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)
- 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.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.
- 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])