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

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])
pdb2pqr.cif.author(block)[source]

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])
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])
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])
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])
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
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])
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])
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])
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])
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])
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])
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])
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])
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])
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])