Builds a PDBFile object from a Structure object.
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__init__(self,
struct,
pdb_file)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature |
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new_atom_serial(self,
atm)
Gets the next available atom serial number for the given atom
instance, and stores a map from atm->atom_serial_num for use when
creating PDB records which require serial number identification of
the atoms. |
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set_from_cifdb(self,
rec,
field,
ctbl,
ccol) |
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add_title_section(self)
HEADER, TITLE, EXPDTA, AUTHOR |
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add_primary_structure_section(self)
DBREF, SEQADV, SEQRES, MODRES |
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add_heterogen_section(self)
HET, HETNAM, HETSYN, FORMUL |
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add_secondary_structure_section(self)
HELIX, SHEET, TURN PDB files do not put separate secondary structure
descriptions within MODEL definitions, so you have to hope the models
do not differ in secondary structure. |
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add_connectivity_annotation_section(self)
SSBOND, LINK, SLTBRG, CISPEP |
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add_miscellaneous_fatures_section(self)
SITE |
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add_crystallographic_coordinate_transformation_section(self)
CRYST1, ORIGXn, SCALEn, MTRIXn, TVECT |
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add_coordinate_section(self)
MODEL, ATOM, SIGATM, ANISOU, SIGUIJ, TER, HETATM, ENDMDL |
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add_atom_records(self)
With a default model set, output all the ATOM and associated records
for the model. |
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add_ATOM(self,
rec_type,
atm)
Adds ATOM/SIGATM/ANISOU/SIGUIJ/TER/HETATM |
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Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__str__ ,
__subclasshook__
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