pymatgen.analysis.functional_groups module
Determine functional groups present in a Molecule.
- class FunctionalGroupExtractor(molecule, optimize=False)[source]
Bases:
objectThis 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)[source]
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)[source]
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)[source]
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)[source]
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)[source]
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)[source]
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