><A NAME="933202"><PRE>
</PRE><A NAME="933203"><PRE> PDBfile *file;
</PRE><A NAME="933076"><PRE> float *fv;
</PRE><A NAME="933205"><PRE>
</PRE><A NAME="933206"><PRE> .
</PRE><A NAME="933208"><PRE> .
</PRE><A NAME="933630"><PRE> .
</PRE><A NAME="933631"><PRE> if (</a>PD_append(file, “x(20)”, fv)) == FALSE)
</PRE><A NAME="933632"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="933634"><PRE> .
</PRE><A NAME="933636"><PRE> .
</PRE><A NAME="933637"><PRE> .
</PRE><a name="933638">
Compare this with the example of </a>PD_write.<p>
</a>
</dl>
<a name="933177">
<h2>4.2 PD_APPEND_ALT</h2>
</a>
<A NAME="933194"><PRE><B>
</B></PRE><A NAME="934356"><PRE><B>int </a>PD_append_alt(PDBfile *file
</B></PRE><A NAME="934357"><PRE><B> char *name,
</B></PRE><A NAME="934358"><PRE><B> void *vr,
</B></PRE><A NAME="934359"><PRE><B> int nd,
</B></PRE><A NAME="934360"><PRE><B> long *ind)
</B></PRE><a name="934061">
</a>Append data to an entry in the specified file. The type is assumed to be the same as for the original entry. The dimensions of the appended data are specified in the ind array. They must match the original entry except for the most slowly varying one. The specification of the most slowly varying dimension must be one of the following;<p>
</a>
<dl>
<a name="933642">
<dt>min:max :stride => new dimension is old_min:old_max+(max-min+1)
</a>
<a name="933643">
<dt> if min is the default_offset for the file
</a>
<a name="933644">
<dt> or
</a>
<a name="933645">
<dt>min:max :stride => new dimension is old_min:max
</a>
<a name="935250">
<dt> if min is old_max+1
</a>
<a name="934067">
The rationale for this function is that some data sets are of unknown size until they are completely written. PDBLib permits any entry to reside in </a>discontiguous blocks of disk space. The library is responsible for reading and writing data correctly across these blocks.<p>
</a>
<a name="934069">
Input to this function is: <em>file</em>, a pointer to a PDBfile, name, an ASCII string containing the name of the variable; vr, a pointer to the data to be appended; nd, an integer number of dimensions; and ind, an array of longs with triples (start, stop, step) defining dimension information.<p>
</a>
<a name="934070">
This function returns TRUE, if successful; otherwise, FALSE.<p>
</a>
<a name="934330">
See also </a>PD_append, </a>PD_append_as, </a>PD_append_as_alt, </a>PD_defent, </a>PD_defent_alt, </a>PD_write, </a>PD_write_alt, </a>PD_write_as, </a>PD_write_as_alt.<p>
</a>
<a name="934331">
<p>
</a>
<A NAME="934332"><PRE><B>int </a>PD_append_alt(PDBfile *file
</B></PRE><A NAME="934333"><PRE><B> char *name,
</B></PRE><A NAME="934334"><PRE><B> void *vr,
</B></PRE><A NAME="934354"><PRE><B> int nd,
</B></PRE><A NAME="934355"><PRE><B> long *ind)
</B></PRE><A NAME="934335"><B>
</B><HR><A NAME="934336"><PRE> #include “pdb.h”
</PRE><A NAME="934337"><PRE>
</PRE><A NAME="934338"><PRE> PDBfile *file;
</PRE><A NAME="934339"><PRE> float *fv;
</PRE><A NAME="934350"><PRE> long ind[3]
</PRE><A NAME="934340"><PRE>
</PRE><A NAME="934341"><PRE> .
</PRE><A NAME="934342"><PRE> .
</PRE><A NAME="934343"><PRE> .
</PRE><A NAME="934344"><PRE> ind[0] = 0L;
</PRE><A NAME="934352"><PRE> ind[1] = 20L;
</PRE><A NAME="934353"><PRE> ind[2] = 1L;
</PRE><A NAME="934351"><PRE> if (</a>PD_append_alt(file, “x”, fv, 1, ind)) == FALSE)
</PRE><A NAME="934345"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="934346"><PRE> .
</PRE><A NAME="934347"><PRE> .
</PRE><A NAME="934348"><PRE> .
</PRE><a name="934349">
Compare this with the example of </a>PD_write_alt.<p>
</a>
</dl>
<a name="933204">
<h2>4.3 PD_APPEND_AS</h2>
</a>
<A NAME="933685"><PRE><B>
</B></PRE><A NAME="933687"><PRE><B>int </a>PD_append_as(PDBfile *file
</B></PRE><A NAME="934361"><PRE><B> char *name,
</B></PRE><A NAME="934436"><PRE><B> char *intype,
</B></PRE><A NAME="934362"><PRE><B> void *vr)
</B></PRE><a name="934363">
</a>Append data to an entry in the specified file. The output type is assumed to be the same as for the original entry. The dimensions of the appended data are specified in the name. They must match the original entry except for the most slowly varying one. The specification of the most slowly varying dimension must be one of the following;<p>
</a>
<dl>
<a name="934063">
<dt>min:max => new dimension is old_min:old_max+(max-min+1)
</a>
<a name="934064">
<dt> if min is the default_offset for the file
</a>
<a name="934065">
<dt> or
</a>
<a name="934066">
<dt>min:max => new dimension is old_min:max
</a>
<a name="935251">
<dt> if min is old_max+1
</a>
<a name="934369">
The rationale for this function is that some data sets are of unknown size until they are completely written. PDBLib permits any entry to reside in </a>discontiguous blocks of disk space. The library is responsible for reading and writing data correctly across these blocks.<p>
</a>
<a name="934370">
The shape or dimensional information of the entry is a part of the name string. In this respect</a> PD_append_as behaves just like </a>PD_write_as.<p>
</a>
<a name="934371">
Input to this function is: <em>file</em>, a pointer to a PDBfile, name, an ASCII string containing the name of the variable and any dimensional information, intype, an ASCII string specifying the type of the data to which vr points; and vr, a pointer to the data to be appended.<p>
</a>
<a name="934372">
This function returns TRUE, if successful; otherwise, FALSE.<p>
</a>
<a name="934373">
See also </a>PD_append, </a>PD_append_alt, </a>PD_append_as_alt, </a>PD_defent, </a>PD_defent_alt, </a>PD_write, </a>PD_write_alt, </a>PD_write_as, </a>PD_write_as_alt.<p>
</a>
<a name="934374">
<p>
</a>
<A NAME="934437"><PRE><B>int </a>PD_append_as(PDBfile *file
</B></PRE><A NAME="934438"><PRE><B> char *name,
</B></PRE><A NAME="934439"><PRE><B> char *intype,
</B></PRE><A NAME="934440"><PRE><B> void *vr)
</B></PRE><A NAME="934378"><B>
</B><HR><A NAME="934379"><PRE> #include “pdb.h”
</PRE><A NAME="934380"><PRE>
</PRE><A NAME="934381"><PRE> PDBfile *file;
</PRE><A NAME="934382"><PRE> double *dv;
</PRE><A NAME="934383"><PRE>
</PRE><A NAME="934384"><PRE> .
</PRE><A NAME="934385"><PRE> .
</PRE><A NAME="934386"><PRE> .
</PRE><A NAME="934387"><PRE> if (</a>PD_append_as(file, “x(20)”, “float”, dv)) == FALSE)
</PRE><A NAME="934388"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="934389"><PRE> .
</PRE><A NAME="934390"><PRE> .
</PRE><A NAME="934391"><PRE> .
</PRE><a name="934392">
Compare this with the example of </a>PD_write_as.<p>
</a>
</dl>
<a name="934393">
<h2>4.4 PD_APPEND_AS_ALT</h2>
</a>
<A NAME="934394"><PRE><B>
</B></PRE><A NAME="934395"><PRE><B>int PD_append_as_alt(PDBfile *file
</B></PRE><A NAME="934396"><PRE><B> char *name,
</B></PRE><A NAME="934375"><PRE><B> char *intype,
</B></PRE><A NAME="934397"><PRE><B> void *vr,
</B></PRE><A NAME="934398"><PRE><B> int nd,
</B></PRE><A NAME="934399"><PRE><B> long *ind)
</B></PRE><a name="934400">
</a>Append data to an entry in the specified file. The output type is assumed to be the same as for the original entry. The dimensions of the appended data are specified in the ind array. They must match the original entry except for the most slowly varying one. The specification of the most slowly varying dimension must be one of the following;<p>
</a>
<dl>
<a name="934365">
<dt>min:max :stride => new dimension is old_min:old_max+(max-min+1)
</a>
<a name="934366">
<dt> if min is the default_offset for the file
</a>
<a name="934367">
<dt> or
</a>
<a name="934368">
<dt>min:max :stride => new dimension is old_min:max
</a>
<a name="935252">
<dt> if min is old_max+1
</a>
<a name="934406">
The rationale for this function is that some data sets are of unknown size until they are completely written. PDBLib permits any entry to reside in </a>discontiguous blocks of disk space. The library is responsible for reading and writing data correctly across these blocks.<p>
</a>
<a name="934408">
Input to this function is: <em>file</em>, a pointer to a PDBfile, name, an ASCII string containing the name of the variable; intype, an ASCII string specifying the type of data to which vr points; vr, a pointer to the data to be appended; nd, an integer number of dimensions; and ind, an array of longs with triples (start, stop, step) defining dimension information.<p>
</a>
<a name="934409">
This function returns TRUE, if successful; otherwise, FALSE.<p>
</a>
<a name="934410">
See also </a>PD_append, </a>PD_append_alt, </a>PD_append_as, </a>PD_defent, </a>PD_defent_alt, </a>PD_write, </a>PD_write_alt, </a>PD_write_as, </a>PD_write_as_alt.<p>
</a>
<a name="934411">
<p>
</a>
<A NAME="934376"><PRE><B>int PD_append_as_alt(PDBfile *file
</B></PRE><A NAME="934377"><PRE><B> char *name,
</B></PRE><A NAME="934441"><PRE><B> char *intype,
</B></PRE><A NAME="934442"><PRE><B> void *vr,
</B></PRE><A NAME="934443"><PRE><B> int nd,
</B></PRE><A NAME="934444"><PRE><B> long *ind)
</B></PRE><A NAME="934417"><B>
</B><HR><A NAME="934418"><PRE> #include “pdb.h”
</PRE><A NAME="934419"><PRE>
</PRE><A NAME="934420"><PRE> PDBfile *file;
</PRE><A NAME="934421"><PRE> float *fv;
</PRE><A NAME="934422"><PRE> long ind[3]
</PRE><A NAME="934423"><PRE>
</PRE><A NAME="934424"><PRE> .
</PRE><A NAME="934425"><PRE> .
</PRE><A NAME="934426"><PRE> .
</PRE><A NAME="934427"><PRE> ind[0] = 0L;
</PRE><A NAME="934428"><PRE> ind[1] = 20L;
</PRE><A NAME="934429"><PRE> ind[2] = 1L;
</PRE><A NAME="934430"><PRE> if (</a>PD_append_as_alt(file, “x”, “double”, fv, 1, ind)) == FALSE)
</PRE><A NAME="934431"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="934432"><PRE> .
</PRE><A NAME="934433"><PRE> .
</PRE><A NAME="934434"><PRE> .
</PRE><a name="934435">
Compare this with the example of </a>PD_write_as_alt.<p>
</a>
</dl>
<a name="933597">
<h2>4.5 PD_CAST</h2>
</a>
<A NAME="932614"><PRE><B>
</B></PRE><A NAME="932613"><PRE><B>int </a>PD_cast(PDBfile *file,
</B></PRE><A NAME="932579"><PRE><B> char *type,
</B></PRE><A NAME="932611"><PRE><B> char *memb,
</B></PRE><A NAME="932612"><PRE><B> char *contr)
</B></PRE><a name="933605">
</a>Dynamically change the type of a structure member. PDBLib supports an extended data typing mechanism called a structure. A </a>structure is a set of declarations of members. Each </a>member is in turn a data type known to the system. In some applications, a structure member is used to point to data of a type which is specified by another member. In the C coding a </a>cast is used to obtain a pointer to the desired data type.<p>
</a>
<a name="933611">
PDBLib supports this same practice by allowing the programmer to override the type of a member as given in the structure definition (see </a>PD_defstr) by supplying the name of a member, whose type must be “char *”, which will contain an ASCII string specifying the actual type of the data to which the first member points.<p>
</a>
<a name="933633">
The arguments to </a>PD_cast are: file, a pointer to a PDBfile; type, an ASCII string containing the name of the data structure type in the PDB file; memb, an ASCII string containing the name of the member whose type is to be overridden; and contr, an ASCII string containing the name of the member (whose type must be “char *”) which will provide the actual type for memb.<p>
</a>
<a name="933635">
The return value is a TRUE if the cast is successful; otherwise, FALSE is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="933641">
<p>
</a>
<a name="932521">
int </a>PD_cast(PDBfile *file,<p>
</a>
<a name="932615">
char *type,<p>
</a>
<a name="932617">
char *memb,<p>
</a>
<a name="932616">
char *contr)<p>
</a>
<A NAME="933647"><B>
</B><HR><A NAME="933650"><PRE> #include “pdb.h”
</PRE><A NAME="933651"><PRE>
</PRE><A NAME="933652"><PRE> PDBfile *file;
</PRE><A NAME="933654"><PRE> struct sample
</PRE><A NAME="933655"><PRE> {char *type;
</PRE><A NAME="933656"><PRE> int *a;};
</PRE><A NAME="933657"><PRE> .
</PRE><A NAME="933658"><PRE> .
</PRE><A NAME="933659"><PRE> .
</PRE><A NAME="933660"><PRE> </a>PD_defstr(file, “sample”, “char *type”, “int *a”, LAST);
</PRE><A NAME="933661"><PRE> </a>PD_cast(file, “sample”, “a”, “type”);
</PRE><A NAME="933662"><PRE> .
</PRE><A NAME="933663"><PRE> .
</PRE><A NAME="933664"><PRE> .
</PRE><a name="935411">
<h2>4.6 PD_CD</h2>
</a>
<A NAME="935412"><PRE><B>
</B></PRE><A NAME="935415"><PRE><B>int </a>PD_cd(PDBfile *file,
</B></PRE><A NAME="935428"><PRE><B> char *dirname)
</B></PRE><a name="935430">
</a>Change the </a>current </a>directory in the specified PDB file.<p>
</a>
<a name="935431">
PDBLib supports an optional </a>hierarchical </a>directory structure inside PDB files. A directory or a variable in a directory may be specified by either a </a>relative path or an </a>absolute path. Slashes separate nodes in a </a>path name. Absolute paths begin with a slash. Nodes consisting of two periods, “..”, refer to the next higher level directory.<p>
</a>
<a name="935432">
The arguments to </a>PD_cd are: file, a pointer to a PDBfile; and dirname, an ASCII string containing the path name of the directory to change to.<p>
</a>
<a name="935529">
If dirname is NULL or an empty string or a slash, it refers to the top level or </a>root directory.<p>
</a>
<a name="935433">
The return value is a TRUE if successful; otherwise, FALSE is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="935416">
See also </a>PD_ln, </a>PD_ls, </a>PD_mkdir, and </a>PD_pwd.<p>
</a>
<a name="935434">
<p>
</a>
<a name="935435">
int </a>PD_cd(PDBfile *file,<p>
</a>
<a name="935438">
char *dirname)<p>
</a>
<A NAME="935439"><B>
</B><HR><A NAME="935440"><PRE> #include “pdb.h”
</PRE><A NAME="935446"><PRE>
</PRE><A NAME="935447"><PRE> PDBfile *file;
</PRE><A NAME="935451"><PRE> .
</PRE><A NAME="935452"><PRE> .
</PRE><A NAME="935453"><PRE> .
</PRE><A NAME="935427"><PRE> if (</a>PD_cd(file, “/animals/mammals”) == FALSE)
</PRE><A NAME="935457"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="935436"><PRE> .
</PRE><A NAME="935437"><PRE> .
</PRE><A NAME="935448"><PRE> .
</PRE><A NAME="935449"><PRE> if (</a>PD_cd(file, “../reptiles”) == FALSE)
</PRE><A NAME="935458"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="935450"><PRE> .
</PRE><A NAME="935454"><PRE> .
</PRE><A NAME="935456"><PRE> .
</PRE><a name="933672">
<h2>4.7 PD_CLOSE</h2>
</a>
<A NAME="933677"><PRE><B>
</B></PRE><A NAME="932618"><PRE><B>int </a>PD_close(PDBfile *file)
</B></PRE><a name="933683">
</a>Close a PDB file. After all data is written to the PDB file, the structure chart and symbol table must be written out to the file and their disk addresses recorded in the file header. Without these operations the file cannot be read back in by PDBLib and all data is lost. All open PDB files must be </a>PD_close’d before exiting the program.<p>
</a>
<a name="933686">
A pointer, file, to the PDBfile associated with the PDB file must be passed to </a>PD_close.<p>
</a>
<a name="933690">
The function returns TRUE if the PDB file is correctly written and closed; otherwise, FALSE is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="933693">
<p>
</a>
<a name="932620">
int </a>PD_close(PDBfile *file)<p>
</a>
<A NAME="933698"><B>
</B><HR><A NAME="933702"><PRE> #include “pdb.h”
</PRE><A NAME="933703"><PRE>
</PRE><A NAME="933704"><PRE> PDBfile *file;
</PRE><A NAME="933705"><PRE> .
</PRE><A NAME="933706"><PRE> .
</PRE><A NAME="933707"><PRE> .
</PRE><A NAME="933708"><PRE> if (</a>PD_close(file) == FALSE)
</PRE><A NAME="933709"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="933710"><PRE> .
</PRE><A NAME="933711"><PRE> .
</PRE><A NAME="933712"><PRE> .
</PRE><a name="932688">
<h2>4.8 PD_DEF_ATTRIBUTE</h2>
</a>
<A NAME="933508"><PRE><B>
</B></PRE><A NAME="934550"><PRE><B>int </a>PD_def_attribute(PDBfile *file,
</B></PRE><A NAME="934551"><PRE><B> char *attr,
</B></PRE><A NAME="934555"><PRE><B> char *type)
</B></PRE><a name="933499">
</a>Define an </a>attribute to the given PDB file. The </a>model of an attribute in PDBLib is an entity that has a name and type. The two supported operations on attributes are to create them and to remove them. An entity in a PDB file can be assigned an </a>attribute value simply by making a call which specifies the entity name, the attribute name, and the attribute value (which is determined by the type). The only association between an entry in a PDB file and any attribute is made by the name in the attribute table and the entry in the symbol table. In particular, this mechanism allows the application developer to define and use entities in a PDB file solely in terms of attributes.<p>
</a>
<a name="934556">
The arguments to this function are: file, a pointer to a PDBfile; name, an ASCII string containing the name of the attribute being defined; and type, an ASCII string containing the name of the data type in the PDB file.<p>
</a>
<a name="934576">
The return value is TRUE if successful, and FALSE otherwise.<p>
</a>
<a name="934558">
See also </a>PD_rem_attribute, </a>PD_set_attribute, and </a>PD_get_attribute.<p>
</a>
<a name="934923">
<p>
</a>
<A NAME="934922"><PRE><B>int </a>PD_def_attribute(PDBfile *file,
</B></PRE><A NAME="934943"><PRE><B> char *attr,
</B></PRE><A NAME="934944"><PRE><B> char *type)
</B></PRE><A NAME="934928"><B>
</B><HR><A NAME="934929"><PRE> #include “pdb.h”
</PRE><A NAME="934930"><PRE>
</PRE><A NAME="934932"><PRE> PDBfile *file;
</PRE><A NAME="934933"><PRE> .
</PRE><A NAME="934934"><PRE> .
</PRE><A NAME="934936"><PRE> .
</PRE><A NAME="934937"><PRE> if (</a>PD_def_attribute(file, “date”, “char *”) == FALSE)
</PRE><A NAME="934938"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="934939"><PRE> .
</PRE><A NAME="934940"><PRE> .
</PRE><A NAME="934942"><PRE> .
</PRE><a name="933498">
<h2>4.9 PD_DEFENT</h2>
</a>
<A NAME="933352"><PRE><B>
</B></PRE><A NAME="932695"><PRE><B>syment *</a>PD_defent(PDBfile *file,
</B></PRE><A NAME="933355"><PRE><B> char *name,
</B></PRE><A NAME="933356"><PRE><B> char *outtype)
</B></PRE><a name="932692">
</a>Define an entry in the </a>symbol table of the PDB file specified by <em>file</em>. This function </a>reserves space on disk but writes no data. The data can be written with later calls to </a>PD_write, </a>PD_write_alt, </a>PD_write_as, or </a>PD_write_as_alt.<p>
</a>
<a name="933353">
The rationale for this function is to </a>block out space in a PDB file corresponding to some logical layout of a piece of data. The data may not exist at the time the space is reserved or for some reason it may be desirable to write out the data in pieces. In any case if the type and shape of a variable is known at some point, an entry may be made in the PDB file without writing any data. The space may filled with other PDBLib calls at some later time.<p>
</a>
<a name="933354">
The shape or dimensional information of the entry is a part of the name string. In this respect </a>PD_defent behaves just like </a>PD_write.<p>
</a>
<a name="932696">
Input to this function is: <em>file</em>, a pointer to a PDBfile, name, an ASCII string containing the name of the variable and any dimensional information, and outtype, an ASCII string specifying the type of data in the file.<p>
</a>
<a name="932698">
This function returns a symbol table entry (syment) pointer, if successful; otherwise, NULL is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="934227">
See also </a>PD_defent_alt, </a>PD_write, </a>PD_write_alt, </a>PD_write_as, </a>PD_write_as_alt.<p>
</a>
<a name="932700">
<p>
</a>
<a name="932701">
syment *</a>PD_defent(PDBfile *file,<p>
</a>
<a name="932715">
char *name,<p>
</a>
<a name="933348">
char *outtype)<p>
</a>
<A NAME="933349"><B>
</B><HR><A NAME="933350"><PRE> #include “pdb.h”
</PRE><A NAME="933351"><PRE>
</PRE><A NAME="933362"><PRE> PDBfile *file;
</PRE><A NAME="933365"><PRE> syment *ep;
</PRE><A NAME="933369"><PRE>
</PRE><A NAME="933370"><PRE> .
</PRE><A NAME="933371"><PRE> .
</PRE><A NAME="933372"><PRE> .
</PRE><A NAME="933373"><PRE> if ((ep = </a>PD_defent(file, “x(20)”, “float”)) == NULL)
</PRE><A NAME="933374"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="933375"><PRE> .
</PRE><A NAME="933376"><PRE> .
</PRE><A NAME="932670"><PRE> .
</PRE><a name="933438">
Compare this with the example of </a>PD_write.<p>
</a>
<a name="932699">
<h2>4.10 PD_DEFENT_ALT</h2>
</a>
<A NAME="932693"><PRE><B>
</B></PRE><A NAME="933357"><PRE><B>syment *</a>PD_defent_alt(PDBfile *file,
</B></PRE><A NAME="933358"><PRE><B> char *name,
</B></PRE><A NAME="933361"><PRE><B> char *outtype,
</B></PRE><A NAME="933360"><PRE><B> int nd,
</B></PRE><A NAME="933359"><PRE><B> long *ind)
</B></PRE><a name="933363">
</a>Define an entry in the </a>symbol table of the PDB file specified by <em>file</em>. This function </a>reserves space on disk but writes no data. The data can be written with later calls to </a>PD_write, </a>PD_write_alt, </a>PD_write_as, or </a>PD_write_as_alt.<p>
</a>
<a name="933368">
This is an alternate form of </a>PD_defent. The difference is that the </a>dimension information is supplied via the nd and ind arguments instead of being a part of the name string. In this respect it behaves as </a>PD_write_alt does.<p>
</a>
<a name="933364">
The rationale for this function is to </a>block out space in a PDB file corresponding to some logical layout of a piece of data. The data may not exist at the time the space is reserved or for some reason it may be desirable to write out the data in pieces. In any case if the type and shape of a variable is known at some point, an entry may be made in the PDB file without writing any data. The space may filled with other PDBLib calls at some later time.<p>
</a>
<a name="933366">
Input to this function is: <em>file</em>, a pointer to a PDBfile, name, an ASCII string containing the name of the variable only, outtype, an ASCII string specifying the type of data in the file; nd, an integer specifying the number of dimensions; and ind, an array of long integers containing the minimum and maximum values of the index for each dimension pairwise.<p>
</a>
<a name="933367">
This function returns a symbol table entry (syment) pointer, if successful; otherwise, NULL is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="934228">
See also </a>PD_defent, </a>PD_write, </a>PD_write_alt, </a>PD_write_as, </a>PD_write_as_alt.<p>
</a>
<a name="933425">
<p>
</a>
<a name="933426">
syment *</a>PD_defent_alt(PDBfile *file,<p>
</a>
<a name="933427">
char *name,<p>
</a>
<a name="933428">
char *outtype,<p>
</a>
<a name="933430">
int nd,<p>
</a>
<a name="933431">
long *ind)<p>
</a>
<A NAME="933432"><B>
</B><HR><A NAME="933433"><PRE> #include “pdb.h”
</PRE><A NAME="933434"><PRE>
</PRE><A NAME="933435"><PRE> PDBfile *file;
</PRE><A NAME="933436"><PRE> syment *ep;
</PRE><A NAME="933437"><PRE> long ind[4];
</PRE><A NAME="933439"><PRE> .
</PRE><A NAME="933440"><PRE> .
</PRE><A NAME="933441"><PRE> .
</PRE><A NAME="933442"><PRE> ind[0] = 0L;
</PRE><A NAME="933443"><PRE> ind[1] = 19L;
</PRE><A NAME="933444"><PRE> ind[2] = -2L;
</PRE><A NAME="933445"><PRE> ind[3] = 2L;
</PRE><A NAME="933446"><PRE> if ((ep = </a>PD_defent_alt(file, “x”, “float”, 2, ind)) == NULL)
</PRE><A NAME="933447"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="933448"><PRE> .
</PRE><A NAME="933449"><PRE> .
</PRE><A NAME="933394"><PRE> .
</PRE><a name="933429">
Compare this with the example of </a>PD_write_alt and note the absence of a two dimensional array in this call.<p>
</a>
<a name="933157">
<h2>4.11 PD_DEFIX</h2>
</a>
<A NAME="933197"><PRE><B>
</B></PRE><A NAME="933158"><PRE><B>defstr *</a>PD_defix(PDBfile *file,
</B></PRE><A NAME="933193"><PRE><B> char *name,
</B></PRE><A NAME="933543"><PRE><B> long bytespitem,
</B></PRE><A NAME="933542"><PRE><B> int align,
</B></PRE><A NAME="933541"><PRE><B> int flg)
</B></PRE><a name="933200">
</a>Define a primitive integral type (</a>fixed point type) in the PDB file specified by <em>file</em>. <p>
</a>
<a name="933166">
Input to PD_defix is: <em>file</em>, a pointer to a PDBfile; name, an ASCII string containing the name of the new data type; bytespitem, the number of bytes required for 1 item of the new type; align, the byte alignment for the type; and flg, a flag indicating whether the byte ordering of the type is normal or reverse ordered.<p>
</a>
<a name="933160">
PDBLib supplies two </a>#</a>define’d constants which define the two ordering schemes used for fixed point types: </a>NORMAL_ORDER and </a>REVERSE_ORDER. NORMAL_ORDER means that the byte ordering from lowest to highest address as occurs on most CPU’s. REVERSE_ORDER means that the byte order goes from highest to lowest address as happens with INTEL and other CPU’s.<p>
</a>
<a name="933161">
Compare this information with that found in the discussion of data conversion later in this manual.<p>
</a>
<a name="933209">
A pointer to the new type’s defstr is returned if the call is successful; otherwise, NULL is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="933201">
<p>
</a>
<A NAME="933544"><PRE><B>defstr *</a>PD_defix(PDBfile *file,
</B></PRE><A NAME="933545"><PRE><B> char *name,
</B></PRE><A NAME="933546"><PRE><B> long bytespitem,
</B></PRE><A NAME="933547"><PRE><B> int align,
</B></PRE><a name="933207">
int flg)<p>
</a>
<A NAME="933231"><B>
</B><HR><A NAME="933232"><PRE> #include “pdb.h”
</PRE><A NAME="933233"><PRE>
</PRE><A NAME="933234"><PRE> PDBfile *file;
</PRE><A NAME="933239"><PRE> defstr *ptr;
</PRE><A NAME="933240"><PRE> .
</PRE><A NAME="933241"><PRE> .
</PRE><A NAME="933242"><PRE> .
</PRE><A NAME="933244"><PRE> ptr = </a>PD_defix(file, “int40”, 5, 1, </a>NORMAL_ORDER);
</PRE><A NAME="933245"><PRE> .
</PRE><A NAME="933246"><PRE> .
</PRE><A NAME="933210"><PRE> .
</PRE><a name="933169">
<h2>4.12 PD_DEFLOAT</h2>
</a>
<A NAME="933192"><PRE><B>
</B></PRE><A NAME="933530"><PRE><B>defstr *</a>PD_defloat(PDBfile *file,
</B></PRE><A NAME="933531"><PRE><B> char *name,
</B></PRE><A NAME="933532"><PRE><B> long bytespitem,
</B></PRE><A NAME="933533"><PRE><B> int align,
</B></PRE><A NAME="933534"><PRE><B> int *ordr,
</B></PRE><A NAME="933535"><PRE><B> long expb,
</B></PRE><A NAME="933536"><PRE><B> long mantb,
</B></PRE><A NAME="933537"><PRE><B> long sbs,
</B></PRE><A NAME="933538"><PRE><B> long sbe,
</B></PRE><A NAME="933539"><PRE><B> long sbm,
</B></PRE><A NAME="933540"><PRE><B> long hmb,
</B></PRE><A NAME="933196"><PRE><B> long bias)
</B></PRE><a name="933171">
</a>Define a new floating point type to the PDB file specified by <em>file</em>.<p>
</a>
<a name="933187">
Input to </a>PD_defloat is: <em>file</em>, a pointer to a PDBfile; n<em>ame</em>, an ASCII string containing the name of the variable in the PDB file; b<em>ytespitem, the number of bytes required for an item of the new type; </em>align, the byte alignment for this type; ordr, an array of bytespitem integers specifying the byte order; expb, the number of exponent bits; mantb, the number of mantissa bits; sbs, the position of the sign bit; sbe, the starting bit of the exponent; sbm, the starting bit of the mantissa; hmb, the value of the high order mantissa bit; and bias, the bias of the exponent.<p>
</a>
<a name="933167">
Compare this information with that found in the discussion of data conversion later in this manual.<p>
</a>
<a name="933217">
A pointer to the new type’s defstr is returned if the call is successful; otherwise, NULL is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="933211">
<p>
</a>
<A NAME="933212"><PRE><B>defstr *</a>PD_defloat(PDBfile *file,
</B></PRE><A NAME="933500"><PRE><B> char *name,
</B></PRE><A NAME="933501"><PRE><B> long bytespitem,
</B></PRE><A NAME="933523"><PRE><B> int align,
</B></PRE><A NAME="933502"><PRE><B> int *ordr,
</B></PRE><A NAME="933213"><PRE><B> long expb,
</B></PRE><A NAME="933524"><PRE><B> long mantb,
</B></PRE><A NAME="933529"><PRE><B> long sbs,
</B></PRE><A NAME="933528"><PRE><B> long sbe,
</B></PRE><A NAME="933527"><PRE><B> long sbm,
</B></PRE><A NAME="933526"><PRE><B> long hmb,
</B></PRE><A NAME="933525"><PRE><B> long bias)
</B></PRE><A NAME="933214"><B>
</B><HR><A NAME="933215"><PRE> #include “pdb.h”
</PRE><A NAME="933216"><PRE>
</PRE><A NAME="933226"><PRE> int ord_int24[] = {1, 3, 2};
</PRE><A NAME="933222"><PRE>
</PRE><A NAME="933221"><PRE> PDBfile *file;
</PRE><A NAME="933218"><PRE> defstr *ptr;
</PRE><A NAME="933223"><PRE> .
</PRE><A NAME="933224"><PRE> .
</PRE><A NAME="933225"><PRE> .
</PRE><A NAME="933220"><PRE> ptr = </a>PD_defloat(file, “fp24”, 3, 1, ord_int24,
</PRE><A NAME="933219"><PRE> 7L, 16L, 0L, 1L, 8L, 0L, 0x3F)
</PRE><A NAME="933228"><PRE> .
</PRE><A NAME="933229"><PRE> .
</PRE><A NAME="933195"><PRE> .
</PRE><a name="933559">
<h2>4.13 PD_DEFNCV</h2>
</a>
<A NAME="933562"><PRE><B>
</B></PRE><A NAME="933563"><PRE><B>defstr *</a>PD_defncv(PDBfile *file,
</B></PRE><A NAME="933565"><PRE><B> char *name,
</B></PRE><A NAME="933566"><PRE><B> long bytespitem,
</B></PRE><A NAME="933569"><PRE><B> int align)
</B></PRE><a name="933570">
</a>Define a primitive type that will not undergo format conversion from platform to platform in the PDB file specified by <em>file</em>. Certain data types commonly defined in C programs are used as flags or character holders. With such data types the actual bit pattern contains the meaningful information. This information would be lost under a data conversion operation. This function provides users with a means to define primitive types which will not be converted under any circumstances and therefore preserve the meaningful bit patterns which constitute the intended data.<p>
</a>
<a name="933571">
Input to </a>PD_defncv is: <em>file</em>, a pointer to a PDBfile; name, an ASCII string containing the name of the new data type; bytespitem, the number of bytes required for 1 item of the new type; and align, the byte alignment for the type.<p>
</a>
<a name="933573">
Compare this information with that found in the discussion of data conversion later in this manual.<p>
</a>
<a name="933574">
A pointer to the new type’s defstr is returned if the call is successful; otherwise, NULL is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="933575">
<p>
</a>
<A NAME="933576"><PRE><B>defstr *PD_defncv(PDBfile *file,
</B></PRE><A NAME="933577"><PRE><B> char *name,
</B></PRE><A NAME="933578"><PRE><B> long bytespitem,
</B></PRE><a name="933580">
int align)<p>
</a>
<A NAME="933581"><B>
</B><HR><A NAME="933582"><PRE> #include “pdb.h”
</PRE><A NAME="933583"><PRE>
</PRE><A NAME="933584"><PRE> PDBfile *file;
</PRE><A NAME="933586"><PRE> defstr *ptr;
</PRE><A NAME="933587"><PRE> .
</PRE><A NAME="933588"><PRE> .
</PRE><A NAME="933589"><PRE> .
</PRE><A NAME="933590"><PRE> /* define a type like the FORTRAN character*8 */
</PRE><A NAME="933567"><PRE> ptr = </a>PD_defncv(file, “char_8”, 8, 1);
</PRE><A NAME="933591"><PRE> .
</PRE><A NAME="935810"><PRE> .
</PRE><A NAME="933592"><PRE> .
</PRE><a name="933720">
<h2>4.14 PD_DEFSTR</h2>
</a>
<A NAME="933726"><PRE><B>
</B></PRE><A NAME="932622"><PRE><B>defstr *</a>PD_defstr(PDBfile *file,
</B></PRE><A NAME="932623"><PRE><B> char *name,
</B></PRE><A NAME="932625"><PRE><B> char *mem1, ..., memn,
</B></PRE><A NAME="932624"><PRE><B> int *LAST)
</B></PRE><a name="933736">
</a>Define a data </a>structure for a PDB file. As a matter of programming efficiency and clarity it is useful to be able to refer to more complex structural units than the primitive types: short integers, integers, long integers, floating point numbers, double precision floating point numbers, and characters. Arrays do this in a very simple-minded way. Many modern languages support extended types or structures which allow the programmer to group diverse types of data together in a very sophisticated way.<p>
</a>
<a name="933746">
PDBLib supports an extended data typing mechanism called a structure. A </a>structure is a set of declarations of members. Each member is in turn a data type known to the system. Much of the style and usage of structures comes from the C struct. Because of the memory management features upon which PDBLib now depends, even members whose types are pointers are allowed. The only </a>restrictions on member types are that they not be function pointers and that they be expressible without parentheses. Again any member which is a pointer must have its memory allocated by a SCORE </a>memory management function or macro. See the Memory Management section near the beginning of this manual. <p>
</a>
<a name="933758">
</a>PD_defstr defines structures to the PDB system so that they can be read and written as a whole in a single statement. The members of the </a>structure are processed and an entry in the structure chart is made. Then subsequent references to the new structure type are processed using information from the structure chart. The syntax by which members of a structure are specified is like that for C structs. The formal definition is given below ([ ] enclose optional elements). </a>Self-referential structures are allowed providing the reference is through pointers (like C). The actual type name is used in the reference since PDBLib checks that all member types are already known or are the type being defined.<p>
</a>
<dl>
<a name="933761">
<dt>
</a>
<a name="932523">
<dt> <member> := <type> [*...*]<member name>[(<dimensions>)]
</a>
<a name="933763">
<dt> <type> := <primitive type> | <derived type>
</a>
<a name="933766">
<dt> <member name> := an ascii string representing the name of the member
</a>
<a name="933768">
<dt> <primitive type> := short | integer | long | float | double | char
</a>
<a name="933770">
<dt> <derived type> := any </a>PD_defstr’d type
</a>
<a name="933773">
<dt> <dimensions> := <integer> |
</a>
<a name="933620">
<dt> <integer : integer> |
</a>
<a name="933621">
<dt> <integer>, <dimensions> |
</a>
<a name="932524">
<dt> <integer : integer> <dimensions>
</a>
<a name="933782">
Dimensions can be given in two ways. If the default offset value for the PDB file can be taken as the minimum value for the range which a dimension index can legally run, the maximum value may be specified alone. Alternatively, the minimum value followed by a colon and the maximum value may be specified. For example,<p>
</a>
<a name="933785">
<dd> integer a(30,1:10)<P>
</a>
<a name="933791">
The arguments to </a>PD_defstr are: file, a pointer to a PDBfile; name, an ASCII string containing the name of the data structure type in the PDB file; and memi, a list of ASCII strings each representing the declaration of a member of a </a>structure are defined above. LAST must terminate the list of members.<p>
</a>
<a name="933612">
The return value is a pointer to the entry made in the structure chart if the call is successful; otherwise, NULL is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="933793">
<p>
</a>
<a name="933799">
<p>
</a>
<a name="932626">
defstr *PD_defstr(PDBfile *file,<p>
</a>
<a name="932627">
char *name,<p>
</a>
<a name="932628">
char *mem1, ..., memn,<p>
</a>
<a name="932629">
int *LAST)<p>
</a>
<A NAME="933805"><B>
</B><HR><A NAME="933808"><PRE> #include “pdb.h”
</PRE><A NAME="933809"><PRE>
</PRE><A NAME="933810"><PRE> PDBfile *file;
</PRE><A NAME="933811"><PRE> defstr *ptr;
</PRE><A NAME="933812"><PRE> struct sample
</PRE><A NAME="933813"><PRE> {float x[20];
</PRE><A NAME="933814"><PRE> float y[20];
</PRE><A NAME="933815"><PRE> int number;};
</PRE><A NAME="933816"><PRE> .
</PRE><A NAME="933817"><PRE> .
</PRE><A NAME="933818"><PRE> .
</PRE><A NAME="933819"><PRE> ptr = </a>PD_defstr(file, “sample”, “float x(20)”, “float y(20)”,
</PRE><A NAME="933820"><PRE> “int number”, LAST);
</PRE><A NAME="933821"><PRE> .
</PRE><A NAME="933822"><PRE> .
</PRE><A NAME="933823"><PRE> .
</PRE></dl>
<a name="934412">
<h2>4.15 PD_DEFSTR_ALT</h2>
</a>
<A NAME="934413"><PRE><B>
</B></PRE><a name="934498">
defstr *</a>PD_defstr_alt(PDBfile *file,<p>
</a>
<a name="934499">
char *name,<p>
</a>
<a name="934500">
int nmemb,<p>
</a>
<a name="934501">
char **members)<p>
</a>
<a name="934446">
</a>Define a data </a>structure for a PDB file. As a matter of programming efficiency and clarity it is useful to be able to refer to more complex structural units than the primitive types: short integers, integers, long integers, floating point numbers, double precision floating point numbers, and characters. Arrays do this in a very simple-minded way. Many modern languages support extended types or structures which allow the programmer to group diverse types of data together in a very sophisticated way.<p>
</a>
<a name="934447">
PDBLib supports an extended data typing mechanism called a structure. A </a>structure is a set of declarations of members. Each member is in turn a data type known to the system. Much of the style and usage of structures comes from the C struct. Because of the memory management features upon which PDBLib now depends, even members whose types are pointers are allowed. The only </a>restrictions on member types are that they not be function pointers and that they be expressible without parentheses. Again any member which is a pointer must have its memory allocated by a SCORE </a>memory management function or macro. See the Memory Management section near the beginning of this manual. <p>
</a>
<a name="934448">
</a>PD_defstr defines structures to the PDB system so that they can be read and written as a whole in a single statement. The members of the </a>structure are processed and an entry in the structure chart is made. Then subsequent references to the new structure type are processed using information from the structure chart. The syntax by which members of a structure are specified is like that for C structs. The formal definition is given below ([ ] enclose optional elements). </a>Self-referential structures are allowed providing the reference is through pointers (like C). The actual type name is used in the reference since PDBLib checks that all member types are already known or are the type being defined.<p>
</a>
<dl>
<a name="934449">
<dt>
</a>
<a name="934450">
<dt> <member> := <type> [*...*]<member name>[(<dimensions>)]
</a>
<a name="934451">
<dt> <type> := <primitive type> | <derived type>
</a>
<a name="934452">
<dt> <member name> := an ascii string representing the name of the member
</a>
<a name="934453">
<dt> <primitive type> := short | integer | long | float | double | char
</a>
<a name="934454">
<dt> <derived type> := any </a>PD_defstr’d type
</a>
<a name="934455">
<dt> <dimensions> := <integer> |
</a>
<a name="934456">
<dt> <integer : integer> |
</a>
<a name="934457">
<dt> <integer>, <dimensions> |
</a>
<a name="934458">
<dt> <integer : integer> <dimensions>
</a>
<a name="934459">
Dimensions can be given in two ways. If the default offset value for the PDB file can be taken as the minimum value for the range which a dimension index can legally run, the maximum value may be specified alone. Alternatively, the minimum value followed by a colon and the maximum value may be specified. For example,<p>
</a>
<a name="934460">
<dd> integer a(30,1:10)<P>
</a>
<a name="934461">
The arguments to </a>PD_defstr are: file, a pointer to a PDBfile; name, an ASCII string containing the name of the data structure type in the PDB file; nmemb, an integer number of strings in the members array; and members, an array of ASCII strings each representing the declaration of a member of a </a>structure are defined above.<p>
</a>
<a name="934462">
The return value is a pointer to the entry made in the structure chart if the call is successful; otherwise, NULL is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="934463">
<p>
</a>
<a name="934464">
<p>
</a>
<a name="934465">
defstr *</a>PD_defstr_alt(PDBfile *file,<p>
</a>
<a name="934466">
char *name,<p>
</a>
<a name="934468">
int nmemb,<p>
</a>
<a name="934467">
char **members)<p>
</a>
<A NAME="934469"><B>
</B><HR><A NAME="934470"><PRE> #include “pdb.h”
</PRE><A NAME="934471"><PRE>
</PRE><A NAME="934472"><PRE> PDBfile *file;
</PRE><A NAME="934473"><PRE> defstr *ptr;
</PRE><A NAME="934497"><PRE> char **members;
</PRE><A NAME="934475"><PRE> struct sample
</PRE><A NAME="934476"><PRE> {float x[20];
</PRE><A NAME="934477"><PRE> float y[20];
</PRE><A NAME="934478"><PRE> int number;};
</PRE><A NAME="934479"><PRE> .
