pymatgen.analysis.functional_groups module

Determine functional groups present in a Molecule.

class FunctionalGroupExtractor(molecule, optimize=False)

Bases: object

This class is used to algorithmically parse a molecule (represented by an instance of pymatgen.analysis.graphs.MoleculeGraph) and determine arbitrary functional groups.

Instantiation method for FunctionalGroupExtractor.

Parameters:

• molecule – Either a filename, a pymatgen.core.structure.Molecule object, or a pymatgen.analysis.graphs.MoleculeGraph object.

• optimize – Default False. If True, then the input molecule will be modified, adding Hydrogens, performing a simple conformer search, etc.

categorize_functional_groups(groups)

Determine classes of functional groups present in a set.

Parameters:

groups – Set of functional groups.

Returns:

dict containing representations of the groups, the indices of where the group occurs in the MoleculeGraph, and how many of each type of group there is.

get_all_functional_groups(elements=None, func_groups=None, catch_basic=True)

Identify all functional groups (or all within a certain subset) in the molecule, combining the methods described above.

Parameters:

• elements – List of elements that will qualify a carbon as special (if only certain functional groups are of interest). Default None.

• func_groups – List of strs representing the functional groups of interest. Default to None, meaning that all of the functional groups defined in this function will be sought.

• catch_basic – bool. If True, use get_basic_functional_groups and other methods

Returns:

list of sets of ints, representing groups of connected atoms

get_basic_functional_groups(func_groups=None)

Identify functional groups that cannot be identified by the Ertl method of get_special_carbon and get_heteroatoms, such as benzene rings, methyl groups, and ethyl groups.

TODO: Think of other functional groups that are important enough to be added (ex: do we need ethyl, butyl, propyl?)

Parameters:

func_groups – List of strs representing the functional groups of interest. Default to None, meaning that all of the functional groups defined in this function will be sought.

Returns:

list of sets of ints, representing groups of connected atoms

get_heteroatoms(elements=None)

Identify non-H, non-C atoms in the MoleculeGraph, returning a list of their node indices.

Parameters:

elements – List of elements to identify (if only certain functional groups are of interest).

Returns:

set of ints representing node indices

get_special_carbon(elements=None)

Identify Carbon atoms in the MoleculeGraph that fit the characteristics defined Ertl (2017), returning a list of their node indices.

The conditions for marking carbon atoms are (quoted from Ertl):

“- atoms connected by non-aromatic double or triple bond to any heteroatom - atoms in nonaromatic carbon-carbon double or triple bonds - acetal carbons, i.e. sp3 carbons connected to two or more oxygens, nitrogens or sulfurs; these O, N or S atoms must have only single bonds - all atoms in oxirane, aziridine and thiirane rings”

Parameters:

elements – List of elements that will qualify a carbon as special (if only certain functional groups are of interest). Default None.

Returns:

set of ints representing node indices

link_marked_atoms(atoms)

Take a list of marked “interesting” atoms (heteroatoms, special carbons) and attempt to connect them, returning a list of disjoint groups of special atoms (and their connected hydrogens).

Parameters:

atoms – set of marked “interesting” atoms, presumably identified using other functions in this class.

Returns:

list of sets of ints, representing groups of connected atoms