Package mmLib :: Module PDBBuilder :: Class PDBFileBuilder
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Class PDBFileBuilder

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object --+
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        PDBFileBuilder

Builds a PDBFile object from a Structure object.

Instance Methods [hide private]
 
__init__(self, struct, pdb_file)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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next_serial_number(self) source code
 
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) source code
 
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_connectivity_section(self)
CONECT
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bookkeeping_section(self)
MASTER, END
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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__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, struct, pdb_file)
(Constructor)

source code 

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

add_secondary_structure_section(self)

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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. mmLib allows separate MODELs to have different secondary structure, but one MODEL must be chosen for the PDF file, so the default Model of the Structure is used.