mmLib.PDBBuilder.PDBFileBuilder

Package mmLib :: Module PDBBuilder :: Class PDBFileBuilder

[show private | hide private]

Type PDBFileBuilder

object --+
         |
        PDBFileBuilder

Builds a PDBFile object from a Structure object.

Method Summary
	`__init__(self, struct, pdb_file)`
	`add_ATOM(self, rec_type, atm)` Adds ATOM/SIGATM/ANISOU/SIGUIJ/TER/HETATM
	`add_atom_records(self)` With a default model set, output all the ATOM and associated records for the model.
	`add_connectivity_annotation_section(self)` SSBOND,LINK,SLTBRG,CISPEP
	`add_connectivity_section(self)` CONECT
	`add_coordinate_section(self)` MODEL,ATOM,SIGATM,ANISOU,SIGUIJ,TER,HETATM,ENDMDL
	`add_crystallographic_coordinate_transformation_section(self)` CRYST1,ORIGXn,SCALEn,MTRIXn,TVECT
	`add_heterogen_section(self)` HET,HETNAM,HETSYN,FORMUL
	`add_miscellaneous_fatures_section(self)` SITE
	`add_primary_structure_section(self)` DBREF,SEQADV,SEQRES,MODRES
	`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.
	`add_title_section(self)` HEADER, TITLE, EXPDTA, AUTHOR
	`bookkeeping_section(self)` MASTER,END
	`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.
	`next_serial_number(self)`
	`set_from_cifdb(self, rec, field, ctbl, ccol)`
Inherited from object
	`__delattr__(...)` x.__delattr__('name') <==> del x.name
	`__getattribute__(...)` x.__getattribute__('name') <==> x.name
	`__hash__(x)` x.__hash__() <==> hash(x)
	`__new__(T, S, ...)` T.__new__(S, ...) -> a new object with type S, a subtype of T
	`__reduce__(...)` helper for pickle
	`__reduce_ex__(...)` helper for pickle
	`__repr__(x)` x.__repr__() <==> repr(x)
	`__setattr__(...)` x.__setattr__('name', value) <==> x.name = value
	`__str__(x)` x.__str__() <==> str(x)

Method Details

add_ATOM(self, rec_type, atm)

Adds ATOM/SIGATM/ANISOU/SIGUIJ/TER/HETATM

add_atom_records(self)

With a default model set, output all the ATOM and associated records for the model.

add_connectivity_annotation_section(self)

SSBOND,LINK,SLTBRG,CISPEP

add_connectivity_section(self)

CONECT

add_coordinate_section(self)

MODEL,ATOM,SIGATM,ANISOU,SIGUIJ,TER,HETATM,ENDMDL

add_crystallographic_coordinate_transformation_section(self)

CRYST1,ORIGXn,SCALEn,MTRIXn,TVECT

add_heterogen_section(self)

HET,HETNAM,HETSYN,FORMUL

add_miscellaneous_fatures_section(self)

SITE

add_primary_structure_section(self)

DBREF,SEQADV,SEQRES,MODRES

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. 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.

add_title_section(self)

HEADER, TITLE, EXPDTA, AUTHOR

bookkeeping_section(self)

MASTER,END

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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