molecupy.converters.pdbdatafile2model (PDB Data File to Model)

This module handles the logic of converting a PdbDataFile to a Model

molecupy.converters.pdbdatafile2model.model_from_pdb_data_file(data_file, model_id=1)[source]

Takes a PdbDataFile, converts it to a Model, and returns it.

PdbDataFile objects can contain multiple models. By default, model 1 will be used, but you can specify specific models with the model_id argument.

Parameters:
  • data_file (PdbDataFile) – The PdbDataFile to convert.
  • model_id (int) – The ID of the model in the data fileto be used for conversion.
Return type:

Model
molecupy.converters.pdbdatafile2model.add_small_molecules_to_model(model, data_file, model_id)[source]

Takes a Model and creates SmallMolecule objects in it based on the heteroatoms in the provided PdbDataFile.

Parameters:
  • model (Model) – the model to update.
  • data_file (PdbDataFile) – The source Pdb Data File
  • model_id (int) – The ID of the model in the data fileto be used for conversion.
molecupy.converters.pdbdatafile2model.add_chains_to_model(model, data_file, model_id)[source]

Takes a Model and creates Chain objects in it based on the atoms in the provided PdbDataFile.

Parameters:
  • model (Model) – the model to update.
  • data_file (PdbDataFile) – The source Pdb Data File
  • model_id (int) – The ID of the model in the data fileto be used for conversion.
molecupy.converters.pdbdatafile2model.connect_atoms(model, data_file, model_id)[source]

Takes a Model and creates Bond objects between atoms in it based on the connections in the provided PdbDataFile.

Parameters:
  • model (Model) – the model to update.
  • data_file (PdbDataFile) – The source Pdb Data File
  • model_id (int) – The ID of the model in the data fileto be used for conversion.
molecupy.converters.pdbdatafile2model.bond_residue_atoms(model, data_file, model_id)[source]

Takes a Model and creates Bond objects within the residues of the Model, based on a pre-defined dictionary of how residues are connected internally.

Parameters:
  • model (Model) – the model to update.
  • data_file (PdbDataFile) – The source Pdb Data File
  • model_id (int) – The ID of the model in the data fileto be used for conversion.
molecupy.converters.pdbdatafile2model.bond_residues_together(model, data_file, model_id)[source]

Takes a Model and creates Bond objects between the residues of chains in the model.

Parameters:
  • model (Model) – the model to update.
  • data_file (PdbDataFile) – The source Pdb Data File
  • model_id (int) – The ID of the model in the data fileto be used for conversion.
molecupy.converters.pdbdatafile2model.make_disulphide_bonds(model, data_file, model_id)[source]

Takes a Model and creates disulphide Bond objects in it based on the ss_bonds in the provided PdbDataFile.

Parameters:
  • model (Model) – the model to update.
  • data_file (PdbDataFile) – The source Pdb Data File
  • model_id (int) – The ID of the model in the data fileto be used for conversion.

Takes a Model and creates specified Bond objects in it based on the links in the provided PdbDataFile.

Parameters:
  • model (Model) – the model to update.
  • data_file (PdbDataFile) – The source Pdb Data File
  • model_id (int) – The ID of the model in the data fileto be used for conversion.
molecupy.converters.pdbdatafile2model.give_model_sites(model, data_file, model_id)[source]

Takes a Model and creates BindSite objects in it based on the sites in the provided PdbDataFile.

Parameters:
  • model (Model) – the model to update.
  • data_file (PdbDataFile) – The source Pdb Data File
  • model_id (int) – The ID of the model in the data fileto be used for conversion.
molecupy.converters.pdbdatafile2model.map_sites_to_ligands(model, data_file, model_id)[source]

Takes a Model and assocated ligands and binding sites to each other based on 800-remarks in the provided PdbDataFile.

Parameters:
  • model (Model) – the model to update.
  • data_file (PdbDataFile) – The source Pdb Data File
  • model_id (int) – The ID of the model in the data fileto be used for conversion.
molecupy.converters.pdbdatafile2model.give_model_alpha_helices(model, data_file, model_id)[source]

Takes a Model and creates AlphaHelix objects in it based on the helices in the provided PdbDataFile.

Parameters:
  • model (Model) – the model to update.
  • data_file (PdbDataFile) – The source Pdb Data File
  • model_id (int) – The ID of the model in the data fileto be used for conversion.
molecupy.converters.pdbdatafile2model.give_model_beta_strands(model, data_file, model_id)[source]

Takes a Model and creates BetaStrand objects in it based on the sheets in the provided PdbDataFile.

Parameters:
  • model (Model) – the model to update.
  • data_file (PdbDataFile) – The source Pdb Data File
  • model_id (int) – The ID of the model in the data fileto be used for conversion.
molecupy.converters.pdbdatafile2model.give_model_complexes(model, data_file, model_id)[source]

Takes a Model and creates Complex objects in it based on the compounds in the provided PdbDataFile.

Parameters:
  • model (Model) – the model to update.
  • data_file (PdbDataFile) – The source Pdb Data File
  • model_id (int) – The ID of the model in the data fileto be used for conversion.