</PRE><A NAME="934480"><PRE> .
</PRE><A NAME="934481"><PRE> .
</PRE><A NAME="934489"><PRE> members = MAKE_N(char *, 3);
</PRE><A NAME="934490"><PRE> members[0] = SC_strsave(“float x[20]”);
</PRE><A NAME="934491"><PRE> members[1] = SC_strsave(“float y[20]”);
</PRE><A NAME="934492"><PRE> members[2] = SC_strsave(“integer number”);
</PRE><A NAME="934483"><PRE> ptr = </a>PD_defstr_alt(file, “sample”, 3, members);
</PRE><A NAME="934484"><PRE>
</PRE><A NAME="934493"><PRE> SFREE(members[0]);
</PRE><A NAME="934494"><PRE> SFREE(members[1]);
</PRE><A NAME="934495"><PRE> SFREE(members[3]);
</PRE><A NAME="934496"><PRE> SFREE(members);
</PRE><A NAME="934485"><PRE> .
</PRE><A NAME="934486"><PRE> .
</PRE><A NAME="934487"><PRE> .
</PRE></dl>
<a name="935904">
<h2>4.16 PD_FAMILY</h2>
</a>
<A NAME="935907"><PRE><B>
</B></PRE><A NAME="935970"><PRE><B>PDBfile *</a>PD_family(PDBfile *file, int flag)
</B></PRE><a name="935971">
This function checks to see whether the specified file has exceeded it size limit. If it has a new file is opened and returns. If not the given file pointer is returned. The flag is set to TRUE if you want </a>PD_family to close the file it is given. Otherwise the application is responsible for closing the file<p>
</a>
<a name="935985">
The arguments to this function are: file, the pointer to the PDBfile structure returned by a previous call to </a>PD_open; and flag an integer value (either TRUE or FALSE).<p>
</a>
<a name="935990">
This function returns a pointer to a PDBfile.<p>
</a>
<a name="935995">
<p>
</a>
<a name="935996">
PDBfile *</a>PD_family(PDBfile *file, int flag)<p>
</a>
<A NAME="935997"><B>
</B><HR><A NAME="935998"><PRE> #include “pdb.h”
</PRE><A NAME="935999"><PRE>
</PRE><A NAME="936000"><PRE> PDBfile *old, *new;
</PRE><A NAME="936001"><PRE> .
</PRE><A NAME="936003"><PRE> .
</PRE><A NAME="936004"><PRE> .
</PRE><A NAME="936005"><PRE> new = PD_family(old, FALSE);
</PRE><A NAME="935323"><PRE> if (new != old)
</PRE><A NAME="935324"><PRE> {PD_close(old);
</PRE><A NAME="935325"><PRE> .
</PRE><A NAME="935524"><PRE> .
</PRE><A NAME="935811"><PRE> .
</PRE><A NAME="935972"><PRE> old = new;};
</PRE><A NAME="936008"><PRE> .
</PRE><A NAME="936009"><PRE> .
</PRE><A NAME="936010"><PRE> .
</PRE><a name="933831">
<h2>4.17 PD_FLUSH</h2>
</a>
<A NAME="934268"><PRE><B>
</B></PRE><A NAME="934275"><PRE><B>int </a>PD_flush(PDBfile *file)
</B></PRE><a name="934277">
This function writes out the information which describes the </a>contents of the PDB file specified. Normally, </a>PD_close calls this routine, but applications that want to protect themselves from system failures or other problems may chose to periodically use this function. After a successful return and until or unless more data is written to the file or space reserved for future writes, the PDB file is valid in the sense that if the application terminates unexpectedly before calling PD_close, the file can be </a>PD_open’d successfully.<p>
</a>
<a name="934276">
NOTE: this call does NOT obviate PD_close!<p>
</a>
<a name="934278">
The argument to this function is file, the pointer to the PDBfile structure returned by a previous call to PD_open.<p>
</a>
<a name="934279">
This function returns TRUE if successful and FALSE otherwise.<p>
</a>
<a name="934281">
<p>
</a>
<a name="934282">
int </a>PD_flush(PDBfile *file)<p>
</a>
<A NAME="934283"><B>
</B><HR><A NAME="934284"><PRE> #include “pdb.h”
</PRE><A NAME="934285"><PRE>
</PRE><A NAME="934286"><PRE> PDBfile *file;
</PRE><A NAME="934287"><PRE> .
</PRE><A NAME="934288"><PRE> .
</PRE><A NAME="934289"><PRE> .
</PRE><A NAME="934290"><PRE> if (</a>PD_flush(file) == FALSE)
</PRE><A NAME="934291"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="934292"><PRE> .
</PRE><A NAME="934293"><PRE> .
</PRE><A NAME="934280"><PRE> .
</PRE><a name="934559">
<h2>4.18 PD_GET_ATTRIBUTE</h2>
</a>
<A NAME="934560"><PRE><B>
</B></PRE><A NAME="934561"><PRE><B>void *</a>PD_get_attribute(PDBfile *file,
</B></PRE><A NAME="934562"><PRE><B> char *vr,
</B></PRE><A NAME="934567"><PRE><B> char *attr)
</B></PRE><a name="934564">
</a>Return the value of the specified </a>attribute for the named entity.<p>
</a>
<a name="934563">
The </a>model of an attribute in PDBLib is an entity that has a name and type. The two supported operations on attributes are to create them and to remove them. An entity in a PDB file can be assigned an </a>attribute value simply by calling </a>PD_set_attribute. The only association between an entry in a PDB file and any attribute is made by the name in the attribute table and the entry in the symbol table. In particular, this mechanism allows the application developer to define and use entities in a PDB file solely in terms of attributes.<p>
</a>
<a name="934565">
Attribute values are always assigned by </a>reference and </a>PD_get_attribute returns them the same way. The application may have to make a cast on the returned pointer.<p>
</a>
<a name="934566">
The arguments to this function are: file, a pointer to a PDBfile; vr, an ASCII string containing the name of an entity in the PDB file; and attr, an ASCII string containing the name of the attribute being sought.<p>
</a>
<a name="934579">
The return value is a pointer to the value of the attribute if one exists and NULL otherwise.<p>
</a>
<a name="934568">
See also </a>PD_def_attribute, </a>PD_rem_attribute, and </a>PD_set_attribute.<p>
</a>
<a name="934946">
<p>
</a>
<A NAME="934924"><PRE><B>void *</a>PD_get_attribute(PDBfile *file,
</B></PRE><A NAME="934966"><PRE><B> char *vr,
</B></PRE><A NAME="934967"><PRE><B> char *attr)
</B></PRE><A NAME="934951"><B>
</B><HR><A NAME="934952"><PRE> #include “pdb.h”
</PRE><A NAME="934953"><PRE>
</PRE><A NAME="934954"><PRE> PDBfile *file;
</PRE><A NAME="934947"><PRE> char *dt;
</PRE><A NAME="934955"><PRE> .
</PRE><A NAME="934957"><PRE> .
</PRE><A NAME="934958"><PRE> .
</PRE><A NAME="934959"><PRE> dt = (char *) </a>PD_get_attribute(file, “foo”, “date”);
</PRE><A NAME="934960"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="934961"><PRE> .
</PRE><A NAME="934962"><PRE> .
</PRE><A NAME="934964"><PRE> .
</PRE><a name="935459">
<h2>4.19 PD_LN</h2>
</a>
<A NAME="935460"><PRE><B>
</B></PRE><A NAME="935462"><PRE><B>int </a>PD_ln(PDBfile *file,
</B></PRE><A NAME="935464"><PRE><B> char *var,
</B></PRE><A NAME="935498"><PRE><B> char *link)
</B></PRE><a name="935465">
</a>Create a link to a variable in the specified PDB file.<p>
</a>
<a name="935467">
PDBLib supports an optional </a>hierarchical </a>directory structure inside PDB files. A directory or a variable in a directory may be specified by either a </a>relative path or an </a>absolute path. Slashes separate nodes in a </a>path name. Absolute paths begin with a slash. Nodes consisting of two periods, “..”, refer to the next higher level directory.<p>
</a>
<a name="935468">
The arguments to </a>PD_ln are: file, a pointer to a PDBfile; var, an ASCII string containing the path name of an existing variable; and link, an ASCII string containing the path name of the new link.<p>
</a>
<a name="935469">
The return value is a TRUE if successful; otherwise, FALSE is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="935470">
See also </a>PD_cd, </a>PD_ls, </a>PD_mkdir, and </a>PD_pwd.<p>
</a>
<a name="935471">
<p>
</a>
<a name="935472">
int </a>PD_ln(PDBfile *file,<p>
</a>
<a name="935473">
char *var,<p>
</a>
<a name="935499">
char *link)<p>
</a>
<A NAME="935474"><B>
</B><HR><A NAME="935475"><PRE> #include “pdb.h”
</PRE><A NAME="935476"><PRE>
</PRE><A NAME="935477"><PRE> PDBfile *file;
</PRE><A NAME="935478"><PRE> .
</PRE><A NAME="935479"><PRE> .
</PRE><A NAME="935480"><PRE> .
</PRE><A NAME="935481"><PRE> if (</a>PD_ln(file, “/animals/mammals/chimpanzee”, “/chimp”) == FALSE)
</PRE><A NAME="935483"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="935484"><PRE> .
</PRE><A NAME="935486"><PRE> .
</PRE><A NAME="935492"><PRE> .
</PRE><a name="935493">
<h2>4.20 PD_LS</h2>
</a>
<A NAME="935494"><PRE><B>
</B></PRE><A NAME="935495"><PRE><B>char **PD_ls(PDBfile *file,
</B></PRE><A NAME="935496"><PRE><B> char *path,
</B></PRE><A NAME="935526"><PRE><B> char *type,
</B></PRE><A NAME="935497"><PRE><B> int *num)
</B></PRE><a name="935501">
</a>Return a list of names of entries (variables and directories) in PDB file file that are of type type and that are in the </a>directory and match the variable name pattern specified by path.<p>
</a>
<a name="935542">
PDBLib supports an optional </a>hierarchical </a>directory structure inside PDB files. A directory or a variable in a directory may be specified by either a </a>relative path or an </a>absolute path. Slashes separate nodes in a </a>path name. Absolute paths begin with a slash. Nodes consisting of two periods, “..”, refer to the next higher level directory.<p>
</a>
<a name="935527">
The arguments to </a>PD_ls are: file, a pointer to a PDBfile; <em>path</em>, an ASCII string containing the path name of the directory to search and/or the variable name pattern to match; <em>type</em>, an ASCII string containing the type of entries to return; and num, a pointer to an integer to contain the number of entries returned.<p>
</a>
<a name="935530">
If path is NULL, the contents of the </a>current directory are listed. If type is NULL, all types are returned.<p>
</a>
<a name="935500">
The terminal node of path may contain meta characters “*” and “?”. Each “*” matches any zero or more characters and each “?” matches any single character.<p>
</a>
<a name="935503">
For the sake of efficiency, the returned names are not duplicated. That is, the caller should not free the space associated with each of the individual strings, but should free the char ** pointer. This should be done using the SFREE macro as shown in the example.<p>
</a>
<a name="935502">
The return value is a pointer to an array of strings, if successful; otherwise, NULL is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="935504">
See also </a>PD_cd, </a>PD_ln, </a>PD_mkdir, and </a>PD_pwd.<p>
</a>
<a name="935505">
<p>
</a>
<a name="935506">
int </a>PD_ls(PDBfile *file,<p>
</a>
<a name="935507">
char *path,<p>
</a>
<a name="935509">
char *type,<p>
</a>
<a name="935531">
int *num)<p>
</a>
<A NAME="935510"><B>
</B><HR><A NAME="935511"><PRE> #include “pdb.h”
</PRE><A NAME="935512"><PRE>
</PRE><A NAME="935513"><PRE> PDBfile *file;
</PRE><A NAME="935543"><PRE> char **list;
</PRE><A NAME="935580"><PRE> int num;
</PRE><A NAME="935514"><PRE> .
</PRE><A NAME="935516"><PRE> .
</PRE><A NAME="935517"><PRE> .
</PRE><A NAME="935518"><PRE> /* get a list of all directories in the current directory */
</PRE><A NAME="935519"><PRE> list = </a>PD_ls(file, NULL, “Directory”, &num);
</PRE><A NAME="935521"><PRE> if (list == NULL)
</PRE><A NAME="935522"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="935523"><PRE> .
</PRE><A NAME="935541"><PRE> .
</PRE><A NAME="935544"><PRE> .
</PRE><A NAME="935545"><PRE> SFREE(list);
</PRE><A NAME="935546"><PRE> .
</PRE><A NAME="935548"><PRE> .
</PRE><A NAME="935549"><PRE> .
</PRE><A NAME="935550"><PRE> /* get a list of the variables of type char * in directory animals */
</PRE><A NAME="935551"><PRE> list = </a>PD_ls(file, “animals”, “char *”, &num);
</PRE><A NAME="935553"><PRE> if (list == NULL)
</PRE><A NAME="935554"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="935555"><PRE> .
</PRE><A NAME="935556"><PRE> .
</PRE><A NAME="935559"><PRE> .
</PRE><A NAME="935560"><PRE> SFREE(list);
</PRE><A NAME="935577"><PRE> .
</PRE><A NAME="935578"><PRE> .
</PRE><A NAME="935579"><PRE> .
</PRE><a name="935581">
<h2>4.21 PD_MKDIR</h2>
</a>
<A NAME="935583"><PRE><B>
</B></PRE><A NAME="935584"><PRE><B>int </a>PD_mkdir(PDBfile *file,
</B></PRE><A NAME="935594"><PRE><B> char *dirname)
</B></PRE><a name="935595">
</a>Create a new directory in the specified PDB file.<p>
</a>
<a name="935596">
PDBLib supports an optional </a>hierarchical </a>directory structure inside PDB files. A directory or a variable in a directory may be specified by either a </a>relative path or an </a>absolute path. Slashes separate nodes in a </a>path name. Absolute paths begin with a slash. Nodes consisting of two periods, “..”, refer to the next higher level directory.<p>
</a>
<a name="935597">
The arguments to </a>PD_mkdir are: file, a pointer to a PDBfile and dirname, an ASCII string containing the path name of the new directory.<p>
</a>
<a name="935593">
The </a>root directory, “/”, does not have to be created.<p>
</a>
<a name="935598">
The return value is a TRUE if successful; otherwise, FALSE is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="935599">
See also </a>PD_cd, </a>PD_ln, </a>PD_ls, and </a>PD_pwd.<p>
</a>
<a name="935600">
<p>
</a>
<a name="935602">
int </a>PD_mkdir(PDBfile *file,<p>
</a>
<a name="935604">
char *dirname)<p>
</a>
<A NAME="935605"><B>
</B><HR><A NAME="935606"><PRE> #include “pdb.h”
</PRE><A NAME="935607"><PRE>
</PRE><A NAME="935608"><PRE> PDBfile *file;
</PRE><A NAME="935609"><PRE> .
</PRE><A NAME="935610"><PRE> .
</PRE><A NAME="935611"><PRE> .
</PRE><A NAME="935612"><PRE> if (</a>PD_mkdir(file, “/animals/mammals) == FALSE)
</PRE><A NAME="935613"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="935614"><PRE> .
</PRE><A NAME="935615"><PRE> .
</PRE><A NAME="935616"><PRE> .
</PRE><a name="934232">
<h2>4.22 PD_OPEN</h2>
</a>
<A NAME="933834"><PRE><B>
</B></PRE><A NAME="932630"><PRE><B>PDBfile *</a>PD_open(char *filename,
</B></PRE><A NAME="932631"><PRE><B> char *mode)
</B></PRE><a name="933848">
</a>Open an existing PDB file or </a>create a new PDB file. Depending on the value of the mode argument, PDBLib attempts to open the file filename in read-only binary mode, open the file in append binary </a>mode, or create a new file in read-write binary mode. Any string which begins with “</a>r” causes the file to be opened in </a>read-only mode, any string beginning with “</a>a” causes the file to be opened in </a>append mode, and any string beginning with “</a>w” causes a file to be </a>created in </a>read-write mode. Next the beginning of the file is searched for the header which identifies the file as having been generated by PDBLib. The addresses of the structure chart and symbol table are then sought.<p>
</a>
<a name="933857">
The structure chart from the file is read in. The structure chart contains information about data types (e.g. floats), their sizes in bytes and their structures if any. By default there are six </a>primitive </a>data types that PDBLib knows about: short integers, integers, long integers, floating point numbers, double precision floating point numbers, characters, and pointers. The sizes of these types varies from machine to machine, but PDBLib hides this from the user.<p>
</a>
<a name="933863">
The symbol table from the file is read in. The symbol table contains the list of variables in the file, their types as defined in the structure chart, and dimensioning information for arrays. Each read from the file first consults the symbol table to see if the requested variable is present in the PDB file.<p>
</a>
<a name="933868">
Both the structure chart and the symbol table are implemented as hash tables, although their shapes are different. This makes lookups as efficient as possible given an unknown amount of data in the file.<p>
</a>
<a name="933871">
The arguments to </a>PD_open are: filename, an ASCII string, which is the name of the file to be created or opened; and mode, an ASCII string, which is the mode (either “w” for create, “r” for read-only or “a” for append).<p>
</a>
<a name="933878">
The function returns a pointer to a PDBfile. This PDBfile identifies the particular file to PDBLib. As such, if it is overwritten the file is lost. The number of PDB files which can be open simultaneously is machine or operating system dependent, but each open file has a unique PDBfile associated with it.<p>
</a>
<a name="933881">
If any aspect of the PDB file opening process fails a NULL pointer is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="933884">
<p>
</a>
<a name="932633">
PDBfile *</a>PD_open(char *filename,<p>
</a>
<a name="932634">
char *mode)<p>
</a>
<A NAME="933889"><B>
</B><HR><A NAME="933893"><PRE> #include “pdb.h”
</PRE><A NAME="933894"><PRE>
</PRE><A NAME="933895"><PRE> PDBfile *file;
</PRE><A NAME="933896"><PRE> .
</PRE><A NAME="933897"><PRE> .
</PRE><A NAME="933898"><PRE> .
</PRE><A NAME="933899"><PRE> if ((file = </a>PD_open(“filenam”, “r”)) == NULL)
</PRE><A NAME="933900"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="933901"><PRE> .
</PRE><A NAME="933902"><PRE> .
</PRE><A NAME="933903"><PRE> .
</PRE><a name="935603">
<h2>4.23 PD_PWD</h2>
</a>
<A NAME="935617"><PRE><B>
</B></PRE><A NAME="935618"><PRE><B>char *PD_pwd(PDBfile *file)
</B></PRE><a name="935620">
</a>Return the </a>current </a>directory for the specified PDB file.<p>
</a>
<a name="935621">
PDBLib supports an optional </a>hierarchical </a>directory structure inside PDB files. A directory or a variable in a directory may be specified by either a </a>relative path or an </a>absolute path. Slashes separate nodes in a </a>path name. Absolute paths begin with a slash. Nodes consisting of two periods, “..”, refer to the next higher level directory.<p>
</a>
<a name="935622">
The argument to </a>PD_pwd is file, a pointer to a PDBfile.<p>
</a>
<a name="935619">
If no directory has been created, “/” is returned.<p>
</a>
<a name="935624">
The return value is a pointer to a string containing the path name of the current directory if successful; otherwise, NULL is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="935625">
See also </a>PD_cd, </a>PD_ln, </a>PD_ls, and </a>PD_mkdir.<p>
</a>
<a name="935626">
<p>
</a>
<a name="935627">
int </a>PD_pwd(PDBfile *file)<p>
</a>
<A NAME="935629"><B>
</B><HR><A NAME="935630"><PRE> #include “pdb.h”
</PRE><A NAME="935631"><PRE>
</PRE><A NAME="935632"><PRE> PDBfile *file;
</PRE><A NAME="935623"><PRE> char *dirname;
</PRE><A NAME="935633"><PRE> .
</PRE><A NAME="935635"><PRE> .
</PRE><A NAME="935636"><PRE> .
</PRE><A NAME="935637"><PRE> if ((dirname = </a>PD_pwd(file)) == NULL)
</PRE><A NAME="935638"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="935639"><PRE> .
</PRE><A NAME="935640"><PRE> .
</PRE><A NAME="935641"><PRE> .
</PRE><a name="933911">
<h2>4.24 PD_READ</h2>
</a>
<A NAME="933914"><PRE><B>
</B></PRE><A NAME="932635"><PRE><B>int </a>PD_read(PDBfile *file,
</B></PRE><A NAME="932636"><PRE><B> char *name,
</B></PRE><A NAME="932637"><PRE><B> void *var)
</B></PRE><a name="933921">
</a>Read all or part of a data entry from an open PDB file. The symbol table of the given PDB file is searched for the given name and if it is found the information there is used to read the proper number of bytes from the file, do any conversions, and put the result in memory pointed to by var.<p>
</a>
<a name="933057">
The arguments to </a>PD_read are: file, a pointer to a PDBfile which designates the PDB file from which to attempt the read; name, an ASCII string containing the specification of data to be read; and var, a pointer to the location where the data is to be placed.<p>
</a>
<a name="932809">
Note: In each </a>PD_read operation, the type of var must be a pointer to the type of the variable name.<p>
</a>
<a name="933053">
Note: PDBLib can only read part of an entry if the type of the terminal node is primitive or a structure which contains no indirections and whose descendant members contain no indirections. <p>
</a>
<a name="933929">
Note: When reading part of a variable, especially a structured variable, the path to the desired part must contain one array reference for each level of </a>indirection traversed.<p>
</a>
<a name="933933">
The return value is TRUE, if successful; otherwise, FALSE is returned and the ASCII string PD_err contains any error messages.<p>
</a>
<a name="934226">
See also </a>PD_read_alt, </a>PD_read_as, </a>PD_read_as_alt.<p>
</a>
<a name="933939">
<p>
</a>
<a name="932639">
int </a>PD_read(PDBfile *file,<p>
</a>
<a name="932641">
char *name,<p>
</a>
<a name="932642">
void *var)<p>
</a>
<A NAME="933944"><B>
</B><HR><A NAME="933948"><PRE> #include “pdb.h”
</PRE><A NAME="933949"><PRE>
</PRE><A NAME="933950"><PRE> PDBfile *file;
</PRE><A NAME="933951"><PRE> float x[20];
</PRE><A NAME="933952"><PRE> .
</PRE><A NAME="933953"><PRE> .
</PRE><A NAME="933954"><PRE> .
</PRE><A NAME="933955"><PRE> if (</a>PD_read(file, “x”, x) == FALSE)
</PRE><A NAME="933956"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="933957"><PRE> .
</PRE><A NAME="933958"><PRE> .
</PRE><A NAME="933959"><PRE> .
</PRE><a name="932648">
<h2>4.25 PD_READ_ALT</h2>
</a>
<A NAME="932649"><PRE><B>
</B></PRE><A NAME="932650"><PRE><B>int </a>PD_read_alt(PDBfile *file,
</B></PRE><A NAME="932651"><PRE><B> char *name,
</B></PRE><A NAME="932652"><PRE><B> void *var,
</B></PRE><A NAME="932653"><PRE><B> long *ind)
</B></PRE><a name="932654">
</a>Read all or part of a data entry from an open PDB file. The symbol table of the given PDB file is searched for the given name and if it is found the information there is used to read the proper number of bytes from the file, do any conversions, and put the result in memory pointed to by var.<p>
</a>
<a name="932676">
The arguments to </a>PD_read_alt are: file, a pointer to a PDBfile which designates the PDB file from which to attempt the read; name, an ASCII string containing the specification of the data to be read; var, a pointer to the location where the data is to be placed; and ind, an array of long integers consisting of three indexes (start, stop, and step) for each dimension of the entry.<p>
</a>
<a name="932677">
Note: In each </a>PD_read_alt operation, the type of var must be a pointer to the type of the variable name.<p>
</a>
<a name="933937">
Note: PDBLib can only read part of an entry if the type of the terminal node is primitive or a structure which contains no indirections and whose descendant members contain no indirections. <p>
</a>
<a name="932678">
Note: When reading part of a variable, especially a structured variable, the path to the desired part must contain one array reference for each level of </a>indirection traversed.<p>
</a>
<a name="932680">
The return value is TRUE, if successful; otherwise, FALSE is returned and the ASCII string PD_err contains any error messages.<p>
</a>
<a name="934225">
See also </a>PD_read, </a>PD_read_as, </a>PD_read_as_alt.<p>
</a>
<a name="932681">
<p>
</a>
<a name="932682">
int </a>PD_read_alt(PDBfile *file,<p>
</a>
<a name="932683">
char *name,<p>
</a>
<a name="932684">
void *var,<p>
</a>
<a name="932685">
long *ind)<p>
</a>
<A NAME="932686"><B>
</B><HR><A NAME="932986"><PRE> #include “pdb.h”
</PRE><A NAME="932990"><PRE>
</PRE><A NAME="932991"><PRE> PDBfile *file;
</PRE><A NAME="932995"><PRE> long ind[3];
</PRE><A NAME="932996"><PRE> float x[20];
</PRE><A NAME="932997"><PRE> .
</PRE><A NAME="932998"><PRE> .
</PRE><A NAME="933000"><PRE> .
</PRE><A NAME="933040"><PRE> ind[0] = 3;
</PRE><A NAME="933044"><PRE> ind[1] = 18;
</PRE><A NAME="933334"><PRE> ind[2] = 2;
</PRE><A NAME="933335"><PRE> if (</a>PD_read_alt(file, “x”, x, ind) == FALSE)
</PRE><A NAME="933336"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="933337"><PRE> .
</PRE><A NAME="933338"><PRE> .
</PRE><A NAME="933339"><PRE> .
</PRE><a name="932598">
<h2>4.26 PD_READ_AS</h2>
</a>
<A NAME="932600"><PRE><B>
</B></PRE><A NAME="932601"><PRE><B>int </a>PD_read_as(PDBfile *file,
</B></PRE><A NAME="932602"><PRE><B> char *name,
</B></PRE><A NAME="932603"><PRE><B> char *type,
</B></PRE><A NAME="933098"><PRE><B> void *var)
</B></PRE><a name="932604">
</a>Read data from an open PDB file. The symbol table of the given PDB file is searched for the given name and if it is found the information there is used with the type specified by type to read the proper number of bytes from the file, do any conversions, and put the result in memory pointed to by var. The type specified overrides the type in the symbol table entry as far as deciding on data conversions goes.<p>
</a>
<a name="933099">
This function is generally used to read floats as doubles and so on. However with sufficient care and understanding of both the file data and C data structuring, it can be used to transmute structured data.<p>
</a>
<a name="932606">
The arguments to </a>PD_read_as are: file, a pointer to a PDBfile which designates the PDB file from which to attempt the read; name, an ASCII string containing the specification for the data to be read;<em> type</em>, an ASCII string containing the type of the data desired; and var, a pointer to the location where the data is to be placed.<p>
</a>
<a name="932607">
Note: In each </a>PD_read_as operation, the type of var must be a pointer to the type specified by type.<p>
</a>
<a name="934313">
Note: PDBLib can only read part of an entry if the type of the terminal node is primitive or a structure which contains no indirections and whose descendant members contain no indirections. <p>
</a>
<a name="932608">
Note: When reading part of a variable, especially a structured variable, the path to the desired part must contain one array reference for each level of </a>indirection traversed.<p>
</a>
<a name="932609">
The return value is TRUE, if successful; otherwise, FALSE is returned and the ASCII string PD_err contains any error messages.<p>
</a>
<a name="934212">
See also </a>PD_read, </a>PD_read_alt, </a>PD_read_as_alt.<p>
</a>
<a name="932610">
<p>
</a>
<a name="933067">
int </a>PD_read_as(PDBfile *file,<p>
</a>
<a name="933069">
char *name,<p>
</a>
<a name="933072">
char *type,<p>
</a>
<a name="933095">
void *var)<p>
</a>
<A NAME="933075"><B>
</B><HR><A NAME="933077"><PRE> #include “pdb.h”
</PRE><A NAME="933078"><PRE>
</PRE><A NAME="933079"><PRE> PDBfile *file;
</PRE><A NAME="933081"><PRE> float x[20];
</PRE><A NAME="933082"><PRE> .
</PRE><A NAME="933083"><PRE> .
</PRE><A NAME="933085"><PRE> .
</PRE><A NAME="933086"><PRE> /* x is a double in the file */
</PRE><A NAME="933096"><PRE> if (</a>PD_read_as(file, “x”, “float”, x) == FALSE)
</PRE><A NAME="933087"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="933090"><PRE> .
</PRE><A NAME="933092"><PRE> .
</PRE><A NAME="933094"><PRE> .
</PRE><A NAME="932526"><PRE>
</PRE><a name="932862">
<h2>4.27 PD_READ_AS_ALT</h2>
</a>
<A NAME="932870"><PRE><B>
</B></PRE><A NAME="933045"><PRE><B>int </a>PD_read_as_alt(PDBfile *file,
</B></PRE><A NAME="933049"><PRE><B> char *name,
</B></PRE><A NAME="933050"><PRE><B> char *type,
</B></PRE><A NAME="933051"><PRE><B> void *var,
</B></PRE><A NAME="933052"><PRE><B> long *ind)
</B></PRE><a name="933054">
</a>Read all or part of a data entry from an open PDB file. The symbol table of the given PDB file is searched for the given name and if it is found the information there is used with the type specified by type to read the proper number of bytes from the file, do any conversions, and put the result in memory pointed to by var. The type specified overrides the type in the symbol table entry as far as deciding on data conversions goes.<p>
</a>
<a name="933285">
This function is generally used to read floats as doubles and so on. However with sufficient care and understanding of both the file data and C data structuring, it can be used to transmute structured data.<p>
</a>
<a name="933309">
The arguments to </a>PD_read_as_alt are: file, a pointer to a PDBfile which designates the PDB file from which to attempt the read; name, an ASCII string containing the specification of the data to be read;<em> type</em>, an ASCII string containing the type of the data desired; var, a pointer to the location where the data is to be placed; and ind, an array of long integers consisting of three indexes (start, stop, and step) for each dimension of the entry.<p>
</a>
<a name="933310">
Note: In each </a>PD_read_as_alt operation, the type of var must be a pointer to the type specified by type.<p>
</a>
<a name="934314">
Note: PDBLib can only read part of an entry if the type of the terminal node is primitive or a structure which contains no indirections and whose descendant members contain no indirections. <p>
</a>
<a name="933311">
Note: When reading part of a variable, especially a structured variable, the path to the desired part must contain one array reference for each level of </a>indirection traversed.<p>
</a>
<a name="933312">
The return value is TRUE, if successful; otherwise, FALSE is returned and the ASCII string PD_err contains any error messages.<p>
</a>
<a name="933989">
See also </a>PD_read, </a>PD_read_as, </a>PD_read_alt.<p>
</a>
<a name="933313">
<p>
</a>
<A NAME="933314"><PRE><B>int </a>PD_read_as_alt(PDBfile *file,
</B></PRE><A NAME="933319"><PRE><B> char *name,
</B></PRE><A NAME="933320"><PRE><B> char *type,
</B></PRE><A NAME="933321"><PRE><B> void *var,
</B></PRE><A NAME="933322"><PRE><B> long *ind)
</B></PRE><A NAME="933323"><B>
</B><HR><A NAME="933324"><PRE> #include “pdb.h”
</PRE><A NAME="933325"><PRE>
</PRE><A NAME="933326"><PRE> PDBfile *file;
</PRE><A NAME="933327"><PRE> long ind[3];
</PRE><A NAME="933328"><PRE> float x[20];
</PRE><A NAME="933329"><PRE> .
</PRE><A NAME="933330"><PRE> .
</PRE><A NAME="933331"><PRE> .
</PRE><A NAME="933340"><PRE> ind[0] = 2;
</PRE><A NAME="933341"><PRE> ind[1] = 10;
</PRE><A NAME="933342"><PRE> ind[2] = 2;
</PRE><A NAME="933343"><PRE>
</PRE><A NAME="933344"><PRE> /* x is a double in the file */
</PRE><A NAME="933345"><PRE> if (</a>PD_read_as_alt(file, “x”, “float”, x, ind) == FALSE)
</PRE><A NAME="933346"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="933572"><PRE> .
</PRE><A NAME="933579"><PRE> .
</PRE><A NAME="933593"><PRE> .
</PRE><a name="934188">
<h2>4.28 PD_RESET_PTR_LIST</h2>
</a>
<A NAME="936825"><PRE><B>
</B></PRE><A NAME="936827"><PRE><B>int </a>PD_reset_ptr_list(PDBfile *file)
</B></PRE><a name="936829">
Free the list of pointers which the PDB file file knows about. This includes both pointers in memory acquired during write operations and pointers in the file acquired during read operations.<p>
</a>
<a name="936830">
Rationale: When reading or writing indirectly referenced data, PDBLib, maintains an array of pointers encountered in write operations and an array of pointers encountered in read operations. This is done on a per file basis. These arrays are the basis on which PDBLIb can determine how to preserve the connectivity of data trees when they are moved between memory and files. Because of the difference between memory and disk files, it is important for applications to be able to clear out these arrays and start over. See the discussion on </a>Using Pointers earlier in the manual.<p>
</a>
<a name="936828">
The argument to this function is file a pointer to a PDBfile.<p>
</a>
<a name="936832">
The return value is TRUE if successful, and FALSE otherwise.<p>
</a>
<a name="936833">
<p>
</a>
<A NAME="936834"><PRE><B>int </a>PD_reset_ptr_list(PDBfile *file)
</B></PRE><A NAME="936835"><B>
</B><HR><A NAME="936836"><PRE> #include “pdb.h”
</PRE><A NAME="936837"><PRE>
</PRE><A NAME="936839"><PRE> PDBfile *file;
</PRE><A NAME="936840"><PRE> .
</PRE><A NAME="936841"><PRE> .
</PRE><A NAME="936842"><PRE> .
</PRE><A NAME="936843"><PRE> if (</a>PD_reset_ptr_list(file) == FALSE)
</PRE><A NAME="936844"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="936845"><PRE> .
</PRE><A NAME="936846"><PRE> .
</PRE><a name="934569">
<h2>4.29 PD_REM_ATTRIBUTE</h2>
</a>
<A NAME="934570"><PRE><B>
</B></PRE><A NAME="934571"><PRE><B>int </a>PD_rem_attribute(PDBfile *file,
</B></PRE><A NAME="934573"><PRE><B> char *attr)
</B></PRE><a name="934574">
</a>Remove the specified </a>attribute. Any entities which have a value for this </a>attribute will have it removed by PDBLib.<p>
</a>
<a name="934575">
The </a>model of an attribute in PDBLib is an entity that has a name and type. The two supported operations on attributes are to create them and to remove them. An entity in a PDB file can be assigned an </a>attribute value simply by calling </a>PD_set_attribute. The only association between an entry in a PDB file and any attribute is made by the name in the attribute table and the entry in the symbol table. In particular, this mechanism allows the application developer to define and use entities in a PDB file solely in terms of attributes.<p>
</a>
<a name="934577">
The arguments to this function are: file, a pointer to a PDBfile; and attr, an ASCII string containing the name of the attribute being removed.<p>
</a>
<a name="934578">
The return value is TRUE if successful, and FALSE otherwise.<p>
</a>
<a name="934572">
See also </a>PD_def_attribute, </a>PD_get_attribute, and </a>PD_set_attribute.<p>
</a>
<a name="934950">
<p>
</a>
<A NAME="934948"><PRE><B>int </a>PD_rem_attribute(PDBfile *file,
</B></PRE><A NAME="934993"><PRE><B> char *attr)
</B></PRE><A NAME="934976"><B>
</B><HR><A NAME="934977"><PRE> #include “pdb.h”
</PRE><A NAME="934979"><PRE>
</PRE><A NAME="934980"><PRE> PDBfile *file;
</PRE><A NAME="934981"><PRE> .
</PRE><A NAME="934986"><PRE> .
</PRE><A NAME="934987"><PRE> .
</PRE><A NAME="934988"><PRE> if (</a>PD_rem_attribute(file, “date”) == FALSE)
</PRE><A NAME="934989"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="934990"><PRE> .
</PRE><A NAME="934991"><PRE> .
</PRE><A NAME="934992"><PRE> .
</PRE><a name="934580">
<h2>4.30 PD_SET_ATTRIBUTE</h2>
</a>
<A NAME="934581"><PRE><B>
</B></PRE><A NAME="934582"><PRE><B>int </a>PD_set_attribute(PDBfile *file,
</B></PRE><A NAME="934583"><PRE><B> char *vr,
</B></PRE><A NAME="934585"><PRE><B> char *attr,
</B></PRE><A NAME="934598"><PRE><B> void *vl)
</B></PRE><a name="934593">
</a>Set the value of the specified </a>attribute for the named entity. Attribute values are always assigned by </a>reference.<p>
</a>
<a name="934592">
The </a>model of an attribute in PDBLib is an entity that has a name and type. The two supported operations on attributes are to create them and to remove them. An entity in a PDB file can be assigned an </a>attribute value simply by calling </a>PD_set_attribute. The only association between an entry in a PDB file and any attribute is made by the name in the attribute table and the entry in the symbol table. In particular, this mechanism allows the application developer to define and use entities in a PDB file solely in terms of attributes.<p>
</a>
<a name="934595">
The arguments to this function are: file, a pointer to a PDBfile; vr, an ASCII string containing the name of an entity in the PDB file; attr, an ASCII string containing the name of the attribute being set; and vl, a pointer to data whose type matches the attribute type.<p>
</a>
<a name="934596">
The return value is TRUE if successful and FALSE otherwise.<p>
</a>
<a name="934597">
See also </a>PD_def_attribute, </a>PD_rem_attribute, and </a>PD_get_attribute.<p>
</a>
<a name="934969">
<p>
</a>
<A NAME="934968"><PRE><B>int </a>PD_set_attribute(PDBfile *file,
</B></PRE><A NAME="935012"><PRE><B> char *vr,
</B></PRE><A NAME="935013"><PRE><B> char *attr,
</B></PRE><A NAME="935014"><PRE><B> void *vl)
</B></PRE><A NAME="934997"><B>
</B><HR><A NAME="934998"><PRE> #include “pdb.h”
</PRE><A NAME="934999"><PRE>
</PRE><A NAME="935000"><PRE> PDBfile *file;
</PRE><A NAME="935001"><PRE> char *dt;
</PRE><A NAME="935002"><PRE> .
</PRE><A NAME="935003"><PRE> .
</PRE><A NAME="935004"><PRE> .
</PRE><A NAME="935005"><PRE> dt = SC_strsave(“Mon March 23, 1921”);
</PRE><A NAME="934975"><PRE> if (</a>PD_set_attribute(file, “foo”, “date”, dt) == FALSE)
</PRE><A NAME="935007"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="935008"><PRE> .
</PRE><A NAME="935009"><PRE> .
</PRE><A NAME="935011"><PRE> .
