conkit.io.pdb module

Parser module specific to Pdb files

ATOM

alias of Atom

class GenericStructureParser[source]

Bases: conkit.io._parser.ContactFileParser

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

Methods

read()
write()
class MmCifParser[source]

Bases: conkit.io.pdb.GenericStructureParser

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

Methods

read(f_handle[, f_id, distance_cutoff, …]) Read a contact file
write(f_handle, hierarchy) Write a contact file instance to to file
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:

ContactFile
write(f_handle, hierarchy)[source]

Write a contact file instance to to file

Parameters:

f_handle

Open file handle [write permissions]

hierarchy : ContactFile, ContactMap
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

Methods

read(f_handle[, f_id, distance_cutoff, …]) Read a contact file
write(f_handle, hierarchy) Write a contact file instance to to file
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:

ContactFile
write(f_handle, hierarchy)[source]

Write a contact file instance to to file

Parameters:

f_handle

Open file handle [write permissions]

hierarchy : ContactFile, ContactMap
Raises:

NotImplementedError

Write function not available