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/*! \mainpage Clipper-MMDB interface.
MMDB is a powerful package for the storage and manipulation of atomic
coordinate models, by E. Krissinel. Full documentation for the MMDB
package is available here: http://msd.ebi.ac.uk/~keb/cldoc/
The Clipper-MMDB interface package provides an interface to allow MMDB
models to interact with other types of crystallographic data as part
of a structure solution application. It is designed to be minimally
intrusive on both packages, so that either package may be used alone,
or in conjunction with other software.
The most common interactions between atomic models, structure factors,
maps, and masks come in the form of the generation of structure
factors, electron density and masks from a model. For these purposes,
most of the information in an atomic model (e.g. bonding, residue
types), is redundant; all we need is a list of atomic coordinates,
elements, occupancies and temperature factors (U-values). These are
handled by the Clipper classes clipper::Atom and clipper::Atom_list.
MMDB describes atom lists in terms of an array of pointers to atoms,
and a count (of types PPCAtom and int). These are commonly generated
using a selection function to select some portion of the stored atomic
model.
The main component of the Clipper-MMDB interface is therefore a class
which communicated atom lists from one package to the other.
\section s_mmdb_atom_list The clipper::MMDBAtom_list class.
The clipper::MMDBAtom_list class is a trivial derivation of the
clipper::Atom_list class which can be constructed from an MMDB atom
list. This involves extracting all the relevant information from MMDB
and building a new list of clipper::Atom objects, but this list is
both small and quickly created in comparison to any purpose for which
it will be used. The clipper::MMDBAtom_list class may be used
wherever a clipper::Atom_list would be used, e.g. in a structure
factor calculation.
A typical usage is therefore as follows:
- Perform an atom selection in MMDB using the MMDB selection functions.
- Call the MMDB GetSelIndex() method to return a PPCAtom and a count.
- Give these to the constructor of clipper::MMDBAtom_list.
- Use the resulting atom list in Clipper.
For example, the following code reads a PDB file from disk, selects
all the atoms from the model, and uses them to perform a structure
factors calculation:
\code
/* mmdb part of the calculation */
CMMDBManager mmdb;
mmdb.ReadPDBASCII( "input.pdb" ); // read pdb file
int hndl = mmdb.NewSelection(); // make selection handle
mmdb.SelectAtoms( hndl, 0, 0, SKEY_NEW ); // select all atoms
PPCAtom psel;
int nsel;
mmdb.GetSelIndex( hndl, psel, nsel ); // get the selection
/* Clipper part of the calculation */
clipper::HKL_info hkls; // make reflection lists for result
/* *********************************************************** */
/* NOTE: we need to initialise the reflection list 'hkls' here */
/* *********************************************************** */
clipper::HKL_data<clipper::data32::F_phi> fphi(hkls); // and data list
clipper::MMDBAtom_list atoms( psel, nsel ); // make atom list
clipper::SFcalc_aniso_fft<float>( fphi, atoms ); // and do SF calc
\endcode
Note that we have assumed that the reflection list has been
initialised in the intervening code. For this, spacegroup and cell
information are required. If that information is to be obtained from
the PDB file from MMDB, some additional functions are required, which
will be described below.
\section s_mmdb_other Other Classes.
Sometimes we need to communicate other information between Clipper and
MMDB. For example, as above, we may want to use the spacegroup or cell
information from MMDB in Clipper.
For this purpose, additional classes are provided. In every case,
these are trivial derivations of MMDB classes (i.e. adding no
additional data members), which simply add additional functions for
communicating information to or from MMDB in terms of Clipper
types. The following classes are provided:
- clipper::MMDBManager derives from CMMDBManager
- clipper::MMDBModel derives from CModel
- clipper::MMDBChain derives from CChain
- clipper::MMDBResidue derives from CResidue
- clipper::MMDBAtom derives from CAtom
Of these, the clipper::MMDBManager and clipper::MMDBAtom classes are
probably the most useful.
Since these classes are trivial derivations, you can safely cast a
pointer or reference to your MMDB object to the derived type in order
to gain access to the addition methods. C and C++ casts are
permissible, although the C++ static_cast mechanism provides better
type safety.
\subsection ss_mmdb_manager The clipper::MMDBManager class.
This provides 4 additional methods in addition to the MMDB
version. These are used for getting and setting the cell and
spacegroup information. They are:
- clipper::MMDBManager::spacegroup()
- clipper::MMDBManager::cell()
- clipper::MMDBManager::set_spacegroup( const Spacegroup& )
- clipper::MMDBManager::set_cell( const Cell& )
The first two return the spacegroup and cell from MMDB, and the last
two set the spacegroup and cell.
When fetching the MMDB spacegroup, if the operators are present then
these will be used to determine the Clipper spacegroup. If the
operators are missing, the spacegroup name will be used. When setting
the spacegroup the name is always set, however the operators will only
be set if MMDB recognizes the Clipper spacegroup name.
Therefore, to return a clipper::Cell from a PDB file, the
following code is used:
\code
CMMDBManager mmdb;
mmdb.ReadPDBASCII( "input.pdb" ); // read pdb file
clipper::Cell cell = static_cast<clipper::MMDBManager&>(mmdb).cell();
\endcode
(Alternatively, if we created a clipper::MMDBManager in the first place,
no cast would be required.)
The following example shows how a reference to the CMMDBManager in the
structure factor calculation above could be cast to return the
spacegroup and cell information.
\code
clipper::MMDBManager& cmmdb = static_cast<clipper::MMDBManager&>( mmdb );
hkls.init( cmmdb.spacegroup(), cmmdb.cell(), clipper::Resolution(2.0) );
\endcode
\subsection ss_mmdb_atom The clipper::MMDBAtom class.
The clipper::MMDBAtom class is used in exactly the same way as the
previous class to obtain access to atom properties as Clipper data
items. For example, given a pointer to an MMDB CAtom, the coordinates,
occupancy and anisotropic U could be extracted as follows:
\code
PCAtom atom;
/* set the atom pointer here */
clipper::MMDBAtom* catom = static_cast<clipper::MMDBAtom*>( atom );
clipper::Coord_orth coord = catom->coord_orth();
double occup = catom->occupancy();
clipper::U_aniso_orth uanis = catom->u_aniso_orth();
\endcode
If the requested property of the MMDB atom is not set, then the
corresponding Clipper object will be set to its null state, which is
tested by the corresponding is_null method,
e.g. clipper::Coord_orth::is_null(). In the case of numeric
properties, if they are missing the result will be NaN, testable by
the clipper::Util::is_nan() method.
Write accessors ('set' methods) are also provided for all properties
where MMDB permits. Null objects will be translated to unset
properties in MMDB.
*/
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