</PRE><a name="934174">
<h2>4.31 PD_TARGET</h2>
</a>
<A NAME="934175"><PRE><B>
</B></PRE><A NAME="932671"><PRE><B>int </a>PD_target(data_standard *std,
</B></PRE><A NAME="932672"><PRE><B> data_alignment *align)
</B></PRE><a name="934186">
Write the next PDB file according to the specified data standard and alignment. PDBLib has a general binary data conversion mechanism called </a>parametrized </a>data </a>conversion (</a>PDC). The an integer type is described by one set of parameters and a floating point type is described by another. A general purpose conversion routine takes the description of the input type and a description of the desired output type and does the conversion. In this way, PDBLib avoids an N2 increase in data conversion routines as it ports to new machines. In fact, the number of data standards and alignments grows more slowly than N because many machines share common formats.<p>
</a>
<a name="934190">
An additional advantage to PDC is that by specifying a format involving the minimal number of bits to represent the data for a file, PDBLib can carry out a large class of </a>data </a>compressions.<p>
</a>
<a name="934196">
For programmer convenience, PDBLib carries several data standards and alignments. </a>Data standards: </a>IEEEA_STD, </a>IEEEB_STD, </a>IEEEC_STD, </a>INTELA_STD, </a>INTELB_STD, </a>VAX_STD, and </a>CRAY_STD. </a>Data </a>alignments: </a>DEF_ALIGNMENT, </a>SPARC_ALIGNMENT, </a>MIPS_ALIGNMENT, </a>M68000_ALIGNMENT, </a>INTEL_ALIGNMENT, and </a>CRAY_ALIGNMENT.<p>
</a>
<a name="934198">
Some common </a>configurations are:<p>
</a>
<dl>
<a name="934203">
<dt> Motorola - </a>PD_target(&IEEEA_STD, &M68000_ALIGNMENT)
</a>
<a name="934204">
<dt> SPARC - PD_target(&IEEEA_STD, &SPARC_ALIGNMENT)
</a>
<a name="933307">
<dt>MIPS, SGI - PD_target(&IEEEA_STD, &MIPS_ALIGNMENT)
</a>
<a name="934205">
<dt>IBM RS6000 - PD_target(&IEEEA_STD, &RS6000_ALIGNMENT)
</a>
<a name="934206">
<dt>Mac/Think C - PD_target(&IEEEB_STD, &M68000_ALIGNMENT)
</a>
<a name="934207">
<dt>Mac/MPW - PD_target(&IEEEC_STD, &M68000_ALIGNMENT)
</a>
<a name="934208">
<dt>DOS - PD_target(&INTELA_STD, &INTEL_ALIGNMENT)
</a>
<a name="934209">
<dt>Intel 80x86 UNIX - PD_target(&INTELB_STD, &INTEL_ALIGNMENT)
</a>
<a name="934210">
<dt>DEC Vax - PD_target(&VAX_STD, &DEF_ALIGNMENT)
</a>
<a name="934211">
<dt>DEC 3100 - PD_target(&INTELB_STD, &MIPS_ALIGNMENT)
</a>
<a name="934213">
<dt>UNICOS Cray - </a>PD_target(&CRAY_STD, &UNICOS_ALIGNMENT)
</a>
<a name="934219">
The argument, std, is a pointer to a data_standard structure, and the argument, align, is a pointer to a data_alignment structure. See the section on Data Structures.<p>
</a>
<a name="933333">
The return value is TRUE, if successful; otherwise, FALSE is returned and the ASCII string PD_err contains any error messages.<p>
</a>
<a name="934224">
<p>
</a>
<a name="932674">
int </a>PD_target(data_standard *std,<p>
</a>
<a name="932675">
data_alignment *align)<p>
</a>
<A NAME="934229"><B>
</B><HR><A NAME="934233"><PRE> #include “pdb.h”
</PRE><A NAME="934234"><PRE>
</PRE><A NAME="934235"><PRE> void test_target(tgt, base, n, fname, datfile)
</PRE><A NAME="934236"><PRE> char *tgt, *base;
</PRE><A NAME="934237"><PRE> int n;
</PRE><A NAME="934238"><PRE> char *fname, *datfile;
</PRE><A NAME="934239"><PRE> {if (tgt != NULL)
</PRE><A NAME="934240"><PRE>
</PRE><A NAME="934241"><PRE> /* for DOS machines */
</PRE><A NAME="934242"><PRE> {if (strcmp(tgt, “dos”) == 0)
</PRE><A NAME="934243"><PRE> </a>PD_target(&</a>INTEL_STD, &</a>INTEL_ALIGNMENT);
</PRE><A NAME="934244"><PRE>
</PRE><A NAME="934245"><PRE> /* for CRAY computers */
</PRE><A NAME="934246"><PRE> else if (strcmp(tgt, “cray”) == 0)
</PRE><A NAME="934247"><PRE> </a>PD_target(&</a>CRAY_STD, &</a>UNICOS_ALIGNMENT);
</PRE><A NAME="934248"><PRE>
</PRE><A NAME="934249"><PRE> /* for DEC VAX machines */
</PRE><A NAME="934250"><PRE> else if (strcmp(tgt, “vax”) == 0)
</PRE><A NAME="934251"><PRE> </a>PD_target(&</a>VAX_STD, &</a>DEF_ALIGNMENT);
</PRE><A NAME="934252"><PRE>
</PRE><A NAME="934253"><PRE> /* for MIPS based machines */
</PRE><A NAME="934254"><PRE> else if (strcmp(tgt, “mips”) == 0)
</PRE><A NAME="934255"><PRE> </a>PD_target(&</a>IEEEA_STD, &</a>MIPS_ALIGNMENT);
</PRE><A NAME="934256"><PRE>
</PRE><A NAME="934257"><PRE> /* for standard M68000 machines */
</PRE><A NAME="934258"><PRE> else if (strcmp(tgt, “sun3”) == 0)
</PRE><A NAME="934259"><PRE> </a>PD_target(&</a>IEEEA_STD, &</a>M68000_ALIGNMENT);
</PRE><A NAME="934260"><PRE>
</PRE><A NAME="934261"><PRE> /* for SPARC machines */
</PRE><A NAME="934262"><PRE> else if (strcmp(tgt, “sun4”) == 0)
</PRE><A NAME="934263"><PRE> </a>PD_target(&</a>IEEEA_STD, &</a>SPARC_ALIGNMENT);
</PRE><A NAME="934264"><PRE>
</PRE><A NAME="934265"><PRE> /* for Macintosh */
</PRE><A NAME="934266"><PRE> else if (strcmp(tgt, “mac”) == 0)
</PRE><A NAME="934267"><PRE> </a>PD_target(&</a>IEEEB_STD, &</a>M68000_ALIGNMENT);
</PRE><A NAME="932593"><PRE>
</PRE><A NAME="932594"><PRE> sprintf(fname, “%s-%s.rs%d”, base, tgt, n);
</PRE><A NAME="934269"><PRE> sprintf(datfile, “%s-%s.db%d”, base, tgt, n);}
</PRE><A NAME="934270"><PRE> else
</PRE><A NAME="934271"><PRE> {sprintf(fname, “%s-nat.rs%d”, base, n);
</PRE><A NAME="934272"><PRE> sprintf(datfile, “%s-nat.db%d”, base, n);};
</PRE><A NAME="934273"><PRE>
</PRE><A NAME="934274"><PRE> return;}
</PRE><A NAME="934474"><PRE>
</PRE></dl>
<a name="934415">
<h2>4.32 PD_TYPEDEF</h2>
</a>
<A NAME="934416"><PRE><B>
</B></PRE><a name="934445">
defstr *</a>PD_typedef(PDBfile *file,<p>
</a>
<a name="934502">
char *oname,<p>
</a>
<A NAME="934503"><PRE><B> char *tname)
</B></PRE><a name="934504">
</a>Define a an alternate name for an existing type. The intended use of this function is to allow users to make their PDB data types match their C types as closely as possible. It does this by mimicking the C </a>typedef mechanism in a limited way. More accurately it provides an </a>aliasing capability. This can be used in conjunction with either </a>PD_defix or </a>PD_defloat to install a definition of a data type in the host chart (</a>PD_defix and </a>PD_defloat define their types to the file chart only).<p>
</a>
<a name="934506">
Input to </a>PD_defix is: <em>file</em>, a pointer to a PDBfile; oname, an ASCII string containing the name of the original data type; tname, an ASCII string containing the name of the alias.<p>
</a>
<a name="934507">
A pointer to the original type’s defstr is returned if the call is successful; otherwise, NULL is returned and the ASCII string PD_err contains any error message that was generated.<p>
</a>
<a name="934508">
<p>
</a>
<a name="934509">
defstr *</a>PD_typedef(PDBfile *file,<p>
</a>
<a name="934510">
char *oname,<p>
</a>
<a name="934511">
char *tname)<p>
</a>
<A NAME="934512"><B>
</B><HR><A NAME="934513"><PRE> #include “pdb.h”
</PRE><A NAME="934515"><PRE>
</PRE><A NAME="934516"><PRE> PDBfile *file;
</PRE><A NAME="934517"><PRE> defstr *ptr;
</PRE><A NAME="934518"><PRE> .
</PRE><A NAME="934519"><PRE> .
</PRE><A NAME="934520"><PRE> .
</PRE><A NAME="934521"><PRE> /* define “enum” as an alias for “integer” */
</PRE><A NAME="934522"><PRE> ptr = </a>PD_typedef(file, “integer”, “enum”);
</PRE><A NAME="934523"><PRE> .
</PRE><A NAME="934524"><PRE> .
</PRE><A NAME="934629"><PRE>
</PRE><a name="934482">
<h2>4.33 PD_WRITE</h2>
</a>
<a name="934586">
<p>
</a>
<a name="934591">
int </a>PD_write(PDBfile *file,<p>
</a>
<a name="934587">
char *name,<p>
</a>
<a name="934589">
char *type,<p>
</a>
<a name="934590">
void *var)<p>
</a>
<a name="932742">
</a>Write data to a PDB file. If an entry already exists in the file, the data overwrites the specified file data; otherwise, before writing data to the PDB file an entry is prepared for the symbol table consisting of the name, the type, the </a>dimension information, the disk address to which the data will be written, and the total number of bytes as computed with the help of the structure chart. After the entry is installed in the symbol table the data from memory is converted (only if the </a>target machine type is different from the current machine type) and then written out to disk starting at the current disk address.<p>
</a>
<a name="934505">
The </a>primitive </a>data types which the PDBLib system knows about by default are: “short”, “integer”, “long”, “float”, “double”, and “char” for short integer, integer, long integer, floating point or real number, double precision floating point number, and character or single byte respectively. Additional types may be added using </a>PD_defstr.<p>
</a>
<a name="934514">
PDBLib supports arbitrary levels of </a>indirections. This means that all types of pointers (except function pointers) can be traced down to the actual data to which they point and that data will be written out into the PDB file in such a way that the read operations can reconstruct the data as it exists prior to the write operation. There is one crucial restriction. That is that the memory associated with any pointer must have been allocated using a SCORE memory management function or macro. See the memory management section near the beginning of this document.<p>
</a>
<a name="934526">
Rationale: When writing out scalar variables (i.e. non-dimensioned variables - structured variables are scalars unless specifically dimensioned) this function is the most convenient to use since it involves no variable argument list and hence no worries about terminating the list. Another situation, which is more common than expected, in which </a>PD_write would be preferred is when it is desirable to make entries in a PDB file which do not correspond to any variables in the application program. Since string manipulations might be involved in preparing the name under which to write the data, coding in the dimensional information is not any less efficient.<p>
</a>
<a name="934531">
Dimensions can be given in two ways. If the default offset value for the PDB file can be taken as the minimum value for the range which a dimension index can legally run, the maximum value may be specified alone. Alternatively, the minimum value, maximum value, and stride (separated by colons) may be specified. The stride is optional and defaults to 1.<p>
</a>
<a name="934539">
The arguments to </a>PD_write are: file, a pointer to a PDBfile which designates the PDB file to which to attempt to write; name, an ASCII string containing the name of the variable to install in the symbol table; type, an ASCII string specifying the variable type; and var, a pointer to the data to be written. This pointer must be consistent with the type specified, that is it must be a pointer to data with type, type. For example:<p>
</a>
<a name="934543">
<dd>char **s, **t;<P>
</a>
<a name="934544">
<dd>integer *u;<P>
</a>
<a name="934546">
<dd><P>
</a>
<a name="932527">
<dd>PD_write(file, “s”, “char **”, &s);<P>
</a>
<a name="934547">
<dd>PD_write(file, “t(3)”, “char *”, t);<P>
</a>
<a name="934548">
<dd>PD_write(file, “u(30,1:10)”, “integer”, u);<P>
</a>
<a name="934553">
The </a>dimension information is encoded in the ASCII string, name, as if in a FORTRAN dimension statement.<p>
</a>
<a name="934315">
Note: PDBLib can only write part of an entry if the type of the terminal node is primitive or a structure which contains no indirections and whose descendant members contain no indirections. <p>
</a>
<a name="934316">
Note: When writing part of a variable, especially a structured variable, the path to the desired part must contain one array reference for each level of </a>indirection traversed.<p>
</a>
<a name="932744">
The return value is TRUE if successful; otherwise, FALSE is returned and the ASCII string PD_err contains any error messages.<p>
</a>
<a name="933496">
See also </a>PD_write_alt and </a>PD_defent.<p>
</a>
<a name="932746">
<p>
</a>
<a name="933249">
int </a>PD_write(PDBfile *file,<p>
</a>
<a name="932747">
char *name,<p>
</a>
<a name="932748">
char *type,<p>
</a>
<a name="933046">
void *var)<p>
</a>
<A NAME="933047"><B>
</B><HR><A NAME="933181"><PRE> #include “pdb.h”
</PRE><A NAME="933185"><PRE>
</PRE><A NAME="933189"><PRE> PDBfile *file;
</PRE><A NAME="933227"><PRE> float x[20];
</PRE><A NAME="933230"><PRE> .
</PRE><A NAME="933235"><PRE> .
</PRE><A NAME="933236"><PRE> .
</PRE><A NAME="933237"><PRE> if (!</a>PD_write(file, “x(20)”, “float”, x))
</PRE><A NAME="933238"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="933243"><PRE> .
</PRE><A NAME="933247"><PRE> .
</PRE><A NAME="933248"><PRE> .
</PRE><a name="934557">
<p>
</a>
<a name="933347">
<h2>4.34 PD_WRITE_ALT</h2>
</a>
<A NAME="933377"><PRE><B>
</B></PRE><A NAME="933378"><PRE><B>int </a>PD_write_alt(PDBfile *file,
</B></PRE><A NAME="933379"><PRE><B> char *name,
</B></PRE><A NAME="933380"><PRE><B> char *type,
</B></PRE><A NAME="933381"><PRE><B> void *var,
</B></PRE><A NAME="933422"><PRE><B> int nd,
</B></PRE><A NAME="933423"><PRE><B> long *ind)
</B></PRE><a name="933382">
</a>Write data to a PDB file. This is an alternate form to </a>PD_write. If an entry already exists in the file, the data overwrites the specified file data; otherwise, before writing data to the PDB file an entry is prepared for the symbol table consisting of the name, the type, the </a>dimension information, the disk address to which the data will be written, and the total number of bytes as computed with the help of the structure chart. After the entry is installed in the symbol table the data from memory is converted (only if the </a>target machine type is different from the current machine type) and then written out to disk starting at the current disk address.<p>
</a>
<a name="933383">
The </a>primitive </a>data types which the PDBLib system knows about by default are: “short”, “integer”, “long”, “float”, “double”, and “char” for short integer, integer, long integer, floating point or real number, double precision floating point number, and character or single byte respectively. Additional types may be added using </a>PD_defstr.<p>
</a>
<a name="933384">
PDBLib supports arbitrary levels of </a>indirections. This means that, subject to the restrictions spelled out in the section on rules, pointers (except function pointers) can be traced down to the actual data to which they point and that data will be written out into the PDB file in such a way that the read operations can reconstruct the data as it exists prior to the write operation. There is one crucial restriction. That is that the memory associated with any pointer must have been allocated by a SCORE memory management function or macro. See the Memory Management section near the beginning of this document.<p>
</a>
<a name="933386">
The rationale for this function is that in some situations, it is desirable to be able to specify the dimensions without building them into an ASCII string.<p>
</a>
<a name="933385">
The arguments to </a>PD_write_alt are: file, a pointer to a PDBfile which designates the PDB file to which to attempt to write; name, an ASCII string containing the name of the variable to install in the symbol table; type, an ASCII string specifying the variable type; var, a pointer to the data to be written; nd, then number of dimensions for the variable; and ind, an array of long integers containing (min, max, stride) triples specifying the ranges and strides of the dimensions. The pointer, var, must be consistent with the type specified, that is it must be a pointer to data with type, type. For example:<p>
</a>
<a name="933388">
<dd>char **s, **t;<P>
</a>
<a name="933389">
<dd>integer *u;<P>
</a>
<a name="933391">
<dd>PD_write_alt(file, “s”, “char **”, &s, ...);<P>
</a>
<a name="933392">
<dd>PD_write_alt(file, “t”, “char *”, t, ...);<P>
</a>
<a name="933393">
<dd>PD_write_alt(file, “u”, “integer”, u, ...);<P>
</a>
<a name="934318">
Note: PDBLib can only write part of an entry if the type of the terminal node is primitive or a structure which contains no indirections and whose descendant members contain no indirections. <p>
</a>
<a name="933395">
Note: When writing part of a variable, especially a structured variable, the path to the desired part must contain one array reference for each level of </a>indirection traversed.<p>
</a>
<a name="934317">
The return value is TRUE if successful; otherwise, FALSE is returned and the ASCII string PD_err contains any error messages.<p>
</a>
<a name="933396">
<p>
</a>
<a name="933397">
int </a>PD_write_alt(PDBfile *file,<p>
</a>
<a name="933398">
char *name,<p>
</a>
<a name="933399">
char *type,<p>
</a>
<a name="933400">
void *var,<p>
</a>
<a name="933414">
int nd,<p>
</a>
<a name="933416">
long *ind)<p>
</a>
<A NAME="933401"><B>
</B><HR><A NAME="933402"><PRE> #include “pdb.h”
</PRE><A NAME="933403"><PRE>
</PRE><A NAME="933404"><PRE> PDBfile *file;
</PRE><A NAME="933406"><PRE> long ind[6];
</PRE><A NAME="933417"><PRE> float x[20][5];
</PRE><A NAME="933407"><PRE> .
</PRE><A NAME="933408"><PRE> .
</PRE><A NAME="933409"><PRE> .
</PRE><A NAME="933410"><PRE> ind[0] = 0L;
</PRE><A NAME="933419"><PRE> ind[1] = 19L;
</PRE><A NAME="933420"><PRE> ind[2] = 1L;
</PRE><A NAME="933421"><PRE> ind[3] = -2L;
</PRE><A NAME="934326"><PRE> ind[4] = 2L;
</PRE><A NAME="934327"><PRE> ind[5] = 1L;
</PRE><A NAME="933418"><PRE> if (!</a>PD_write_alt(file, “x”, “float”, x, 2, ind))
</PRE><A NAME="933411"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="933412"><PRE> .
</PRE><A NAME="933413"><PRE> .
</PRE><A NAME="933415"><PRE> .
</PRE><a name="933182">
<h2>4.35 PD_WRITE_AS</h2>
</a>
<A NAME="933165"><PRE><B>
</B></PRE><A NAME="933183"><PRE><B>int </a>PD_write_as(PDBfile *file,
</B></PRE><A NAME="933475"><PRE><B> char *name,
</B></PRE><A NAME="933476"><PRE><B> char *intype,
</B></PRE><A NAME="933477"><PRE><B> char *outtype,
</B></PRE><A NAME="933478"><PRE><B> void *var)
</B></PRE><a name="933172">
</a>Write the data pointed to by <em>var</em> under <em>name</em> and with <em>intype</em> in PDB file <em>file</em> as data of outtype.<p>
</a>
<a name="933264">
The rationale for this function is that in some situations, it is desirable to not only convert the formats of data of a specified type, but to convert between types. An example that occurs in practice often enough is converting a 32 bit int to a 32 bit long on a machine which only has a 16 bit int.<p>
</a>
<a name="933178">
Input to </a>PD_write_as is: <em>file</em>, a pointer to a PDBfile; <em>name</em>, an ASCII string containing the name of the variable in the PDB file; <em>intype</em>, an ASCII string containing the type of the variable; <em>outtype</em>, an ASCII string containing the output type of the variable; and <em>var</em>, a pointer to the location where the data is to be stored in memory.<p>
</a>
<a name="934320">
Note: PDBLib can only write part of an entry if the type of the terminal node is primitive or a structure which contains no indirections and whose descendant members contain no indirections. <p>
</a>
<a name="933162">
Note: When writing part of a variable, especially a structured variable, the path to the desired part must contain one array reference for each level of </a>indirection traversed.<p>
</a>
<a name="934319">
</a>PD_write_as returns TRUE if successful; otherwise, FALSE is returned and the ASCII string PD_err contains any error messages.<p>
</a>
<a name="933495">
See also </a>PD_write_as_alt and </a>PD_defent_alt.<p>
</a>
<a name="933176">
<p>
</a>
<a name="933175">
int </a>PD_write_as(PDBfile *file,<p>
</a>
<a name="933479">
char *name,<p>
</a>
<a name="933480">
char *intype,<p>
</a>
<a name="933481">
char *outtype,<p>
</a>
<a name="933482">
void *var)<p>
</a>
<A NAME="933173"><B>
</B><HR><A NAME="933250"><PRE> #include “pdb.h”
</PRE><A NAME="933251"><PRE>
</PRE><A NAME="933252"><PRE> PDBfile *file;
</PRE><A NAME="933254"><PRE> float x[20];
</PRE><A NAME="933255"><PRE> .
</PRE><A NAME="933256"><PRE> .
</PRE><A NAME="933257"><PRE> .
</PRE><A NAME="933263"><PRE> if (!</a>PD_write_as(file, “x(20)”, “float”, “double”, x))
</PRE><A NAME="933259"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="933260"><PRE> .
</PRE><A NAME="933261"><PRE> .
</PRE><A NAME="933262"><PRE> .
</PRE><a name="933451">
<h2>4.36 PD_WRITE_AS_ALT</h2>
</a>
<A NAME="933452"><PRE><B>
</B></PRE><A NAME="933453"><PRE><B>int </a>PD_write_as_alt(PDBfile *file,
</B></PRE><A NAME="933483"><PRE><B> char *name,
</B></PRE><A NAME="933484"><PRE><B> char *intype,
</B></PRE><A NAME="933485"><PRE><B> char *outtype,
</B></PRE><A NAME="933486"><PRE><B> void *var,
</B></PRE><A NAME="933487"><PRE><B> int nd,
</B></PRE><A NAME="933488"><PRE><B> long *ind)
</B></PRE><a name="933454">
</a>Write the data pointed to by <em>var</em> under <em>name</em> and with <em>intype</em> in PDB file <em>file</em> as data of outtype. This is an alternate form of </a>PD_write_as.<p>
</a>
<a name="933455">
The rationale for this function is that in some situations, it is desirable to be able to specify the dimensions without building them into an ASCII string.<p>
</a>
<a name="933456">
Input to </a>PD_write_as_alt is: <em>file</em>, a pointer to a PDBfile; <em>name</em>, an ASCII string containing the name of the variable in the PDB file; <em>intype</em>, an ASCII string containing the type of the variable; <em>outtype</em>, an ASCII string containing the output type of the variable; <em>var</em>, a pointer to the location where the data is to be stored in memory; nd, an integer number of dimensions; and ind, an array of long integers specifying the ranges of each dimension (min, max, stride).<p>
</a>
<a name="934322">
Note: PDBLib can only write part of an entry if the type of the terminal node is primitive or a structure which contains no indirections and whose descendant members contain no indirections. <p>
</a>
<a name="933457">
Note: When writing part of a variable, especially a structured variable, the path to the desired part must contain one array reference for each level of </a>indirection traversed.<p>
</a>
<a name="934321">
PD_write_as_alt returns TRUE if successful; otherwise, FALSE is returned and the ASCII string PD_err contains any error messages.<p>
</a>
<a name="933458">
<p>
</a>
<a name="933459">
int </a>PD_write_as_alt(PDBfile *file,<p>
</a>
<a name="933489">
char *name,<p>
</a>
<a name="933490">
char *intype,<p>
</a>
<a name="933494">
char *outtype,<p>
</a>
<a name="933493">
void *var,<p>
</a>
<a name="933492">
int nd,<p>
</a>
<a name="933491">
long *ind)<p>
</a>
<A NAME="933460"><B>
</B><HR><A NAME="933461"><PRE> #include “pdb.h”
</PRE><A NAME="933462"><PRE>
</PRE><A NAME="933463"><PRE> PDBfile *file;
</PRE><A NAME="933387"><PRE> long ind[6];
</PRE><A NAME="933390"><PRE> float x[20][5];
</PRE><A NAME="933424"><PRE> .
</PRE><A NAME="933466"><PRE> .
</PRE><A NAME="933467"><PRE> .
</PRE><A NAME="933468"><PRE> ind[0] = 0L;
</PRE><A NAME="933469"><PRE> ind[1] = 19L;
</PRE><A NAME="933613"><PRE> ind[2] = 1L;
</PRE><A NAME="933614"><PRE> ind[3] = -2L;
</PRE><A NAME="934328"><PRE> ind[4] = 2L;
</PRE><A NAME="934329"><PRE> ind[5] = 1L;
</PRE><A NAME="933470"><PRE> if (!</a>PD_write_as_alt(file, “x”, “float”, “double”, x, 2, ind))
</PRE><A NAME="933471"><PRE> printf(“%s”, PD_err);
</PRE><A NAME="933472"><PRE> .
</PRE><A NAME="933473"><PRE> .
</PRE><A NAME="933474"><PRE> .
</PRE><a name="932587">
<h1>5.0 </a>Summary of the </a>FORTRAN </a>API</h1>
</a>
<a name="932589">
There is a hierarchy of routines in PDBLib from high to low level. The </a>high level routines form the API while the lower level routines are modularized to perform the actual work. It should be noted that the lower level routines are sufficiently well modularized so as to make it possible to build entirely different API’s for PDBLib. <p>
</a>
<a name="932815">
The high level PDBLib routines have a strict </a>naming convention. All routines in the FORTRAN API begin with ‘</a>PF’.<p>
</a>
<a name="932590">
Note: many of these functions return integer values. The </a>implicit typing convention in FORTRAN would indicate that they return real values. Application programs must explicitly type these functions as integers.<p>
</a>
<a name="932595">
When an error condition is detected by PDBLib it saves a message in a global C character string. FORTRAN programs can access this </a>error message by invoking function </a><em>PFGERR</em>. The message contains the name of the function in which the error occurred thus eliminating the need for a cross reference document on error codes. In this way applications programs can check for error conditions themselves and decide in what manner to use the PDBLib error messages instead of having error messages printed by the system routines. Error messages are not stacked and must be processed by the application before any other PDBLib calls are made in order to avoid potential overwrites. See the FORTRAN API section for more information about which routines return error messages<p>
</a>
<a name="934654">
<h2>5.1 Some Guidance in Using the FORTRAN API to PDBLib</h2>
</a>
<a name="934656">
PDBLib offers a great deal of flexibility to its users. In some cases the flexibility results in a bewildering assortment of function calls from which the application developer must choose. This section is intended to offer some guidance and enable developers to home in on the functions they need to use.<p>
</a>
<a name="934657">
<h3>5.1.1 Opening, Creating and Closing PDB Files</h3>
</a>
<a name="934658">
These are the most fundamental operations involving PDBLib. The function </a>PFOPEN is used to either open an existing file or create a new one. </a>PFCLOS is used to close a PDB file so that it can be recognized by PDBLib for future operations.<p>
</a>
<a name="934659">
PDBLib allows applications to specify the binary format in which a newly created file will be written. </a>PFTRGT does this work. It is not necessary to invoke </a>PFTRGT before creating a new PDB file.<p>
</a>
<a name="934662">
<h3>5.1.2 Writing Data to PDB Files</h3>
</a>
<a name="934663">
The following paragraphs describe a sequence of increasingly more elaborate output operations for PDB files. They are all compatible with one another so users can select the ones which match their needs best. The most straightforward operations are first.<p>
</a>
<a name="934664">
There are two forms for the most basic data writing operations. These have to do with how the application wants to handle the dimension specifications. The two functions are: </a>PFWRTA and </a>PFWRTD.<p>
</a>
<a name="934666">
PDBLib supports the notion of writing data of one type out into a file as another type. More precisely, an integer type of data can be written to a file in the format of any other integer type, and similarly for floating point types. The application must take all responsibility for ensuring the appropriateness of this type of conversion (e.g. underflows and overflows). The functions which support this are </a>PFWRAS and </a>PFWRAD.<p>
</a>
<a name="936499">
PDBLib allows applications to append data to existing entries. This is handy in situations where the total amount of data is not known in advance, but a logical ordering of the data is apparent which matches the order in which data will be written. The functions which do this are </a>PFAPPA, </a>PFAPPD, </a>PFAPAS and </a>PFAPAD.<p>
</a>
<a name="934667">
Finally, PDBLib allows applications to reserve space on disk and then let subsequent writes fill in that space with values. This is handy in instances where an application knows a logical structure for a data set but needs to write it out in smaller pieces and not necessarily in the order implied by its logical structure. The functions which let applications reserve space are </a>PFDEFA, and </a>PFDEFD. Reserved spaces may be written to with </a>PFWRTA, </a>PFWRTD, </a>PFWRAS or </a>PFWRAD.<p>
</a>
<a name="934668">
<h3>5.1.3 Reading Data from PDB Files</h3>
</a>
<a name="932491">
Since data in a file has a definite size and shape, the reading operations in PDBLib are somewhat simpler than the writing operations. The functions </a>PFREAD, </a>PFPTRD, </a>PFRDAS, and </a>PFRDAD, the counterparts of </a>PFWRTA, </a>PFWRTD, </a>PFWRAS, and </a>PFWRAD, do all of the work in reading data from files.<p>
</a>
<a name="934671">
<h3>5.1.4 Defining New Data Types</h3>
</a>
<a name="934672">
To aid application developers in using structured data PDBLib lets applications define new data types in a PDBfile. New data types may either be derived from other existing data types or they may be primitive (integer types, floating point types, or byte sequences). To define derived types applications should use </a>PFDEFS.<p>
</a>
<a name="934675">
<h3>5.1.5 Defining Attributes</h3>
</a>
<a name="934677">
PDBLib supports a general mechanism for managing a class of data which is variously referred to as attributes or meta data. In a great many cases, the careful design of data structures obviates the need for this kind of data. Nevertheless, PDBLib supplies four functions to manage attributive data: </a>PFDATT, </a>PFRATT, </a>PFSVAT, and </a>PFGVAT.<p>
</a>
<a name="934653">
<h3>5.1.6 Queries</h3>
</a>
<a name="934660">
The FORTRAN API supports several query operations to help applications interpret the contents of a PDB file. The current functions are: </a>PFGBFS, </a>PFGERR, </a>PFGMOD, </a>PFGOFF, </a>PFITYP, and </a>PFIVAR.<p>
</a>
<a name="933691">
A few definitions must be given first to keep the following summary concise. Some of these will be elaborated upon in the next section.<p>
</a>
<a name="932847">
<p>
</a>
<A NAME="932849"></a>PDBfile: for the purposes of a program this is a collection of all the relevant information about one of these data files.See the section on Data Structures for more information.
<BR><A NAME="932848">
<BR><A NAME="932850"><strong></a>ASCII:</strong><em> </em>an array of characters
<BR><a name="932851">
<p>
</a>
<A NAME="932852"></a>VOID: any FORTRAN data type
<BR><a name="932858">
<p>
</a>
<A NAME="932860"><strong></a>LAST:</strong> the value 0
<BR><a name="932861">
<p>
</a>
<A NAME="932863"><strong></a>ENTRY: </strong>for the purposes of a program this is a collection of all the relevant information about a variable written to a PDB file.
<BR><a name="932846">
<p>
</a>
<A NAME="932864"><strong></a>DEFSTR:</strong> for the purposes of a program this is a collection of all the relevant information about a data type in a PDB file.
<BR><a name="932865">
<p>
</a>
<A NAME="932868"><strong></a>REAL*8:</strong> an eight byte floating point number.
<BR><a name="932866">
<h2>5.2 </a>Function Summary</h2>
</a>
<a name="932867">
These routines form the </a>interface between FORTRAN applications programs and the PDBLib system.<p>
</a>
<A NAME="936511"><P><B></a>PFAPAD(fileid, nchr, name, ntype, type, space, nd, ind)
</B><BR><A NAME="936512"></a> </a>Append the data from spaceof type type to the entry name in a PDB file. In this alternate to </a>PFAPAS the dimensions are specified via the array ind.
<BR><dl>
<a name="936513">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="936514">
<dd>nchr, the number of characters in name,<P>
</a>
<a name="936515">
<dd>name, an ASCII string containing the name of the variable,<P>
</a>
<a name="936516">
<dd><em>ntype</em>, the number of characters in <em>type</em>,<P>
</a>
<a name="936517">
<dd><em>type</em>, an ASCII string containing the type of the variable in space,<P>
</a>
<a name="936518">
<dd><em>space</em>, the variable containing the data,<P>
</a>
<a name="936519">
<dd>nd, the number of dimensions of the entry,<P>
</a>
<a name="936520">
<dd>ind, an array containing (start, stop, step) index range triples for each dimension.<P>
</a>
<a name="936521">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="932925"><P><B></a>PFAPAS(fileid, nchr, name, ntype, type, space)
</B><BR><A NAME="932926"></a>Append the data from spaceof type type to the entry name in a PDB file. Dimensions
are specified in the text of name.
<BR><a name="932928">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="932929">
<dd>nchr, the number of characters in name,<P>
</a>
<a name="932933">
<dd>name, an ASCII string containing the name of the variable and any dimensional information,<P>
</a>
<a name="936509">
<dd><em>ntype</em>, the number of characters in <em>type</em>,<P>
</a>
<a name="936510">
<dd><em>type</em>, an ASCII string containing the type of the variable in space,<P>
</a>
<a name="932934">
<dd><em>space</em>,the variable containing the data.<P>
</a>
<a name="932935">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="935061"><P><B></a>PFAPPA(fileid, nchr, name, space)
</B><BR><A NAME="935067"></a>Append data to an entry in a PDB file. In this alternate to </a>PFAPPD dimensions are
specified in the text of name.
<BR><a name="935068">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="935069">
<dd>nchr, the number of characters in name,<P>
</a>
<a name="935070">
<dd>name, an ASCII string containing the name of the variable and any dimensional information,<P>
</a>
<a name="935071">
<dd><em>space</em>, the variable containing the data.<P>
</a>
<a name="935072">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="934867"><P><B></a>PFAPPD(fileid, nchr, name, space, nd, ind)
</B><BR><A NAME="934883"></a>Append data to an entry in a PDB file. The dimensions are specified via the array ind.
<BR><a name="935037">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="935048">
<dd>nchr, the number of characters in name,<P>
</a>
<a name="935059">
<dd>name, an ASCII string containing the name of the variable,<P>
</a>
<a name="935060">
<dd><em>space</em>, the variable containing the data,<P>
</a>
<a name="935073">
<dd>nd, the number of dimensions of the entry,<P>
</a>
<a name="935074">
<dd>ind, an array containing (start, stop, step) index range triples for each dimension.<P>
</a>
<a name="932869">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="932912"><P><B>[</a>PFCD(fileid, nchr, dirname)
</B><BR><A NAME="933640"></a>Change the </a>current </a>directory in a PDB file.
<BR><a name="934062">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="934101">
<dd>nchr, the number of characters in dirname,<P>
</a>
<a name="934364">
<dd>dirname, an ASCII string containing the path name of the directory to change to.<P>
</a>
<a name="934530">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="932871"><P><B></a>PFCLOS(fileid)
</B><BR><A NAME="932872"></a>Complete and close the PDB file<em> fileid</em>.
<BR><a name="932873">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number.
</a>
<a name="934913">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="935066"><P><B></a>PFDATT(fileid, na, attr, nt, type)
</B><BR><A NAME="934914">Define an attribute in a PDB file.
<BR><a name="934917">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="934926">
<dd><em>na</em>, an integer number of characters in attr,<P>
</a>
<a name="934927">
<dd>attr, an ASCII string naming the attribute,<P>
</a>
<a name="934919">
<dd><em>nt</em>, an integer number of characters in type,<P>
</a>
<a name="934921">
<dd>type, an ASCII string specifying the attribute type.<P>
</a>
<a name="934925">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="934144"><P><B></a>PFDEFA(fileid, nchr, name, ntype, outtype)
</B><BR><A NAME="934145"></a>Define an entry in the symbol table of a PDB file. This function </a>reserves space on disk
but writes no data. The data can be written with later PDBLib calls.
<BR><a name="934146">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="934147">
<dd>nchr, the number of characters in name,<P>
</a>
<a name="934150">
<dd>name, an ASCII string containing the name of the variable and any dimensional information,<P>
</a>
<a name="934151">
<dd><em>ntype</em>, the number of characters in <em>outtype</em>,<P>
</a>
<a name="934148">
<dd>outtype, an ASCII string specifying the type of data in the file.<P>
</a>
<a name="934149">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="932883"><P><B></a>PFDEFD(fileid, nchr, name, ntype, outtype, nd, ind)
</B><BR><A NAME="934153"></a>Define an entry in the symbol table of a PDB file. This function </a>reserves space on disk
but writes no data. The data can be written with later calls. In this alternate to </a>PFDEFA
the dimensions are specified via the array ind.
<BR><a name="934154">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="934160">
<dd>nchr, the number of characters in name,<P>
</a>
<a name="934155">
<dd>name, an ASCII string containing the name of the variable (no dimensional information can be supplied with the name),<P>
</a>
<a name="934161">
<dd><em>ntype</em>, the number of characters in <em>outtype</em>,<P>
</a>
<a name="934156">
<dd>outtype, an ASCII string specifying the type of data in the file,<P>
</a>
<a name="934157">
<dd>nd, the number of dimensions of the entry,<P>
</a>
<a name="934158">
<dd>ind, an array containing (min, max) index range pairs for each dimension.<P>
</a>
<a name="934159">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="935099"><P><B></a>PFDEFS(fileid, nchr, name, ncm1, mem1, ..., ncmn, memn, LAST)
</B><BR><A NAME="935100"></a>Define a data structure for a PDB file. LAST must terminate the list of members.
<BR><a name="935104">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="935105">
<dd>nchr, the number of characters in name,<P>
</a>
<a name="935108">
<dd>name, an ASCII string containing the structure name,<P>
</a>
<a name="935146">
<dd>ncmi,the number of characters in memi,<P>
</a>
<a name="935147">
<dd>memi, an ASCII string containing the member declaration.<P>
</a>
<a name="935148">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="933063"><P><B></a>PFDEFT(fileid, nchr, name, nm, nc, memb)
</B><BR><A NAME="933064"></a>Define a data structure for a PDB file.
<BR><a name="933068">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="933303">
<dd>nchr, the number of characters in name,<P>
</a>
<a name="933304">
<dd>name, an ASCII string containing the structure name,<P>
</a>
<a name="933305">
<dd>nm,the number of members,<P>
</a>
<a name="935149">
<dd>nc, the array of offset, length pairs,<P>
</a>
<a name="933306">
<dd>memb, an ASCII string containing the member declarations.<P>
</a>
<a name="933288">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="935253"><P><B></a>PFDLS()
</B><BR><A NAME="935254"></a>Release table create by </a>PFLST.
<BR><a name="935271">
<dt>Input: <em>None</em>.
</a>
<a name="935272">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="935348"><P><B></a>PFDVAR()
</B><BR><A NAME="935349"></a>Release table create by </a>PFVART.
<BR><a name="935350">
<dt>Input: <em>None</em>.
</a>
<a name="935351">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="936236"><P><B></a>PFFAMI(fileid, flag)
</B><BR><A NAME="936237">If the <em>file indicated by</em> <em>fileid</em> has exceeded its size limit, open and return a new member
of the </a>file family. If flag is TRUE close the old file.
<BR><a name="936238">
<dt>Input: <em>fileid</em>, an integer file identifier
</a>
<a name="936247">
<dd>flag, an integer flag.<P>
</a>
<a name="936254">
<dt>Output: an integer file identifier
</a>
<A NAME="935182"><P><B></a>PFFLSH(fileid)
</B><BR><A NAME="935183"></a>Flush the PDB file<em> fileid</em>.
<BR><a name="935185">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number.
</a>
<a name="935236">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="932874"><P><B></a>PFGBFS()
</B><BR><A NAME="932875"></a>Get the current buffer size which PDBLib uses for all PDB files and return it.
<BR><a name="932876">
<dt>Input: <em>None.</em>
</a>
<a name="932877">
<dt>Output: Return the current buffer size in bytes, if previously set; otherwise, return -1.
</a>
<A NAME="932878"><P><B></a>PFGERR(nchr, err)
</B><BR><A NAME="932879"></a>Get the current PDBLib error message. Return the length of the error message in <em>nchr</em>
and the actual message in <em>err</em>. The space for <em>err</em> should be 255 characters long.
<BR><a name="932880">
<dt>Input:<em> </em>None.
</a>
<a name="932882">
<dt>Output: Return 1 if successful, 0 otherwise,
</a>
<a name="934152">
<dd><em>nchr</em>, the length of the error message,<P>
</a>
<a name="937567">
<dd><em>err</em>, an ASCII string into which the message is copied.<P>
</a>
<A NAME="937578"><P><B></a>PFGLS(n, nchr, name)
</B><BR><a name="935346">
<dt></a>Get the name of the nth entry in the internal table generated by </a>PFLST.
</a>
<a name="935347">
<dt>Input: <em>n</em>, an integer ordinal index into the internal table.
</a>
<a name="935353">
<dt>Output: Return 1 if successful, 0 otherwise,
</a>
<a name="935354">
<dd>nchr, the number of characters returned in name,<P>
</a>
<a name="935355">
<dd>name, an ASCII string to contain the entry name.<P>
</a>
<A NAME="934215"><P><B></a>PFGMOD(fileid)
</B><BR><A NAME="934216"></a>Get the current mode of PDB file<em> fileid</em>: 2 (append - ’a’), 3 (open - ’r’), 4 (create - ’w’).
<BR><a name="934217">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number.
</a>
<a name="934218">
<dt>Output: Return the integer value of the current mode.
</a>
<A NAME="937609"><P><B></a>PFGMXS(fileid)
</B><BR><a name="937610">
<dt></a>Get the current maximum file size of PDB file <em>fileid</em>.
</a>
<a name="937611">
<dt>Input: <em>fileid</em>, an integer <strong>PDBfile</strong> identification number.
</a>
<a name="937612">
<dt>Output: Return the integer value of the current maximum file size.
</a>
<A NAME="937584"><P><B></a>PFGNM(fileid, nchr, name)
</B><BR><A NAME="937586">Return the </a>name of a PDB file.
<BR><a name="937587">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="937588">
<dd>nchr, the number of characters in name,<P>
</a>
<a name="937589">
<dd>name, an ASCII string to contain the file name.<P>
</a>
<a name="937590">
<dt>Output: Return 1 if successful, 0 otherwise,
</a>
<a name="937591">
<dd>name, an ASCII string containing the file name.<P>
</a>
<A NAME="937581"><P><B></a>PFGOFF(fileid)
</B><BR><A NAME="934201"></a>Get the current default offset for PDB file<em> fileid</em>.
<BR><a name="934202">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number.
</a>
<a name="934214">
<dt>Output: Return the integer value of the default offset.
</a>
<A NAME="933271"><P><B></a>PFGVAR(n, nchr, name)
</B><BR><A NAME="933276"></a>Get the name of the nth variable in the internal sorted table generated by </a>PFVART.
<BR><a name="933278">
<dt>Input: <em>n</em>, integer ordinal index into the internal sorted name table.
</a>
<a name="933279">
<dt>Output: Return 1 if successful, 0 otherwise,
</a>
<a name="933280">
<dd>nchr, the number of characters in the name,<P>
</a>
<a name="935280">
<dd>name, an ASCII array in which the name is returned.<P>
</a>
<A NAME="934855"><P><B></a>PFGVAT(fileid, nv, var, na, attr, value)
</B><BR><A NAME="934862"></a>Get the value of an attribute for an entity in a PDB file.
<BR><a name="934895">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="934896">
<dd><em>nv</em>, an integer number of characters in var,<P>
</a>
<a name="934897">
<dd>var, an ASCII string naming an entity,<P>
</a>
<a name="934906">
<dd><em>na</em>, an integer number of characters in attr,<P>
</a>
<a name="934907">
<dd>attr, an ASCII string naming an existing attribute,<P>
</a>
<a name="934908">
<dd>value, the data for the attribute value.<P>
</a>
<a name="934909">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="936255"><P><B></a>PFIMBR(file, ntype, type, n, size, space)
</B><BR><A NAME="936256"></a>Inquire about the nth member of the type <em>type</em> in PDB file<em> fileid</em>.
<BR><a name="936257">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="936258">
<dd><em>ntype</em>, the number of characters in <em>type</em>,<P>
</a>
<a name="936260">
<dd><em>type</em>, an ASCII string containing the name of the type,<P>
</a>
<a name="936265">
<dd>n, an integer specifying the member,<P>
</a>
<a name="936267">
<dd>size, an integer character size of the space buffer,<P>
</a>
<a name="936268">
<dd>space, an character buffer to hold the member description.<P>
</a>
<a name="936261">
<dt>Output: Return 1 if successful, 0 otherwise,
</a>
<a name="936262">
<dd><em>size</em>, the number of characters in the member description,<P>
</a>
<a name="936263">
<dd><em>space</em>, the member description.<P>
</a>
<A NAME="936264"><P><B></a>PFITYP(fileid, ntype, type, size, align, ind)
</B><BR><A NAME="932893"></a>Inquire about type <em>type</em> in PDB file<em> fileid</em>.
<BR><a name="932894">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="932895">
<dd><em>ntype</em>, the number of characters in <em>type</em>,<P>
</a>
<a name="932896">
<dd><em>type</em>, an ASCII string containing the name of the type.<P>
</a>
<a name="932897">
<dt>Output: Return 1 if successful, 0 otherwise,
</a>
<a name="932898">
<dd><em>size</em>, the number of bytes necessary to represent the type,<P>
</a>
<a name="932899">
<dd><em>align</em>, the alignment of <em>type</em> in bytes,<P>
</a>
<a name="932900">
<dd><em>ind</em>, the number of members which are pointers if <em>type</em> is a derived type.<P>
</a>
<A NAME="932901"><P><B></a>PFIVAR(fileid, nchr, name, ntype, type, size, ndims, dims)
</B><BR><A NAME="932902"></a>Inquire about variable <em>name</em> in PDB file<em> fileid</em>.
