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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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])