pdom.Molecule

class pdom.Molecule(identifier, properties, save=True)

This class should not be initialised directly. Use one of the following class methods instead: from_chem_id(), from_folder(), from_inchi(), from_inchi_key(), from_iupac_name(), from_name()

Parameters:

• identifier (dict) –
  • name common name
  • iupac_name IUPAC name (can be the same as common name)
  • chem_id compound ID from PubChem
  • inchi IUPAC International Chemical Identifier (human readable)
  • inchi_key IUPAC International Chemical Identifier (hash)
• properties (dict) –
  • chem_formula chemical formula e.g. ‘C10H22’
  • chem_formdic chemical formula as dict
  • mol_weight molecular weight in g/mol
  • mol_volume molecular volume in cm^3/mol
  • mol_surface largest projected surface area m^2/molecule
  • excess_bonds number of bonds in excess of a simple carbon chain
  • structure_3d atom position list
• save (bool) – save data to the user cache

classmethod from_chem_id(chem_id, name=None, inchi_key=None)

Create Molecule instance identified by a chemID from PubChem data.

Note:

if molecule is cached in Molecule.db_folder load from there

Parameters:

• chem_id (int) –

  compound ID from PubChem

• name (str, optional) – overwrite compound name
• inchi_key (str, optional) – IUPAC International Chemical Identifier (to check cache quickly)

Returns:

Molecule instance

classmethod from_folder(folder)

create Molecule instance from a folder created by save

Parameters:folder (str, folder) – molecule folder Returns:Molecule instance

classmethod from_name(name)

Create Molecule instance identified by a name if unique

Note:queries chem_id and calls from_chem_id() Parameters:name (str) – unique compound name Returns:Molecule instance

identifier = None

dict of identifiers as described in Molecule

properties = None

dict of properties as described in Molecule

save(folder=None, name=None)

saves the molecule information to disk, can be loaded with from_folder()

Note:

If called without parameters the molecule is saved in an appropriate cache folder Molecule.db_folder.

Parameters:

• folder (str, Path) – parent folder
• name (str) – molecule folder name (default INCHI key)

structure_3d(rotated=True)

Returned 3d structure of the molecule

Parameters:rotated (bool) – if True the structure is rotated to cover the maximum surface in the xy space Returns:3D structure (symbol, x, y, z) Return type:list