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void OEWritePDBFile(oemolostream &ofs, OEMolBase &mol,
unsigned int flavor = OEPDBOFlag::DEFAULT)
Write the molecule as a Brookhaven PDB format file to the output stream ofs. A number of different PDB format variants are supported by use of the bits in the ``flavor'' parameter.
The OEPDBOFlag::BONDS flag is used to control whether the OEChem
PDB file writer includes CONECT records to describe the connectivity of
the molecule. If this flag is given without OEPDBOFlag::ORDERS
all bonds are written as ``single'' bonds. OEPDBOFlag::BONDS is
off by default.
The OEPDBOFlag::ORDERS flag is used to control whether the PDB file
writer should use repeated CONECT records to represent multiple bond
orders (i.e. double and triple bonds). If this flag is given without
OEPDBOFlag::BONDS only double and triple bonds are written to the
file. OEPDBOFlag::ORDERS is off by default.
The OEPDBOFlag::BOTH flag is used to control whether CONECT records
are written bi-directionally. Conventionally, PDB files list connect records
both from source atom to destination atom, and again from destination to
source. This duplication doubles the number/size of CONECT records with
redundant information, as most readers (if they honor CONECT records at
all) can work with uni-directional CONECT records. By default, OEChem's
PDB writer only output uni-directional CONECT records where the source
atom's serial number is always less than the destination atom's. The
OEPDBOFlag::BOTH can be used to request full bi-directional PDB files.
The OEPDBOFlag::CHARGE flag can be used to instruct the OEChem PDB
file writer to take the value for the PDB file's B-factor field from the
atom's partial charge property. A number of applications, including
Delphi, (ab)use the PDB file format specification to store atomic
partial charges in the b-factor field rather instead of crystallographically
determined anisotropic temperature factors. OEPDBOFlag::CHARGE is
off by default.
The OEPDBOFlag::RADIUS flag can be used to instruct the OEChem PDB
file writer to take the value for the PDB file's occupancy field from the
atom's radius property. A number of applications, including Delphi,
(ab)use the PDB file format specification to store radii in the occupancy
field rather instead of crystallographically determined anisotropic
occupancies. OEPDBOFlag::RADIUS is off by default.
The OEPDBOFlag::DELPHI flag is just the combination of the
OEPDBOFlag::CHARGE and OEPDBOFlag::RADIUS flags.
The OEPDBOFlag::TER flag can be used to instruct the OEChem PDB file
writer to terminate each connection table with a TER record rather than
an END record. Some dubious molecular graphics software, such as Grasp,
requires that multiple compounds be separated by the chain/fragment
separator TER, rather than the molecule separator END.
OEPDBOFlag::TER is off by default.
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