molecupy.converters.pdbfile2pdbdatafile (PDB File to PDB Data File)

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

molecupy.converters.pdbfile2pdbdatafile.pdb_data_file_from_pdb_file(pdb_file)[source]

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

Parameters:pdb_file (PdbFile) – The PdbFile to convert.
Return type:PdbDataFile
molecupy.converters.pdbfile2pdbdatafile.process_header_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the HEADER records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_obslte_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the OBSLTE records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_title_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the TITLE records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_split_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the SPLIT records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_caveat_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the CAVEAT records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_compnd_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the COMPND records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_source_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the SOURCE records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_keywd_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the KEYWD records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_expdta_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the EXPDTA records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_nummdl_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the NUMMDL records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_mdltyp_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the MDLTYP records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_author_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the AUTHOR records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_revdat_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the REVDAT records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_sprsde_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the SPRSDE records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_jrnl_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the JRNL records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_remark_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the REMARK records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_dbref_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the DBREF records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_seqadv_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the SEQADV records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_seqres_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the SEQRES records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_modres_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the MODRES records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_het_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the HET records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_hetnam_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the HETNAM records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_hetsyn_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the HETSYN records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_formul_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the FORMUL records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_helix_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the HELIX records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_sheet_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the SHEET records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_ssbond_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the SSBOND records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File

Takes a PdbDataFile and updates it based on the LINK records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_cispep_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the CISPEP records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_site_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the SITE records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_cryst1_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the CRYST1 records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_origx_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the ORIGX records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_scale_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the SCALE records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_mtrix_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the MTRIX records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_model_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the MODEL records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_atom_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the ATOM records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_anisou_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the ANISOU records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_ter_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the TER records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_hetatm_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the HETATM records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_conect_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the CONECT records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File
molecupy.converters.pdbfile2pdbdatafile.process_master_records(data_file, pdb_file)[source]

Takes a PdbDataFile and updates it based on the MASTER records in the provided PdbFile

Parameters:
  • data_file (PdbDataFile) – the Data File to update.
  • pdb_file (PdbFile) – The source Pdb File