<BR><a name="932903">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="932905">
<dd><em>nchr</em>, the number of characters in <em>name</em>,<P>
</a>
<a name="932906">
<dd><em>name</em>, an ASCII string containing the name of the variable.<P>
</a>
<a name="932908">
<dt>Output: Return 1 if successful, 0 otherwise,
</a>
<a name="932909">
<dd><em>ntype</em>, the number of characters in <em>type</em>,<P>
</a>
<a name="932910">
<dd><em>type</em>, an ASCII string containing the type of the variable,<P>
</a>
<a name="932911">
<dd><em>size</em>, the number of elements in the variable,<P>
</a>
<a name="932913">
<dd><em>ndims</em>, the number of dimensions which the variable has,<P>
</a>
<a name="932914">
<dd><em>dims</em>, an array of the dimensions given as (min, max) pairs.<P>
</a>
<A NAME="935326"><P><B></a>PFLN(fileid, nvar, var, nlink, link)
</B><BR><A NAME="935327"></a>Create a </a>link to a variable in a PDB file.
<BR><a name="935328">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="935329">
<dd>nvar, the number of characters in var,<P>
</a>
<a name="935330">
<dd>var, an ASCII string containing the path name of an existing variable,<P>
</a>
<a name="935331">
<dd>nlink, the number of characters in link,<P>
</a>
<a name="935332">
<dd>link, an ASCII string containing the path name of the new link.<P>
</a>
<a name="935333">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="935334"><P><B></a>PFLST(fileid, npath, path, ntype, type, num)
</B><BR><a name="935335">
<dt></a>Generate an internal table of </a>variables and/or </a>directories in a PDB file.
</a>
<a name="935336">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="935337">
<dd>npath, the number of characters in path,<P>
</a>
<a name="935338">
<dd>path, an ASCII string containing the directory and/or variable name pattern,<P>
</a>
<a name="935340">
<dd>ntype, the number of characters in type,<P>
</a>
<a name="935341">
<dd>type, an ASCII string containing the type of entries to return.<P>
</a>
<a name="935342">
<dt>Output: Return 1 if successful, 0 otherwise,
</a>
<a name="935344">
<dd>num, the number of entries in the table.<P>
</a>
<A NAME="935356"><P><B></a>PFMKDR(fileid, nchr, dirname)
</B><BR><A NAME="935357"></a>Create a new </a>directory in a PDB file.
<BR><a name="935359">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="935360">
<dd>nchr, the number of characters in dirname,<P>
</a>
<a name="935361">
<dd>dirname, an ASCII string containing the path name of the new directory.<P>
</a>
<a name="935375">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="932915"><P><B></a>PFOPEN(nchr, name, mode)
</B><BR><A NAME="932917"></a>Open a PDB file on disk named <em>name</em> in one of three </a>modes: ‘</a>w’ for </a>create, ‘</a>r’ for </a>read-
only, or ‘</a>a’ for </a>append.
<BR><a name="932919">
<dt>Input: <em>nchr</em>, the number of characters in name,
</a>
<a name="932920">
<dd><em>name</em>, an ASCII string naming the file,<P>
</a>
<a name="932922">
<dd><em>mode</em>, an ASCII string, either ‘w’ for create, ‘r’ for read, or ‘a’ for append.<P>
</a>
<a name="932924">
<dt>Output: Return an integer PDBfile identification number, if successful, and 0 otherwise.
</a>
<A NAME="932937"><P><B></a>PFPTRD(fileid, nchr, name, space, ind)
</B><BR><A NAME="932938"></a>Read <em>part of variable</em> <em>name</em> from PDB file <em>fil</em>eid and put it into <em>space</em>.
<BR><a name="932939">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="932940">
<dd><em>nchr</em>, the number of characters in <em>name</em>,<P>
</a>
<a name="932941">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="932944">
<dd><em>space</em>, the variable where the data is to be placed,<P>
</a>
<a name="932946">
<dd><em>ind</em>, the array of dimension index specifications (start, stop, step triplets for each dimension).<P>
</a>
<a name="932948">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="935362"><P><B></a>PFPWD(fileid, nchr, dirname)
</B><BR><A NAME="935369"></a>Get the </a>current </a>directory for a PDB file.
<BR><a name="935392">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number.
</a>
<a name="935273">
<dt>Output: Return 1 if successful, 0 otherwise,
</a>
<a name="935413">
<dd>nchr, the number of characters returned in dirname,<P>
</a>
<a name="935414">
<dd>dirname, an ASCII string to contain the path name of the current directory.<P>
</a>
<A NAME="934910"><P><B></a>PFRATT(fileid, na, attr)
</B><BR><A NAME="934911">Remove an attribute from a PDB file.
<BR><a name="934912">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="934915">
<dd><em>na</em>, an integer number of characters in attr,<P>
</a>
<a name="934916">
<dd>attr, an ASCII string naming an existing attribute.<P>
</a>
<a name="934918">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="936500"><P><B></a>PFRDAD(fileid, nchr, name, ntype, type, space, ind)
</B><BR><A NAME="936794"></a>Read <em>part of variable</em> <em>name</em> from PDB file <em>fil</em>eid as variable type type and put it into
<em>space</em>.
<BR><a name="936501">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="936502">
<dd><em>nchr</em>, the number of characters in <em>name</em>,<P>
</a>
<a name="936503">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="936504">
<dd><em>ntype</em>, the number of characters in <em>type</em>,<P>
</a>
<a name="936505">
<dd><em>type</em>, an ASCII string containing the type of the variable in space,<P>
</a>
<a name="936506">
<dd><em>space</em>, the variable where the data is to be placed,<P>
</a>
<a name="936507">
<dd><em>ind</em>, the array of dimension index specifications (start, stop, step triplets for each dimension).<P>
</a>
<a name="936508">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="936482"><P><B></a>PFRDAS(fileid, nchr, name, ntype, type, space)
</B><BR><A NAME="936483"></a>Read variable <em>name</em> from PDB file<em> fileid</em> as variable type type and put it into <em>space</em>.
<BR><a name="936484">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="936486">
<dd><em>nchr</em>, the number of characters in <em>name</em>,<P>
</a>
<a name="936487">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="936497">
<dd><em>ntype</em>, the number of characters in <em>type</em>,<P>
</a>
<a name="936498">
<dd><em>type</em>, an ASCII string containing the type of the variable in space,<P>
</a>
<a name="936488">
<dd><em>space</em>, the variable where the data is to be placed.<P>
</a>
<a name="936489">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="936490"><P><B></a>PFREAD(fileid, nchr, name, space)
</B><BR><A NAME="936491"></a>Read variable <em>name</em> from PDB file<em> fileid</em> and put it into <em>space</em>.
<BR><a name="936492">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="936493">
<dd><em>nchr</em>, the number of characters in <em>name</em>,<P>
</a>
<a name="936494">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="936495">
<dd><em>space</em>, the variable where the data is to be placed.<P>
</a>
<a name="936496">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="932950"><P><B></a>PFSBFS(v)
</B><BR><A NAME="932952"></a>Set the buffer size which PDBLib will use for all PDB files to <em>v</em>.
<BR><a name="932953">
<dt>Input: <em>v</em>, an integer value for the buffer size in bytes.
</a>
<a name="932954">
<dt>Output: Return the integer value of the buffer size in bytes.
</a>
<A NAME="937619"><P><B></a>PFSMXS(fileid, v)
</B><BR><a name="937620">
<dt></a>Set the maximum file size for PDB file <em>fileid</em> to <em>v</em>.
</a>
<a name="937621">
<dt>Input: <em>fileid</em>, an integer <strong>PDBfile</strong> identification number.
</a>
<a name="937622">
<dd><em>v</em>, an integer value for the maximum file size.<P>
</a>
<a name="937623">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="932956"><P><B></a>PFSOFF(fileid, v)
</B><BR><A NAME="932957"></a>Set the default offset for PDB file<em> fileid</em> to <em>v</em>.
<BR><a name="932958">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="932959">
<dd><em>v</em>, an integer value for the default offset.<P>
</a>
<a name="932960">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="934898"><P><B></a>PFSVAT(fileid, nv, var, na, attr, value)
</B><BR><A NAME="934899"></a>Set the value of an attribute for an entity in a PDB file.
<BR><a name="934900">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="934902">
<dd><em>nv</em>, an integer number of characters in var,<P>
</a>
<a name="934904">
<dd>var, an ASCII string naming an entity,<P>
</a>
<a name="934894">
<dd><em>na</em>, an integer number of characters in attr,<P>
</a>
<a name="934905">
<dd>attr, an ASCII string naming an existing attribute,<P>
</a>
<a name="934863">
<dd>value, the data for the attribute value.<P>
</a>
<a name="934903">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="933289"><P><B></a>PFTRGT(is, ia)
</B><BR><A NAME="933290">Write the next PDB file to be created according to the specified </a>data standard and </a>alignment.
<BR><a name="933291">
<dt>Input: <em>is</em>, an index specifying the data standard,
</a>
<a name="933292">
<dd><em>ia</em>, an index specifying the data alignment.<P>
</a>
<a name="933293">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="932885"><P><B></a>PFVART(fileid, order, nvars)
</B><BR><A NAME="932886"></a>Generate an internal </a>table of </a>variables in PDB file<em> fileid</em> which is sorted according to the
specification, order.
<BR><a name="932887">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="932889">
<dd>order, an integer specifying the order (1, alphabetic; 2, disk address order).<P>
</a>
<a name="933267">
<dt>Output: Return 1 if successful, 0 otherwise,
</a>
<a name="935283">
<dd>nvars, the number of variables in the file.<P>
</a>
<A NAME="932962"><P><B></a>PFWIMA(fileid, nchr, name, pkn, pkx, pln, plx, data, pxn, pxx, pyn, pyx, pim)
</B><BR><A NAME="932963">Write the given information out to file<em> fileid</em> as a PD_image.
<BR><a name="932964">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="932966">
<dd><em>nchr</em>, the number of characters in the image name,<P>
</a>
<a name="932968">
<dd><em>name</em>, an ASCII string containing the </a>image name,<P>
</a>
<a name="932969">
<dd><em>pkn</em>, an integer containing the minimum column index of data,<P>
</a>
<a name="932970">
<dd><em>pkx</em>, an integer containing the maximum column index of data,<P>
</a>
<a name="933646">
<dd><em>pln</em>, an integer containing the minimum row index of data,<P>
</a>
<a name="933648">
<dd><em>plx</em>, an integer containing the maximum row index of data,<P>
</a>
<a name="932971">
<dd><em>data</em>, a real*8 array containing the range data,<P>
</a>
<a name="932973">
<dd><em>pxn</em>, a real*8 constant specifying the minimum column index in image,<P>
</a>
<a name="932976">
<dd><em>pxx</em>, a real*8 constant specifying the maximum column index in image,<P>
</a>
<a name="932977">
<dd><em>pyn</em>, a real*8 constant specifying the minimum row index in image,<P>
</a>
<a name="932978">
<dd><em>pyx</em>, a real*8 constant specifying the maximum row index in image,<P>
</a>
<a name="934221">
<dd>pim, an integer containing the image number.<P>
</a>
<a name="932981">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="932983"><P><B></a>PFWMAP(fileid, dname, dp, dm, rname, rp, rm, pim)
</B><BR><A NAME="932984">Write the given information out to <em>file fileid</em> as a </a>PM_mapping. The number <em>pim</em> represents the </a>mapping number and must be unique.
<BR><a name="932985">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="932987">
<dd><em>dname</em>, an ASCII string containing the domain name,<P>
</a>
<a name="932988">
<dd><em>dp</em>, an integer array of parameters defining the domain,<P>
</a>
<a name="932989">
<dd><em>dm</em>, a real*8 array containing the domain data,<P>
</a>
<a name="932992">
<dd><em>rname</em>, an ASCII string containing the range name,<P>
</a>
<a name="932993">
<dd><em>rp</em>, an integer array of parameters defining the range,<P>
</a>
<a name="932994">
<dd><em>rm</em>, a real*8 array containing the range data,<P>
</a>
<a name="932999">
<dd><em>pim</em>, an integer containing the mapping number.<P>
</a>
<a name="933001">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="936531"><P><B></a>PFWRAD(fileid, nchr, name, ntypin, intype, ntypout, outtype, space, nd, ind)
</B><BR><A NAME="936532"></a>Write the data pointed to by <em>space</em> under <em>name</em> and with <em>type</em> in PDB file <em>fileid</em>. Array
ind contains nd triples indicating the minimum and maximum index and the stride for
each dimension.
<BR><a name="936533">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="936534">
<dd><em>nchr</em>, the number of characters in <em>name</em>,<P>
</a>
<a name="936535">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="936538">
<dd><em>ntypin</em>, the number of characters in <em>intype</em>,<P>
</a>
<a name="936539">
<dd><em>intype</em>, an ASCII string containing the type of the variable in space,<P>
</a>
<a name="936540">
<dd><em>ntypout</em>, the number of characters in <em>outtype</em>,<P>
</a>
<a name="936541">
<dd><em>outtype</em>, an ASCII string containing the type of the variable in name,<P>
</a>
<a name="936624">
<dd><em>space</em>, the variable containing the data,<P>
</a>
<a name="936741">
<dd><em>nd</em>, an integer number of dimensions,<P>
</a>
<a name="936742">
<dd>ind, an array of nd integer (min, max, stride) triples.<P>
</a>
<a name="936746">
<dt>Output: Return 1 if successful, 0 otherwise.AS</a>(fileid, nchr, name, ntypin, intype, ntypout, outtype, space)
</a>
<A NAME="933002"><P><B></a>PFWRAN(fileid, dname, nchr, rname, rp, rm, pim)
</B><BR><A NAME="933003">Write the given information out to file <em>fileid</em> as a </a>PM_mapping. The number <em>pim</em> represents the </a>mapping number and must be unique.
<BR><a name="933005">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="933006">
<dd><em>dname</em>, an ASCII string containing the domain name,<P>
</a>
<a name="933007">
<dd><em>nchr</em>, the number of characters in the domain name,<P>
</a>
<a name="933008">
<dd><em>rname</em>, an ASCII string containing the range name,<P>
</a>
<a name="933009">
<dd><em>rp</em>, an integer array of parameters defining the range,<P>
</a>
<a name="933012">
<dd><em>rm</em>, a real*8 array containing the range data,<P>
</a>
<a name="933013">
<dd><em>pim</em>, an integer containing the mapping number.<P>
</a>
<a name="933014">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="936522"><P><B></a>PFWRAS(fileid, nchr, name, ntypin, intype, ntypout, outtype, space)
</B><BR><A NAME="936523"></a>Write the data pointed to by <em>space of type</em> intype in PDB file<em> fileid</em> under <em>name</em> and with
type outtype. An arbitrary number of dimensions may be included in the <em>name</em> string.
<BR><a name="936524">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="936525">
<dd><em>nchr</em>, the number of characters in name,<P>
</a>
<a name="936526">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="936527">
<dd><em>ntypin</em>, the number of characters in <em>intype</em>,<P>
</a>
<a name="936528">
<dd><em>intype</em>, an ASCII string containing the type of the variable in space,<P>
</a>
<a name="936544">
<dd><em>ntypout</em>, the number of characters in <em>outtype</em>,<P>
</a>
<a name="936545">
<dd><em>outtype</em>, an ASCII string containing the type of the variable in name,<P>
</a>
<a name="936529">
<dd><em>space</em>, the variable containing the data.<P>
</a>
<a name="936530">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="933017"><P><B></a>PFWRTA(fileid, nchr, name, ntype, type, space)
</B><BR><A NAME="933020"></a>Write the data pointed to by <em>space</em> under <em>name</em> and with t<em>ype</em> in PDB file<em> fileid</em>. An arbitrary number of dimensions may be included in the <em>name</em> string.
<BR><a name="933022">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="933023">
<dd><em>nchr</em>, the number of characters in name,<P>
</a>
<a name="933024">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="933026">
<dd><em>ntype</em>, the number of characters in <em>type</em>,<P>
</a>
<a name="933027">
<dd><em>type</em>, an ASCII string containing the type of the variable,<P>
</a>
<a name="933028">
<dd><em>space</em>, the variable containing the data.<P>
</a>
<a name="933031">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="933032"><P><B></a>PFWRTD(fileid, nchr, name, ntype, type, space, nd, ind)
</B><BR><A NAME="933034"></a>Write the data pointed to by <em>space</em> under <em>name</em> and with <em>type</em> in PDB file <em>fileid</em>. Array
ind contains nd triples indicating the minimum and maximum index and the stride for
each dimension.
<BR><a name="933035">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="933037">
<dd><em>nchr</em>, the number of characters in <em>name</em>,<P>
</a>
<a name="933038">
<dd><em>name</em>, an ASCII string containing the name of the variable in the PDB file,<P>
</a>
<a name="933039">
<dd><em>ntype</em>, the number of characters in <em>type</em>,<P>
</a>
<a name="933041">
<dd><em>type</em>, an ASCII string containing the type of the variable,<P>
</a>
<a name="933617">
<dd><em>space</em>, the variable containing the data,<P>
</a>
<a name="933042">
<dd><em>nd</em>, an integer number of dimensions,<P>
</a>
<a name="934071">
<dd>ind, an array of nd integer (min, max, stride) triples.<P>
</a>
<a name="933043">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="933294"><P><B></a>PFWSET(fileid, dname, dp, dm)
</B><BR><a name="933296">
<dt>Build a </a>PM_set structure out of the given input data and write it to a PDB file.
</a>
<a name="933295">
<dt>Input: <em>fileid</em>, an integer PDBfile identification number,
</a>
<a name="933297">
<dd><em>dname</em>, an ASCII string containing the set name,<P>
</a>
<a name="933298">
<dd><em>dp</em>, an integer array of parameters defining the </a>PM_set,<P>
</a>
<a name="933299">
<dd><em>dm</em>, an array of real*8 values containing the set elements.<P>
</a>
<a name="933302">
<dt>Output: Return 1 if successful, 0 otherwise.
</a>
<A NAME="934584"><PRE>
</PRE></dl>
<a name="934594">
<h1>6.0 The </a>FORTRAN </a>API</h1>
</a>
<a name="932479">
In this section a more formal description of the FORTRAN API for PDBLib is given including a more detailed account of their workings.<p>
</a>
<a name="936585">
<h2>6.1 PFAPAD — (PD_append_as_alt)</h2>
</a>
<A NAME="936586"><PRE><B>
</B></PRE><A NAME="936587"><PRE><B>integer </a>PFAPAD(integer fileid,
</B></PRE><A NAME="936588"><PRE><B> integer nchr,
</B></PRE><A NAME="934669"><PRE><B> character name,
</B></PRE><A NAME="936589"><PRE><B> integer ntype,
</B></PRE><A NAME="936590"><PRE><B> character intype,
</B></PRE><A NAME="936796"><PRE><B> void space,
</B></PRE><A NAME="936591"><PRE><B> integer nd,
</B></PRE><A NAME="936592"><PRE><B> integer ind)
</B></PRE><a name="936593">
</a>Append data of type intype to an entry in the specified file. The outtype is assumed to be the same as for the original entry. The dimensions of the appended data are specified in nd and ind. They must match the original entry except for the most slowly varying one. The specification of the most slowly varying dimension must be one of the following;<p>
</a>
<dl>
<a name="936594">
<dt>min:max :stride => new dimension is old_min:old_max+(max-min+1)
</a>
<a name="936595">
<dt> if min is the default_offset for the file
</a>
<a name="936596">
<dt> or
</a>
<a name="936597">
<dt>min:max :stride => new dimension is old_min:max
</a>
<a name="936598">
<dt> if min is old_max+1
</a>
<a name="936599">
The rationale for this function is that some data sets are of unknown size until they are completely written. PDBLib permits any entry to reside in </a>discontiguous blocks of disk space. The library is responsible for reading and writing data correctly across these blocks.<p>
</a>
<a name="936600">
The shape or dimensional information of the entry is specified in nd and ind. In this respect PFAPAD behaves just like </a>PFWRTD.<p>
</a>
<a name="936601">
The arguments to PFAPAD are: fileid, an integer identifier which designates the PDB file to which to write; nchr, an integer number of characters in the name string; name, an ASCII string containing the name of the variable to install in the symbol table; ntype, an integer number of characters in the intype string; intype, an ASCII string specifying the type of data to which space points; space, the data to be written; nd, an integer number of dimensions; and ind, an array of nd integer triples containing the minimum and maximum index and the stride for each dimension.<p>
</a>
<a name="936602">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function </a>PFGERR.<p>
</a>
<a name="936603">
See also PFAPAS, PFAPPA, PFAPPD, PFWRAD, PFWRAS, PFWRTA, and PFWRTD.<p>
</a>
<a name="936604">
<p>
</a>
<A NAME="936605"><PRE><B>integer </a>PFAPAD(integer fileid,
</B></PRE><A NAME="936606"><PRE><B> integer nchr,
</B></PRE><A NAME="936607"><PRE><B> character name,
</B></PRE><A NAME="936563"><PRE><B> integer ntype,
</B></PRE><A NAME="936798"><PRE><B> character intype,
</B></PRE><A NAME="936608"><PRE><B> void space,
</B></PRE><A NAME="936609"><PRE><B> integer nd,
</B></PRE><A NAME="936610"><PRE><B> integer ind)
</B></PRE><A NAME="936611"><B>
</B><HR><A NAME="936612"><PRE> character*8 intype
</PRE><A NAME="936807"><PRE> integer pfapad, pfwrtd
</PRE><A NAME="936613"><PRE> integer fileid, ntype, nd, ind(3)
</PRE><A NAME="936614"><PRE> real x(20)
</PRE><A NAME="936799"><PRE> real*8 y(10)
</PRE><A NAME="936615"><PRE> .
</PRE><A NAME="936616"><PRE> .
</PRE><A NAME="936617"><PRE> .
</PRE><A NAME="936618"><PRE> c write array x
</PRE><A NAME="936619"><PRE> ind(1) = 1
</PRE><A NAME="936620"><PRE> ind(2) = 20
</PRE><A NAME="936621"><PRE> ind(3) = 1
</PRE><A NAME="936622"><PRE> if (</a>pfwrtd(fileid, 1, ‘x’, 5, ‘float’, x, 1, ind) .eq. 0)
</PRE><A NAME="936623"><PRE> $ call errproc
</PRE><A NAME="936732"><PRE> .
</PRE><A NAME="936733"><PRE> .
</PRE><A NAME="936740"><PRE> .
</PRE><A NAME="936625"><PRE> c append to x
</PRE><A NAME="936626"><PRE> ind(2) = 10
</PRE><A NAME="936627"><PRE> if (</a>pfapad(fileid, 1, ‘x’, 6, ‘double’, y, 1, ind) .eq. 0)
</PRE><A NAME="936628"><PRE> $ call errproc
</PRE><A NAME="936629"><PRE> .
</PRE><A NAME="936630"><PRE> .
</PRE><A NAME="936546"><PRE> .
</PRE><A NAME="936558"><PRE> Compare this with the example of </a>PFWRAD.
</PRE></dl>
<a name="936631">
<h2>6.2 PFAPAS — (PD_append_as)</h2>
</a>
<A NAME="936547"><PRE><B>
</B></PRE><A NAME="936548"><PRE><B>integer </a>PFAPAS(integer fileid,
</B></PRE><A NAME="936549"><PRE><B> integer nchr,
</B></PRE><A NAME="936550"><PRE><B> character name,
</B></PRE><A NAME="936801"><PRE><B> integer ntype,
</B></PRE><A NAME="936802"><PRE><B> character intype,
</B></PRE><A NAME="936551"><PRE><B> void space)
</B></PRE><a name="936552">
</a>Append data to an entry in the specified file. The outtype is assumed to be the same as for the original entry. The dimensions of the appended data are specified in name. They must match the original entry except for the most slowly varying one. The specification of the most slowly varying dimension must be one of the following;<p>
</a>
<dl>
<a name="936553">
<dt>min:max => new dimension is old_min:old_max+(max-min+1)
</a>
<a name="936554">
<dt> if min is the default_offset for the file
</a>
<a name="936555">
<dt> or
</a>
<a name="936556">
<dt>min:max => new dimension is old_min:max
</a>
<a name="936557">
<dt> if min is old_max+1
</a>
<a name="936665">
The rationale for this function is that some data sets are of unknown size until they are completely written. PDBLib permits any entry to reside in </a>discontiguous blocks of disk space. The library is responsible for reading and writing data correctly across these blocks.<p>
</a>
<a name="936559">
The shape or dimensional information of the entry is a part of the name string. In this respect </a>PFAPAS behaves just like </a>PFWRAS.<p>
</a>
<a name="936560">
The arguments to </a>PFAPAS are: fileid, an integer identifier which designates the PDB file to which to write; nchr, an integer number of characters in the name string; name, an ASCII string containing the name of the variable and any dimensional information, ntype, an integer number of characters in the intype string; intype, an ASCII string specifying the type of data to which space points and space, the data to be appended.<p>
</a>
<a name="936561">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function </a>PFGERR.<p>
</a>
<a name="936562">
See also PFAPAD, PFAPPA, PFAPPD, PFWRAD, PFWRAS, PFWRTA, and PFWRTD.<p>
</a>
<a name="936564">
<p>
</a>
<A NAME="936797"><PRE><B>integer </a>PFAPAS(integer fileid,
</B></PRE><A NAME="936565"><PRE><B> integer nchr,
</B></PRE><A NAME="936566"><PRE><B> character name,
</B></PRE><A NAME="936805"><PRE><B> integer ntype,
</B></PRE><A NAME="936806"><PRE><B> character intype,
</B></PRE><A NAME="936567"><PRE><B> void space)
</B></PRE><A NAME="936568"><B>
</B><HR><A NAME="936808"><PRE> character*8 intype
</PRE><A NAME="936569"><PRE> integer pfapas, pfwrta
</PRE><A NAME="936570"><PRE> integer fileid, nchr, ntype
</PRE><A NAME="936571"><PRE> real x(20)
</PRE><A NAME="936803"><PRE> real*8 y(10)
</PRE><A NAME="936572"><PRE> .
</PRE><A NAME="936573"><PRE> .
</PRE><A NAME="936574"><PRE> .
</PRE><A NAME="936575"><PRE> c write array x
</PRE><A NAME="936576"><PRE> if (</a>pfwrta(fileid, 5, ‘x(20)’, 5, ‘float’, x) .eq. 0)
</PRE><A NAME="936577"><PRE> $ call errproc
</PRE><A NAME="936747"><PRE> .
</PRE><A NAME="936748"><PRE> .
</PRE><A NAME="936749"><PRE> .
</PRE><A NAME="936579"><PRE> c append to x
</PRE><A NAME="936580"><PRE> if (</a>pfapas(fileid, 7, ‘x(1:10)’, 6, ‘double’, y) .eq. 0)
</PRE><A NAME="936581"><PRE> $ call errproc
</PRE><A NAME="936582"><PRE> .
</PRE><A NAME="936578"><PRE> .
</PRE><A NAME="936583"><PRE> .
</PRE><a name="932907">
Compare this with the example of </a>PFWRAS.<p>
</a>
</dl>
<a name="936804">
<h2>6.3 PFAPPA — (PD_append)</h2>
</a>
<A NAME="933517"><PRE><B>
</B></PRE><A NAME="933518"><PRE><B>integer </a>PFAPPA(integer fileid,
</B></PRE><A NAME="934125"><PRE><B> integer nchr,
</B></PRE><A NAME="934525"><PRE><B> character name,
</B></PRE><A NAME="934527"><PRE><B> void space)
</B></PRE><a name="934528">
</a>Append data to an entry in the specified file. The type is assumed to be the same as for the original entry. The dimensions of the appended data are specified in name. They must match the original entry except for the most slowly varying one. The specification of the most slowly varying dimension must be one of the following;<p>
</a>
<dl>
<a name="934529">
<dt>min:max => new dimension is old_min:old_max+(max-min+1)
</a>
<a name="934532">
<dt> if min is the default_offset for the file
</a>
<a name="934533">
<dt> or
</a>
<a name="934534">
<dt>min:max => new dimension is old_min:max
</a>
<a name="934538">
<dt> if min is old_max+1
</a>
<a name="934599">
The rationale for this function is that some data sets are of unknown size until they are completely written. PDBLib permits any entry to reside in </a>discontiguous blocks of disk space. The library is responsible for reading and writing data correctly across these blocks.<p>
</a>
<a name="934622">
The shape or dimensional information of the entry is a part of the name string. In this respect </a>PFAPPA behaves just like </a>PFWRTA.<p>
</a>
<a name="934627">
The arguments to </a>PFAPPA are: fileid, an integer identifier which designates the PDB file to which to write; nchr, an integer number of characters in the name string; name, an ASCII string containing the name of the variable to install in the symbol table; and space, the data to be written.<p>
</a>
<a name="934688">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function </a>PFGERR.<p>
</a>
<a name="934722">
See also PFAPAD, PFAPAS, PFAPPD, PFWRAD, PFWRAS, PFWRTA, and PFWRTD.<p>
</a>
<a name="935241">
<p>
</a>
<A NAME="934724"><PRE><B>integer </a>PFAPPA(integer fileid,
</B></PRE><A NAME="934725"><PRE><B> integer nchr,
</B></PRE><A NAME="934726"><PRE><B> character name,
</B></PRE><A NAME="934728"><PRE><B> void space)
</B></PRE><A NAME="934696"><B>
</B><HR><A NAME="934697"><PRE> integer pfappa, pfwrta
</PRE><A NAME="934699"><PRE> integer fileid
</PRE><A NAME="934700"><PRE> real x(20), y(10)
</PRE><A NAME="934703"><PRE> .
</PRE><A NAME="934704"><PRE> .
</PRE><A NAME="934705"><PRE> .
</PRE><A NAME="934707"><PRE> c write array x
</PRE><A NAME="934708"><PRE> if (</a>pfwrta(fileid, 5, ‘x(20)’, 5, ‘float’, x) .eq. 0)
</PRE><A NAME="934709"><PRE> $ call errproc
</PRE><A NAME="934711"><PRE>
</PRE><A NAME="934712"><PRE> c append to x
</PRE><A NAME="934713"><PRE> if (</a>pfappa(fileid, 7, ‘x(1:10)’, y) .eq. 0)
</PRE><A NAME="934714"><PRE> $ call errproc
</PRE><A NAME="934715"><PRE> .
</PRE><A NAME="934716"><PRE> .
</PRE><A NAME="934689"><PRE> .
</PRE></dl>
<a name="934690">
<h2>6.4 PFAPPD — (PD_append_alt)</h2>
</a>
<A NAME="934718"><PRE><B>
</B></PRE><A NAME="934776"><PRE><B>integer </a>PFAPPD(integer fileid,
</B></PRE><A NAME="934777"><PRE><B> integer nchr,
</B></PRE><A NAME="934779"><PRE><B> character name,
</B></PRE><A NAME="934780"><PRE><B> void space,
</B></PRE><A NAME="934781"><PRE><B> integer nd,
</B></PRE><A NAME="934782"><PRE><B> integer ind)
</B></PRE><a name="934701">
</a>Append data to an entry in the specified file. The type is assumed to be the same as for the original entry. The dimensions of the appended data are specified in nd and ind. They must match the original entry except for the most slowly varying one. The specification of the most slowly varying dimension must be one of the following;<p>
</a>
<dl>
<a name="935244">
<dt>min:max :stride => new dimension is old_min:old_max+(max-min+1)
</a>
<a name="935245">
<dt> if min is the default_offset for the file
</a>
<a name="935246">
<dt> or
</a>
<a name="935247">
<dt>min:max :stride => new dimension is old_min:max
</a>
<a name="935248">
<dt> if min is old_max+1
</a>
<a name="934736">
The rationale for this function is that some data sets are of unknown size until they are completely written. PDBLib permits any entry to reside in </a>discontiguous blocks of disk space. The library is responsible for reading and writing data correctly across these blocks.<p>
</a>
<a name="934737">
The shape or dimensional information of the entry is specified in nd and ind. In this respect </a>PFAPPD behaves just like </a>PFWRTD.<p>
</a>
<a name="934691">
The arguments to </a>PFAPPD are: fileid, an integer identifier which designates the PDB file to which to write; nchr, an integer number of characters in the name string; name, an ASCII string containing the name of the variable to install in the symbol table; space, the data to be written; nd, an integer number of dimensions; and ind, an array of nd integer triples containing the minimum and maximum index and the stride for each dimension.<p>
</a>
<a name="934739">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function </a>PFGERR.<p>
</a>
<a name="934740">
See also PFAPAD, PFAPAS, PFAPPA, PFWRAD, PFWRAS, PFWRTA, and PFWRTD.<p>
</a>
<a name="934742">
<p>
</a>
<A NAME="936810"><PRE><B>integer </a>PFAPPD(integer fileid,
</B></PRE><A NAME="934744"><PRE><B> integer nchr,
</B></PRE><A NAME="934745"><PRE><B> character name,
</B></PRE><A NAME="934746"><PRE><B> void space,
</B></PRE><A NAME="934774"><PRE><B> integer nd,
</B></PRE><A NAME="934775"><PRE><B> integer ind)
</B></PRE><A NAME="934747"><B>
</B><HR><A NAME="934748"><PRE> integer pfappd, pfwrtd
</PRE><A NAME="934750"><PRE> integer fileid, ind(3)
</PRE><A NAME="934751"><PRE> real x(20), y(10)
</PRE><A NAME="934752"><PRE> .
</PRE><A NAME="934754"><PRE> .
</PRE><A NAME="934755"><PRE> .
</PRE><A NAME="934756"><PRE> c write array x
</PRE><A NAME="934757"><PRE> ind(1) = 1
</PRE><A NAME="934771"><PRE> ind(2) = 20
</PRE><A NAME="934772"><PRE> ind(3) = 1
</PRE><A NAME="934770"><PRE> if (</a>pfwrtd(fileid, 1, ‘x’, 5, ‘float’, x, 1, ind) .eq. 0)
</PRE><A NAME="934759"><PRE> $ call errproc
</PRE><A NAME="934760"><PRE>
</PRE><A NAME="934761"><PRE> c append to x
</PRE><A NAME="934773"><PRE> ind(2) = 10
</PRE><A NAME="934762"><PRE> if (</a>pfappd(fileid, 1, ‘x’, y, 1, ind) .eq. 0)
</PRE><A NAME="934763"><PRE> $ call errproc
</PRE><A NAME="934764"><PRE> .
</PRE><A NAME="934766"><PRE> .
</PRE><A NAME="934767"><PRE> .
</PRE></dl>
<a name="935628">
<h2>6.5 </a>PFCD — (PD_cd)</h2>
</a>
<A NAME="935642"><PRE><B>
</B></PRE><A NAME="935643"><PRE><B>integer </a>PFCD(integer fileid,
</B></PRE><A NAME="935646"><PRE><B> integer nchr,
</B></PRE><A NAME="935645"><PRE><B> char *dirname)
</B></PRE><a name="935644">
</a>Change the </a>current </a>directory in a PDB file.<p>
</a>
<a name="935647">
PDBLib supports an optional </a>hierarchical </a>directory structure inside PDB files. A directory or a variable in a directory may be specified by either a </a>relative path or an </a>absolute path. Slashes separate nodes in a </a>path name. Absolute paths begin with a slash. Nodes consisting of two periods, “..”, refer to the next higher level directory.<p>
</a>
<a name="935648">
The arguments to </a>PFCD are: fileid, an integer file identifier; nchr, an integer number of characters in string dirname; and dirname, an ASCII string containing the path name of the directory to change to.<p>
</a>
<a name="935649">
If dirname is an empty string or a slash, it refers to the top level or </a>root directory.<p>
</a>
<a name="935650">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="935651">
See also </a>PFDLS, </a>PFGLS, </a>PFLN, </a>PFLST, </a>PFMKDR, </a>PFPWD.<p>
</a>
<a name="935652">
<p>
</a>
<A NAME="935653"><PRE><B>integer </a>PFCD(integer fileid,
</B></PRE><A NAME="935656"><PRE><B> integer nchr,
</B></PRE><A NAME="935657"><PRE><B> char *dirname)
</B></PRE><A NAME="935659"><B>
</B><HR><A NAME="935660"><PRE> integer pfcd
</PRE><A NAME="935661"><PRE> integer fileid
</PRE><A NAME="935662"><PRE> .
</PRE><A NAME="935663"><PRE> .
</PRE><A NAME="935664"><PRE> .
</PRE><A NAME="935654"><PRE> if (</a>pfcd(fileid, 16, ‘/animals/mammals’) .eq. 0)
</PRE><A NAME="935655"><PRE> $ call errproc
</PRE><A NAME="935665"><PRE> .
</PRE><A NAME="935666"><PRE> .
</PRE><A NAME="935667"><PRE> .
</PRE><A NAME="935668"><PRE> if (</a>pfcd(fileid, 11, ‘../reptiles’) .eq. 0)
</PRE><A NAME="935669"><PRE> $ call errproc
</PRE><A NAME="935670"><PRE> .
</PRE><A NAME="935671"><PRE> .
</PRE><A NAME="935672"><PRE> .
</PRE><a name="934616">
<h2>6.6 PFCLOS — (PD_close)</h2>
</a>
<A NAME="934619"><PRE><B>
</B></PRE><A NAME="932750"><PRE><B>integer </a>PFCLOS(integer fileid)
</B></PRE><a name="934625">
</a>Close a PDB file. After all data is written to the PDB file, the structure chart and symbol table must be written out to the file and their disk addresses recorded in the file header. Without these operations the file cannot be read back in by PDBLib and all data is lost.<p>
</a>
<a name="934630">
All open PDB files must be </a>PFCLOS’d before exiting the program. The integer identifier <em>fileid</em> associated with the PDB file must be passed to </a>PFCLOS.<p>
</a>
<a name="932483">
This function returns 1 if the PDB file is correctly written and closed; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="933692">
<p>
</a>
<A NAME="933694"><PRE><B>integer </a>PFCLOS(integer fileid)
</B></PRE><A NAME="932859"><B>
</B><HR><A NAME="932888"><PRE> integer </a>pfclos
</PRE><A NAME="933841"><PRE> integer fileid
</PRE><A NAME="933843"><PRE> .
</PRE><A NAME="933844"><PRE> .
</PRE><A NAME="933842"><PRE> .
</PRE><A NAME="933845"><PRE> if (</a>pfclos(fileid) .eq. 0)
</PRE><A NAME="933846"><PRE> $ call errproc
</PRE><A NAME="933849"><PRE> .
</PRE><A NAME="933850"><PRE> .
</PRE><A NAME="933851"><PRE> .
</PRE><a name="934588">
<h2>6.7 PFDATT — (PD_def_attribute)</h2>
</a>
<A NAME="934600"><PRE><B>
</B></PRE><A NAME="934601"><PRE><B>integer </a>PFDATT(integer fileid,
</B></PRE><A NAME="934608"><PRE><B> integer na,
</B></PRE><A NAME="934602"><PRE><B> char *attr,
</B></PRE><A NAME="934609"><PRE><B> integer nt,
</B></PRE><A NAME="934603"><PRE><B> char *type)
</B></PRE><a name="934604">
</a>Define an </a>attribute to the given PDB file. The </a>model of an attribute in PDBLib is an entity that has a name and type. The two supported operations on attributes are to create them and to remove them. An entity in a PDB file can be assigned an </a>attribute value simply by making a call which specifies the entity name, the attribute name, and the attribute value (which is determined by the type). The only association between an entry in a PDB file and any attribute is made by the name in the attribute table and the entry in the symbol table. In particular, this mechanism allows the application developer to define and use entities in a PDB file solely in terms of attributes.<p>
</a>
<a name="934610">
The arguments to </a>PFDATT are: fileid, an integer identifier which designates the PDB file in which the attribute is being defined; na, an integer number of characters in the attr string; attr, an ASCII string containing the name of the attribute; nt, an integer number of characters in the type string; and type, an ASCII string containing the type of the attribute;<p>
</a>
<a name="933972">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="934607">
See also </a>PFRATT, </a>PFGVAT, and </a>PFSVAT.<p>
</a>
<a name="934693">
<p>
</a>
<A NAME="934692"><PRE><B>integer </a>PFDATT(integer fileid,
</B></PRE><A NAME="934808"><PRE><B> integer na,
</B></PRE><A NAME="934810"><PRE><B> char *attr,
</B></PRE><A NAME="934811"><PRE><B> integer nt,
</B></PRE><A NAME="934812"><PRE><B> char *type)
</B></PRE><A NAME="934786"><B>
</B><HR><A NAME="934787"><PRE> integer pfdatt
</PRE><A NAME="934788"><PRE> integer fileid
</PRE><A NAME="934791"><PRE> .
</PRE><A NAME="934792"><PRE> .
</PRE><A NAME="934794"><PRE> .
</PRE><A NAME="934796"><PRE> if (</a>pfdatt(fileid, 4, ‘date’, 6, ‘char *’) .eq. 0)
</PRE><A NAME="934798"><PRE> $ call errproc
</PRE><A NAME="934804"><PRE> .
</PRE><A NAME="934805"><PRE> .
</PRE><A NAME="934807"><PRE> .
</PRE><a name="935077">
<h2>6.8 PFDEFA — (PD_defent)</h2>
</a>
<A NAME="935078"><PRE><B>
</B></PRE><A NAME="935075"><PRE><B>integer </a>PFDEFA(integer fileid,
</B></PRE><A NAME="935152"><PRE><B> integer nc,
</B></PRE><A NAME="935153"><PRE><B> char *name,
</B></PRE><A NAME="935154"><PRE><B> integer nt,
</B></PRE><A NAME="935155"><PRE><B> char *type)
</B></PRE><a name="935123">
</a>Define an entry in the </a>symbol table of the PDB file specified by <em>fileid</em>. This function </a>reserves space on disk but writes no data. The data can be written with later calls to </a>PFWRTA or </a>PFWRTD.<p>
</a>
<a name="935124">
The shape or dimensional information of the entry is a part of the name string. In this respect it behaves as </a>PFWRTA.<p>
</a>
<a name="935138">
The rationale for this function is to </a>block out space in a PDB file corresponding to some logical layout of a piece of data. The data may not exist at the time the space is reserved or for some reason it may be desirable to write out the data in pieces. In any case if the type and shape of a variable is known at some point, an entry may be made in the PDB file without writing any data. The space may filled with other PDBLib calls at some later time.<p>
</a>
<a name="935139">
The arguments to this function are: fileid, an integer identifier which designates the PDB file in which to define an entry; nchr, an integer number of characters in the name string; name, an ASCII string containing the name of the variable to install in the symbol table; ntype, an integer number of characters in the type string; and type, an ASCII string specifying the variable type.<p>
</a>
<a name="935140">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="935141">
See also </a>PFAPAD, </a>PFAPAS, </a>PFAPPA, </a>PFAPPD, </a>PFDEFD, </a>PFWRAD, </a>PFWRAS, </a>PFWRTA, and </a>PFWRTD.<p>
</a>
<a name="935088">
<p>
</a>
<A NAME="935080"><PRE><B>integer </a>PFDEFA(integer fileid,
</B></PRE><A NAME="935157"><PRE><B> integer nc,
</B></PRE><A NAME="935158"><PRE><B> char *name,
</B></PRE><A NAME="935159"><PRE><B> integer nt,
</B></PRE><A NAME="935160"><PRE><B> char *type)
</B></PRE><A NAME="935093"><B>
</B><HR><A NAME="934040"><PRE> integer </a>pfdefa
</PRE><A NAME="935081"><PRE> integer fileid
</PRE><A NAME="935086"><PRE> .
</PRE><A NAME="935087"><PRE> .
</PRE><A NAME="935142"><PRE> .
