conkit.io.pdb module

Parser module specific to Pdb files

ATOM

alias of conkit.io.pdb.Atom

class GenericStructureParser[source]

Bases: conkit.io._parser.ContactFileParser

Parent class to parse a PDB file and extract distance restraints as residue-residue contacts

class MmCifParser[source]

Bases: conkit.io.pdb.GenericStructureParser

Class to parse a mmCIF file and extract distance restraints as residue-residue contacts

read(f_handle, f_id='mmcif', distance_cutoff=8, atom_type='CB')[source]

Read a contact file

Parameters:
  • f_handle – Open file handle [read permissions]
  • f_id (str, optional) – Unique contact file identifier
  • distance_cutoff (int, optional) – Distance cutoff for which to determine contacts [default: 8]
  • atom_type (str, optional) – Atom type between which distances are calculated [default: CB]
Returns:
Return type:

ContactFile
write(f_handle, hierarchy)[source]

Write a contact file instance to to file

Parameters:
Raises:

NotImplementedError – Write function not available
class PdbParser[source]

Bases: conkit.io.pdb.GenericStructureParser

Class to parse a PDB file and extract distance restraints as residue-residue contacts

read(f_handle, f_id='pdb', distance_cutoff=8, atom_type='CB')[source]

Read a contact file

Parameters:
  • f_handle – Open file handle [read permissions]
  • f_id (str, optional) – Unique contact file identifier
  • distance_cutoff (int, optional) – Distance cutoff for which to determine contacts [default: 8]
  • atom_type (str, optional) – Atom type between which distances are calculated [default: CB]
Returns:
Return type:

ContactFile
write(f_handle, hierarchy)[source]

Write a contact file instance to to file

Parameters:
Raises:

NotImplementedError – Write function not available