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/*
o-------------------------------------------------------------------o
| |
| Copyright (C) 2000 Damir Zucic |
| |
| This program is free software; you can redistribute it and/or |
| modify it under the terms of the GNU General Public License |
| as published by the Free Software Foundation, version 2. |
| |
| This program is distributed in the hope that it will be useful, |
| but WITHOUT ANY WARRANTY; without even the implied warranty of |
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| GNU General Public License for more details. |
| |
| You should have received a copy of the GNU General Public License |
| along with this program; if not, write to the |
| Free Software Foundation, Inc., |
| 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
| |
o-------------------------------------------------------------------o
*/
/*=============================================================================
garlic.c
Molecular visualization and analyzing tool
General description:
Garlic is molecular visualization program written for investigation
of membrane proteins. It may be used to visualize other proteins,
as well as some geometric objects. The name should has something to
do with the structure and operation of this program. This version
of garlic recognizes PDB format version 2.1; see pdb_atom.c for
details about this format.
Author:
Damir Zucic (zucic@pref.etfos.hr), University of Osijek, Croatia.
-------------------------------------------------------------------------------
Naming conventions:
(1) xxx_yyy Simple variable; lowercase, underline separates
adjacent words.
(2) xxx_yyyI Index (array index usually).
(3) xxx_yyyN Number of array elements.
(4) xxx_yyyID Identifier (integer or long integer).
(5) xxx_yyyF Flag (usually integer, value 0 or 1).
(6) XxxYyyS New data type (typedef struct XxxYyyS).
(7) xxx_yyyS Structure (type: XxxYyyS).
(8) xxx_yyyP Pointer.
(9) xxx_yyySP Pointer to structure.
(10) xxx_yyyA[] Array; no space before left bracket.
(11) xxx_yyyAA[][] Two dimensional array.
(12) xxx_yyySA[] Array of structures.
(13) xxx_yyyPA[] Array of pointers.
(14) XXXYYYZZZ Symbol (#define).
(15) XxxYyy_ () Function; the first character in each word is in
uppercase; the last character is underline; one
space (exactly one!) used to separate underline
and left parenthesis; underline is not used to
separate words.
(16) xxx_yyyGC Graphics context (pointer to _XGC structure).
Programming style:
When this project was started RAM and hard disk became quite cheap.
Thus:
(1) Whenever choosing between brute force and intelligence, choose
force: it is cheaper, simpler and more reliable. Of course, use
brain if there is no other choice.
(2) Comment everything, including trivial things, so that hackers
find this program disgusting.
(3) Never put two functions in the same file, even if it seems to
be reasonable.
(4) Use verbose function and variable names.
(5) Indentation is one tab (eight characters), except in functions
which draw atoms and bonds (four characters).
(6) Each brace should be placed in a separate line.
(7) Avoid global scope data.
(8) Use auxiliary structures when some function requires a lot of
input data. Pass pointer to the structure to this function,
instead of a large number of arguments.
Portability:
Garlic should be ANSI C and/or POSIX compliant. All functions fit
into one of these standards:
(1) ANSI C programming language.
(2) Xlib, X Window System (X11R6).
Development platform:
Pentium MMX 166 MHz, 128 MB RAM, running Linux Slackware 3.4, with
updated kernel (version 2.0.34). Compiled with GNU C compiler
(version 2.7.2.3).
History:
(1) 30.09.1998 Created (and forgotten).
(2) 27.12.1998 Project reactivated.
(3) 14.01.1999 Heavily redesigned.
(4) 16.01.1999 I got the idea that this program may be
used for more general purpose than molec.
visualization.
(5) 12.01.2000 Capable to load more than one molecule. Few
commands implemented (quit, load, discard).
From /usr/games/fortunes/fortunes file (Linux Slackware 3.4):
"What garlic is to food, insanity is to art."
-------------------------------------------------------------------------------
Purpose of this file:
The main function is in this file. The real job is done by called
functions.
Return value / exit status:
(1) EXIT_SUCCESS on success.
(2) EXIT_FAILURE on failure.
(3) EXIT_SUCCESS if help, version info or regist. required.