</PRE><A NAME="935143"><PRE> c define and reserve array x
</PRE><A NAME="935083"><PRE> c declaration for x would be: real x(20)
</PRE><A NAME="935082"><PRE>
</PRE><A NAME="935144"><PRE> if (</a>pfdefa(fileid, 5, ‘x(20)’, 5, ‘float’) .eq. 0)
</PRE><A NAME="935145"><PRE> $ call errproc
</PRE><A NAME="935101"><PRE> .
</PRE><A NAME="935102"><PRE> .
</PRE><A NAME="935103"><PRE> .
</PRE><a name="935110">
Compare this with the example of </a>PFWRTA.<p>
</a>
<a name="935111">
<h2>6.9 PFDEFD — (PD_defent_alt)</h2>
</a>
<A NAME="935112"><PRE><B>
</B></PRE><A NAME="935079"><PRE><B>integer </a>PFDEFD(integer fileid,
</B></PRE><A NAME="935090"><PRE><B> integer nc,
</B></PRE><A NAME="935091"><PRE><B> char *name,
</B></PRE><A NAME="935092"><PRE><B> integer nt,
</B></PRE><A NAME="935161"><PRE><B> char *type,
</B></PRE><A NAME="935117"><PRE><B> integer nd,
</B></PRE><A NAME="935118"><PRE><B> integer ind)
</B></PRE><a name="935119">
</a>Define an entry in the </a>symbol table of the PDB file specified by <em>fileid</em>. This function </a>reserves space on disk but writes no data. The data can be written with later calls to </a>PFWRTA or </a>PFWRTD.<p>
</a>
<a name="935120">
This is an alternate form of </a>PFDEFA. The difference is that the </a>dimension information is supplied via the nd and ind arguments instead of being a part of the name string. In this respect it behaves as </a>PFWRTD.<p>
</a>
<a name="935122">
The rationale for this function is to </a>block out space in a PDB file corresponding to some logical layout of a piece of data. The data may not exist at the time the space is reserved or for some reason it may be desirable to write out the data in pieces. In any case if the type and shape of a variable is known at some point, an entry may be made in the PDB file without writing any data. The space may filled with other PDBLib calls at some later time.<p>
</a>
<a name="935136">
The arguments to this function are: fileid, an integer identifier which designates the PDB file in which to define an entry; nchr, an integer number of characters in the name string; name, an ASCII string containing the name of the variable to install in the symbol table; ntype, an integer number of characters in the type string; type, an ASCII string specifying the variable type; nd, an integer number of dimensions; and ind, an array of nd integer pairs containing the minimum and maximum index for each dimension.<p>
</a>
<a name="935137">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="934741">
See also </a>PFAPAD, </a>PFAPAS, </a>PFAPPA, </a>PFAPPD, </a>PFDEFA, </a>PFWRAD, </a>PFWRAS, </a>PFWRTA, and </a>PFWRTD.<p>
</a>
<a name="935125">
See also </a>PFAPPA, </a>PFAPPD, </a>PFDEFA, </a>PFWRTA, and </a>PFWRTD.<p>
</a>
<a name="935127">
<p>
</a>
<A NAME="935113"><PRE><B>integer </a>PFDEFD(integer fileid,
</B></PRE><A NAME="935114"><PRE><B> integer nc,
</B></PRE><A NAME="935116"><PRE><B> char *name,
</B></PRE><A NAME="935162"><PRE><B> integer nt,
</B></PRE><A NAME="935164"><PRE><B> char *type,
</B></PRE><A NAME="935165"><PRE><B> integer nd,
</B></PRE><A NAME="935166"><PRE><B> integer ind)
</B></PRE><A NAME="935133"><B>
</B><HR><A NAME="935128"><PRE> integer </a>pfdefd
</PRE><A NAME="935129"><PRE> integer fileid, nd, ind(4)
</PRE><A NAME="935131"><PRE> .
</PRE><A NAME="935132"><PRE> .
</PRE><A NAME="935151"><PRE> .
</PRE><A NAME="935167"><PRE> c define and reserve array c
</PRE><A NAME="935130"><PRE> c declaration for c would be: real c(2,2:4)
</PRE><A NAME="935134"><PRE>
</PRE><A NAME="935168"><PRE> nd = 2
</PRE><A NAME="935169"><PRE> ind(1) = 1
</PRE><A NAME="935170"><PRE> ind(2) = 2
</PRE><A NAME="935171"><PRE> ind(3) = 2
</PRE><A NAME="935172"><PRE> ind(4) = 4
</PRE><A NAME="935176"><PRE> if (</a>pfdefd(fileid, 1, ‘c’, 5, ‘float’, nd, ind) .eq. 0)
</PRE><A NAME="935177"><PRE> $ call errproc
</PRE><A NAME="935178"><PRE> .
</PRE><A NAME="935179"><PRE> .
</PRE><A NAME="935180"><PRE> .
</PRE><a name="935135">
Compare with the example for </a>PFWRTD.<p>
</a>
<a name="933695">
<h2>6.10 PFDEFS — (PD_defstr))</h2>
</a>
<A NAME="934645"><PRE><B>
</B></PRE><A NAME="932751"><PRE><B>integer </a>PFDEFS(integer fileid,
</B></PRE><A NAME="932752"><PRE><B> integer nchr,
</B></PRE><A NAME="932753"><PRE><B> character name,
</B></PRE><A NAME="932754"><PRE><B> integer ncm1, character mem1,
</B></PRE><A NAME="932757"><PRE><B> ...,
</B></PRE><A NAME="932758"><PRE><B> integer ncmn, character memn,
</B></PRE><A NAME="932756"><PRE><B> integer LAST)
</B></PRE><a name="934655">
</a>Define a data structure for a PDB file. As a matter of programming efficiency and clarity it is useful to be able to refer to more complex structural units than the </a>primitive types: short integers, integers, long integers, floating point numbers, double precision floating point numbers, and characters. Arrays do this in a very simple-minded way. Many modern languages support </a>extended types or structures which allow the programmer to group diverse types of data together in a very sophisticated way.<p>
</a>
<a name="934661">
PDBLib supports an </a>extended </a>data typing mechanism called a structure. A </a>structure is a set of declarations of members. Each </a>member is in turn a data type known to the system. Much of the style and usage of structures comes from the C struct. Note: because FORTRAN 77 lacks a </a>pointer type, structures defined with this function should not contain pointered members.<p>
</a>
<a name="934670">
</a>PFDEFS defines data structures to the PDB system so that instances of such extended types can be read and written as a whole in a single statement. The members of the structure are processed and an entry in the structure chart is made. Subsequent references to the new structure type are processed using information from the structure chart. The syntax by which members of a structure are specified is like that for C structs. The formal definition is given below ([ ] enclose optional elements). Note: </a>self-referential structures should not be used in FORTRAN applications.<p>
</a>
<dl>
<a name="934674">
<dt> <member> := <type> <member name>[(<dimensions>)]
</a>
<a name="934676">
<dt> <type> := <primitive type> | <derived type>
</a>
<a name="934679">
<dt> <member name> := an ASCII string representing the name of the member
</a>
<a name="934681">
<dt> <primitive type> := short | integer | long | float | double | char
</a>
<a name="934683">
<dt> <derived type> := any PFDEFS’d type
</a>
<a name="934685">
<dt> <dimensions> := <integer> |
</a>
<a name="933618">
<dt> <integer : integer> |
</a>
<a name="933619">
<dt> <integer>, <dimensions> |
</a>
<a name="934687">
<dt> <integer : integer>, <dimensions> |
</a>
<a name="934695">
Dimensions can be given in two ways. If the default offset value for the PDB file can be taken as the minimum value for the range which a dimension index can legally run, the maximum value may be specified alone. Alternatively, the minimum value followed by a colon and the maximum value may be specified. For example,<p>
</a>
<a name="934698">
<dd>integer a(30,1:10)<P>
</a>
<a name="934706">
The arguments to </a>PFDEFS are: fileid, an integer identifier which designates the PDB file to which to write; nchr, the integer number of characters in the name string; name, an ASCII string containing the name of the variable to install in the symbol table; a list of pairs where ncmi is an integer number of characters in the memi string which follows it; and a terminating LAST.<p>
</a>
<a name="934710">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="933697">
<p>
</a>
<A NAME="933699"><PRE><B>integer </a>PFDEFS(integer fileid,
</B></PRE><A NAME="933760"><PRE><B> integer nchr,
</B></PRE><A NAME="933762"><PRE><B> character name,
</B></PRE><A NAME="933764"><PRE><B> integer ncm1, character mem1,
</B></PRE><A NAME="933765"><PRE><B> ...,
</B></PRE><A NAME="933767"><PRE><B> integer ncmn, character memn,
</B></PRE><A NAME="933769"><PRE><B> integer LAST)
</B></PRE><A NAME="933700"><B>
</B><HR><A NAME="933852"><PRE> parameter(LAST = 0)
</PRE><A NAME="933875"><PRE> integer </a>pfdefs
</PRE><A NAME="933853"><PRE> integer fileid
</PRE><A NAME="933867"><PRE> common /abc/ a(2), b, c(2,2:4)
</PRE><A NAME="933869"><PRE> real a, b, c
</PRE><A NAME="933854"><PRE> common /jkl/ j, k, l
</PRE><A NAME="934009"><PRE> integer j, k, l
</PRE><A NAME="934010"><PRE> .
</PRE><A NAME="933866"><PRE> .
</PRE><A NAME="933855"><PRE> .
</PRE><A NAME="933856"><PRE> if (</a>pfdefs(fileid,
</PRE><A NAME="933858"><PRE> $ 3, ’abc’,
</PRE><A NAME="933859"><PRE> $ 10, ’float a(2)’,
</PRE><A NAME="933864"><PRE> $ 7, ’float b’,
</PRE><A NAME="933865"><PRE> $ 14, ’float c(2,2:4)’,
</PRE><A NAME="933870"><PRE> $ LAST) .eq. 0)
</PRE><A NAME="933873"><PRE> $ call errproc
</PRE><A NAME="934011"><PRE>
</PRE><A NAME="934056"><PRE> if (</a>pfdefs(fileid,
</PRE><A NAME="934012"><PRE> $ 3, ’jkl’,
</PRE><A NAME="934013"><PRE> $ 9, ’integer j’,
</PRE><A NAME="934014"><PRE> $ 9, ’integer k’,
</PRE><A NAME="934015"><PRE> $ 9, ’integer l’,
</PRE><A NAME="934016"><PRE> $ LAST) .eq. 0)
</PRE><A NAME="934017"><PRE> $ call errproc
</PRE><A NAME="933860"><PRE> .
</PRE><A NAME="933861"><PRE> .
</PRE><A NAME="933862"><PRE> .
</PRE></dl>
<a name="935084">
<h2>6.11 PFDEFT — (PD_defstr_alt)</h2>
</a>
<A NAME="935095"><PRE><B>
</B></PRE><A NAME="935202"><PRE><B>integer </a>PFDEFT(integer fileid,
</B></PRE><A NAME="935203"><PRE><B> integer nchr,
</B></PRE><A NAME="935209"><PRE><B> character name,
</B></PRE><A NAME="935210"><PRE><B> integer nm,
</B></PRE><A NAME="935216"><PRE><B> integer nc(2*nm),
</B></PRE><A NAME="935217"><PRE><B> character *memb)
</B></PRE><A NAME="935106"><PRE><B>
</B></PRE><a name="935107">
</a>Define a data structure for a PDB file. This is an alternate form of PFDEFS (see the description above for a discussion of structured data types).<p>
</a>
<a name="935186">
The arguments to </a>PFDEFT are: fileid, an integer identifier which designates the PDB file to which to write; nchr, the integer number of characters in the name string; name, an ASCII string containing the name of the variable to install in the symbol table; nm, an integer specifying how many members the type has; nc, an array of integer pairs specifying the 0 based offset into the nm array and the number of characters for each member; and nm, an array of characters containing the member specifications.<p>
</a>
<a name="935187">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="935096">
See also </a>PFDEFS.<p>
</a>
<a name="935188">
<p>
</a>
<A NAME="935189"><PRE><B>integer </a>PFDEFT(integer fileid,
</B></PRE><A NAME="935190"><PRE><B> integer nchr,
</B></PRE><A NAME="935191"><PRE><B> character name,
</B></PRE><A NAME="935192"><PRE><B> integer nm,
</B></PRE><A NAME="935193"><PRE><B> integer nc(2*nm),
</B></PRE><A NAME="935194"><PRE><B> character *memb)
</B></PRE><A NAME="935196"><B>
</B><HR><A NAME="935198"><PRE> integer </a>pfdeft
</PRE><A NAME="935199"><PRE> integer fileid, nc(6)
</PRE><A NAME="935200"><PRE> character*8 nm(4)
</PRE><A NAME="935195"><PRE> common /abc/ a(2), b, c(2,2:4)
</PRE><A NAME="935204"><PRE> .
</PRE><A NAME="935205"><PRE> .
</PRE><A NAME="935207"><PRE> .
</PRE><A NAME="935211"><PRE> nc(1) = 0
</PRE><A NAME="935212"><PRE> nc(2) = 10
</PRE><A NAME="935213"><PRE> nc(3) = 10
</PRE><A NAME="935214"><PRE> nc(4) = 7
</PRE><A NAME="935215"><PRE> nc(5) = 17
</PRE><A NAME="935228"><PRE> nc(6) = 14
</PRE><A NAME="935229"><PRE> nm(1) = ‘float a(‘
</PRE><A NAME="935230"><PRE> nm(2) = ‘2)float ‘
</PRE><A NAME="935231"><PRE> nm(3) = ‘bfloat c’
</PRE><A NAME="935232"><PRE> nm(4) = ‘(2,2:4) ‘
</PRE><A NAME="935208"><PRE> if (pfdeft(fileid, 3, ’abc’, 3, nc, nm) .eq. 0)
</PRE><A NAME="935197"><PRE> call errproc
</PRE><A NAME="935223"><PRE> .
</PRE><A NAME="935224"><PRE> .
</PRE><A NAME="935225"><PRE> .
</PRE><a name="935097">
Compare with the example for </a>PFDEFS.<p>
</a>
<a name="935322">
<h2>6.12 PFFAMI — (PD_family)</h2>
</a>
<A NAME="936007"><PRE><B>
</B></PRE><A NAME="936012"><PRE><B>integer </a>PFFAMI(integer fileid, integer flag)
</B></PRE><a name="936013">
This function checks to see whether the specified file has exceeded it size limit. If it has a new file is opened and returns. If not the given file pointer is returned. The flag is set to TRUE if you want </a>PFFAMI to close the file it is given. Otherwise the application is responsible for closing the file<p>
</a>
<a name="936014">
The arguments to this function are: fileid, an integer file identifier returned by a previous call to </a>PFOPEN; and flag an integer value (either TRUE or FALSE).<p>
</a>
<a name="936015">
This function returns an integer file identifier.<p>
</a>
<a name="936017">
<p>
</a>
<a name="936018">
integer </a>PFFAMI(integer fileid, integer flag)<p>
</a>
<A NAME="936019"><B>
</B><HR><A NAME="936099"><PRE> integer old, new
</PRE><A NAME="936097"><PRE> integer </a>pffami
</PRE><A NAME="936102"><PRE> .
</PRE><A NAME="936165"><PRE> .
</PRE><A NAME="936166"><PRE> .
</PRE><A NAME="936167"><PRE> new = pffami(old, 0)
</PRE><A NAME="936168"><PRE> if (new .ne. old) then
</PRE><A NAME="936169"><PRE> pfclos(old)
</PRE><A NAME="936170"><PRE> .
</PRE><A NAME="936171"><PRE> .
</PRE><A NAME="936173"><PRE> .
</PRE><A NAME="936174"><PRE> old = new
</PRE><A NAME="936098"><PRE> endif
</PRE><A NAME="936175"><PRE> .
</PRE><A NAME="936177"><PRE> .
</PRE><A NAME="936178"><PRE> .
</PRE><a name="935150">
<h2>6.13 PFFLSH — (PD_flush)</h2>
</a>
<A NAME="935173"><PRE><B>
</B></PRE><A NAME="935175"><PRE><B>integer </a>PFFLSH(integer fileid)
</B></PRE><a name="935237">
This function writes out the information which describes the </a>contents of the PDB file specified. Normally, </a>PFCLOS calls this routine, but applications that want to protect themselves from system failures or other problems may chose to periodically use this function. After a successful return and until or unless more data is written to the file or space reserved for future writes, the PDB file is valid in the sense that if the application terminates unexpectedly before calling </a>PFCLOS, the file can be </a>PFOPEN’d successfully.<p>
</a>
<a name="935238">
NOTE: this call does NOT obviate </a>PFCLOS!<p>
</a>
<a name="935239">
The argument to this function is file, the pointer to the PDBfile structure returned by a previous call to PD_open.<p>
</a>
<a name="933275">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="935184">
<p>
</a>
<A NAME="935181"><PRE><B>integer </a>PFFLSH(integer fileid)
</B></PRE><A NAME="935201"><B>
</B><HR><A NAME="935218"><PRE> integer </a>pfflsh
</PRE><A NAME="935219"><PRE> integer fileid
</PRE><A NAME="935220"><PRE> .
</PRE><A NAME="935221"><PRE> .
</PRE><A NAME="935222"><PRE> .
</PRE><A NAME="935226"><PRE> if (</a>pfflsh(fileid) .eq. 0)
</PRE><A NAME="935227"><PRE> $ call errproc
</PRE><A NAME="935233"><PRE> .
</PRE><A NAME="935234"><PRE> .
</PRE><A NAME="935235"><PRE> .
</PRE><a name="932854">
<h2>6.14 PFGFNM</h2>
</a>
<A NAME="932855"><PRE><B>
</B></PRE><A NAME="935261"><PRE><B>integer </a>PFGFNM(integer fileid,
</B></PRE><A NAME="935262"><PRE><B> integer nchr,
</B></PRE><A NAME="935270"><PRE><B> character name)
</B></PRE><a name="934405">
Return the name of the specified PDB file. The nchr argument contains the length of the buffer on input and the length of the file name on output. If the buffer is not long enough, the length of the file name is returned in nchr and a value of 0 is returned.<p>
</a>
<a name="932856">
The arguments to </a>PFGFNM are: fileid, an integer identifier which designates the PDB file in question; nchr, an integer number of characters in the name string; name, an ASCII string which will contain the file name upon successful completion.<p>
</a>
<a name="935255">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="935257">
<p>
</a>
<A NAME="935258"><PRE><B>integer </a>PFGFNM(integer fileid,
</B></PRE><A NAME="935259"><PRE><B> integer nchr,
</B></PRE><A NAME="935260"><PRE><B> character name)
</B></PRE><A NAME="935263"><B>
</B><HR><A NAME="935264"><PRE> integer pfgfnm
</PRE><A NAME="935265"><PRE> integer fileid
</PRE><A NAME="935266"><PRE> character*8 name(4)
</PRE><A NAME="935267"><PRE> .
</PRE><A NAME="935268"><PRE> .
</PRE><A NAME="935269"><PRE> .
</PRE><A NAME="935274"><PRE> if (</a>pfgfnm(fileid, 32, name) .eq. 0)
</PRE><A NAME="935275"><PRE> $ call errproc
</PRE><A NAME="935276"><PRE> .
</PRE><A NAME="935277"><PRE> .
</PRE><A NAME="935278"><PRE> .
</PRE><a name="935673">
<h2>6.15 PFGLS</h2>
</a>
<A NAME="935674"><PRE><B>
</B></PRE><A NAME="935675"><PRE><B>integer </a>PFGLS(integer n,
</B></PRE><A NAME="935676"><PRE><B> integer nchr,
</B></PRE><A NAME="935677"><PRE><B> char *name)
</B></PRE><a name="935679">
</a>Get the name of the nth entry in the internal table generated by </a>PFLST.<p>
</a>
<a name="935678">
PDBLib supports an optional </a>hierarchical </a>directory structure inside PDB files. A directory or a variable in a directory may be specified by either a </a>relative path or an </a>absolute path. Slashes separate nodes in a </a>path name. Absolute paths begin with a slash. Nodes consisting of two periods, “..”, refer to the next higher level directory.<p>
</a>
<a name="935680">
The arguments to </a>PFGLS are: n, an integer ordinal index into the internal table; nchr, an integer to contain the number of characters returned in string name; and name, an ASCII string to contain the returned entry name.<p>
</a>
<a name="935681">
Calls to </a>PFGLS must be preceded by a call to </a>PFLST to set up an internal table of directory and/or variable names.<p>
</a>
<a name="935806">
This function copies the name of a symbol table entry into the name, if successful. The application must ensure that name is large enough to contain the </a>longest name in the symbol table (although PDBLib permits names of arbitrary length, 256 characters would probably be more than enough). <p>
</a>
<a name="935682">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="935683">
See also </a>PFCD, </a>PFDLS, </a>PFLN, </a>PFLST, </a>PFMKDR, </a>PFPWD.<p>
</a>
<a name="935684">
<p>
</a>
<A NAME="935685"><PRE><B>integer </a>PFGLS(integer n,
</B></PRE><A NAME="935686"><PRE><B> integer nchr,
</B></PRE><A NAME="935687"><PRE><B> char *name)
</B></PRE><A NAME="935688"><B>
</B><HR><A NAME="935689"><PRE> integer pfgls
</PRE><A NAME="935704"><PRE> integer i, nvar, nchr
</PRE><A NAME="935699"><PRE> character name(256)
</PRE><A NAME="935691"><PRE> .
</PRE><A NAME="935692"><PRE> .
</PRE><A NAME="935693"><PRE> .
</PRE><A NAME="935690"><PRE> do 100 i = 1, nvar
</PRE><A NAME="935694"><PRE> if (</a>pfgls(i, nchr, name) .eq. 0)
</PRE><A NAME="935695"><PRE> $ call errproc
</PRE><A NAME="935696"><PRE> .
</PRE><A NAME="935697"><PRE> .
</PRE><A NAME="935698"><PRE> .
</PRE><A NAME="935705"><PRE> 100 continue
</PRE><A NAME="935701"><PRE> .
</PRE><A NAME="935702"><PRE> .
</PRE><A NAME="935703"><PRE> .
</PRE><a name="933286">
<h2>6.16 PFGVAR</h2>
</a>
<A NAME="933281"><PRE><B>
</B></PRE><A NAME="933287"><PRE><B>integer </a>PFGVAR(n, nchr, name)
</B></PRE><a name="933282">
</a>Get the name of the nth variable in the internal table generated by a previous call to </a>PFVART. The table will have been sorted in a particular order and this function allows applications to access the variables in the sorted order, not the default hash ordering that would normally apply.<p>
</a>
<a name="933284">
This function copies the name into the array name, if successful. The application must ensure that name is large enough to contain the </a>longest name in the symbol table (although PDBLib permits names of arbitrary length, 256 characters would probably be more than enough). <p>
</a>
<a name="935282">
The arguments to </a>PFGVAR are: n, an integer ordinal index into the internal sorted name table; nchr, an integer in which the number of characters in the name string is returned; name, an ASCII string which will contain the variable name upon successful completion.<p>
</a>
<a name="933277">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="934617">
See also </a>PFVART and </a>PFDVAR.<p>
</a>
<a name="933713">
<p>
</a>
<A NAME="933714"><PRE><B>integer </a>PFGVAR(n, nchr, name)
</B></PRE><A NAME="933715"><B>
</B><HR><A NAME="933701"><PRE> integer </a>pfgvar
</PRE><A NAME="933876"><PRE> integer i, n, nvar, nchar
</PRE><A NAME="933892"><PRE> character vname(256)
</PRE><A NAME="933891"><PRE> .
</PRE><A NAME="933888"><PRE> .
</PRE><A NAME="933890"><PRE> .
</PRE><A NAME="933872"><PRE> c print out the table of variable names created by pfvart
</PRE><A NAME="934027"><PRE> write(6,700)
</PRE><A NAME="933874"><PRE> 700 format(/,’Alphabetic list of variables:’)
</PRE><A NAME="933877"><PRE> do 701 n = 1, nvar
</PRE><A NAME="933879"><PRE> if (</a>pfgvar(n, nchar, vname) .eq. 0)
</PRE><A NAME="933882"><PRE> $ call errproc
</PRE><A NAME="933883"><PRE> write(6,702) (vname(i), i=1,nchar)
</PRE><A NAME="933885"><PRE> 702 format(’ ’,256a1)
</PRE><A NAME="933886"><PRE> 701 continue
</PRE><A NAME="933909"><PRE> .
</PRE><A NAME="933910"><PRE> .
</PRE><A NAME="933912"><PRE> .
</PRE><a name="932918">
<h2>6.17 PFGVAT — (PD_get_attribute)</h2>
</a>
<A NAME="932923"><PRE><B>
</B></PRE><A NAME="933696"><PRE><B>integer </a>PFGVAT(integer fileid,
</B></PRE><A NAME="934068"><PRE><B> integer nv,
</B></PRE><A NAME="934407"><PRE><B> char *var,
</B></PRE><A NAME="934605"><PRE><B> integer na
</B></PRE><A NAME="934611"><PRE><B> char *attr,
</B></PRE><A NAME="934612"><PRE><B> void value)
</B></PRE><a name="934613">
</a>Get the value of the specified </a>attribute for the named entity. The application must ensure that there is sufficient space to receive the attribute value.<p>
</a>
<a name="934614">
The </a>model of an attribute in PDBLib is an entity that has a name and type. The two supported operations on attributes are to create them and to remove them. An entity in a PDB file can be assigned an </a>attribute value simply by calling </a>PFSVAT. The only association between an entry in a PDB file and any attribute is made by the name in the attribute table and the entry in the symbol table. In particular, this mechanism allows the application developer to define and use entities in a PDB file solely in terms of attributes.<p>
</a>
<a name="934615">
The arguments to </a>PFGVAT are: fileid, an integer identifier which designates the PDB file from which to get the attribute; nv, an integer number of characters in the var string; var, an ASCII string containing the name of an entity; na, an integer number of characters in the attr string; attr, an ASCII string containing the name of the attribute; and value into which the attribute value will be copied.<p>
</a>
<a name="934606">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="934621">
See also </a>PFDATT, </a>PFRATT, and </a>PFSVAT.<p>
</a>
<a name="934694">
<p>
</a>
<A NAME="933887"><PRE><B>integer </a>PFGVAT(integer fileid,
</B></PRE><A NAME="934820"><PRE><B> integer nv,
</B></PRE><A NAME="934821"><PRE><B> char *var,
</B></PRE><A NAME="934823"><PRE><B> integer na
</B></PRE><A NAME="934824"><PRE><B> char *attr,
</B></PRE><A NAME="934826"><PRE><B> void value)
</B></PRE><A NAME="934799"><B>
</B><HR><A NAME="934801"><PRE> integer pfgvat
</PRE><A NAME="934802"><PRE> integer fileid
</PRE><A NAME="934738"><PRE> character*8 dt(10)
</PRE><A NAME="934803"><PRE> .
</PRE><A NAME="934813"><PRE> .
</PRE><A NAME="934814"><PRE> .
</PRE><A NAME="934815"><PRE> if (</a>pfgvat(fileid, 3, ‘foo’, 4, ‘date’, dt) .eq. 0)
</PRE><A NAME="934816"><PRE> $ call errproc
</PRE><A NAME="934817"><PRE> .
</PRE><A NAME="934818"><PRE> .
</PRE><A NAME="934819"><PRE> .
</PRE><a name="932890">
<h2>6.18 PFIMBR</h2>
</a>
<A NAME="936352"><PRE><B>
</B></PRE><A NAME="936353"><PRE><B>integer </a>PFIMBR(integer fileid,
</B></PRE><A NAME="936354"><PRE><B> integer ntype,
</B></PRE><A NAME="936355"><PRE><B> char *type,
</B></PRE><A NAME="936357"><PRE><B> integer n
</B></PRE><A NAME="936476"><PRE><B> integer size
</B></PRE><A NAME="936358"><PRE><B> char *space)
</B></PRE><a name="936360">
</a>Inquire about the nth member of the type <em>type</em> in PDB file<em> fileid</em>. Return the description of the member in the character buffer, space. On input size is the number of characters in the buffer space. If the member description requires more space, size is set to the number of bytes required and 0 is returned.<p>
</a>
<a name="936362">
Input to this function is: <em>fileid</em>, an integer PDBfile identification number<em>; ntype</em>, the number of characters in <em>type</em>; <em>type</em>, an ASCII string containing the name of the type; n, an integer specifying the member; size, an integer character size of the space buffer; and space, an character buffer to hold the member description.<p>
</a>
<a name="936485">
Output from this function is: <em>size</em>, the number of characters in the member description; and <em>space</em>, the member description.<p>
</a>
<a name="936361">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="936359">
See also </a>PFDEFS.<p>
</a>
<a name="936365">
<p>
</a>
<A NAME="936363"><PRE><B>integer </a>PFIMBR(integer fileid,
</B></PRE><A NAME="936364"><PRE><B> integer ntype,
</B></PRE><A NAME="936478"><PRE><B> char *type,
</B></PRE><A NAME="936479"><PRE><B> integer n
</B></PRE><A NAME="936480"><PRE><B> integer size
</B></PRE><A NAME="936481"><PRE><B> char *space)
</B></PRE><A NAME="936464"><B>
</B><HR><A NAME="936465"><PRE> integer pfimbr
</PRE><A NAME="936466"><PRE> integer fileid
</PRE><A NAME="936467"><PRE> character*8 type(10), desc(10), bdesc(100)
</PRE><A NAME="936468"><PRE> .
</PRE><A NAME="936469"><PRE> .
</PRE><A NAME="936470"><PRE> .
</PRE><A NAME="936471"><PRE> size = 80
</PRE><A NAME="936366"><PRE> if (</a>pfimbr(fileid, 3, ‘foo’, 4, size, desc) .eq. 0) then
</PRE><A NAME="936472"><PRE> if (size .le. 800) then
</PRE><A NAME="936368"><PRE> if (</a>pfimbr(fileid, 3, ‘foo’, 4, size, bdesc) .eq. 0) then
</PRE><A NAME="936367"><PRE> $ call errproc
</PRE><A NAME="936369"><PRE> endif
</PRE><A NAME="936371"><PRE> endif
</PRE><A NAME="936473"><PRE> endif
</PRE><A NAME="936372"><PRE> .
</PRE><A NAME="936474"><PRE> .
</PRE><A NAME="936475"><PRE> .
</PRE><a name="935700">
<h2>6.19 PFLN — (PD_ln)</h2>
</a>
<A NAME="935706"><PRE><B>
</B></PRE><A NAME="935707"><PRE><B>integer </a>PFLN(integer fileid,
</B></PRE><A NAME="935708"><PRE><B> integer nvar,
</B></PRE><A NAME="935709"><PRE><B> char *var,
</B></PRE><A NAME="935737"><PRE><B> integer nlink,
</B></PRE><A NAME="935738"><PRE><B> char *link)
</B></PRE><a name="935710">
</a>Create a </a>link to a variable in a PDB file.<p>
</a>
<a name="935711">
PDBLib supports an optional </a>hierarchical </a>directory structure inside PDB files. A directory or a variable in a directory may be specified by either a </a>relative path or an </a>absolute path. Slashes separate nodes in a </a>path name. Absolute paths begin with a slash. Nodes consisting of two periods, “..”, refer to the next higher level directory.<p>
</a>
<a name="935712">
The arguments to </a>PFLN are: fileid, an integer file identifier; nvar, an integer number of characters in string var; var, an ASCII string containing the path name of an existing variable; nlink, an integer number of characters in string link; and link, an ASCII string containing the path name of the new link.<p>
</a>
<a name="935714">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="935715">
See also </a>PFCD, </a>PFDLS, </a>PFGLS, </a>PFLST, </a>PFMKDR, </a>PFPWD.<p>
</a>
<a name="935716">
<p>
</a>
<A NAME="935717"><PRE><B>integer </a>PFLN(integer fileid,
</B></PRE><A NAME="935713"><PRE><B> integer nvar,
</B></PRE><A NAME="935718"><PRE><B> char *var,
</B></PRE><A NAME="935719"><PRE><B> integer nlink,
</B></PRE><A NAME="935739"><PRE><B> char *link)
</B></PRE><A NAME="935720"><B>
</B><HR><A NAME="935721"><PRE> integer pfln
</PRE><A NAME="935722"><PRE> integer fileid
</PRE><A NAME="935724"><PRE> .
</PRE><A NAME="935725"><PRE> .
</PRE><A NAME="935726"><PRE> .
</PRE><A NAME="935728"><PRE> if (</a>pfln(fileid, 27, ‘/animals/mammals/chimpanzee’,
</PRE><A NAME="935723"><PRE> $ 6, ‘/chimp’) .eq. 0)
</PRE><A NAME="935729"><PRE> $ call errproc
</PRE><A NAME="935732"><PRE> .
</PRE><A NAME="935733"><PRE> .
</PRE><A NAME="935734"><PRE> .
</PRE><a name="934717">
<h2>6.20 PFLST — (PD_ls)</h2>
</a>
<A NAME="935727"><PRE><B>
</B></PRE><A NAME="935730"><PRE><B>integer </a>PFLST(integer fileid,
</B></PRE><A NAME="935731"><PRE><B> integer npath,
</B></PRE><A NAME="935736"><PRE><B> char *path,
</B></PRE><A NAME="935740"><PRE><B> integer ntype,
</B></PRE><A NAME="935741"><PRE><B> char *type,
</B></PRE><A NAME="935776"><PRE><B> integer num)
</B></PRE><a name="935742">
</a>Generate an internal table of names of entries (variables and/or directories) in a PDB file that are of a specified type and that are in the directory and match the variable name pattern specified.<p>
</a>
<a name="935743">
PDBLib supports an optional </a>hierarchical </a>directory structure inside PDB files. A directory or a variable in a directory may be specified by either a </a>relative path or an </a>absolute path. Slashes separate nodes in a </a>path name. Absolute paths begin with a slash. Nodes consisting of two periods, “..”, refer to the next higher level directory.<p>
</a>
<a name="935744">
The arguments to </a>PFLST are: fileid, an integer file identifier; npath, an integer number of characters in string path; path, an ASCII string containing the path name of the directory to search and/or the variable name pattern to match; ntype, an integer number of characters in string type; type, an ASCII string containing the type of entries to return; and num, an integer to contain the number of entries returned.<p>
</a>
<a name="935766">
If npath is zero, the contents of the </a>current </a>directory are listed. If ntype is zero, all types are returned.<p>
</a>
<a name="935767">
The terminal node of path may contain meta characters “*” and “?”. Each “*” matches any zero or more characters and each “?” matches any single character.<p>
</a>
<a name="935765">
Call </a>PFGLS to get an entry from the internal table generated by </a>PFLST. Call </a>PFDLS to release the table. </a>PFLST automatically releases tables created by previous calls.<p>
</a>
<a name="935745">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="935746">
See also </a>PFCD, </a>PFDLS, </a>PFGLS, </a>PFLN, </a>PFMKDR, </a>PFPWD.<p>
</a>
<a name="935747">
<p>
</a>
<A NAME="935748"><PRE><B>integer </a>PFLST(integer fileid,
</B></PRE><A NAME="935749"><PRE><B> integer npath,
</B></PRE><A NAME="935750"><PRE><B> char *path,
</B></PRE><A NAME="935751"><PRE><B> integer ntype,
</B></PRE><A NAME="935752"><PRE><B> char *type,
</B></PRE><A NAME="935768"><PRE><B> integer num)
</B></PRE><A NAME="935753"><B>
</B><HR><A NAME="935754"><PRE> integer pflst, pfdls
</PRE><A NAME="935755"><PRE> integer fileid, num
</PRE><A NAME="935756"><PRE> .
</PRE><A NAME="935757"><PRE> .
</PRE><A NAME="935758"><PRE> .
</PRE><A NAME="935785"><PRE> c generate a table of all directories in the current directory
</PRE><A NAME="935759"><PRE> if (</a>pflst(fileid, 0, ‘’, 9, ‘Directory’, num) .eq. 0)
</PRE><A NAME="935761"><PRE> $ call errproc
</PRE><A NAME="935773"><PRE> .
</PRE><A NAME="935774"><PRE> .
</PRE><A NAME="935777"><PRE> .
</PRE><A NAME="935783"><PRE> c generate a table of the variables of type char * in directory animals
</PRE><A NAME="935771"><PRE> if (</a>pflst(fileid, 7, ‘animals’, 6, ‘char *’, num) .eq. 0)
</PRE><A NAME="935772"><PRE> $ call errproc
</PRE><A NAME="935762"><PRE> .
</PRE><A NAME="935763"><PRE> .
</PRE><A NAME="935764"><PRE> .
</PRE><a name="935760">
<h2>6.21 PFMKDR — (PD_mkdir)</h2>
</a>
<A NAME="935769"><PRE><B>
</B></PRE><A NAME="935770"><PRE><B>integer </a>PFMKDR(integer fileid,
</B></PRE><A NAME="935778"><PRE><B> integer nchr,
</B></PRE><A NAME="935780"><PRE><B> char *dirname)
</B></PRE><a name="935781">
</a>Create a new </a>directory in a PDB file.<p>
</a>
<a name="935782">
PDBLib supports an optional </a>hierarchical </a>directory structure inside PDB files. A directory or a variable in a directory may be specified by either a </a>relative path or an </a>absolute path. Slashes separate nodes in a </a>path name. Absolute paths begin with a slash. Nodes consisting of two periods, “..”, refer to the next higher level directory.<p>
</a>
<a name="935784">
The arguments to </a>PFMKDR are: fileid, an integer file identifier; nchr, an integer number of characters in string dirname; and dirname, an ASCII string containing the path name of the new directory.<p>
</a>
<a name="935787">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="935788">
See also </a>PFCD, </a>PFDLS, </a>PFGLS, </a>PFLN, </a>PFLST, </a>PFPWD.<p>
</a>
<a name="935789">
<p>
</a>
<A NAME="935790"><PRE><B>integer PFMKDR(integer fileid,
</B></PRE><A NAME="935791"><PRE><B> integer nchr,
</B></PRE><A NAME="935792"><PRE><B> char *dirname)
</B></PRE><A NAME="935793"><B>
</B><HR><A NAME="935794"><PRE> integer pfmkdr
</PRE><A NAME="935795"><PRE> integer fileid
</PRE><A NAME="935796"><PRE> .
</PRE><A NAME="935797"><PRE> .
</PRE><A NAME="935798"><PRE> .
</PRE><A NAME="935799"><PRE> if (</a>pfmkdr(fileid, 16, ‘/animals/mammals’) .eq. 0)
</PRE><A NAME="935800"><PRE> $ call errproc
</PRE><A NAME="935801"><PRE> .
</PRE><A NAME="935802"><PRE> .
</PRE><A NAME="935804"><PRE> .
</PRE><a name="935735">
<h2>6.22 PFOPEN — (PD_open)</h2>
</a>
<A NAME="934720"><PRE><B>
</B></PRE><A NAME="932760"><PRE><B>integer </a>PFOPEN(integer nchr,
</B></PRE><A NAME="932764"><PRE><B> character name,
</B></PRE><A NAME="932766"><PRE><B> character mode)
</B></PRE><a name="934727">
</a>Open an existing PDB file or </a>create a new PDB file. Depending on the value of mode, PDBLib attempts to open the file name in </a>read-only binary mode, open the file in </a>append binary mode, or </a>create a new file in </a>read-write binary mode.<p>
</a>
<a name="934731">
Any string which begins with ‘</a>r’ causes the file to be opened in read-only mode, any string beginning with ‘</a>a’ causes the file to be opened in append mode, and any string beginning with ‘</a>w’ causes a file to be created in read-write mode.<p>
</a>
<a name="934734">
Next, the beginning of the file is searched for the header which identifies the file as having been generated by PDBLib. The addresses of the structure chart and symbol table are then sought.<p>
</a>
<a name="934743">
The structure chart from the file is read in. The structure chart contains information about data types (e.g. floats), their sizes in bytes and their structures, if any. By default there are six </a>primitive </a>data types that PDBLib knows about: short integers, integers, long integers, floating point numbers, double precision floating point numbers, characters, and pointers. The sizes of these types varies from machine to machine, but PDBLib hides this from the user.<p>
</a>
<a name="934749">
The symbol table from the file is read in. The symbol table contains the list of variables in the file, their types as defined in the structure chart, and dimensioning information for arrays. Each read from the file first consults the symbol table to see if the requested variable is present in the PDB file.<p>
</a>
<a name="934753">
Both the structure chart and the symbol table are implemented as hash tables, although their shapes are different. This makes lookups as efficient as possible given an unknown amount of data in the file.<p>
</a>
<a name="934758">
The arguments to </a>PFOPEN are: nchr, the number of characters in the string containing the file name; name, an ASCII string, which is the name of the file to be opened/created; and mode, an ASCII string, which is the mode (either ‘w’ for create, ‘r’ for read-only or ‘a’ for append).<p>
</a>
<a name="934765">
The function returns an integer identifier for the PDB file opened/created. This identifies the particular file to PDBLib. As such, if it is overwritten the file is lost. The number of PDB files which can be open simultaneously is machine or operating system dependent, but each open PDB file has a unique identifier associated with it.<p>
</a>
<a name="934769">
If any aspect of the PDB file opening process fails 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="933717">
<p>
</a>
<A NAME="933718"><PRE><B>integer </a>PFOPEN(integer nchr,
</B></PRE><A NAME="933771"><PRE><B> character name,
</B></PRE><A NAME="933772"><PRE><B> character mode)
</B></PRE><A NAME="933719"><B>
</B><HR><A NAME="933716"><PRE> integer </a>pfopen
</PRE><A NAME="933904"><PRE> integer fileid
</PRE><A NAME="933913"><PRE> .
</PRE><A NAME="933915"><PRE> .
</PRE><A NAME="933916"><PRE> .
</PRE><A NAME="933905"><PRE> fileid = </a>pfopen(8, ’file.pdb’, ’r’)
</PRE><A NAME="933906"><PRE> if (fileid .eq. 0)
</PRE><A NAME="933907"><PRE> $ call errproc
</PRE><A NAME="933917"><PRE> .
</PRE><A NAME="933918"><PRE> .
</PRE><A NAME="933919"><PRE> .
</PRE><a name="932741">
<h2>6.23 PFPTRD — (PD_read_alt)</h2>
</a>
<A NAME="932743"><PRE><B>
</B></PRE><A NAME="932945"><PRE><B>integer </a>PFPTRD(integer fileid,
</B></PRE><A NAME="933010"><PRE><B> integer nchr,
</B></PRE><A NAME="933011"><PRE><B> character name,
</B></PRE><A NAME="933497"><PRE><B> void space
</B></PRE><A NAME="934540"><PRE><B> integer ind)
</B></PRE><a name="934552">
</a>Read all or part of a data entry from an open PDB file. The symbol table of the given PDB file is searched for the given name and if it is found the information there is used to read the proper number of bytes from the file, do any conversions, and put the result in memory pointed to by var.<p>
</a>
<a name="934554">
The elements to be read from an array are designated by start, stop, step triples (one for each dimension) passed in the argument ind.<p>
</a>
<a name="933509">
The arguments to </a>PFPTRD are: fileid, an integer identifier which designates the PDB file from which to attempt the read; nchr, an integer number of characters in the name string; name, an ASCII string containing the name of the variable to lookup; space, the location where the data is to be placed; and ind, an array of integers which specify the elements to be read.<p>
</a>
<a name="933503">
Note: In each </a>PFPTRD operation, the type of space must be a pointer to the type of name.<p>
</a>
<a name="933504">
Note: When reading part of a variable, especially a structured variable, the path to the desired part must contain one array reference for each level of </a>indirection traversed.<p>
</a>
<a name="933505">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="933510">
See also </a>PFREAD, </a>PFRDAS, and </a>PFRDAD.<p>
</a>
<a name="933506">
<p>
</a>
<A NAME="933507"><PRE><B>integer </a>PFPTRD(integer fileid,
</B></PRE><A NAME="934541"><PRE><B> integer nchr,
</B></PRE><A NAME="934542"><PRE><B> character name,
</B></PRE><A NAME="934545"><PRE><B> void space
</B></PRE><A NAME="934549"><PRE><B> integer ind)
</B></PRE><A NAME="933511"><B>
</B><HR><A NAME="933512"><PRE> integer </a>pfptrd
</PRE><A NAME="933513"><PRE> integer fileid, ind(3)
</PRE><A NAME="933514"><PRE> real xodd(10)
</PRE><A NAME="933519"><PRE> .
