molecupy.pdb.access (PDB Access)

This module contains the functions used to access PDB files themselves. These are the only functions to be imported into the top level directory, and so are all accesisble by importing molecupy itself.

molecupy.pdb.access.pdb_from_string(text)[source]

Creates a Pdb object from the text of a PDB file.

Parameters:string (str) – The raw text of a PDB file.
Return type:Pdb
molecupy.pdb.access.pdb_data_file_from_string(text)[source]

Creates a PdbDataFile object from the text of a PDB file.

Parameters:string (str) – The raw text of a PDB file.
Return type:PdbDataFile
molecupy.pdb.access.pdb_file_from_string(text)[source]

Creates a PdbFile object from the text of a PDB file.

Parameters:string (str) – The raw text of a PDB file.
Return type:PdbFile
molecupy.pdb.access.get_pdb_from_file(path, processing='pdb')[source]

Creates a Pdb, PdbDataFile, or PdbFile from a file path on disk - the default behaviour being to create a Pdb.

Parameters:
  • path (str) – The location of the PDB file on disk.
  • processing (str) – The level of processing you want the returned object to have. Propviding "pdbfile" will just return a PdbFile, "datafile" will return a PdbDataFile, and "pdb" (the default) will return a fully processed Pdb object.
Raises:

FileNotFoundError – if there is no file at the specified location.
molecupy.pdb.access.get_pdb_remotely(code, processing='pdb')[source]

Creates a Pdb, PdbDataFile, or PdbFile from a 4-letter PDB code - the default behaviour being to create a Pdb.

Parameters:
  • code (str) – The 4-letter PDB code.
  • processing (str) – The level of processing you want the returned object to have. Propviding "pdbfile" will just return a PdbFile, "datafile" will return a PdbDataFile, and "pdb" (the default) will return a fully processed Pdb object.
Raises:

InvalidPdbCodeError – if there is no PDB with the given code.