PDB files (chemistry_files.pdb)

The PDB file format.

class qcip_tools.chemistry_files.pdb.File

classmethod attempt_identification(f)

A PDB file has a lot of specific keywords

file_type = 'PDB_FILE'

The identifier

classmethod from_molecule(molecule, *args, **kwargs)

Create a file from molecule

Parameters:

molecule (qcip_tools.molecule.Molecule) – the molecule

Return type:

qcip_tools.chemistry_files.pdb.File

classmethod possible_file_extensions()

Return the common extention of this kind of files

Return type:

list

read(f)

Format is described in - http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM - http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#HETATM - http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#TER

Parameters:

f (file) – File

to_string()

Return type:

str