conkit.io.pdb module¶
Parser module specific to Pdb files
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ATOM
¶ alias of
conkit.io.pdb.Atom
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class
GenericStructureParser
[source]¶ Bases:
conkit.io._parser.ContactFileParser
Parent class to parse a PDB file and extract distance restraints as residue-residue contacts
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class
MmCifParser
[source]¶ Bases:
conkit.io.pdb.GenericStructureParser
Class to parse a mmCIF file and extract distance restraints as residue-residue contacts
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read
(f_handle, f_id='mmcif', distance_cutoff=8, atom_type='CB')[source]¶ Read a contact file
Parameters: Returns: Return type:
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write
(f_handle, hierarchy)[source]¶ Write a contact file instance to to file
Parameters: - f_handle – Open file handle [write permissions]
- hierarchy (
ContactFile
,ContactMap
) – orContact
Raises: NotImplementedError
– Write function not available
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class
PdbParser
[source]¶ Bases:
conkit.io.pdb.GenericStructureParser
Class to parse a PDB file and extract distance restraints as residue-residue contacts
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read
(f_handle, f_id='pdb', distance_cutoff=8, atom_type='CB')[source]¶ Read a contact file
Parameters: Returns: Return type:
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write
(f_handle, hierarchy)[source]¶ Write a contact file instance to to file
Parameters: - f_handle – Open file handle [write permissions]
- hierarchy (
ContactFile
,ContactMap
) – orContact
Raises: NotImplementedError
– Write function not available
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