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bool OEReadPDBFile(oemolistream &ifs, OEMolBase &mol,
unsigned int flavor = OEPDBIFlag::DEFAULT)
Read a molecule from the specified input stream, ifs, in Brookhaven PDB file format. A number of different PDB format variants are supported by the use of the bits in the ``flavor'' parameter. This function returns true if the operation was successful, and false if an end-of-file was encountered.
The OEPDBIFlag::TER, OEPDBIFlag::END and
OEPDBIFlag::ENDM flags are used
to inform the OEChem PDB file reader of the records used to separate
consecutive molecules in a single PDB file. The flags correspond to
the PDB file format's TER, END and ENDMOD records respectively. If all
of these flags are turned off, all of the ATOM and HETATM records in a
single PDB file will be read into a single OEMolBase. By default, only
OEPDBIFlag::END and OEPDBIFlag::ENDM are on (and
OEPDBIFlag::TER is off),
meaning that different chains are read into the a single molecule, but
different NMR models and concatenated PDB files are treated as sequential
molecules.
The OEPDBIFlag::ALL flag is used to indicate that all of the
atom records in the input file should be read into the OEMolBase. By
default, the OEReadPDBFile function ignores/omits ATOM and HETATM
records that represent pseudo or dummy atoms and/or alternate conformations.
Without OEPDBIFlag::ALL, the PDB file reader ignores all atoms whose
alternate location indicator is other than ' ', A or 1,
all atoms with atom names begining " Q", all atoms with residue name
"DUM", and all atoms with co-ordinates 9999.000, 9999.000, 9999.000
(as used by XPLOR/CNS to represent dummy atoms).
The OEPDBIFlag::DATA flag is used to instruct the OEChem PDB file
reader to preserve the PDB file's header data in the OEMolBase's generic
data. This option currently preserves AUTHOR, CAVEAT, COMPND, CRSYT1,
EXPDTA, FORMUL, HEADER, HELIX, HET, HETNAM, HETSYM, JRNL, KEYWDS, MODRES,
OBSLTE, ORIGX1, ORIGX2, ORIGX3, REMARK, REVDAT, SCALE1, SCALE2, SCALE3,
SEQRES, SHEET, SITE, SOURCE, SPRSDE, SSBOND, TITLE and TURN records.
Note that modifying or reordering the molecule may invalidate the atom
serial numbers used in some of the PDB records.
The OEPDBIFlag::CHARGE flag is used to indicate that the contents
of the b-factor column in the input PDB file contains a partial charge,
and should be stored in the `partial charge' property of an atom, instead
of the `b-factor' property. This value can then be retrieved using the
OEAtomBase::GetPartialCharge method.
The OEPDBIFlag::RADIUS flag is used to indicate the the contents
of the occupancy column in the input PDB file contains a radius, and
should be stored in the `radius' property of an atom instead of the
`occupancy' property. This value can then be retrieved using the
OEAtomBase::GetRadius method.
The OEPDBIFlag::DELPHI flag is just the combination of the
OEPDBIFlag::CHARGE and OEPDBIFlag::RADIUS flags above.
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