vermouth.pdb.cif module

Provides functionality to read CIF files.

class vermouth.pdb.cif.CIFReader(file, exclude, ignh, modelidx=1)

Bases: object

reader()

vermouth.pdb.cif.casting(value, typeto)

Cast a value to its correct type with an exception value: value to cast type: the expected output type of the value

vermouth.pdb.cif.cif_entry_reader(cf, entry, cif_categories_all, cif_category_names, cif_category_types, essential_properties, modelidx, exclude, ignh)

Read a single entry of a parsed cif file

Parameters:

• cf – CIF file object parsed by PyCifRW

• entry (str) – Key of the cf dict

• cif_categories_all (list) – List of valid category keys contained within a cif file entry

• cif_category_names (list) – Common name for category entries

• cif_category_types (list) – Type to cast CIF data to

• essential_properties (list) – List of properties which must be contained

• modelidx (int) – If the cif file contains multiple models, which one to select.

• exclude (collections.abc.Container[str]) – Atoms that have one of these residue names will not be included.

• ignh (bool) – Whether hydrogen atoms should be ignored.

Returns:

A parsed molecule. Will not contain edges

Return type:

vermouth.molecule.Molecule

vermouth.pdb.cif.read_cif_file(file_name, exclude=('SOL', 'HOH'), ignh=False, modelidx=1)

Parse a CIF file to create a list of molecules using the PyCIFRW library

Parameters:

• file_name (str) – The file to read.

• exclude (collections.abc.Container[str]) – Atoms that have one of these residue names will not be included.

• ignh (bool) – Whether hydrogen atoms should be ignored.

• modelidx (int) – If the cif file contains multiple models, which one to select.

Returns:

The parsed molecules. Will not contain edges

Return type:

list[vermouth.molecule.Molecule]