</PRE><A NAME="933520"><PRE> .
</PRE><A NAME="933521"><PRE> .
</PRE><A NAME="933522"><PRE> c read the first 10 odd elements of x into array xodd
</PRE><A NAME="932921"><PRE> ind(1) = 1
</PRE><A NAME="933515"><PRE> ind(2) = 20
</PRE><A NAME="933516"><PRE> ind(3) = 2
</PRE><A NAME="934298"><PRE> if (</a>pfptrd(fileid, 1, ’x’, xodd, ind) .eq. 0)
</PRE><A NAME="934488"><PRE> $ call errproc
</PRE><A NAME="934535"><PRE> .
</PRE><A NAME="934536"><PRE> .
</PRE><A NAME="934537"><PRE> .
</PRE><a name="935786">
<h2>6.24 PFPWD</h2>
</a>
<A NAME="935812"><PRE><B>
</B></PRE><A NAME="935813"><PRE><B>integer </a>PFPWD(integer fileid,
</B></PRE><A NAME="935814"><PRE><B> integer nchr,
</B></PRE><A NAME="935815"><PRE><B> char *dirname)
</B></PRE><a name="935816">
</a>Get the </a>current </a>directory for a PDB file.<p>
</a>
<a name="935817">
PDBLib supports an optional </a>hierarchical </a>directory structure inside PDB files. A directory or a variable in a directory may be specified by either a </a>relative path or an </a>absolute path. Slashes separate nodes in a </a>path name. Absolute paths begin with a slash. Nodes consisting of two periods, “..”, refer to the next higher level directory.<p>
</a>
<a name="935818">
The arguments to </a>PFPWD are: fileid, an integer file identifier; nchr, an integer to contain the number of characters returned in string dirname; and dirname, an ASCII string to contain the path name of the </a>current </a>directory.<p>
</a>
<a name="935808">
This function copies the path name of a directory into the dirname, if successful. The application must ensure that dirname is large enough to contain the longest directory name (although PDBLib permits names of arbitrary length, 256 characters would probably be more than enough). <p>
</a>
<a name="935819">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="935821">
See also </a>PFCD, </a>PFDLS, </a>PFGLS, </a>PFLN, </a>PFLST, </a>PFMKDR.<p>
</a>
<a name="935822">
<p>
</a>
<A NAME="935905"><PRE><B>integer </a>PFPWD(integer fileid,
</B></PRE><A NAME="935906"><PRE><B> integer nchr,
</B></PRE><A NAME="935909"><PRE><B> char *dirname)
</B></PRE><A NAME="935910"><B>
</B><HR><A NAME="935911"><PRE> integer pfpwd
</PRE><A NAME="935912"><PRE> integer fileid, nchr
</PRE><A NAME="935805"><PRE> character dirname(256)
</PRE><A NAME="935914"><PRE> .
</PRE><A NAME="935915"><PRE> .
</PRE><A NAME="935917"><PRE> .
</PRE><A NAME="935918"><PRE> if (</a>pfpwd(fileid, nchr, dirname) .eq. 0)
</PRE><A NAME="935967"><PRE> $ call errproc
</PRE><A NAME="935991"><PRE> .
</PRE><A NAME="935992"><PRE> .
</PRE><A NAME="935993"><PRE> .
</PRE><a name="934618">
<h2>6.25 PFRATT — (PD_rem_attribute)</h2>
</a>
<A NAME="934620"><PRE><B>
</B></PRE><A NAME="934628"><PRE><B>integer </a>PFRATT(integer fileid,
</B></PRE><A NAME="934633"><PRE><B> integer na
</B></PRE><A NAME="934634"><PRE><B> char *attr)
</B></PRE><a name="934636">
</a>Remove the specified </a>attribute. PDBLib will remove the values of this attribute which may be associated with entities in the file.<p>
</a>
<a name="934637">
The </a>model of an attribute in PDBLib is an entity that has a name and type. The two supported operations on attributes are to create them and to remove them. An entity in a PDB file can be assigned an </a>attribute value simply by calling </a>PFSVAT. The only association between an entry in a PDB file and any attribute is made by the name in the attribute table and the entry in the symbol table. In particular, this mechanism allows the application developer to define and use entities in a PDB file solely in terms of attributes.<p>
</a>
<a name="934638">
The arguments to </a>PFRATT are: fileid, an integer identifier which designates the PDB file from which to remove the attribute; na, an integer number of characters in the attr string; and attr, an ASCII string containing the name of the attribute.<p>
</a>
<a name="934639">
The return value is 1 if successful and 0 otherwise.<p>
</a>
<a name="934640">
See also </a>PFDATT, </a>PFGVAT, and </a>PFSVAT.<p>
</a>
<a name="934784">
<p>
</a>
<A NAME="934851"><PRE><B>integer </a>PFRATT(integer fileid,
</B></PRE><A NAME="934853"><PRE><B> integer na
</B></PRE><A NAME="934854"><PRE><B> char *attr)
</B></PRE><A NAME="934831"><B>
</B><HR><A NAME="934833"><PRE> integer pfratt
</PRE><A NAME="934834"><PRE> integer fileid
</PRE><A NAME="934836"><PRE> .
</PRE><A NAME="934838"><PRE> .
</PRE><A NAME="934839"><PRE> .
</PRE><A NAME="934840"><PRE> if (</a>pfratt(fileid, 4, ‘date’) .eq. 0)
</PRE><A NAME="934841"><PRE> $ call errproc
</PRE><A NAME="934849"><PRE> .
</PRE><A NAME="934850"><PRE> .
</PRE><A NAME="934783"><PRE> .
</PRE><a name="936536">
<h2>6.26 PFRDAD — (PD_read_as_alt)</h2>
</a>
<A NAME="936537"><PRE><B>
</B></PRE><A NAME="936542"><PRE><B>integer </a>PFRDAD(integer fileid,
</B></PRE><A NAME="936543"><PRE><B> integer nchr,
</B></PRE><A NAME="936673"><PRE><B> character name,
</B></PRE><A NAME="936809"><PRE><B> integer ntype,
</B></PRE><A NAME="936811"><PRE><B> character intype,
</B></PRE><A NAME="936674"><PRE><B> void space
</B></PRE><A NAME="936675"><PRE><B> integer ind)
</B></PRE><a name="936676">
</a>Read all or part of a data entry from an open PDB file as data type intype. The symbol table of the given PDB file is searched for the given name and if it is found the information there is used to read the proper number of bytes from the file, do any conversions, and put the result in memory pointed to by space.<p>
</a>
<a name="936677">
The elements to be read from an array are designated by start, stop, step triples (one for each dimension) passed in the argument ind.<p>
</a>
<a name="936678">
The arguments to </a>PFRDAD are: fileid, an integer identifier which designates the PDB file from which to attempt the read; nchr, an integer number of characters in the name string; name, an ASCII string containing the name of the variable to lookup; ntype, an integer number of characters in the intype string; intype, an ASCII string specifying the type of data to which space points; space, the location where the data is to be placed; and ind, an array of integers which specify the elements to be read.<p>
</a>
<a name="936679">
Note: In each </a>PFRDAD operation, the type of space must be a pointer to the type of intype.<p>
</a>
<a name="936680">
Note: When reading part of a variable, especially a structured variable, the path to the desired part must contain one array reference for each level of </a>indirection traversed.<p>
</a>
<a name="936681">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="936682">
See also PFPTRD, PFRDAS, and PFREAD.<p>
</a>
<a name="936683">
<p>
</a>
<A NAME="936684"><PRE><B>integer </a>PFRDAD(integer fileid,
</B></PRE><A NAME="936685"><PRE><B> integer nchr,
</B></PRE><A NAME="936686"><PRE><B> character name,
</B></PRE><A NAME="936812"><PRE><B> integer ntype,
</B></PRE><A NAME="936813"><PRE><B> character intype,
</B></PRE><A NAME="936687"><PRE><B> void space
</B></PRE><A NAME="936688"><PRE><B> integer ind)
</B></PRE><A NAME="936689"><B>
</B><HR><A NAME="936690"><PRE> integer </a>pfrdad
</PRE><A NAME="936691"><PRE> integer fileid, ind(3)
</PRE><A NAME="936692"><PRE> real*8 xdd(10)
</PRE><A NAME="936693"><PRE> .
</PRE><A NAME="936694"><PRE> .
</PRE><A NAME="936695"><PRE> .
</PRE><A NAME="936696"><PRE> c read the first 10 elements of float x into array xdd
</PRE><A NAME="936824"><PRE> c as type double.
</PRE><A NAME="936664"><PRE>
</PRE><A NAME="936697"><PRE> ind(1) = 1
</PRE><A NAME="936698"><PRE> ind(2) = 10
</PRE><A NAME="936699"><PRE> ind(3) = 1
</PRE><A NAME="936700"><PRE> if (</a>pfrdad(fileid, 1, ’x’, 6, ‘double’, xdd, ind) .eq. 0)
</PRE><A NAME="936701"><PRE> $ call errproc
</PRE><A NAME="936702"><PRE> .
</PRE><A NAME="936703"><PRE> .
</PRE><A NAME="936704"><PRE> .
</PRE><a name="936632">
<h2>6.27 PFRDAS — (PD_read_as)</h2>
</a>
<A NAME="936633"><PRE><B>
</B></PRE><A NAME="936634"><PRE><B>integer </a>PFRDAS(integer fileid,
</B></PRE><A NAME="936635"><PRE><B> integer nchr,
</B></PRE><A NAME="936636"><PRE><B> character name,
</B></PRE><A NAME="936814"><PRE><B> integer ntype,
</B></PRE><A NAME="936815"><PRE><B> character intype,
</B></PRE><A NAME="936637"><PRE><B> void space)
</B></PRE><a name="936638">
</a>Read data from an open PDB file as data type intype. The symbol table of the given PDB file is searched for the given name and if it is found the information there is used to read the proper number of bytes from the file, do any conversions, and put the result in memory pointed to by space.<p>
</a>
<a name="936639">
The arguments to </a>PFRDAS are: fileid, an integer identifier which designates the PDB file from which to attempt the read; nchr, an integer number of characters in the name string; name, an ASCII string containing the name of the variable to lookup; ntype, an integer number of characters in the intype string; intype, an ASCII string specifying the type of data to which space points; and space, the location where the data is to be placed.<p>
</a>
<a name="936640">
Note: In each </a>PFRDAS operation, the type of space must be a pointer to the type of intype.<p>
</a>
<a name="936641">
Note: When reading part of a variable, especially a structured variable, the path to the desired part must contain one array reference for each level of </a>indirection traversed.<p>
</a>
<a name="936642">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="936826">
See also PFPTRD, PFRDAD, and PFREAD.<p>
</a>
<a name="936643">
<p>
</a>
<A NAME="936644"><PRE><B>integer </a>PFRDAS(integer fileid,
</B></PRE><A NAME="936645"><PRE><B> integer nchr,
</B></PRE><A NAME="936646"><PRE><B> character name,
</B></PRE><A NAME="936816"><PRE><B> integer ntype,
</B></PRE><A NAME="936817"><PRE><B> character intype,
</B></PRE><A NAME="936647"><PRE><B> void space)
</B></PRE><A NAME="936648"><B>
</B><HR><A NAME="936649"><PRE> integer </a>pfrdas
</PRE><A NAME="936650"><PRE> integer fileid
</PRE><A NAME="936651"><PRE> real*8 xx(20)
</PRE><A NAME="936655"><PRE> .
</PRE><A NAME="936657"><PRE> .
</PRE><A NAME="936658"><PRE> .
</PRE><A NAME="936659"><PRE> c read array x into array xx as type double
</PRE><A NAME="936660"><PRE> if (</a>pfrdas(fileid, 1, ’x’, 6, ’double’, xx) .eq. 0)
</PRE><A NAME="936661"><PRE> $ call errproc
</PRE><A NAME="932454"><PRE> .
</PRE><A NAME="936672"><PRE> .
</PRE><A NAME="936584"><PRE> .
</PRE><a name="936671">
<h2>6.28 PFREAD — (PD_read)</h2>
</a>
<A NAME="934778"><PRE><B>
</B></PRE><A NAME="932771"><PRE><B>integer </a>PFREAD(integer fileid,
</B></PRE><A NAME="932772"><PRE><B> integer nchr,
</B></PRE><A NAME="932774"><PRE><B> character name,
</B></PRE><A NAME="932773"><PRE><B> void space)
</B></PRE><a name="934785">
</a>Read data from an open PDB file. The symbol table of the given PDB file is searched for the given name and if it is found the information there is used to read the proper number of bytes from the file, do any conversions, and put the result in memory pointed to by space.<p>
</a>
<a name="934790">
The arguments to </a>PFREAD are: fileid, an integer identifier which designates the PDB file from which to attempt the read; nchr, an integer number of characters in the name string; name, an ASCII string containing the name of the variable to lookup; and space, the location where the data is to be placed.<p>
</a>
<a name="934793">
Note: In each </a>PFREAD operation, the type of space must be a pointer to the type of name.<p>
</a>
<a name="934797">
Note: When reading part of a variable, especially a structured variable, the path to the desired part must contain one array reference for each level of </a>indirection traversed.<p>
</a>
<a name="934800">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="936652">
See also PFPTRD, PFRDAD, and PFRDAS.<p>
</a>
<a name="933722">
<p>
</a>
<A NAME="933723"><PRE><B>integer </a>PFREAD(integer fileid,
</B></PRE><A NAME="933774"><PRE><B> integer nchr,
</B></PRE><A NAME="933775"><PRE><B> character name,
</B></PRE><A NAME="933776"><PRE><B> void space)
</B></PRE><A NAME="933721"><B>
</B><HR><A NAME="933724"><PRE> integer </a>pfread
</PRE><A NAME="933925"><PRE> integer fileid
</PRE><A NAME="934005"><PRE> real x(20)
</PRE><A NAME="933934"><PRE> common /abc/ a(2), b, c(2,2:4)
</PRE><A NAME="933935"><PRE> real a, b, c
</PRE><A NAME="933940"><PRE> common /jkl/ j, k, l
</PRE><A NAME="933922"><PRE> integer j, k, l
</PRE><A NAME="934007"><PRE> .
</PRE><A NAME="933923"><PRE> .
</PRE><A NAME="933924"><PRE> .
</PRE><A NAME="933920"><PRE> c read array x
</PRE><A NAME="934028"><PRE> if (</a>pfread(fileid, 1, ’x’, x) .eq. 0)
</PRE><A NAME="933927"><PRE> $ call errproc
</PRE><A NAME="933936"><PRE>
</PRE><A NAME="934057"><PRE> c read first element of member c of structure abc
</PRE><A NAME="934029"><PRE> if (</a>pfread(fileid, 10, ’abc.c(1,2)’, c) .eq. 0)
</PRE><A NAME="933938"><PRE> $ call errproc
</PRE><A NAME="934006"><PRE>
</PRE><A NAME="934058"><PRE> c read entire structure jkl
</PRE><A NAME="934030"><PRE> if (</a>pfread(fileid, 3, ’jkl’, j) .eq. 0)
</PRE><A NAME="934008"><PRE> $ call errproc
</PRE><A NAME="933930"><PRE> .
</PRE><A NAME="933931"><PRE> .
</PRE><A NAME="933932"><PRE> .
</PRE><a name="934631">
<h2>6.29 PFSVAT — (PD_set_attribute)</h2>
</a>
<A NAME="934632"><PRE><B>
</B></PRE><A NAME="934635"><PRE><B>integer </a>PFSVAT(integer fileid,
</B></PRE><A NAME="934641"><PRE><B> integer nv,
</B></PRE><A NAME="934642"><PRE><B> char *var,
</B></PRE><A NAME="934643"><PRE><B> integer na
</B></PRE><A NAME="934644"><PRE><B> char *attr,
</B></PRE><A NAME="934646"><PRE><B> void value)
</B></PRE><a name="934647">
</a>Set the value of the specified </a>attribute for the named entity.<p>
</a>
<a name="934648">
The </a>model of an attribute in PDBLib is an entity that has a name and type. The two supported operations on attributes are to create them and to remove them. An entity in a PDB file can be assigned an </a>attribute value simply by calling </a>PFSVAT. The only association between an entry in a PDB file and any attribute is made by the name in the attribute table and the entry in the symbol table. In particular, this mechanism allows the application developer to define and use entities in a PDB file solely in terms of attributes.<p>
</a>
<a name="934649">
The arguments to </a>PFSVAT are: fileid, an integer identifier which designates the PDB file in which the attribute is being set; nv, an integer number of characters in the var string; var, an ASCII string containing the name of an entity; na, an integer number of characters in the attr string; attr, an ASCII string containing the name of the attribute being set; and value containing the attribute value.<p>
</a>
<a name="933283">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="934651">
See also </a>PFDATT, </a>PFRATT, and </a>PFGVAT.<p>
</a>
<a name="934795">
<p>
</a>
<A NAME="934789"><PRE><B>integer </a>PFSVAT(integer fileid,
</B></PRE><A NAME="934889"><PRE><B> integer nv,
</B></PRE><A NAME="934890"><PRE><B> char *var,
</B></PRE><A NAME="934891"><PRE><B> integer na
</B></PRE><A NAME="934892"><PRE><B> char *attr,
</B></PRE><A NAME="934893"><PRE><B> void value)
</B></PRE><A NAME="934864"><B>
</B><HR><A NAME="934828"><PRE> integer pfsvat
</PRE><A NAME="934830"><PRE> integer scftcs
</PRE><A NAME="934865"><PRE> integer fileid
</PRE><A NAME="934868"><PRE> character*80 dt
</PRE><A NAME="934869"><PRE> .
</PRE><A NAME="934870"><PRE> .
</PRE><A NAME="934882"><PRE> .
</PRE><A NAME="935026"><PRE> scftcs(dt, ‘Mon March 27, 1921’, 18)
</PRE><A NAME="934827"><PRE> if (pfsvat(fileid, 3, ‘foo’, 4, ‘date’, dt) .eq. 0)
</PRE><A NAME="934884"><PRE> $ call errproc
</PRE><A NAME="934885"><PRE> .
</PRE><A NAME="934886"><PRE> .
</PRE><A NAME="934887"><PRE> .
</PRE><a name="934806">
<h2>6.30 PFTRGT — (PD_target)</h2>
</a>
<A NAME="934809"><PRE><B>
</B></PRE><A NAME="932775"><PRE><B>integer </a>PFTRGT(integer is,
</B></PRE><A NAME="932777"><PRE><B> integer ia)
</B></PRE><a name="934822">
Write the next PDB file to be created according to the specified </a>data standard and </a>alignment. PDBLib has a general binary data conversion mechanism called </a>parametrized </a>data </a>conversion (</a>PDC). An integer type is described by one set of parameters and a floating point type is described by another. A general purpose conversion routine takes the description of the input type and a description of the desired output type and does the conversion. In this way, PDBLib avoids an N2 increase in data conversion routines as it ports to new machines. In fact, the number of data standards and alignments grows more slowly than N because many machines share common formats.<p>
</a>
<a name="934825">
An additional advantage to PDC is that by specifying a format involving the minimal number of bits to represent the data for a file, PDBLib can carry out a large class of data compressions.<p>
</a>
<a name="934829">
PDBLib carries several predefined </a>data_standard and </a>data_alignment structures which describe a large number of binary data formats. In the C API these may be directly referenced and their names are given here for completeness.<p>
</a>
<a name="934832">
Data standards: </a>IEEEA_STD, </a>IEEEB_STD, </a>IEEEC_STD, </a>INTELA_STD, </a>INTELB_STD, </a>VAX_STD, and </a>CRAY_STD.<p>
</a>
<a name="933191">
Data alignments: </a>DEF_ALIGNMENT, </a>SPARC_ALIGNMENT, </a>MIPS_ALIGNMENT, </a>RS6000_ALIGNMENT, </a>68000_ALIGNMENT, </a>INTEL_ALIGNMENT, </a>CRAY_ALIGNMENT, and </a>UNICOS_ALIGNMENT.<p>
</a>
<a name="934835">
In the FORTRAN API, these structures are placed in two arrays and the indices into these arrays are passed into </a>PFTRGT to specify the binary format to be targeted.<p>
</a>
<a name="934837">
The list of standards is:<p>
</a>
<a name="934842">
<dd>1 - </a>IEEEA_STD<P>
</a>
<a name="934843">
<dd>2 - </a>IEEEB_STD<P>
</a>
<a name="934844">
<dd>3 - </a>IEEEC_STD<P>
</a>
<a name="934845">
<dd>4 - </a>INTELA_STD<P>
</a>
<a name="934846">
<dd>5 - </a>INTELB_STD<P>
</a>
<a name="934847">
<dd>6 - </a>VAX_STD<P>
</a>
<a name="934848">
<dd>7 - </a>CRAY_STD<P>
</a>
<a name="934852">
The list of </a>alignments is:<p>
</a>
<dl>
<a name="934856">
<dt>1 - </a>M68000_ALIGNMENT
</a>
<a name="934857">
<dt>2 - </a>SPARC_ALIGNMENT
</a>
<a name="934858">
<dt>3 - </a>MIPS_ALIGNMENT
</a>
<a name="934859">
<dt>4 - </a>INTEL_ALIGNMENT
</a>
<a name="934860">
<dt>5 - </a>DEF_ALIGNMENT
</a>
<a name="934861">
<dt>6 - </a>CRAY_ALIGNMENT
</a>
<a name="933253">
<dt>7 - </a>UNICOS_ALIGNMENT
</a>
<a name="933258">
<dt>8 - </a>RS6000_ALIGNMENT
</a>
<a name="934866">
Some common </a>configurations are:<p>
</a>
<a name="934871">
<dt>Motorola - </a>PFTRGT(1, 1)
</a>
<a name="934872">
<dt>SPARC - PFTRGT(1, 2)
</a>
<a name="933308">
<dt>MIPS, SGI - PFTRGT(1, 3)
</a>
<a name="934873">
<dt>IBM RS6000 - PFTRGT(1, 8)
</a>
<a name="934874">
<dt>Mac/Think C - PFTRGT(2, 1)
</a>
<a name="934875">
<dt>Mac/MPW - PFTRGT(3, 1)
</a>
<a name="934876">
<dt>DOS - PFTRGT(4, 4)
</a>
<a name="934877">
<dt>Intel 80x86 UNIX - PFTRGT(5, 4)
</a>
<a name="934878">
<dt>DEC Vax - PFTRGT(6, 5)
</a>
<a name="934879">
<dt>DEC 3100 - PFTRGT(5, 3)
</a>
<a name="934880">
<dt>NLTSS Cray - PFTRGT(7, 6)
</a>
<a name="934881">
<dt>UNICOS Cray - </a>PFTRGT(7, 7)
</a>
<a name="934888">
The argument, is, is an index corresponding one of the </a>data_standard structures listed above, and the argument, ia, is an index corresponding to one of the </a>data_alignment structures above. See the section on Data Structures later on in this manual.<p>
</a>
<a name="932528">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="933727">
<p>
</a>
<A NAME="933728"><PRE><B>integer </a>PFTRGT(integer is,
</B></PRE><A NAME="933777"><PRE><B> integer ia)
</B></PRE><A NAME="933729"><B>
</B><HR><A NAME="933725"><PRE> integer </a>pftrgt
</PRE><A NAME="933963"><PRE> integer is, ia
</PRE><A NAME="933964"><PRE> .
</PRE><A NAME="933965"><PRE> .
</PRE><A NAME="933966"><PRE> .
</PRE><A NAME="933962"><PRE> c set target architecture (MIPS, SGI)
</PRE><A NAME="933942"><PRE> c IEEEA_STD
</PRE><A NAME="933943"><PRE> is = 1
</PRE><A NAME="933945"><PRE> c MIPS_ALIGNMENT
</PRE><A NAME="933946"><PRE> ia = 3
</PRE><A NAME="933947"><PRE> if (</a>pftrgt(is, ia) .eq. 0)
</PRE><A NAME="933960"><PRE> $ call errproc
</PRE><A NAME="933967"><PRE> .
</PRE><A NAME="933968"><PRE> .
</PRE><A NAME="933969"><PRE> .
</PRE></dl>
<a name="933269">
<h2>6.31 PFVART</h2>
</a>
<A NAME="933274"><PRE><B>
</B></PRE><A NAME="934650"><PRE><B>integer </a>PFVART(integer fileid,
</B></PRE><A NAME="935285"><PRE><B> integer order,
</B></PRE><A NAME="935284"><PRE><B> integer nvars)
</B></PRE><a name="933270">
</a>Generate an internal table of variables in the specified PDB file. With subsequent calls to </a>PFGVAR, each entry can be obtained one at a time by ordinal index. The table is sorted according to a specified scheme. The current choices are alphabetic and by disk address.<p>
</a>
<a name="933272">
The arguments to this function are: <em>fileid, </em>an integer which identifies the PDBfile; order, an integer specifying the </a>sort ordering; and nvars, an integer in which the number of variables in the file is returned. The choices for order are: 1, for an alphabetic sort; and 2, for a disk address order sort.<p>
</a>
<a name="933268">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="935240">
See also </a>PFDVAR and </a>PFGVAR.<p>
</a>
<a name="933730">
<p>
</a>
<A NAME="933880"><PRE><B>integer </a>PFVART(integer fileid,
</B></PRE><A NAME="933731"><PRE><B> integer order,
</B></PRE><A NAME="935287"><PRE><B> integer nvars)
</B></PRE><A NAME="933732"><B>
</B><HR><A NAME="933273"><PRE> integer </a>pfvart
</PRE><A NAME="933975"><PRE> integer fileid, nvar, order
</PRE><A NAME="933976"><PRE> .
</PRE><A NAME="933977"><PRE> .
</PRE><A NAME="933978"><PRE> .
</PRE><A NAME="933941"><PRE> c create table of variable names in alphabetic order
</PRE><A NAME="933970"><PRE> order = 1
</PRE><A NAME="933971"><PRE> if (</a>pfvart(fileid, order, nvar) .eq. 0)
</PRE><A NAME="933973"><PRE> $ call errproc
</PRE><A NAME="933979"><PRE> .
</PRE><A NAME="933980"><PRE> .
</PRE><A NAME="933981"><PRE> .
</PRE><a name="932529">
<h2>6.32 PFWIMA</h2>
</a>
<A NAME="934901"><PRE><B>
</B></PRE><A NAME="932778"><PRE><B>integer </a>PFWIMA(integer fileid,
</B></PRE><A NAME="932779"><PRE><B> integer nchr,
</B></PRE><A NAME="932781"><PRE><B> character name,
</B></PRE><A NAME="932782"><PRE><B> integer pkn,
</B></PRE><A NAME="932783"><PRE><B> integer pkx,
</B></PRE><A NAME="933688"><PRE><B> integer pln,
</B></PRE><A NAME="933689"><PRE><B> integer plx,
</B></PRE><A NAME="932789"><PRE><B> real*8 data,
</B></PRE><A NAME="932800"><PRE><B> real*8 pxn,
</B></PRE><A NAME="932801"><PRE><B> real*8 pxx,
</B></PRE><A NAME="932802"><PRE><B> real*8 pyn,
</B></PRE><A NAME="932803"><PRE><B> real*8 pyx,
</B></PRE><A NAME="934222"><PRE><B> integer pim)
</B></PRE><a name="934230">
</a>Build a PD_image structure out of the given input data and write it to a PDB file.<p>
</a>
<a name="934231">
Rationale: The </a>PD_image structure is a useful and general purpose representation of a </a>raster </a>image. The nature of the generalization is that the values in the raster are floating point numbers. So in addition to the standard data sets that can be rasterized, the PD_image can be used to display the computational matrix of some system of equations, for example. This function is a convenient way for FORTRAN programs to put out their data into PDB files as PD_image’s for later visualization and processing by other programs. It allows a rectangular subset of a two dimensional array to be specified for the PD_image.<p>
</a>
<a name="934920">
The calling application must keep track of how many PM_image’s have been written to each file. PDBLib will write each PM_image under the name composed of the string, ‘Image’, and the integer pim. For example if pim is 9, the PM_image will be written under the name ‘Image9’. If the application passes the same value for pim more than once only the last one will survive in the symbol table even though the data for each PM_image will persist in the file!<p>
</a>
<a name="934931">
The arguments to </a>PFWIMA are: fileid, an integer identifier which designates the PDB file to which to attempt to write; nchr, an integer number of characters in name; name, an ASCII string containing the name of the image; pkn, the integer minimum column index of the data array; pkx, the integer maximum column index of the data array; pln, the integer minimum row index of the data array; plx, the integer maximum row index of the data array; data, an array of real*8 values containing the image data; pxn, a real*8 value specifying the minimum column index in image; pxx, a real*8 value specifying the maximum column index in image; pyn, a real*8 value specifying the minimum row index in image; pyx, a real*8 value specifying the maximum row index in image; and pim, a counter specifying the number of the image being written out.<p>
</a>
<a name="934935">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="933734">
<p>
</a>
<A NAME="933735"><PRE><B>integer </a>PFWIMA(integer fileid,
</B></PRE><A NAME="933778"><PRE><B> integer nchr,
</B></PRE><A NAME="933779"><PRE><B> character name,
</B></PRE><A NAME="933780"><PRE><B> integer pkn,
</B></PRE><A NAME="933781"><PRE><B> integer pkx,
</B></PRE><A NAME="933783"><PRE><B> integer pln,
</B></PRE><A NAME="933784"><PRE><B> integer plx,
</B></PRE><A NAME="933786"><PRE><B> real*8 data,
</B></PRE><A NAME="933787"><PRE><B> real*8 pxn,
</B></PRE><A NAME="933788"><PRE><B> real*8 pxx,
</B></PRE><A NAME="933789"><PRE><B> real*8 pyn,
</B></PRE><A NAME="933790"><PRE><B> real*8 pyx,
</B></PRE><A NAME="934223"><PRE><B> integer pim)
</B></PRE><A NAME="933737"><B>
</B><HR><A NAME="933986"><PRE> integer </a>pfwima
</PRE><A NAME="933985"><PRE> integer fileid, k, l
</PRE><A NAME="933987"><PRE> c these arguments to pfwima must have 8 byte element size
</PRE><A NAME="934034"><PRE> double precision xmin, xmax, ymin, ymax, data(0:10,0:10)
</PRE><A NAME="933733"><PRE> .
</PRE><A NAME="933982"><PRE> .
</PRE><A NAME="933983"><PRE> .
</PRE><A NAME="933984"><PRE> xmin = 0.
</PRE><A NAME="933988"><PRE> xmax = 10.
</PRE><A NAME="933994"><PRE> ymin = 0.
</PRE><A NAME="933999"><PRE> ymax = 10.
</PRE><A NAME="934003"><PRE> do 100 l = 0, 10
</PRE><A NAME="933990"><PRE> do 101 k = 0, 10
</PRE><A NAME="933991"><PRE> data(k, l) = (k - 5)**2 + (l - 5)**2
</PRE><A NAME="933992"><PRE> 101 continue
</PRE><A NAME="933993"><PRE> 100 continue
</PRE><A NAME="933996"><PRE>
</PRE><A NAME="934004"><PRE> if (</a>pfwima(fileid, 10, ’Test image’, 0, 10, 0, 10,
</PRE><A NAME="933997"><PRE> $ data, xmin, xmax, ymin, ymax, 1) .eq. 0)
</PRE><A NAME="933998"><PRE> $ call errproc
</PRE><A NAME="934002"><PRE> .
</PRE><A NAME="934000"><PRE> .
</PRE><A NAME="933995"><PRE> .
</PRE><a name="934941">
<h2>6.33 PFWMAP</h2>
</a>
<A NAME="934945"><PRE><B>
</B></PRE><A NAME="932804"><PRE><B>integer </a>PFWMAP(integer fileid,
</B></PRE><A NAME="932805"><PRE><B> character dname,
</B></PRE><A NAME="932806"><PRE><B> integer dp,
</B></PRE><A NAME="932807"><PRE><B> real*8 dm,
</B></PRE><A NAME="932808"><PRE><B> character rname,
</B></PRE><A NAME="932810"><PRE><B> integer rp,
</B></PRE><A NAME="932811"><PRE><B> real*8 rm,
</B></PRE><A NAME="932812"><PRE><B> integer pim)
</B></PRE><a name="934949">
</a>Build a PM_mapping structure out of the given input data and write it to a PDB file.<p>
</a>
<a name="934956">
Rationale: The </a>PM_mapping structure is a convenient medium of exchange between data production systems such as simulation codes, storage systems such as PDBLib, and </a>visualization systems such as PDBView. This function is a convenient way for FORTRAN programs to put out their data into PDB files as PM_mapping’s for later visualization and processing by other programs. <p>
</a>
<a name="934963">
The PM_mapping is a structure with two main parts: a </a>domain and a </a>range. These two parts are in turn represented by a structure called a </a>PM_set. Because they are both represented as the same type of data object, they are specified similarly in </a>PFWMAP. For each of the domain and range </a>sets the following information is given: a name; an array of integer quantities specifying such information as the </a>dimensionality of the set, the dimensionality of the elements, the number of elements, and so on; and a linear array containing the elements of the set.<p>
</a>
<a name="934965">
The entries in the arrays dp and rp are as follows:<p>
</a>
<dl>
<a name="934970">
<dt>1 - the number of characters in the corresponding set name
</a>
<a name="934971">
<dt>2 - the dimensionality of the set, nd
</a>
<a name="934972">
<dt>3 - the dimensionality of the set elements, nde
</a>
<a name="934973">
<dt>4 - the number of elements in the set, ne
</a>
<a name="934974">
<dt>5 thru 5+ nd-1 - the sizes in each dimension
</a>
<a name="934978">
The layout of the set elements in dm and rm is:<p>
</a>
<a name="934982">
<dt>1 thru ne - values of the first component
</a>
<a name="934983">
<dt>ne+1 thru 2*ne - values of the second component
</a>
<a name="934984">
<dt>... - values of components
</a>
<a name="934985">
<dt>(nde-1)*ne+1 thru nde*ne - values of the nde’th component
</a>
<a name="934996">
The calling application must keep track of how many PM_mapping’s have been written to each file. PDBLib will write each PM_mapping under the name composed of the string, ‘Mapping’, and the integer pim. For example if pim is 9, the PM_mapping will be written under the name ‘Mapping9’. If the application passes the same value for pim more than once only the last one will survive in the symbol table even though the data for each PM_mapping will persist in the file!<p>
</a>
<a name="935006">
The arguments to </a>PFWMAP are: fileid, an integer identifier which designates the PDB file to which to attempt to write; dname, an ASCII string containing the name of the domain set; dp, an integer array of parameters defining the domain set; dm, an array of real*8 values containing the set elements component by component; rname, an ASCII string containing the name of the range set; rp, an integer array of parameters defining the range set; rm, an array of real*8 values containing the range elements component by component; and pim a counter specifying the number of the mapping being written out.<p>
</a>
<a name="935010">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="933739">
<p>
</a>
<A NAME="933740"><PRE><B>integer </a>PFWMAP(integer fileid,
</B></PRE><A NAME="933792"><PRE><B> character dname,
</B></PRE><A NAME="933794"><PRE><B> integer dp,
</B></PRE><A NAME="933795"><PRE><B> real*8 dm,
</B></PRE><A NAME="933796"><PRE><B> character rname,
</B></PRE><A NAME="933797"><PRE><B> integer rp,
</B></PRE><A NAME="933798"><PRE><B> real*8 rm,
</B></PRE><A NAME="933800"><PRE><B> integer pim)
</B></PRE><A NAME="933738"><B>
</B><HR><A NAME="933741"><PRE> integer </a>pfwmap
</PRE><A NAME="934052"><PRE> integer fileid, dp(5), rp(5)
</PRE><A NAME="934073"><PRE> double precision dm(0:99), rm(0:99)
</PRE><A NAME="934074"><PRE> .
</PRE><A NAME="934096"><PRE> .
</PRE><A NAME="934097"><PRE> .
</PRE><A NAME="934076"><PRE> dp(1) = 6
</PRE><A NAME="934077"><PRE> dp(2) = 1
</PRE><A NAME="934078"><PRE> dp(3) = 1
</PRE><A NAME="934079"><PRE> dp(4) = 100
</PRE><A NAME="934080"><PRE> dp(5) = 100
</PRE><A NAME="934081"><PRE> rp(1) = 6
</PRE><A NAME="934082"><PRE> rp(2) = 1
</PRE><A NAME="934083"><PRE> rp(3) = 1
</PRE><A NAME="934084"><PRE> rp(4) = 100
</PRE><A NAME="934085"><PRE> rp(5) = 100
</PRE><A NAME="934086"><PRE>
</PRE><A NAME="934087"><PRE> do 100 i = 0, 99
</PRE><A NAME="934088"><PRE> dm(i) = 6.28*float(i)/99.
</PRE><A NAME="934089"><PRE> rm(i) = sin(6.28*float(i)/99.)
</PRE><A NAME="934090"><PRE> 100 continue
</PRE><A NAME="934091"><PRE>
</PRE><A NAME="934092"><PRE> if (</a>pfwmap(fileid, ‘Domain’, dp, dm, ‘Range’, rp, rm, 0)
</PRE><A NAME="934093"><PRE> $ .eq. 0)
</PRE><A NAME="934094"><PRE> $ call errproc
</PRE><A NAME="934095"><PRE> .
</PRE><A NAME="934098"><PRE> .
</PRE><A NAME="934099"><PRE> .
</PRE></dl>
<a name="936662">
<h2>6.34 PFWRAD — (PD_write_as_alt)</h2>
</a>
<A NAME="936669"><PRE><B>
</B></PRE><A NAME="936670"><PRE><B>integer </a>PFWRAD(integer fileid,
</B></PRE><A NAME="936713"><PRE><B> integer nchr,
</B></PRE><A NAME="936715"><PRE><B> character name,
</B></PRE><A NAME="936716"><PRE><B> integer ntypin,
</B></PRE><A NAME="936717"><PRE><B> character intype,
</B></PRE><A NAME="936718"><PRE><B> integer ntypout,
</B></PRE><A NAME="936750"><PRE><B> character outtype,
</B></PRE><A NAME="936751"><PRE><B> void space,
</B></PRE><A NAME="936752"><PRE><B> integer nd,
</B></PRE><A NAME="936753"><PRE><B> integer ind)
</B></PRE><a name="936754">
Write the data of type intype to the PDB file as data of type outtype.<p>
</a>
<a name="936755">
The rationale for this function is: <br>1) that in some situations, it is desirable to not only convert the formats of data of a specified type, but to convert between types. An example that occurs in practice often enough is converting a 32 bit int to a 32 bit long on a machine which only has a 16 bit int.<br>2) that in some situations, it is desirable to be able to specify the dimensions without building them into an ASCII string.<p>
</a>
<a name="936756">
The arguments to </a>PFWRAD are: fileid, an integer identifier which designates the PDB file to which to write; nchr, an integer number of characters in the name string; name, an ASCII string containing the name of the variable to install in the symbol table; ntypin, an integer number of characters in the intype string; intype, an ASCII string specifying the variable type in space; ntypout, an integer number of characters in the outtype string; outtype, an ASCII string specifying the variable type in the PDB file; space, the data to be written; nd, an integer number of dimensions; and ind, an array of nd integer triples containing the minimum and maximum index and the stride for each dimension.<p>
</a>
<a name="936757">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="936758">
See also PFAPAS, PFAPAD, PFAPPA, PFAPPD, PFWRAS, PFWRTA, and PFWRTD.<p>
</a>
<a name="936759">
<p>
</a>
<a name="936760">
<p>
</a>
<A NAME="936761"><PRE><B>integer </a>PFWRAD(integer fileid,
</B></PRE><A NAME="936762"><PRE><B> integer nchr,
</B></PRE><A NAME="936763"><PRE><B> character name,
</B></PRE><A NAME="936764"><PRE><B> integer ntypin,
</B></PRE><A NAME="936765"><PRE><B> character intype,
</B></PRE><A NAME="936766"><PRE><B> integer ntypout,
</B></PRE><A NAME="936767"><PRE><B> character outtype,
</B></PRE><A NAME="936768"><PRE><B> void space,
</B></PRE><A NAME="936769"><PRE><B> integer nd,
</B></PRE><A NAME="936770"><PRE><B> integer ind)
</B></PRE><A NAME="936771"><B>
</B><HR><A NAME="936772"><PRE> integer </a>pfwrad
</PRE><A NAME="936773"><PRE> integer fileid, nd, ind(6)
</PRE><A NAME="936774"><PRE> real*8 c(2,2:4)
</PRE><A NAME="936775"><PRE> .
</PRE><A NAME="936776"><PRE> .
</PRE><A NAME="936777"><PRE> .
</PRE><A NAME="936778"><PRE> c write array c of type double as type float
</PRE><A NAME="936779"><PRE> nd = 2
</PRE><A NAME="936780"><PRE> ind(1) = 1
</PRE><A NAME="936781"><PRE> ind(2) = 2
</PRE><A NAME="936782"><PRE> ind(3) = 1
</PRE><A NAME="936783"><PRE> ind(4) = 2
</PRE><A NAME="936784"><PRE> ind(5) = 4
</PRE><A NAME="936785"><PRE> ind(6) = 1
</PRE><A NAME="936786"><PRE> if (</a>pfwrad(fileid, 1, ‘c’, 6, ‘double’,
</PRE><A NAME="936792"><PRE> $ 5, ‘float’, c, nd, ind) .eq. 0)
</PRE><A NAME="936788"><PRE> $ call errproc
</PRE><A NAME="936789"><PRE> .
</PRE><A NAME="936790"><PRE> .
</PRE><A NAME="936791"><PRE> .
