cif
¶
CIF parsing methods.
This methods use the pdbx/cif parser provided by WWPDB (http://mmcif.wwpdb.org/docs/sw-examples/python/html/index.html)
Code author: Juan Brandi
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pdb2pqr.cif.
atom_site
(block)[source]¶ Handle ATOM_SITE block.
Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions. (Source: https://j.mp/2Zprx41)
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.ATOM objects, array of things that weren’t handled by parser) Return type: ([Atom], [str])
Handle AUTHOR block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
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pdb2pqr.cif.
cispep
(block)[source]¶ Handle CISPEP block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
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pdb2pqr.cif.
compnd
(block)[source]¶ Handle COMPND block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
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pdb2pqr.cif.
conect
(block)[source]¶ Handle CONECT block.
Data items in the STRUCT_CONN category record details about the connections between portions of the structure. These can be hydrogen bonds, salt bridges, disulfide bridges and so on.
The
STRUCT_CONN_TYPE
records define the criteria used to identify these connections. (Source: https://j.mp/3gPkJT5)Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
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pdb2pqr.cif.
count_models
(block)[source]¶ Count models in structure file block.
Parameters: block ([str]) – PDBx data block Returns: number of models in block Return type: int
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pdb2pqr.cif.
cryst1
(block)[source]¶ Handle CRYST1 block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
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pdb2pqr.cif.
expdata
(block)[source]¶ Handle EXPDTA block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
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pdb2pqr.cif.
header
(block)[source]¶ Handle HEADER block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
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pdb2pqr.cif.
keywds
(block)[source]¶ Handle KEYWDS block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
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pdb2pqr.cif.
origxn
(block)[source]¶ Handle ORIGXn block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
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pdb2pqr.cif.
read_cif
(cif_file)[source]¶ Parse CIF-format data into array of Atom objects.
Todo
Manage several blocks of data.
Parameters: file (file) – open file-like object Returns: (a dictionary indexed by PDBx/CIF record names, a list of record names that couldn’t be parsed) Return type: (dict, [str])
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pdb2pqr.cif.
scalen
(block)[source]¶ Handle SCALEn block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
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pdb2pqr.cif.
source
(block)[source]¶ Handle SOURCE block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
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pdb2pqr.cif.
ssbond
(block)[source]¶ Handle SSBOND block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])
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pdb2pqr.cif.
title
(block)[source]¶ Handle TITLE block.
Parameters: block ([str]) – PDBx data block Returns: (array of pdb.conect objects, array of things that did not parse) Return type: ([pdb.CONECT], [str])