========includes:============================================================*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <X11/Xlib.h>
#include <X11/Xutil.h>
#include <X11/Xos.h>
#include <X11/Xatom.h>
#include "defines.h"
#include "typedefs.h"
/*======defines:=============================================================*/
/* See defines.h for symbols, there is nothing here! */
/*======function prototypes:=================================================*/
void PrintUsage_ (void);
void PrintHelp_ (void);
void PrintVersion_ (void);
int Register_ (void);
void ErrorMessage_ (char *, char *, char *,
char *, char *, char *, char *);
void WarningMessage_ (char *, char *, char *,
char *, char *, char *, char *);
GUIS *AllocateGUIS_ (void);
ConfigS *AllocateConfigS_ (void);
MolComplexS *AllocateMolComplexSA_ (size_t);
void FreeMemory_ (GUIS *, MolComplexS *, int, NearestAtomS *);
int ReadConfig_ (ConfigS *);
int ExtractArgs_ (ConfigS *, GUIS *, char *, int, char **);
void PrintCursorNames_ (void);
int DisplayInit_ (GUIS *);
int DisplayColorCapabilities_ (GUIS *);
int ParseOptions_ (GUIS *, ConfigS *);
int CreateWindows_ (GUIS *, ConfigS *, int, char **);
int CalculateParameters_ (ConfigS *, GUIS *);
void PrintConfig_ (ConfigS *, GUIS *);
int LoadComplex_ (MolComplexS *, int *, int *,
char *, ConfigS *, GUIS *);
NearestAtomS *AllocateNearest_ (size_t *, GUIS *);
void InitNearest_ (NearestAtomS *, size_t);
int ColorSchemes_ (MolComplexS *, int, GUIS *, char *);
int IdentifyButton_ (XButtonEvent *);
int EventLoop_ (MolComplexS *, int *, int *,
NearestAtomS **, size_t *, ConfigS *, GUIS *);
/*======main:================================================================*/
int main (int argc, char *argv[])
{
int mainI = 0; /* Positive on success */
int n; /* Auxiliary integer */
static GUIS *guiSP; /* See typedefs.h */
static ConfigS *configSP; /* Read from .garlicrc */
static char mol_file_nameA[STRINGSIZE]; /* Input file name */
static MolComplexS *mol_complexSP; /* Macromolecular data */
int mol_complexesN = 0; /* Number of mol. complexes */
int next_mol_complexID = 1; /* Initial value should be 1 */
static NearestAtomS *nearest_atomSP; /* Replaces depth sorting */
size_t pixelsN; /* The number of pixels */
/* Write brief introduction - if requested - and exit: */
for (n = 0; n < argc; n++)
{
if ((strcmp (argv[n], "-h") == 0) ||
(strcmp (argv[n], "--help") == 0) ||
(strcmp (argv[n], "-help") == 0))
{
PrintHelp_ ();
exit (EXIT_SUCCESS);
}
}
/* Print version information - if requested - and exit: */
for (n = 0; n < argc; n++)
{
if ((strcmp (argv[n], "-v") == 0) ||
(strcmp (argv[n], "--version") == 0))
{
PrintVersion_ ();
exit (EXIT_SUCCESS);
}
}
/* Register user (send e-mail to the author) - if requested - and exit: */
for (n = 0; n < argc; n++)
{
if ((strcmp (argv[n], "-r") == 0) ||
(strcmp (argv[n], "--register") == 0))
{
Register_ ();
exit (EXIT_SUCCESS);
}
}
/* Formal, single pass loop (many things happen here): */
do
{
/* Allocate memory for GUI data: */
mainI--;
guiSP = AllocateGUIS_ ();
if (guiSP == NULL) break;
/* Initialize the main window drawing mode index: */
mainI--;
guiSP->main_window_modeI = 0;
/* Allocate memory for configuration data: */
mainI--;
configSP = AllocateConfigS_ ();
if (configSP == NULL) break;
/* Allocate memory for macromolecular data: */
mainI--;
mol_complexSP = AllocateMolComplexSA_ (MAXCOMPLEXES);
if (mol_complexSP == NULL) break;
/* Read configuration from $HOME.garlicrc file: */
mainI--;
n = ReadConfig_ (configSP);
/* Extract command line arguments: */
mainI--;
n = ExtractArgs_ (configSP, guiSP, mol_file_nameA, argc, argv);
if (n < 0) break;
/* Print cursor names and exit on request: */
mainI--;
if (configSP->print_cursor_namesF)
{
PrintCursorNames_ ();
break;
}
/* Display related initializations: */
mainI--;
n = DisplayInit_ (guiSP);
if (n < 0)
{
PrintUsage_ ();
fprintf (stderr, "\nUnable to connect to X server,");
fprintf (stderr, " exiting ...\n");
break;
}
/* Color properties of a display: */
mainI--;
n = DisplayColorCapabilities_ (guiSP);
if (n < 0) break;
/* Parse options which require connection to X server: */
mainI--;
n = ParseOptions_ (guiSP, configSP);
if (n < 0) break;
/* Create windows: */
mainI--;
n = CreateWindows_ (guiSP, configSP, argc, argv);
if (n < 0) break;
/* Calculate the remaining parameters: */
mainI--;
n = CalculateParameters_ (configSP, guiSP);
if (n < 0) break;
/* Load macromolecular complex if input file name is specified: */
mainI--;
LoadComplex_ (mol_complexSP, &mol_complexesN, &next_mol_complexID,
mol_file_nameA, configSP, guiSP);
/* Print configuration data, if requested: */
mainI--;
if (configSP->print_configF)
{
PrintConfig_ (configSP, guiSP);
mainI *= -1;
break;
}
/* Allocate the array of NeareastAtomS structures: */
mainI--;
nearest_atomSP = AllocateNearest_ (&pixelsN, guiSP);
if (nearest_atomSP == NULL) break;
/* Initialize the array of NearestAtomS structures: */
InitNearest_ (nearest_atomSP, pixelsN);
/* Prepare the simple color schemes: */
mainI--;
ColorSchemes_ (mol_complexSP, mol_complexesN, guiSP, "dummy");
/* Define dummy buttons in control window: */
mainI--;
IdentifyButton_ ((XButtonEvent *) NULL);
/* Take and process events: */
mainI--;
n = EventLoop_ (mol_complexSP, &mol_complexesN, &next_mol_complexID,
&nearest_atomSP, &pixelsN, configSP, guiSP);
if (n < 0) break;
/* If this point is reached, everything worked */
/* fine; change the sign of mainI to positive: */
mainI *= -1;
} while (0);
/* Free storage used for pixmaps and other data: */
FreeMemory_ (guiSP, mol_complexSP, mol_complexesN, nearest_atomSP);
/* Close connection to X server: */
if (guiSP->displaySP) XCloseDisplay (guiSP->displaySP);
/* Free the array of MolComplexS structures: */
if (mol_complexSP) free (mol_complexSP);
/* Free ConfigS structure: */
if (configSP) free (configSP);
/* Free GUIS structure: */
if (guiSP) free (guiSP);
/* Close log file if used at all: */
if (configSP->log_fileP != NULL) fclose (configSP->log_fileP);
/* Return on failure: */
if (mainI < 0) return (EXIT_FAILURE);
/* Return on success: */
return (EXIT_SUCCESS);
}
/*===========================================================================*/
|