</PRE><a name="935015">
<h2>6.35 PFWRAN</h2>
</a>
<A NAME="935019"><PRE><B>
</B></PRE><A NAME="932813"><PRE><B>integer </a>PFWRAN(integer fileid,
</B></PRE><A NAME="932814"><PRE><B> character dname,
</B></PRE><A NAME="932817"><PRE><B> integer nchr,
</B></PRE><A NAME="932816"><PRE><B> character rname,
</B></PRE><A NAME="932818"><PRE><B> integer rp,
</B></PRE><A NAME="932819"><PRE><B> real*8 rm,
</B></PRE><A NAME="932820"><PRE><B> integer pim)
</B></PRE><a name="935023">
</a>Build a PM_mapping structure out of the given input data and write it to a PDB file.<p>
</a>
<a name="935030">
Rationale: The </a>PM_mapping structure is a convenient medium of exchange between data production systems such as simulation codes, storage systems such as PDBLib, and visualization systems such as PDBView. This function is a convenient way for FORTRAN programs to put out their data into PDB files as PM_mapping’s for later </a>visualization and processing by other programs.<p>
</a>
<a name="935038">
The PM_mapping is a structure with two main parts: a </a>domain and a </a>range. These two parts are in turn represented by a structure called a </a>PM_set. In many cases a number of PM_mapping’s share a common domain set. It is therefore more efficient to write the unique domain </a>sets out separately and use </a>PFWRAN to write out the PM_mapping’s without their domains. Post processor codes such as PDBView (by definition) know how to put the full PM_mapping back together. Note: the domain name given for </a>PFWRAN must be the same as the domain name passed to the corresponding </a>PFWSET call.<p>
</a>
<a name="935043">
For each range set the following information is given: a name; an array of integer quantities specifying such information as the </a>dimensionality of the set, the dimensionality of the elements, the number of elements, and so on; and a linear array containing the elements of the set.<p>
</a>
<a name="935045">
The entries in the array rp are as follows:<p>
</a>
<dl>
<a name="935050">
<dt>1 - the number of characters in the corresponding set name
</a>
<a name="935051">
<dt>2 - the dimensionality of the set, nd
</a>
<a name="935052">
<dt>3 - the dimensionality of the set elements, nde
</a>
<a name="935053">
<dt>4 - the number of elements in the set, ne
</a>
<a name="935054">
<dt>5 thru 5+ nd-1 - the sizes in each dimension
</a>
<a name="935058">
The layout of the set elements in rm is:<p>
</a>
<a name="935062">
<dt>1 thru ne - values of the first component
</a>
<a name="935063">
<dt>ne+1 thru 2*ne - values of the second component
</a>
<a name="935064">
<dt>... - values of components
</a>
<a name="935065">
<dt>(nde-1)*ne+1 thru nde*ne - values of the nde’th component
</a>
<a name="935076">
The calling application must keep track of how many PM_mapping’s have been written to each file. PDBLib will write each PM_mapping under the name composed of the string, ‘Mapping’, and the integer pim. For example if pim is 9, the PM_mapping will be written under the name ‘Mapping9’. If the application passes the same value for pim more than once only the last one will survive in the symbol table even though the data for each PM_mapping will persist in the file.<p>
</a>
<a name="935085">
The arguments to PFWRAN are: fileid, an integer identifier which designates the PDB file to which to attempt to write; dname, an ASCII string containing the name of the domain set; nchr, an integer number of characters in dname; rname, an ASCII string containing the name of the range set; rp, an integer array of parameters defining the range set; rm, an array of real*8 values containing the range elements component by component; and pim a counter specifying the number of the mapping being written out.<p>
</a>
<a name="935089">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="933743">
<p>
</a>
<A NAME="933744"><PRE><B>integer </a>PFWRAN(integer fileid,
</B></PRE><A NAME="933801"><PRE><B> character dname,
</B></PRE><A NAME="933802"><PRE><B> integer nchr,
</B></PRE><A NAME="933803"><PRE><B> character rname,
</B></PRE><A NAME="933804"><PRE><B> integer rp,
</B></PRE><A NAME="933806"><PRE><B> real*8 rm,
</B></PRE><A NAME="933807"><PRE><B> integer pim)
</B></PRE><A NAME="933745"><B>
</B><HR><A NAME="933742"><PRE> integer </a>pfwran
</PRE><A NAME="934075"><PRE> integer fileid, i, pim, rp(5)
</PRE><A NAME="934100"><PRE> double precision rm(0:99)
</PRE><A NAME="934102"><PRE> .
</PRE><A NAME="934103"><PRE> .
</PRE><A NAME="934104"><PRE> .
</PRE><A NAME="934105"><PRE> pim = 0
</PRE><A NAME="934121"><PRE> rp(1) = 6
</PRE><A NAME="934108"><PRE> rp(2) = 1
</PRE><A NAME="934109"><PRE> rp(3) = 1
</PRE><A NAME="934110"><PRE> rp(4) = 100
</PRE><A NAME="934111"><PRE> rp(5) = 100
</PRE><A NAME="934112"><PRE>
</PRE><A NAME="934113"><PRE> do 100 i = 0, 99
</PRE><A NAME="934115"><PRE> rm(i) = sin(6.28*float(i)/99.)
</PRE><A NAME="934116"><PRE> 100 continue
</PRE><A NAME="934117"><PRE>
</PRE><A NAME="934120"><PRE> c ‘Domain’ written previously by pfwset
</PRE><A NAME="934122"><PRE> if (</a>pfwran(fileid, ‘Domain’, 6, ‘Range’, rp, rm, pim)
</PRE><A NAME="934114"><PRE> $ .eq. 0)
</PRE><A NAME="934118"><PRE> $ call errproc
</PRE><A NAME="934119"><PRE> .
</PRE><A NAME="934106"><PRE> .
</PRE><A NAME="934107"><PRE> .
</PRE></dl>
<a name="936705">
<h2>6.36 PFWRAS — (PD_write_as)</h2>
</a>
<A NAME="936706"><PRE><B>
</B></PRE><A NAME="936707"><PRE><B>integer </a>PFWRAS(integer fileid,
</B></PRE><A NAME="936708"><PRE><B> integer nchr,
</B></PRE><A NAME="936709"><PRE><B> character name,
</B></PRE><A NAME="936653"><PRE><B> integer ntypin,
</B></PRE><A NAME="936710"><PRE><B> character intype,
</B></PRE><A NAME="936654"><PRE><B> integer ntypout,
</B></PRE><A NAME="936711"><PRE><B> character outtype,
</B></PRE><A NAME="936712"><PRE><B> void space)
</B></PRE><a name="936714">
Write the data of type intype to the PDB file as data of type outtype.<p>
</a>
<a name="936656">
The rationale for this function is that in some situations, it is desirable to not only convert the formats of data of a specified type, but to convert between types. An example that occurs in practice often enough is converting a 32 bit int to a 32 bit long on a machine which only has a 16 bit int.<p>
</a>
<a name="936663">
The arguments to PFWRAS are: fileid, an integer identifier which designates the PDB file to which to write; nchr, an integer number of characters in the name string; name, an ASCII string containing the name of the variable to install in the symbol table; ntypin, an integer number of characters in the intype string; intype, an ASCII string specifying the variable type in space; ntypout, an integer number of characters in the outtype string; outtype, an ASCII string specifying the variable type in the PDB file; and space, the data to be written.<p>
</a>
<a name="936719">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR<p>
</a>
<a name="936821">
See also PFAPAS, PFAPAD, PFAPPA, PFAPPD, PFWRAD, PFWRTA, and PFWRTD.<p>
</a>
<a name="936720">
<p>
</a>
<A NAME="936721"><PRE><B>integer </a>PFWRAS(integer fileid,
</B></PRE><A NAME="936722"><PRE><B> integer nchr,
</B></PRE><A NAME="936723"><PRE><B> character name,
</B></PRE><A NAME="936724"><PRE><B> integer ntypin,
</B></PRE><A NAME="936725"><PRE><B> character intype,
</B></PRE><A NAME="936667"><PRE><B> integer ntypout,
</B></PRE><A NAME="936668"><PRE><B> character outtype,
</B></PRE><A NAME="936726"><PRE><B> void space)
</B></PRE><A NAME="936727"><B>
</B><HR><A NAME="936728"><PRE> integer </a>pfwras
</PRE><A NAME="936729"><PRE> integer fileid
</PRE><A NAME="936730"><PRE> real*8 x(20)
</PRE><A NAME="936731"><PRE> .
</PRE><A NAME="936734"><PRE> .
</PRE><A NAME="936735"><PRE> .
</PRE><A NAME="936736"><PRE> c write array x of type double as type float
</PRE><A NAME="936737"><PRE> if (</a>pfwras(fileid, 5, ‘x(20)’, 6, ‘double’,
</PRE><A NAME="936666"><PRE> $ 5, ‘float’, x) .eq. 0)
</PRE><A NAME="936738"><PRE> $ call errproc
</PRE><A NAME="936743"><PRE> .
</PRE><A NAME="936744"><PRE> .
</PRE><A NAME="936745"><PRE> .
</PRE><a name="935094">
<h2>6.37 PFWRTA — (PD_write)</h2>
</a>
<A NAME="935098"><PRE><B>
</B></PRE><A NAME="932822"><PRE><B>integer </a>PFWRTA(integer fileid,
</B></PRE><A NAME="932823"><PRE><B> integer nchr,
</B></PRE><A NAME="932828"><PRE><B> character name,
</B></PRE><A NAME="932826"><PRE><B> integer ntype,
</B></PRE><A NAME="932829"><PRE><B> character type,
</B></PRE><A NAME="932827"><PRE><B> void space)
</B></PRE><a name="935109">
</a>Write data to a PDB file. Before writing data to the PDB file an entry is prepared for the symbol table consisting of the name, the type, the </a>dimension information, the disk address to which the data will be written, and the total number of bytes as computed with the help of the structure chart. After the entry is installed in the symbol table the data from memory is converted (only if the </a>target machine type is different from the current machine type) and then written out to disk starting at the current disk address. <p>
</a>
<a name="935115">
The </a>primitive </a>data types which the PDBLib system knows about by default are: ‘short’, ‘integer’, ‘long’, ‘float’, ‘double’, and ‘char’ for short integer, integer, long integer, floating point or real*8 number, double precision floating point number, and character or single byte respectively.<p>
</a>
<a name="935121">
Rationale: When writing out scalar variables (i.e. non-dimensioned variables - structured variables are scalars unless specifically dimensioned) or arrays with fixed dimensions this function is the most convenient to use. Dimension information can be encoded in the name of the entry. PDBLib will strip that information off the name before creating the symbol table entry.<p>
</a>
<a name="935126">
Dimensions can be given in two ways. If the default offset value for the PDB file can be taken as the minimum value for the range which a dimension index can legally run, the maximum value may be specified alone. Alternatively, the minimum value, maximum value, and stride (separated by colons) may be specified. The stride is optional and defaults to 1. For example:<p>
</a>
<a name="933627">
<dd> pfwrta(pid, 10, ‘u(30,1:10)’, 5, ‘float’, u)<P>
</a>
<a name="934323">
The arguments to PFWRTA are: fileid, an integer identifier which designates the PDB file to which to write; nchr, an integer number of characters in the name string; name, an ASCII string containing the name of the variable to install in the symbol table; ntype, an integer number of characters in the type string; type, an ASCII string specifying the variable type; and space, the data to be written.<p>
</a>
<a name="934324">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="936820">
See also PFAPAS, PFAPAD, PFAPPA, PFAPPD, PFWRAD, PFWRAS, and PFWRTD.<p>
</a>
<a name="933748">
<p>
</a>
<A NAME="933749"><PRE><B>integer </a>PFWRTA(integer fileid,
</B></PRE><A NAME="933824"><PRE><B> integer nchr,
</B></PRE><A NAME="933825"><PRE><B> character name,
</B></PRE><A NAME="933826"><PRE><B> integer ntype,
</B></PRE><A NAME="933827"><PRE><B> character type,
</B></PRE><A NAME="933828"><PRE><B> void space)
</B></PRE><A NAME="933750"><B>
</B><HR><A NAME="933747"><PRE> integer </a>pfwrta
</PRE><A NAME="933625"><PRE> integer fileid
</PRE><A NAME="934018"><PRE> real x(20)
</PRE><A NAME="934019"><PRE> common /abc/ a(2), b, c(2,2:4)
</PRE><A NAME="934020"><PRE> real a, b, c
</PRE><A NAME="934024"><PRE> .
</PRE><A NAME="934025"><PRE> .
</PRE><A NAME="934026"><PRE> .
</PRE><A NAME="934023"><PRE> c write array x
</PRE><A NAME="934043"><PRE> if (</a>pfwrta(fileid, 5, ‘x(20)’, 5, ‘float’, x) .eq. 0)
</PRE><A NAME="934031"><PRE> $ call errproc
</PRE><A NAME="934032"><PRE>
</PRE><A NAME="934059"><PRE> c write entire structure abc (previous defined with pfdefs)
</PRE><A NAME="934035"><PRE> if (</a>pfwrta(fileid, 3, ‘abc’, 3, ‘abc’, a) .eq. 0)
</PRE><A NAME="934036"><PRE> $ call errproc
</PRE><A NAME="934001"><PRE> .
</PRE><A NAME="934041"><PRE> .
</PRE><A NAME="934042"><PRE> .
</PRE><a name="935156">
<h2>6.38 PFWRTD — (PD_write_alternate)</h2>
</a>
<A NAME="935163"><PRE><B>
</B></PRE><A NAME="932830"><PRE><B>integer </a>PFWRTD(integer fileid,
</B></PRE><A NAME="932832"><PRE><B> integer nchr,
</B></PRE><A NAME="932837"><PRE><B> character name,
</B></PRE><A NAME="932833"><PRE><B> integer ntype,
</B></PRE><A NAME="932836"><PRE><B> character type,
</B></PRE><A NAME="932834"><PRE><B> void space,
</B></PRE><A NAME="932838"><PRE><B> integer nd,
</B></PRE><A NAME="932840"><PRE><B> integer ind)
</B></PRE><a name="935174">
</a>Write data to a PDB file. Before writing data to the PDB file an entry is prepared for the symbol table consisting of the name, the type, the </a>dimension information, the disk address to which the data will be written, and the total number of bytes as computed with the help of the structure chart. After the entry is installed in the symbol table the data from memory is converted (only if the </a>target machine type is different from the current machine type) and then written out to disk starting at the current disk address.<p>
</a>
<a name="934050">
The </a>primitive </a>data types which the PDBLib system knows about by default are: ‘short’, ‘integer’, ‘long’, ‘float’, ‘double’, and ‘char’ for short integer, integer, long integer, floating point or real number, double precision floating point number, and character or single byte respectively.<p>
</a>
<a name="934051">
The rationale for this function is that in some situations, it is desirable to be able to specify the dimensions without building them into an ASCII string.<p>
</a>
<a name="934072">
The arguments to </a>PFWRTD are: fileid, an integer identifier which designates the PDB file to which to write; nchr, an integer number of characters in the name string; name, an ASCII string containing the name of the variable to install in the symbol table; ntype, an integer number of characters in the type string; type, an ASCII string specifying the variable type; space, the data to be written; nd, an integer number of dimensions; and ind, an array of nd integer triples containing the minimum and maximum index and the stride for each dimension.<p>
</a>
<a name="936822">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="936823">
See also PFAPAS, PFAPAD, PFAPPA, PFAPPD, PFWRAD, PFWRAS, and PFWRTA.<p>
</a>
<a name="935206">
<p>
</a>
<a name="933752">
<p>
</a>
<A NAME="933753"><PRE><B>integer </a>PFWRTD(integer fileid,
</B></PRE><A NAME="933829"><PRE><B> integer nchr,
</B></PRE><A NAME="933830"><PRE><B> character name,
</B></PRE><A NAME="933832"><PRE><B> integer ntype,
</B></PRE><A NAME="933833"><PRE><B> character type,
</B></PRE><A NAME="933835"><PRE><B> void space,
</B></PRE><A NAME="933836"><PRE><B> integer nd,
</B></PRE><A NAME="933837"><PRE><B> integer ind)
</B></PRE><A NAME="933754"><B>
</B><HR><A NAME="934053"><PRE> integer </a>pfwrtd
</PRE><A NAME="933626"><PRE> integer fileid, nd, ind(6)
</PRE><A NAME="934046"><PRE> real c(2,2:4)
</PRE><A NAME="934022"><PRE> .
</PRE><A NAME="934033"><PRE> .
</PRE><A NAME="934037"><PRE> .
</PRE><A NAME="934060"><PRE> c write array c
</PRE><A NAME="933751"><PRE> nd = 2
</PRE><A NAME="934038"><PRE> ind(1) = 1
</PRE><A NAME="934039"><PRE> ind(2) = 2
</PRE><A NAME="933622"><PRE> ind(3) = 1
</PRE><A NAME="934047"><PRE> ind(4) = 2
</PRE><A NAME="934049"><PRE> ind(5) = 4
</PRE><A NAME="934325"><PRE> ind(6) = 1
</PRE><A NAME="934055"><PRE> if (</a>pfwrtd(fileid, 1, ‘c’, 5, ‘float’, c, nd, ind) .eq. 0)
</PRE><A NAME="934054"><PRE> $ call errproc
</PRE><A NAME="934048"><PRE> .
</PRE><A NAME="934045"><PRE> .
</PRE><A NAME="934044"><PRE> .
</PRE><a name="932841">
<h2>6.39 PFWSET)</h2>
</a>
<A NAME="932842"><PRE><B>
</B></PRE><A NAME="932844"><PRE><B>integer </a>PFWSET(integer fileid,
</B></PRE><A NAME="932845"><PRE><B> character dname,
</B></PRE><A NAME="933623"><PRE><B> integer dp,
</B></PRE><A NAME="933649"><PRE><B> real*8 dm)
</B></PRE><a name="933653">
</a>Build a PM_set structure out of the given input data and write it to a PDB file.<p>
</a>
<a name="933665">
Rationale: The </a>PM_set structure is a fundamental component of the </a>PM_mapping structure which is a convenient medium of exchange between data production systems such as simulation codes, storage systems such as PDBLib, and </a>visualization systems such as PDBView. Although the function </a>PFWMAP most conveniently writes a mapping out to a PDB file, it does not make the best use of limited storage space. In many cases a number of PM_mapping’s share a common </a>domain set. It is therefore more efficient to write the unique domain </a>sets out separately and use </a>PFWRAN to write out the PM_mapping’s without their domains. Post processor codes such as PDBView (by definition) know how to put the full PM_mapping back together. Note: the domain name given for </a>PFWSET must be the same as the domain name passed to the corresponding </a>PFWRAN call!<p>
</a>
<a name="933666">
For each PM_set the following information is given: a name; an array of integer quantities specifying such information as the dimensionality of the set, the dimensionality of the elements, the number of elements, etc.; and a linear array containing the elements of the set.<p>
</a>
<a name="933667">
The entries in the array dp are as follows:<p>
</a>
<dl>
<a name="933668">
<dt>1 - the number of characters in the corresponding set name
</a>
<a name="933669">
<dt>2 - the dimensionality of the set, nd
</a>
<a name="933670">
<dt>3 - the dimensionality of the set elements, nde
</a>
<a name="933671">
<dt>4 - the number of elements in the set, ne
</a>
<a name="933673">
<dt>5 thru 5+nd-1 - the sizes in each dimension
</a>
<a name="933674">
The layout of the set elements in dm is:<p>
</a>
<a name="933675">
<dt>1 thru ne - values of the first component
</a>
<a name="933676">
<dt>ne+1 thru 2*ne - values of the second component
</a>
<a name="933678">
<dt>... - values of components
</a>
<a name="933679">
<dt>(nde-1)*ne+1 thru nde*ne - values of the nde’th component
</a>
<a name="933680">
The arguments to </a>PFWSET are: fileid, an integer identifier which designates the PDB file to which to write; dname, an ASCII string containing the name of the PM_set; dp, an integer array of parameters defining the PM_set; and dm, an array of real*8 values containing the set elements component by component.<p>
</a>
<a name="933681">
The return value is 1, if successful; otherwise, 0 is returned and an error message may be retrieved by invoking function PFGERR.<p>
</a>
<a name="933756">
<p>
</a>
<A NAME="933757"><PRE><B>integer </a>PFWSET(integer fileid,
</B></PRE><A NAME="933838"><PRE><B> character dname,
</B></PRE><A NAME="933839"><PRE><B> integer dp,
</B></PRE><A NAME="933840"><PRE><B> real*8 dm)
</B></PRE><A NAME="933759"><B>
</B><HR><A NAME="933755"><PRE> integer </a>pfwset
</PRE><A NAME="934123"><PRE> integer fileid, i, dp(5)
</PRE><A NAME="934124"><PRE> double precision dm(0:99)
</PRE><A NAME="934126"><PRE> .
</PRE><A NAME="934127"><PRE> .
</PRE><A NAME="934128"><PRE> .
</PRE><A NAME="934132"><PRE> dp(1) = 6
</PRE><A NAME="934133"><PRE> dp(2) = 1
</PRE><A NAME="934134"><PRE> dp(3) = 1
</PRE><A NAME="934135"><PRE> dp(4) = 100
</PRE><A NAME="934136"><PRE> dp(5) = 100
</PRE><A NAME="934137"><PRE>
</PRE><A NAME="934143"><PRE> do 100 i = 0, 99
</PRE><A NAME="934129"><PRE> dm(i) = 6.28*float(i)/99.
</PRE><A NAME="934139"><PRE> 100 continue
</PRE><A NAME="934140"><PRE>
</PRE><A NAME="934142"><PRE> if (</a>pfwset(fileid, ‘Domain’, dp, dm) .eq. 0)
</PRE><A NAME="934138"><PRE> $ call errproc
</PRE><A NAME="934141"><PRE> .
</PRE><A NAME="934130"><PRE> .
</PRE><A NAME="934131"><PRE> .
</PRE></dl>
<a name="935279">
<h1>7.0 </a>PDBLib </a>Design Philosophy</h1>
</a>
<a name="935281">
<h2>7.1 Overview</h2>
</a>
<a name="935286">
Perhaps the most fundamental element in the design of PDBLib is the concept of </a>modularity through </a>abstraction barriers. In essence, the functionality is broken down into modular units and abstraction barriers are used to preserve the integrity of the units.<p>
</a>
<a name="935295">
An abstraction barrier is simply a technique or device which allows a section of code to be written assuming other functions or routines are defined and that their internal workings are irrelevant to their use. In this way a routine or module can be changed without any other part of the code which uses it being affected (so long as the definition of its function does not change). Abstraction barriers are most effectively created by a careful choice of the basic functional units and by the interfaces between them.<p>
</a>
<a name="935303">
For example, if all variables in the code were global there would be little or no chance of having any abstraction barriers at all. Similarly, monolithic functions which are defined to ‘solve the worlds problems’ do not lend themselves to the more easy maintenance that abstraction barriers afford a program. For a good discussion of the principles and applications of these ideas see Abelson and Sussman’s marvelous book, The Structure and Interpretation of Computer Programs.<p>
</a>
<a name="935310">
The main </a>functional units in the PDBLib system are: the </a>hash package which controls the maintenance of the data in both the symbol table and structure chart; the </a>conversion package which handles all data format conversions; the </a>data reading routine which is defined to bring data in from the disk, perform any necessary conversion, and store it in the specified location(s) of memory; and the </a>data writing routine which does the reverse of the reading routine.<p>
</a>
<a name="935314">
These units are put together in such a way that they are used over and over again in the process of doing any of the high level functions. In this way the code size was kept relatively small. Again this is one of the rewards of modularity.<p>
</a>
<a name="935316">
<h2>7.2 </a>Data Conversion and </a>Compression</h2>
</a>
<a name="935339">
PDBLib has a quasi-universal </a>data </a>translation capability. It is called </a>Parametrized </a>Data </a>Conversion (</a>PDC). A set of parameters which characterizes a large set of integer and floating point formats was developed. It describes the byte size and order of integer types. For floating point data it describes the bit location and width of the sign, exponent, and mantissa field as well as the byte size and order of the data. Using this information a single integer conversion routine and a single floating point conversion routine handle all of the data conversions in PDBLib. The advantage of this approach is that there is no increase in the size of the library for each port to a new environment. Furthermore, it will allow future releases to auto-configure themselves to the machines on which they run. Another benefit is that a data representation may be targeted without regard to its implementation. This provides a vehicle for developing data representations, evaluating them, or using them in a highly abstract manner. The sole drawback of this approach is that it makes assumptions about the representation of data in computers. While the assumptions are general and the result of incorporating data representations outside these assumptions is more work on the library itself, it is philosophically unsatisfying to make any assumptions about how things are to be done or data to be represented. The other drawback is that by being general purpose the conversion routines are slightly slower than specific ones. This is more than made up for in the saving in library size and ease of porting the library.<p>
</a>
<a name="935345">
Alternative data conversion strategies are either hub and spoke (such as Sun’s </a>XDR) or specific format to format. The latter suffers from an N2 growth in the number of conversion routines where N is the number of machine/architectures which the library supports. On the other hand, hub and spoke strategies necessitate a conversion on each read or write operation.<p>
</a>
<a name="935352">
PDC prevents the conversion problem from being N2. At worst, the PDC method should grow like N in the number of parameter sets required. In practice, it is even better than that. Most computer systems today are based on a handful of CPU’s which are the most constraining factor in binary data formats. For the convenience of the users of PDBLib, several </a>data_standard’s and </a>data_alignment’s are predefined by the library itself.<p>
</a>
<a name="932584">
A significant advantage to PDC is that a class of data compression algorithms is implicit in the method. By simply describing a format which describes data in the correct range (up to a possible overall offset for each type), PDBLib can do all of the work to store and retrieve the data in a compressed form.<p>
</a>
<a name="935358">
<h3>7.2.1 DATA_STANDARD’S</h3>
</a>
<a name="935363">
See the section on the </a>data_standard structure for a detailed discussion of its members. The following is a list of the data_standard’s which PDBLib provides by default. The purpose is twofold: to help users identify target formats; and to guide users who wish to create their own data_standard’s.<p>
</a>
<a name="932530">
The members of the data_standard are indicated in the template:<p>
</a>
<dl>
<a name="932538">
<dt> STAND
</a>
<a name="932548">
<dd>{size of pointer,<P>
</a>
<a name="932539">
<dd> size and order of short,<P>
</a>
<a name="932540">
<dd> size and order of int,<P>
</a>
<a name="932541">
<dd> size and order of long,<P>
</a>
<a name="932542">
<dd> size, format, and order of float,<P>
</a>
<a name="932543">
<dd> size, format, and order of double}<P>
</a>
<a name="932544">
The various variables indicated are defined by PDBLib.<p>
</a>
<a name="932547">
<p>
</a>
<a name="932532">
<dt></a>DEF_STD
</a>
<a name="932550">
<dd>{4,<P>
</a>
<a name="935364">
<dd> 2, NORMAL_ORDER,<P>
</a>
<a name="935365">
<dd> 4, NORMAL_ORDER,<P>
</a>
<a name="935366">
<dd> 4, NORMAL_ORDER,<P>
</a>
<a name="935367">
<dd> 4, def_float, def_float_order,<P>
</a>
<a name="935368">
<dd> 8, def_double, def_double_order}<P>
</a>
<a name="932455">
<p>
</a>
<a name="932531">
<dt> </a>IEEEA_STD
</a>
<a name="932551">
<dd>{4,<P>
</a>
<a name="935370">
<dd> 2, NORMAL_ORDER,<P>
</a>
<a name="935371">
<dd> 4, NORMAL_ORDER,<P>
</a>
<a name="935372">
<dd> 4, NORMAL_ORDER,<P>
</a>
<a name="935373">
<dd> 4, ieee_float, ieee_float_order,<P>
</a>
<a name="935374">
<dd> 8, ieeea_double, ieeea_double_order}<P>
</a>
<a name="932533">
<p>
</a>
<a name="932545">
<dt> </a>IEEEB_STD
</a>
<a name="932559">
<dd>{4,<P>
</a>
<a name="935376">
<dd> 2, NORMAL_ORDER,<P>
</a>
<a name="935377">
<dd> 2, NORMAL_ORDER,<P>
</a>
<a name="935378">
<dd> 4, NORMAL_ORDER,<P>
</a>
<a name="935379">
<dd> 4, ieee_float, ieee_float_order,<P>
</a>
<a name="935380">
<dd> 12, ieeeb_double, ieeeb_double_order}<P>
</a>
<a name="935381">
<p>
</a>
<a name="932534">
<dt> </a>IEEEC_STD
</a>
<a name="932560">
<dd>{4,<P>
</a>
<a name="935382">
<dd> 2, NORMAL_ORDER,<P>
</a>
<a name="935383">
<dd> 4, NORMAL_ORDER,<P>
</a>
<a name="935384">
<dd> 4, NORMAL_ORDER,<P>
</a>
<a name="935385">
<dd> 4, ieee_float, ieee_float_order,<P>
</a>
<a name="935386">
<dd> 12, ieeeb_double, ieeeb_double_order}<P>
</a>
<a name="935387">
<p>
</a>
<a name="932535">
<dt> </a>INTELA_STD
</a>
<a name="932561">
<dd>{4,<P>
</a>
<a name="935388">
<dd> 2, REVERSE_ORDER,<P>
</a>
<a name="935389">
<dd> 2, REVERSE_ORDER,<P>
</a>
<a name="935390">
<dd> 4, REVERSE_ORDER,<P>
</a>
<a name="935391">
<dd> 4, intel_float, intel_float_order,<P>
</a>
<a name="935393">
<dd> 8, intel_double, intel_double_order}<P>
</a>
<a name="932557">
<p>
</a>
<a name="932537">
<dt> </a>INTELB_STD
</a>
<a name="932553">
<dd>{4,<P>
</a>
<a name="935394">
<dd> 2, REVERSE_ORDER,<P>
</a>
<a name="935395">
<dd> 4, REVERSE_ORDER,<P>
</a>
<a name="935396">
<dd> 4, REVERSE_ORDER,<P>
</a>
<a name="935397">
<dd> 4, intel_float, intel_float_order,<P>
</a>
<a name="935398">
<dd> 8, intel_double, intel_double_order},<P>
</a>
<a name="935399">
<p>
</a>
<a name="932556">
<dt> </a>VAX_STD
</a>
<a name="932552">
<dd>{4,<P>
</a>
<a name="935400">
<dd> 2, REVERSE_ORDER,<P>
</a>
<a name="935401">
<dd> 4, REVERSE_ORDER,<P>
</a>
<a name="935402">
<dd> 4, REVERSE_ORDER,<P>
</a>
<a name="935403">
<dd> 4, vax_float, vax_float_order,<P>
</a>
<a name="935404">
<dd> 8, vax_double, vax_double_order}<P>
</a>
<a name="935405">
<p>
</a>
<a name="932555">
<dt> </a>CRAY_STD
</a>
<a name="932554">
<dd>{8,<P>
</a>
<a name="935406">
<dd> 8, NORMAL_ORDER,<P>
</a>
<a name="935407">
<dd> 8, NORMAL_ORDER,<P>
</a>
<a name="935408">
<dd> 8, NORMAL_ORDER,<P>
</a>
<a name="935409">
<dd> 8, cray_float, cray_float_order,<P>
</a>
<a name="935410">
<dd> 8, cray_float, cray_float_order}<P>
</a>
</dl>
<a name="935417">
<h4>7.2.1.1 </a>Floating Point Format Descriptor</h4>
</a>
<a name="935418">
The description of a floating point number consists of an array of 8 long integer parameters. The parameters are:<p>
</a>
<a name="935419">
<dd>format[0] = # of bits per number<P>
</a>
<a name="935420">
<dd>format[1] = # of bits in exponent<P>
</a>
<a name="935421">
<dd>format[2] = # of bits in mantissa<P>
</a>
<a name="935422">
<dd>format[3] = start bit of sign<P>
</a>
<a name="935423">
<dd>format[4] = start bit of exponent<P>
</a>
<a name="935424">
<dd>format[5] = start bit of mantissa<P>
</a>
<a name="935425">
<dd>format[6] = high order mantissa bit<P>
</a>
<a name="935426">
<dd>format[7] = bias of exponent<P>
</a>
<a name="935429">
The following floating point format descriptors are defined in PDBLib and used in the </a>data_standard’s described in the last section:<p>
</a>
<a name="935441">
<dd> </a>ieee_float = {32L, 8L, 23L, 0L, 1L, 9L, 0L, 0x7FL}<P>
</a>
<a name="935442">
<dd> </a>ieeea_double = {64L, 11L, 52L, 0L, 1L, 12L, 0L, 0x3FFL}<P>
</a>
<a name="935443">
<dd> </a>ieeeb_double = {96L, 15L, 64L, 0L, 1L, 32L, 1L, 0x3FFEL}<P>
</a>
<a name="935444">
<dd> </a>intel_float = {32L, 8L, 23L, 0L, 1L, 9L, 0L, 0x7FL}<P>
</a>
<a name="935445">
<dd> </a>intel_double = {64L, 11L, 52L, 0L, 1L, 12L, 0L, 0x3FFL}<P>
</a>
<a name="935455">
<dd> </a>cray_float = {64L, 15L, 48L, 0L, 1L, 16L, 1L, 0x4000L}<P>
</a>
<a name="932572">
Note: There are several variants of floating type format on the VAX. Accordingly the user must decide which one to use and PDBLib has the descriptions:<p>
</a>
<a name="932581">
When using GFLOATs<p>
</a>
<a name="932574">
<dd> </a>vax_float = {32L, 8L, 23L, 0L, 1L, 9L, 0L, 0x81L}<P>
</a>
<a name="932576">
<dd> </a>vax_double = {64L, 11L, 52L, 0L, 1L, 12L, 0L, 0x401L}<P>
</a>
<a name="932577">
otherwise<p>
</a>
<a name="932578">
<dd> </a>vax_float = {32L, 8L, 23L, 0L, 1L, 9L, 0L, 0x81L}<P>
</a>
<a name="932580">
<dd> </a>vax_double = {64L, 8L, 55L, 0L, 1L, 9L, 0L, 0x81L}<P>
</a>
<a name="935461">
<h4>7.2.1.2 </a>Byte Ordering</h4>
</a>
<a name="932573">
There is much discussion in the literature about </a>little endian and </a>big endian machines. Those two refer to two possible byte orderings for binary data. That is not the most general way to talk about byte ordering however. In fact the VAX format exemplifies the need for generality. PDBLib simply uses an array of integers which describe the order of the bytes in memory relative to CPU’s such as the Motorola and SPARC families.<p>
</a>
<a name="932563">
<dd> </a>ieee_float_order = {1, 2, 3, 4}<P>
</a>
<a name="932564">
<dd> </a>ieeea_double_order = {1, 2, 3, 4, 5, 6, 7, 8}<P>
</a>
<a name="932565">
<dd> </a>ieeeb_double_order = {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12}<P>
</a>
<a name="932566">
<dd> </a>intel_float_order = {4, 3, 2, 1}<P>
</a>
<a name="932567">
<dd> </a>intel_double_order = {8, 7, 6, 5, 4, 3, 2, 1}<P>
</a>
<a name="932568">
<dd> </a>vax_float_order = {2, 1, 4, 3}<P>
</a>
<a name="932570">
<dd> </a>vax_double_order = {2, 1, 4, 3, 6, 5, 8, 7}<P>
</a>
<a name="932571">
<dd> </a>cray_float_order = {1, 2, 3, 4, 5, 6, 7, 8}<P>
</a>
<a name="935463">
<h3>7.2.2 </a>DATA_ALIGNMENTS</h3>
</a>
<a name="935466">
The term </a>alignment refers to the fact that many CPU’s require certain data types to begin at memory locations whose addresses are even multiples of some integer number of bytes. So for example, to say that the alignment of a double is 8 means that a double must begin at an address which is a multiple of 8.<p>
</a>
<a name="932562">
Compilers hide this concept from almost all applications. PDBLib is one that must know data alignments precisely. It employs a structure called a </a>data_alignment to record the alignments of the default </a>primitive </a>data types which PDBLib supports. See the discussion of the </a>data_alignment structure in the section on data structures.<p>
</a>
<a name="935482">
The following is the list of </a>data_alignment’s which PDBLib provides automatically (applications can add their own as needed):<p>
</a>
<a name="935485">
<dd> </a>SPARC_ALIGNMENT = {1, 4, 2, 4, 4, 4, 8}<P>
</a>
<a name="933405">
<dd> </a>MIPS_ALIGNMENT = {1, 4, 2, 4, 4, 4, 8}<P>
</a>
<a name="933450">
<dd></a>RS6000_ALIGNMENT = {1, 4, 2, 4, 4, 4, 4}<P>
</a>
<a name="935487">
<dd> </a>CRAY_ALIGNMENT = {8, 8, 8, 8, 8, 8, 8}<P>
</a>
<a name="935488">
<dd> </a>UNICOS_ALIGNMENT = {1, 8, 8, 8, 8, 8, 8}<P>
</a>
<a name="935489">
<dd> </a>M68000_ALIGNMENT = {1, 2, 2, 2, 2, 2, 2}<P>
</a>
<a name="935490">
<dd> </a>INTELA_ALIGNMENT = {1, 2, 2, 2, 2, 2, 2}<P>
</a>
<a name="932442">
<dd> </a>INTELB_ALIGNMENT = {4, 4, 4, 4, 4, 4, 4}<P>
</a>
<a name="932443">
<dd> </a>INTELC_ALIGNMENT = {2, 4, 2, 4, 4, 4, 4}<P>
</a>
<a name="935491">
<dd> </a>DEF_ALIGNMENT = {1, 4, 4, 4, 4, 4, 4}<P>
</a>
<a name="935508">
<h1>8.0 </a>Data Structures in PDBLib</h1>
</a>
<a name="935515">
The data structures with which the PDBLib system works are passed back to the application program as the result of the high level calls. This gives the programmer access to a great deal of information about the PDB file, the symbol table and the structure chart. Hopefully, this also makes the package more powerful without pushing any special responsibility onto the programmer. <p>
</a>
<a name="935520">
For application developers who require all of the information from a PDB file, the hash lookup function, </a>SC_def_lookup, can be used to obtain symbol table entries (</a>syment) and structure definitions (</a>defstr) from the symbol table or structure chart. Examples can be found in the section at the end of the manual.<p>
</a>
<a name="935525">
<h2>8.1 </a>DATA_ALIGNMENT</h2>
</a>
<a name="935528">
The set of </a>alignments for the primitive types is kept in a structure called </a>data_alignment. Its actual definition is:<p>
</a>
<A NAME="932586"><PRE> struct s_data_alignment
</PRE><A NAME="935532"><PRE> {int char_alignment;
</PRE><A NAME="935533"><PRE> int ptr_alignment;
</PRE><A NAME="935534"><PRE> int short_alignment;
</PRE><A NAME="935535"><PRE> int int_alignment;
</PRE><A NAME="935536"><PRE> int long_alignment;
</PRE><A NAME="935537"><PRE> int float_alignment;
</PRE><A NAME="935538"><PRE> int double_alignment;};
</PRE><A NAME="935539"><PRE>
</PRE><A NAME="935540"><PRE> typedef struct s_data_alignment </a>data_alignment;
</PRE><a name="935547">
Each member is an integer which specifies the alignment for a primitive type. The alignment is a number of bytes such that a piece of data of this type must begin at an address which is an even multiple of that number. For example, if ptr_alignment is 4, a pointer must begin at an address divisible by 4.<p>
</a>
<a name="935552">
<h2>8.2 </a>DATA_STANDARD</h2>
</a>
<a name="935557">
The set of information describing all of the </a>primitive </a>data types is organized into a structure called a </a>data_standard. The </a>data_standard characterizes the CPU architecture because all types are either primitive or derived from known types.<p>
</a>
<a name="935558">
Its actual definition is:<p>
</a>
<A NAME="935561"><PRE> struct s_data_standard
</PRE><A NAME="935562"><PRE> {int ptr_bytes;
</PRE><A NAME="935563"><PRE> int short_bytes;
</PRE><A NAME="935564"><PRE> int short_order;
</PRE><A NAME="935565"><PRE> int int_bytes;
</PRE><A NAME="935566"><PRE> int int_order;
</PRE><A NAME="935567"><PRE> int long_bytes;
</PRE><A NAME="935568"><PRE> int long_order;
</PRE><A NAME="935569"><PRE> int float_bytes;
</PRE><A NAME="935570"><PRE> long *float_format;
</PRE><A NAME="935571"><PRE> int *float_order;
</PRE><A NAME="935572"><PRE> int double_bytes;
</PRE><A NAME="935573"><PRE> long *double_format;
</PRE><A NAME="935574"><PRE> int *double_order;};
</PRE><A NAME="935575"><PRE>
</PRE><A NAME="935576"><PRE> typedef struct s_data_standard </a>data_standard;
</PRE><a name="935582">
The integer types only require a number of bytes and their order. The floating point types require additional information describing the bit layout of the components of the number: the sign bit; the exponent; and the mantissa. These are given as an array of 8 integers as follows:<p>
</a>
<a name="935585">
<dd> format[0] = # of bits per number<P>
</a>
<a name="935586">
<dd> format[1] = # of bits in exponent<P>
</a>
<a name="935587">
<dd> format[2] = # of bits in mantissa<P>
</a>
<a name="935588">
<dd> format[3] = start bit of sign<P>
</a>
<a name="935589">
<dd> format[4] = start bit of exponent<P>
</a>
<a name="935590">
<dd> format[5] = start bit of mantissa<P>
</a>
<a name="935591">
<dd> format[6] = high order mantissa bit<P>
</a>
<a name="935592">
<dd> format[7] = bias of exponent<P>
</a>
<a name="932467">
<h2>8.3 </a>DEFSTR</h2>
</a>
<a name="935601">
An entry in the structure chart is represented by a structure called a </a>defstr. It contains information about the </a>data type such as the type name, the byte size and alignment, and a list of members.<p>
</a>
<a name="932468">
<h2>8.4 </a>DIMDES</h2>
</a>
<a name="935634">
A </a>dimdes or </a>dimension descriptor contains the information necessary to characterize a list of dimension specifications. It contains such information as the minimum and maximum values the dimension index may have and the net size of the dimension index range.<p>
</a>
<a name="932469">
<h2>8.5 </a>MEMDES</h2>
</a>
<a name="935658">
A </a>memdes or </a>member descriptor is the structure used to contain the information about a member of a </a>defstr. It contains information about the type of the member, the name of the member, any dimensions which the member may have, and any casts which have been defined via </a>PD_cast.<p>
</a>
<a name="933300">
<h2>8.6 </a>PDBFILE</h2>
</a>
<a name="933301">
The </a>PDBfile is the analog to the </a>FILE structure in standard C I/O. In fact, the PDBfile contains a FILE pointer to access the file via the standard C library functions. In addition, the PDBfile contains information such as: the symbol table, the structure charts for the file and the host platform; </a>data_standard’s and </a>data_alignment’s for the file and the host platform; and a modification date.<p>
</a>
<a name="935775">
<h2>8.7 </a>SYMENT</h2>
</a>
<a name="935779">
Just as the </a>defstr type describes entries in the structure chart the </a>syment type describes entries in the symbol table. The </a>syment includes information about the data type of the entry, the number of elements, the dimensions of the entry, and its disk address.<p>
</a>
<a name="935803">
<h1>9.0 </a>PDBLib by </a>Example</h1>
</a>
<a name="935807">
The following code fragments illustrate the functionality of PDBLib. Some of the code is taken from the validation suite and some from the library itself.<p>
</a>
<a name="935809">
<h2>9.1 Working with PDB files</h2>
</a>
<a name="935820">
This routine is taken from the validation suite for PDBLib. In it, a target for the PDB file is chosen with the routine <em>test_target</em> (see the section on </a><em>PD_target</em> for the definition of this function), a PDB file created, some structures defined, data written, and the file closed. The file is then reopened in append mode, some more data written to the file, and the file is closed again. Finally, the file is opened in read mode, the data read, some comparisons done, and the file is closed. The read and write operations are hidden in this example. The significance of the example is that a PDB file is created, closed, and opened in both append and read-only mode.<p>
</a>
<a name="935823">
<p>
</a>
<A NAME="935824"><PRE> test_1(base, tgt, n)
</PRE><A NAME="935825"><PRE> char *base, *tgt;
</PRE><A NAME="935826"><PRE> int n;
</PRE><A NAME="935827"><PRE> {PDBfile *strm;
</PRE><A NAME="935828"><PRE> char datfile[MAXLINE], fname[MAXLINE];
</PRE><A NAME="935829"><PRE> int err;
</PRE><A NAME="935830"><PRE> FILE *fp;
</PRE><A NAME="935831"><PRE>
</PRE><A NAME="935832"><PRE> /* target the file as asked */
</PRE><A NAME="935833"><PRE> test_target(tgt, base, n, fname, datfile);
</PRE><A NAME="935834"><PRE>
</PRE><A NAME="935835"><PRE> fp = fopen(fname, “w”);
</PRE><A NAME="935836"><PRE>
</PRE><A NAME="935837"><PRE> /* create the named file */
</PRE><A NAME="935838"><PRE> if ((strm = </a>PD_open(datfile, “w”)) == NULL)
</PRE><A NAME="935839"><PRE> {fprintf(fp, “Test couldn’t create file %s\r\n”, datfile);
</PRE><A NAME="935840"><PRE> exit(1);};
</PRE><A NAME="935841"><PRE> fprintf(fp, “File %s created\n”, datfile);
</PRE><A NAME="935842"><PRE>
</PRE><A NAME="935843"><PRE> prep_test_1_data();
</PRE><A NAME="935844"><PRE>
</PRE><A NAME="935845"><PRE> /* make a few defstructs */
</PRE><A NAME="935846"><PRE> </a>PD_defstr(strm, “l_frame”,
</PRE><A NAME="935847"><PRE> “float x_min”, “float x_max”, “float y_min”,
</PRE><A NAME="935848"><PRE> “float y_max”, LAST);
</PRE><A NAME="935849"><PRE> </a>PD_defstr(strm, “plot”,
</PRE><A NAME="935850"><PRE> “float x_axis(10)”, “float y_axis(10)”, “integer npts”,
</PRE><A NAME="935851"><PRE> “char * label”, “l_frame view”, LAST);
</PRE><A NAME="935852"><PRE>
</PRE><A NAME="935853"><PRE> /* write the test data */
</PRE><A NAME="935854"><PRE> write_test_1_data(strm);
</PRE><A NAME="935855"><PRE>
</PRE><A NAME="935856"><PRE> /* close the file */
</PRE><A NAME="935857"><PRE> if (!</a>PD_close(strm))
</PRE><A NAME="935858"><PRE> {fprintf(fp, “Test couldn’t close file %s\r\n”, datfile);
</PRE><A NAME="935859"><PRE> exit(1);};
</PRE><A NAME="935860"><PRE> fprintf(fp, “File %s closed\n”, datfile);
</PRE><A NAME="935861"><PRE>
</PRE><A NAME="935862"><PRE> /* reopen the file to append */
</PRE><A NAME="935863"><PRE> if ((strm = </a>PD_open(datfile, “a”)) == NULL)
</PRE><A NAME="935864"><PRE> {fprintf(fp, “Test couldn’t open file %s to append\r\n”,
</PRE><A NAME="932485"><PRE> datfile);
</PRE><A NAME="935865"><PRE> exit(1);};
</PRE><A NAME="935866"><PRE> fprintf(fp, “File %s opened to append\n”, datfile);
</PRE><A NAME="935867"><PRE>
</PRE><A NAME="935868"><PRE> append_test_1_data(strm);
</PRE><A NAME="935869"><PRE>
</PRE><A NAME="935870"><PRE> /* close the file after append */
</PRE><A NAME="935871"><PRE> if (!</a>PD_close(strm))
</PRE><A NAME="935872"><PRE> {fprintf(fp, “Test couldn’t close file %s after append\r\n”,
</PRE><A NAME="935873"><PRE> datfile);
</PRE><A NAME="935874"><PRE> exit(1);};
</PRE><A NAME="935875"><PRE> fprintf(fp, “File %s closed after append\n”, datfile);
</PRE><A NAME="935876"><PRE>
</PRE><A NAME="935877"><PRE> /* reopen the file */
</PRE><A NAME="935878"><PRE> if ((strm = </a>PD_open(datfile, “r”)) == NULL)
</PRE><A NAME="935879"><PRE> {fprintf(fp, “Test couldn’t open file %s\r\n”, datfile);
</PRE><A NAME="935880"><PRE> exit(1);};
</PRE><A NAME="935881"><PRE> fprintf(fp, “File %s opened\n”, datfile);
</PRE><A NAME="935882"><PRE>
</PRE><A NAME="935883"><PRE> /* dump the symbol table */
</PRE><A NAME="935884"><PRE> dump_test_symbol_table(fp, strm->symtab, 1);
</PRE><A NAME="935885"><PRE>
</PRE><A NAME="935886"><PRE> /* read the data from the file */
</PRE><A NAME="935887"><PRE> read_test_1_data(strm);
</PRE><A NAME="935888"><PRE>
</PRE><A NAME="935889"><PRE> /* compare the original data with that read in */
</PRE><A NAME="935890"><PRE> err = compare_test_1_data(strm, fp);
</PRE><A NAME="935891"><PRE>
</PRE><A NAME="935892"><PRE> /* close the file */
</PRE><A NAME="935893"><PRE> if (!</a>PD_close(strm))
</PRE><A NAME="935894"><PRE> {fprintf(fp, “Test couldn’t close file %s\r\n”, datfile);
</PRE><A NAME="935895"><PRE> exit(1);};
</PRE><A NAME="935896"><PRE> fprintf(fp, “File %s closed\n”, datfile);
</PRE><A NAME="935897"><PRE>
</PRE><A NAME="935898"><PRE> /* print it out to stdout */
</PRE><A NAME="935899"><PRE> print_test_1_data(fp);
</PRE><A NAME="935900"><PRE>
</PRE><A NAME="935901"><PRE> fclose(fp);
</PRE><A NAME="935902"><PRE>
</PRE><A NAME="935903"><PRE> return(err);}
</PRE><a name="935908">
<h2>9.2 </a>Writing Data to PDB files</h2>
</a>
<a name="935913">
These two routines exemplify the various write routines of PDBLib. In particular, they were built to test the spectrum of write calls. Notice their demonstration of the rules for write operations: the variable must be a pointer to data of the type specified.<p>
</a>
<a name="935916">
The identifiers beginning with ‘N_’ are ‘#defined’ constants whose values are irrelevant to these examples.<p>
</a>
<a name="935919">
<p>
</a>
<A NAME="935920"><PRE> static char
</PRE><A NAME="935921"><PRE> cs_w,
</PRE><A NAME="935922"><PRE> ca_w[N_CHAR],
</PRE><A NAME="935923"><PRE> *cap_w[N_DOUBLE];
</PRE><A NAME="935924"><PRE>
</PRE><A NAME="935925"><PRE> static short
</PRE><A NAME="935926"><PRE> ss_w,
</PRE><A NAME="935927"><PRE> sa_w[N_INT];
</PRE><A NAME="935928"><PRE>
</PRE><A NAME="935929"><PRE> static int
</PRE><A NAME="935930"><PRE> is_w,
</PRE><A NAME="935931"><PRE> ia_w[N_INT],
</PRE><A NAME="935932"><PRE> p_w[N_INT],
</PRE><A NAME="935933"><PRE> len;
</PRE><A NAME="935934"><PRE>
</PRE><A NAME="935935"><PRE> static float
</PRE><A NAME="935936"><PRE> fs_w,
</PRE><A NAME="935937"><PRE> fa2_w[N_FLOAT][N_DOUBLE];
</PRE><A NAME="935938"><PRE>
</PRE><A NAME="935939"><PRE> static double
</PRE><A NAME="935940"><PRE> ds_w,
</PRE><A NAME="935941"><PRE> da_w[N_FLOAT];
</PRE><A NAME="935942"><PRE>
</PRE><A NAME="935943"><PRE> static plot
</PRE><A NAME="935944"><PRE> graph_w;
</PRE><A NAME="935945"><PRE>
</PRE><A NAME="935946"><PRE> static l_frame
</PRE><A NAME="935947"><PRE> view_w;
</PRE><A NAME="935948"><PRE>
</PRE><A NAME="935949"><PRE> static lev1
</PRE><A NAME="935950"><PRE> *tar_w;
</PRE><A NAME="935951"><PRE>
</PRE><A NAME="935952"><PRE> /*-----------------------------------------------------------------*/
</PRE><A NAME="935953"><PRE> /*-----------------------------------------------------------------*/
</PRE><A NAME="935954"><PRE>
</PRE><A NAME="935955"><PRE> void write_test_1_data(strm)
</PRE><A NAME="935956"><PRE> PDBfile *strm;
</PRE><A NAME="935957"><PRE> {
</PRE><A NAME="935958"><PRE>
</PRE><A NAME="935959"><PRE> /* write scalars into the file */
</PRE><A NAME="935960"><PRE> </a>PD_write(strm, “cs”, “char”, &cs_w);
</PRE><A NAME="935961"><PRE> PD_write(strm, “ss”, “short”, &ss_w);
</PRE><A NAME="935962"><PRE> PD_write(strm, “is”, “integer”, &is_w);
</PRE><A NAME="935963"><PRE> PD_write(strm, “fs”, “float”, &fs_w);
</PRE><A NAME="935964"><PRE> PD_write(strm, “ds”, “double”, &ds_w);
</PRE><A NAME="935965"><PRE>
</PRE><A NAME="935966"><PRE> /* write primitive arrays into the file */
</PRE><A NAME="935968"><PRE> PD_write(strm, “sa(5)”, “short”, sa_w);
</PRE><A NAME="935969"><PRE> PD_write(strm, “ia(5)”, “integer”, ia_w);
</PRE><A NAME="935973"><PRE>
</PRE><A NAME="935974"><PRE> /* write structures into the file */
</PRE><A NAME="935975"><PRE> PD_write(strm, “view”, “l_frame”, &view_w);
</PRE><A NAME="935976"><PRE> PD_write(strm, “graph”, “plot”, &graph_w);
</PRE><A NAME="935977"><PRE>
</PRE><A NAME="935978"><PRE> return;}
</PRE><A NAME="935979"><PRE>
</PRE><A NAME="935980"><PRE> /*-----------------------------------------------------------------*/
</PRE><A NAME="935981"><PRE> /*-----------------------------------------------------------------*/
</PRE><A NAME="935982"><PRE>
</PRE><A NAME="935983"><PRE> void write_test_2_data(strm)
</PRE><A NAME="935984"><PRE> PDBfile *strm;
</PRE><A NAME="933624"><PRE> {
</PRE><A NAME="933628"><PRE>
</PRE><A NAME="935986"><PRE> </a>PD_write(strm, “tar”, “lev1 *”, &tar_w);
</PRE><A NAME="932486"><PRE>
</PRE><A NAME="932487"><PRE> return;}
</PRE><A NAME="935987"><PRE>
</PRE><A NAME="935988"><PRE> /*-----------------------------------------------------------------*/
</PRE><A NAME="935989"><PRE> /*-----------------------------------------------------------------*/
</PRE><a name="935994">
<h2>9.3 </a>Reading Data from PDB files</h2>
</a>
<a name="936002">
These two routines exemplify the various read routines of PDBLib. In particular, they were built to test the spectrum of read operations. They read the data written out in the previous example. Notice their demonstration of the rules for read operations: the variable must be a pointer to data of the type specified. This is often a more difficult proposition for reads since the type information isn’t supplied in the read call.<p>
</a>
<a name="936006">
The member read operations at the end of the first routine should be studied carefully. They are not the most general read example, but they are among the most useful.<p>
</a>
<a name="936011">
The second routine reads not only the entire structure, but picks out each part individually. It demonstrates the rule about dereferencing pointers in the partial read operation. Study the structures of this example carefully!<p>
</a>
<a name="936016">
The identifiers beginning with ‘N_’ are ‘#defined’ constants whose values are irrelevant to these examples. Also, take for granted that the unspecified variables to contain parts of the structures have the correct declarations.<p>
</a>
<A NAME="936020"><PRE>
</PRE><A NAME="932484"><PRE> struct s_lev2
</PRE><A NAME="936021"><PRE> {char **s;
</PRE><A NAME="936022"><PRE> int type;};
</PRE><A NAME="936023"><PRE>
</PRE><A NAME="936024"><PRE> typedef struct s_lev2 lev2;
</PRE><A NAME="936025"><PRE>
</PRE><A NAME="936026"><PRE> struct s_lev1
</PRE><A NAME="936027"><PRE> {int *a;
</PRE><A NAME="936028"><PRE> double *b;
</PRE><A NAME="936029"><PRE> lev2 *c;};
</PRE><A NAME="936030"><PRE>
</PRE><A NAME="936031"><PRE> typedef struct s_lev1 lev1;
</PRE><A NAME="936032"><PRE>
</PRE><A NAME="936033"><PRE> static char
</PRE><A NAME="936034"><PRE> cs_r,
</PRE><A NAME="936035"><PRE> ca_r[N_CHAR],
</PRE><A NAME="936036"><PRE> *cap_r[N_DOUBLE];
</PRE><A NAME="936037"><PRE>
</PRE><A NAME="936038"><PRE> static short
</PRE><A NAME="936039"><PRE> ss_r,
</PRE><A NAME="936040"><PRE> sa_r[N_INT];
</PRE><A NAME="936041"><PRE>
</PRE><A NAME="936042"><PRE> static int
</PRE><A NAME="936043"><PRE> is_r,
</PRE><A NAME="936044"><PRE> ia_r[N_INT];
</PRE><A NAME="936045"><PRE>
</PRE><A NAME="936046"><PRE> static float
</PRE><A NAME="936047"><PRE> fs_r,
</PRE><A NAME="936048"><PRE> fs_app_r,
</PRE><A NAME="936049"><PRE> fs_p1_r,
</PRE><A NAME="936050"><PRE> fs_p2_r,
</PRE><A NAME="936051"><PRE> fs_p3_r,
</PRE><A NAME="936052"><PRE> fa2_r[N_FLOAT][N_DOUBLE],
</PRE><A NAME="936053"><PRE> fa2_app_r[N_FLOAT][N_DOUBLE];
</PRE><A NAME="936054"><PRE>
</PRE><A NAME="936055"><PRE> static double
</PRE><A NAME="936056"><PRE> ds_r,
</PRE><A NAME="936057"><PRE> da_r[N_FLOAT];
</PRE><A NAME="936058"><PRE>
</PRE><A NAME="936059"><PRE> static plot
</PRE><A NAME="936060"><PRE> graph_r;
</PRE><A NAME="936061"><PRE>
</PRE><A NAME="936062"><PRE> static l_frame
</PRE><A NAME="936063"><PRE> view_r;
</PRE><A NAME="936064"><PRE>
</PRE><A NAME="936065"><PRE> static lev1
</PRE><A NAME="936066"><PRE> *tar_r;
</PRE><A NAME="936067"><PRE>
</PRE><A NAME="936068"><PRE> /*-----------------------------------------------------------------*/
</PRE><A NAME="936069"><PRE> /*-----------------------------------------------------------------*/
</PRE><A NAME="936070"><PRE>
</PRE><A NAME="936071"><PRE> void read_test_1_data(strm)
</PRE><A NAME="936072"><PRE> PDBfile *strm;
</PRE><A NAME="936073"><PRE> {
</PRE><A NAME="936074"><PRE>
</PRE><A NAME="936075"><PRE> /* read the scalar data from the file */
</PRE><A NAME="936076"><PRE> </a>PD_read(strm, “cs”, &cs_r);
</PRE><A NAME="936077"><PRE> PD_read(strm, “ss”, &ss_r);
</PRE><A NAME="936078"><PRE> PD_read(strm, “is”, &is_r);
</PRE><A NAME="936079"><PRE> PD_read(strm, “fs”, &fs_r);
</PRE><A NAME="936080"><PRE> PD_read(strm, “ds”, &ds_r);
</PRE><A NAME="936081"><PRE>
</PRE><A NAME="936082"><PRE> /* read the primitive arrays from the file */
</PRE><A NAME="936083"><PRE> PD_read(strm, “ca”, ca_r);
</PRE><A NAME="936084"><PRE> PD_read(strm, “sa”, sa_r);
</PRE><A NAME="936085"><PRE> PD_read(strm, “ia”, ia_r);
</PRE><A NAME="936086"><PRE> PD_read(strm, “fa2”, fa2_r);
</PRE><A NAME="936087"><PRE> PD_read(strm, “da”, da_r);
</PRE><A NAME="936088"><PRE> PD_read(strm, “cap”, cap_r);
</PRE><A NAME="936089"><PRE>
</PRE><A NAME="936090"><PRE> /* read the entire structures from the file */
</PRE><A NAME="936091"><PRE> PD_read(strm, “view”, &view_r);
</PRE><A NAME="936092"><PRE> PD_read(strm, “graph”, &graph_r);
</PRE><A NAME="936093"><PRE>
</PRE><A NAME="936094"><PRE> /* read the appended data from the file */
</PRE><A NAME="936095"><PRE> PD_read(strm, “fs_app”, &fs_app_r);
</PRE><A NAME="936096"><PRE> PD_read(strm, “fa2_app”, fa2_app_r);
</PRE><A NAME="936100"><PRE>
</PRE><A NAME="936101"><PRE> /* struct member test */
</PRE><A NAME="936103"><PRE> PD_read(strm, “graph.view.x_max”, &fs_p2_r);
</PRE><A NAME="936104"><PRE> </a>PD_read(strm, “view.y_max”, &fs_p3_r);
</PRE><A NAME="936105"><PRE>
</PRE><A NAME="936106"><PRE> return;}
</PRE><A NAME="936107"><PRE>
</PRE><A NAME="936108"><PRE> /*-----------------------------------------------------------------*/
</PRE><A NAME="936109"><PRE> /*-----------------------------------------------------------------*/
</PRE><A NAME="936110"><PRE>
</PRE><A NAME="936111"><PRE> /* READ_TEST_2_DATA - read the test data from the file */
</PRE><A NAME="936112"><PRE>
</PRE><A NAME="936113"><PRE> void read_test_2_data(strm)
</PRE><A NAME="936114"><PRE> PDBfile *strm;
</PRE><A NAME="936115"><PRE> {do_r = strm->default_offset;
</PRE><A NAME="936116"><PRE>
</PRE><A NAME="936117"><PRE> </a>PD_read(strm, “tar”, &tar_r);
</PRE><A NAME="936118"><PRE> PD_read(strm, “p”, p_r);
</PRE><A NAME="936119"><PRE>
</PRE><A NAME="936120"><PRE> PD_read(strm, “tar(0).a”, &ap1);
</PRE><A NAME="936121"><PRE> PD_read(strm, “tar(1).a”, &ap2);
</PRE><A NAME="936122"><PRE>
</PRE><A NAME="936123"><PRE> PD_read(strm, “tar(0).a(0)”, &aa[0]);
</PRE><A NAME="936124"><PRE> PD_read(strm, “tar(0).a(1)”, &aa[1]);
</PRE><A NAME="936125"><PRE> PD_read(strm, “tar(1).a(0)”, &aa[2]);
</PRE><A NAME="936126"><PRE> PD_read(strm, “tar(1).a(1)”, &aa[3]);
</PRE><A NAME="936127"><PRE>
</PRE><A NAME="936128"><PRE> PD_read(strm, “tar(0).b”, &bp1);
</PRE><A NAME="936129"><PRE> PD_read(strm, “tar(1).b”, &bp2);
</PRE><A NAME="936130"><PRE>
</PRE><A NAME="936131"><PRE> PD_read(strm, “tar(0).b(0)”, &ba[0]);
</PRE><A NAME="936132"><PRE> PD_read(strm, “tar(0).b(1)”, &ba[1]);
</PRE><A NAME="936133"><PRE> PD_read(strm, “tar(1).b(0)”, &ba[2]);
</PRE><A NAME="936134"><PRE> PD_read(strm, “tar(1).b(1)”, &ba[3]);
</PRE><A NAME="936135"><PRE>
</PRE><A NAME="936136"><PRE> PD_read(strm, “tar(0).c”, &cp1);
</PRE><A NAME="936137"><PRE> PD_read(strm, “tar(1).c”, &cp2);
</PRE><A NAME="936138"><PRE>
</PRE><A NAME="936139"><PRE> PD_read(strm, “tar(0).c(0)”, &ca[0]);
</PRE><A NAME="936140"><PRE> PD_read(strm, “tar(0).c(1)”, &ca[1]);
</PRE><A NAME="936141"><PRE> PD_read(strm, “tar(1).c(0)”, &ca[2]);
</PRE><A NAME="936142"><PRE> PD_read(strm, “tar(1).c(1)”, &ca[3]);
</PRE><A NAME="936143"><PRE>
</PRE><A NAME="936144"><PRE> PD_read(strm, “tar(0).c(0).s”, &sp1);
</PRE><A NAME="936145"><PRE> PD_read(strm, “tar(0).c(1).s”, &sp2);
</PRE><A NAME="936146"><PRE> PD_read(strm, “tar(1).c(0).s”, &sp3);
</PRE><A NAME="936147"><PRE> PD_read(strm, “tar(1).c(1).s”, &sp4);
</PRE><A NAME="936148"><PRE>
</PRE><A NAME="936149"><PRE> PD_read(strm, “tar(0).c(0).s(0)”, &tp1);
</PRE><A NAME="936150"><PRE> PD_read(strm, “tar(0).c(0).s(1)”, &tp2);
</PRE><A NAME="936151"><PRE> PD_read(strm, “tar(0).c(1).s(0)”, &tp3);
</PRE><A NAME="936152"><PRE> PD_read(strm, “tar(0).c(1).s(1)”, &tp4);
</PRE><A NAME="936153"><PRE>
</PRE><A NAME="936154"><PRE> PD_read(strm, “tar(0).c(0).s(0)(2)”, &ta[0]);
</PRE><A NAME="936155"><PRE> PD_read(strm, “tar(0).c(0).s(1)(1)”, &ta[1]);
</PRE><A NAME="936156"><PRE> PD_read(strm, “tar(0).c(1).s(0)(3)”, &ta[2]);
</PRE><A NAME="936157"><PRE> PD_read(strm, “tar(0).c(1).s(1)(2)”, &ta[3]);
</PRE><A NAME="936158"><PRE>
</PRE><A NAME="936159"><PRE> PD_read(strm, “tar(1).c(0).s(0)”, &tp5);
</PRE><A NAME="936160"><PRE> PD_read(strm, “tar(1).c(0).s(1)”, &tp6);
</PRE><A NAME="936161"><PRE> PD_read(strm, “tar(1).c(1).s(0)”, &tp7);
</PRE><A NAME="936162"><PRE> </a>PD_read(strm, “tar(1).c(1).s(1)”, &tp8);
</PRE><A NAME="936163"><PRE>
</PRE><A NAME="936164"><PRE> return;}
</PRE><a name="936172">
<h2>9.4 </a>Inquiries in PDBLib</h2>
</a>
<a name="936176">
The following fragments show how to obtain information about PDB files and their contents.<p>
</a>
<A NAME="936179"><PRE>
</PRE><A NAME="932488"><PRE> /*-----------------------------------------------------------------*/
</PRE><A NAME="936180"><PRE> /*-----------------------------------------------------------------*/
</PRE><A NAME="936181"><PRE>
</PRE><A NAME="936182"><PRE> myread(file, name, var, offset, number)
</PRE><A NAME="936183"><PRE> PDBfile *file;
</PRE><A NAME="936184"><PRE> char *name;
</PRE><A NAME="936185"><PRE> void *var;
</PRE><A NAME="936186"><PRE> long offset, number;
</PRE><A NAME="936187"><PRE> {long addr, num;
</PRE><A NAME="936188"><PRE> char *token, *type, memb[MAXLINE];
</PRE><A NAME="936189"><PRE> dimdes *dims;
</PRE><A NAME="936190"><PRE> syment *ep;
</PRE><A NAME="936191"><PRE>
</PRE><A NAME="936192"><PRE> strcpy(memb, name);
</PRE><A NAME="936193"><PRE> token = strtok(memb, “.([“);
</PRE><A NAME="936194"><PRE>
</PRE><A NAME="936195"><PRE> /* look up the variable name */
</PRE><A NAME="936196"><PRE> ep = </a>PD_inquire_entry(file, token);
</PRE><A NAME="932716"><PRE> if (ep == NULL)
</PRE><A NAME="936197"><PRE> PD_error(“VARIABLE NOT IN SYMBOL TABLE - MYREAD”,
</PRE><A NAME="932489"><PRE> READ);
</PRE><A NAME="936198"><PRE>
</PRE><A NAME="936199"><PRE> addr = </a>PD_entry_address(ep);
</PRE><A NAME="936200"><PRE> dims = </a>PD_entry_dimensions(ep);
</PRE><A NAME="936201"><PRE> num = </a>PD_entry_number(ep);
</PRE><A NAME="936202"><PRE> type = </a>PD_entry_type(ep);
</PRE><A NAME="936203"><PRE>
</PRE><A NAME="936204"><PRE> /* with ep in hand, we know the variable type, number of elements,
</PRE><A NAME="936205"><PRE> * dimensions, and disk address
</PRE><A NAME="936206"><PRE> */
</PRE><A NAME="936207"><PRE> .
</PRE><A NAME="936208"><PRE> .
</PRE><A NAME="936209"><PRE> .
</PRE><A NAME="936210"><PRE>
</PRE><A NAME="936211"><PRE> /*-----------------------------------------------------------------*/
</PRE><A NAME="936212"><PRE> /*-----------------------------------------------------------------*/
</PRE><A NAME="936213"><PRE>
</PRE><A NAME="936214"><PRE> _PD_wr_leaf(file, var, nitems, type)
</PRE><A NAME="936215"><PRE> PDBfile *file;
</PRE><A NAME="936216"><PRE> char *var;
</PRE><A NAME="936217"><PRE> long nitems;
</PRE><A NAME="936218"><PRE> char *type;
</PRE><A NAME="936219"><PRE> {char *svar;
</PRE><A NAME="936220"><PRE> int size;
</PRE><A NAME="936221"><PRE> FILE *fp;
</PRE><A NAME="936222"><PRE> defstr *dp;
</PRE><A NAME="936223"><PRE> memdes *desc, *mem_lst;
</PRE><A NAME="936224"><PRE>
</PRE><A NAME="936225"><PRE> fp = file->stream;
</PRE><A NAME="936226"><PRE> .
</PRE><A NAME="936227"><PRE> .
</PRE><A NAME="936228"><PRE> .
</PRE><A NAME="936229"><PRE>
</PRE><A NAME="936230"><PRE> /* dispatch all other writes */
</PRE><A NAME="936231"><PRE> if (file->conversions)
</PRE><A NAME="936232"><PRE> .
</PRE><A NAME="936233"><PRE> .
</PRE><A NAME="936234"><PRE> .
</PRE><A NAME="936235"><PRE>
</PRE><A NAME="932492"><PRE> /* obtain a pointer to the defstr associated with type */
</PRE><A NAME="932493"><PRE> dp = PD_inquire_host_type(file, type);
</PRE><A NAME="932495"><PRE> if (dp == NULL)
</PRE><A NAME="932494"><PRE> PD_error(“BAD TYPE - WR-LEAF”, WRITE);
</PRE><A NAME="936239"><PRE>
</PRE><A NAME="936240"><PRE> /* if the structure has any pointered members loop over the members */
</PRE><A NAME="936241"><PRE> if (dp->n_indirects && ((mem_lst = dp->members) != NULL))
</PRE><A NAME="936242"><PRE> {size = dp->size;
</PRE><A NAME="936243"><PRE> for (svar = var, offset = 0L, i = 0L; i < nitems; i++)
</PRE><A NAME="936244"><PRE> {for (desc = mem_lst; desc != NULL; desc = desc->next)
</PRE><A NAME="936245"><PRE> { ... };
</PRE><A NAME="936246"><PRE> svar += size;};};
</PRE><A NAME="936248"><PRE> .
</PRE><A NAME="936249"><PRE> .
</PRE><A NAME="936250"><PRE> .
</PRE><A NAME="936251"><PRE>
</PRE><A NAME="936252"><PRE> /*-----------------------------------------------------------------*/
</PRE><A NAME="936253"><PRE> /*-----------------------------------------------------------------*/
</PRE><a name="936259">
<h2>9.5 </a>Writing PM_mappings with </a>PFWMAP</h2>
</a>
<a name="936266">
The following fragment shows how to write a </a>PM_mapping to a PDB file from a FORTRAN program. This example uses PFWMAP. PFWMAP writes out both </a>domain and </a>range as a complete mapping. The drawback to this approach is that many mappings might have the same domain which would be written out over and over again. This could lead to unacceptably large data files. See the next example for a more space saving approach.<p>
</a>
<A NAME="936269"><PRE> c
</PRE><A NAME="936270"><PRE> c************************************************************
</PRE><A NAME="936271"><PRE> c************************************************************
</PRE><A NAME="936272"><PRE> c
</PRE><A NAME="936273"><PRE> subroutine sxdmp(namesx, namelen)
</PRE><A NAME="936274"><PRE>
</PRE><A NAME="936275"><PRE> c traverse plot list to make dumps suitable for sx
</PRE><A NAME="936276"><PRE>
</PRE><A NAME="936277"><PRE> integer </a>pfopen, </a>pfclos, </a>pfgerr, </a>pfwmap, </a>pfwset, </a>pfwran
</PRE><A NAME="936278"><PRE> integer zscanleq
</PRE><A NAME="936279"><PRE>
</PRE><A NAME="936280"><PRE> integer pderr(32), rp(6), dp(6)
</PRE><A NAME="936281"><PRE> integer fileid, pim, dmnsn
</PRE><A NAME="936282"><PRE>
</PRE><A NAME="936283"><PRE> double precision rm(nsavept), dm(nsavept)
</PRE><A NAME="936284"><PRE>
</PRE><A NAME="936285"><PRE> c ... set up
</PRE><A NAME="936286"><PRE> .
</PRE><A NAME="936287"><PRE> .
</PRE><A NAME="936288"><PRE> .
</PRE><A NAME="936289"><PRE>
</PRE><A NAME="936290"><PRE> c ... open the file
</PRE><A NAME="936291"><PRE> fileid = </a>pfopen(namelen, namesx, ’w’)
</PRE><A NAME="936292"><PRE> if (fileid .eq. -1) then
</PRE><A NAME="936293"><PRE> iplpderr = </a>pfgerr(nchr, pderr)
</PRE><A NAME="936294"><PRE> call errproc(pderr, nchr, 0, 0)
</PRE><A NAME="936295"><PRE> endif
</PRE><A NAME="936296"><PRE>
</PRE><A NAME="936297"><PRE> pim = 0
</PRE><A NAME="936298"><PRE>
</PRE><A NAME="936299"><PRE> c ... loop over plots
</PRE><A NAME="936300"><PRE> do ...
</PRE><A NAME="936301"><PRE>
</PRE><A NAME="936302"><PRE> c ... setup domain
</PRE><A NAME="936303"><PRE> dname = <domain name>
</PRE><A NAME="936304"><PRE> dp(1) = <length of domain name>
</PRE><A NAME="936305"><PRE>
</PRE><A NAME="936306"><PRE> select case (dmnsn)
</PRE><A NAME="936307"><PRE> case (’d2r1’)
</PRE><A NAME="936308"><PRE> dp(2) = 2
</PRE><A NAME="936309"><PRE> dp(3) = 2
</PRE><A NAME="936310"><PRE> dp(4) = nr
</PRE><A NAME="936311"><PRE> dp(5) = kmax
</PRE><A NAME="936312"><PRE> dp(6) = lmax
</PRE><A NAME="936313"><PRE> call zmovewrd(dm(1), x2d, nr)
</PRE><A NAME="936314"><PRE> call zmovewrd(dm(nr+1), y2d, nr)
</PRE><A NAME="936315"><PRE> case (’d1r1’)
</PRE><A NAME="936316"><PRE> dp(2) = 1
</PRE><A NAME="936317"><PRE> dp(3) = 1
</PRE><A NAME="936318"><PRE> dp(4) = nr
</PRE><A NAME="936319"><PRE> dp(5) = nr
</PRE><A NAME="936320"><PRE> call zmovewrd(dm(1), <domain data>, nr)
</PRE><A NAME="936321"><PRE> endselect
</PRE><A NAME="936322"><PRE>
</PRE><A NAME="936323"><PRE> c ... set up range
</PRE><A NAME="936324"><PRE> rname = <range name>
</PRE><A NAME="936325"><PRE> rp(1) = <length of range name>
</PRE><A NAME="936326"><PRE>
</PRE><A NAME="936327"><PRE> rp(2) = dp(2)
</PRE><A NAME="936328"><PRE> rp(3) = 1
</PRE><A NAME="936329"><PRE> rp(4) = nr
</PRE><A NAME="936330"><PRE> rp(5) = dp(5)
</PRE><A NAME="936331"><PRE> rp(6) = dp(6)
</PRE><A NAME="936332"><PRE> call zmovewrd(rm(1), <range data>, nr)
</PRE><A NAME="936333"><PRE>
</PRE><A NAME="936334"><PRE> c ... write the mapping
</PRE><A NAME="936335"><PRE> ierr = </a>pfwmap(fileid, dname, dp, dm, rname, rp, rm, pim)
</PRE><A NAME="936336"><PRE> if (ierr.eq.0) then
</PRE><A NAME="936337"><PRE> </a>pfgerr(nchr, pderr)
</PRE><A NAME="936338"><PRE> call errproc(pderr, nchr, 0, 0)
</PRE><A NAME="936339"><PRE> endif
</PRE><A NAME="936340"><PRE> pim = pim + 1
</PRE><A NAME="936341"><PRE> repeat
</PRE><A NAME="936342"><PRE>
</PRE><A NAME="936343"><PRE> c ... close the file
</PRE><A NAME="936344"><PRE> icloseok = </a>pfclos(fileid)
</PRE><A NAME="936345"><PRE> if (icloseok.eq.0) then
</PRE><A NAME="936346"><PRE> </a>pfgerr(nchr, pderr)
</PRE><A NAME="936347"><PRE> call errproc(pderr, nchr, 0, 0)
</PRE><A NAME="936348"><PRE> endif
</PRE><A NAME="936349"><PRE>
</PRE><A NAME="936350"><PRE> return
</PRE><A NAME="936351"><PRE> end
</PRE><a name="936356">
<h2>9.6 </a>Writing PM_mappings with </a>PFWSET and </a>PFWRAN</h2>
</a>
<a name="936370">
The following fragment shows how to write a </a>PM_mapping to a PDB file from a FORTRAN program. This example uses </a>PFWSET and </a>PFWRAN. With PFWSET and PFWRAN an application can write mappings in the most space efficient way. Instead of writing the same domains over and over again as would be done with </a>PFWMAP, the application can select the unique domains and write them out with PFWSET. Then all mappings can be written using PFWRAN which writes out a PM_mapping with a null </a>domain. The post processing tools (such as PDBView) reconstruct the complete PM_mapping by looking for the domain as a variable with the same name as the domain component of the mapping name. This approach is clearly a little more involved than using PFWMAP and application developers should weigh the advantages and disadvantages before selecting one method over the other. See the previous example for an illustration of the use of PFWMAP.<p>
</a>
<A NAME="936373"><PRE> c
</PRE><A NAME="936374"><PRE> c************************************************************
</PRE><A NAME="936375"><PRE> c************************************************************
</PRE><A NAME="936376"><PRE> c
</PRE><A NAME="936377"><PRE> subroutine sxdmp(namesx, namelen)
</PRE><A NAME="936378"><PRE>
</PRE><A NAME="936379"><PRE> c traverse plot list to make dumps suitable for sx
</PRE><A NAME="936380"><PRE>
</PRE><A NAME="936381"><PRE> integer </a>pfopen, </a>pfclos, </a>pfgerr, </a>pfwmap, </a>pfwset, </a>pfwran
</PRE><A NAME="936382"><PRE> integer zscanleq
</PRE><A NAME="936383"><PRE>
</PRE><A NAME="936384"><PRE> integer pderr(32), rp(6), dp(6)
</PRE><A NAME="936385"><PRE> integer fileid, pim, dmnsn
</PRE><A NAME="936386"><PRE>
</PRE><A NAME="936387"><PRE> double precision rm(nsavept), dm(nsavept)
</PRE><A NAME="936388"><PRE>
</PRE><A NAME="936389"><PRE> c ... set up
</PRE><A NAME="936390"><PRE> .
</PRE><A NAME="936391"><PRE> .
</PRE><A NAME="936392"><PRE> .
</PRE><A NAME="936393"><PRE>
</PRE><A NAME="936394"><PRE> c ... open the file
</PRE><A NAME="936395"><PRE> fileid = </a>pfopen(namelen, namesx, ’w’)
</PRE><A NAME="936396"><PRE> if (fileid .eq. -1) then
</PRE><A NAME="936397"><PRE> iplpderr = </a>pfgerr(nchr, pderr)
</PRE><A NAME="936398"><PRE> call errproc(pderr, nchr, 0, 0)
</PRE><A NAME="936399"><PRE> endif
</PRE><A NAME="936400"><PRE>
</PRE><A NAME="936401"><PRE> pim = 0
</PRE><A NAME="936402"><PRE>
</PRE><A NAME="936403"><PRE> c ... loop over plots
</PRE><A NAME="936404"><PRE> do ...
</PRE><A NAME="936405"><PRE>
</PRE><A NAME="936406"><PRE> c ... setup domain
</PRE><A NAME="936407"><PRE> dname = <domain name>
</PRE><A NAME="936408"><PRE> dp(1) = <length of domain name>
</PRE><A NAME="936409"><PRE>
</PRE><A NAME="936410"><PRE> select case (dmnsn)
</PRE><A NAME="936411"><PRE> case (’d2r1’)
</PRE><A NAME="936412"><PRE> dp(2) = 2
</PRE><A NAME="936413"><PRE> dp(3) = 2
</PRE><A NAME="936414"><PRE> dp(4) = nr
</PRE><A NAME="936415"><PRE> dp(5) = kmax
</PRE><A NAME="936416"><PRE> dp(6) = lmax
</PRE><A NAME="936417"><PRE> call zmovewrd(dm(1), x2d, nr)
</PRE><A NAME="936418"><PRE> call zmovewrd(dm(nr+1), y2d, nr)
</PRE><A NAME="936419"><PRE> case (’d1r1’)
</PRE><A NAME="936420"><PRE> dp(2) = 1
</PRE><A NAME="936421"><PRE> dp(3) = 1
</PRE><A NAME="936422"><PRE> dp(4) = nr
</PRE><A NAME="936423"><PRE> dp(5) = nr
</PRE><A NAME="936424"><PRE> call zmovewrd(dm(1), <domain data>, nr)
</PRE><A NAME="936425"><PRE> endselect
</PRE><A NAME="936426"><PRE>
</PRE><A NAME="936427"><PRE> if <unique domain> then
</PRE><A NAME="936428"><PRE> ierr = </a>pfwset(fileid, dname, dp, dm)
</PRE><A NAME="936429"><PRE> if (ierr.eq.0) then
</PRE><A NAME="936430"><PRE> iplpderr = </a>pfgerr(nchr, pderr)
</PRE><A NAME="936431"><PRE> call errproc(pderr, nchr, 0, 0)
</PRE><A NAME="936432"><PRE> endif
</PRE><A NAME="936433"><PRE> endif
</PRE><A NAME="936434"><PRE>
</PRE><A NAME="936435"><PRE> c ... set up range
</PRE><A NAME="936436"><PRE> rname = <range name>
</PRE><A NAME="936437"><PRE> rp(1) = <length of range name>
</PRE><A NAME="936438"><PRE>
</PRE><A NAME="936439"><PRE> rp(2) = dp(2)
</PRE><A NAME="936440"><PRE> rp(3) = 1
</PRE><A NAME="936441"><PRE> rp(4) = nr
</PRE><A NAME="936442"><PRE> rp(5) = dp(5)
</PRE><A NAME="936443"><PRE> rp(6) = dp(6)
</PRE><A NAME="936444"><PRE> call zmovewrd(rm(1), <range data>, nr)
</PRE><A NAME="936445"><PRE>
</PRE><A NAME="936446"><PRE> c ... write out range
</PRE><A NAME="936447"><PRE> ierr = </a>pfwran(fileid, dname, dp(1), rname, rp, rm, pim)
</PRE><A NAME="936448"><PRE> if (ierr.eq.0) then
</PRE><A NAME="936449"><PRE> </a>pfgerr(nchr, pderr)
</PRE><A NAME="936450"><PRE> call errproc(pderr, nchr, 0, 0)
</PRE><A NAME="936451"><PRE> endif
</PRE><A NAME="936452"><PRE> pim = pim+1
</PRE><A NAME="936453"><PRE> repeat
</PRE><A NAME="936454"><PRE>
</PRE><A NAME="936455"><PRE> c ... close the file
</PRE><A NAME="936456"><PRE> icloseok = </a>pfclos(fileid)
</PRE><A NAME="936457"><PRE> if (icloseok.eq.0) then
</PRE><A NAME="936458"><PRE> </a>pfgerr(nchr, pderr)
</PRE><A NAME="936459"><PRE> call errproc(pderr, nchr, 0, 0)
</PRE><A NAME="936460"><PRE> endif
</PRE><A NAME="936461"><PRE>
</PRE><A NAME="936462"><PRE> return
</PRE><A NAME="936463"><PRE> end
</PRE><a name="936477">
<h1>10.0 Related </a>Documentation</h1>
</a>
<a name="932583">
PDBLib is one part of a collection of libraries called </a>PACT. PDBLib uses the </a>SCORE library in PACT for memory management, hash table, and string handling support. Interested readers should consult the SCORE manual as well as the PDBView manual, the ULTRA II manual, and the PANACEA manual for more information on how PDBLib is used.<p>
</a>
<a name="933048">
The list of </a>PACT documents is:<p>
</a>
<A NAME="933615"><PRE> PACT User’s Guide, UCRL-MA-112087
</PRE><A NAME="934299"><PRE> SCORE User’s Manual, UCRL-MA-108976 Rev.1
</PRE><A NAME="934300"><PRE> PPC User’s Manual UCRL-MA-108964 Rev.1
</PRE><A NAME="932596"><PRE> PML User’s Manual, UCRL-MA-108965 Rev.1
</PRE><A NAME="932597"><PRE> PDBLib User’s Manual, M-270 Rev.2 (this document)
</PRE><A NAME="932719"><PRE> PGS User’s Manual, UCRL-MA-108966 Rev.1
</PRE><A NAME="934304"><PRE> PANACEA User’s Manual, M-276 Rev.2
</PRE><A NAME="934305"><PRE> ULTRA II User’s Manual, UCRL-MA-108967 Rev.1
</PRE><A NAME="934306"><PRE> PDBDiff User’s Manual, UCRL-MA-108975 Rev.1
</PRE><A NAME="934307"><PRE> PDBView User’s Manual, UCRL-MA-108968 Rev.1
</PRE><A NAME="934308"><PRE> SX User’s Manual, UCRL-MA-112315
</PRE><a name="932582">
<p>
</a>
<p><hr>
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