tqchem.functional_groups

Functions

match_atomic_numbers(molecule_node, subgraph_node)	Determine if a node in the molecule matches a node in the subgraph
match_bond_order_range(molecule_edge, subgraph_edge)	Determine if the bond order of the molecule is inside a range defined for the subgraph
bonds_from_isomorphism_mappings(→ set[tuple[int, int]])	Converts bonds defined on the subgraph to bonds on the graph
find_methyl_groups(→ set[tuple[int, int]])	Get set of bonds matching an atom being bonded to a methyl group
find_single_bonded_chalcogen(→ set[tuple[int, int]])	Get set of bonds matching R-O-R or R-S-R bonds
single_bonded_chalcogens_grid(→ dict[None])	Returns Dictionary mapping chalcogen single bonds to their grid
find_amide_groups(→ set[tuple[int, int]])	Get set of bonds matching the C-N bond in amide groups
amide_bonds_grid(→ dict[None])	Returns Dictionary mapping amide bonds to their dihedral grid
find_amino_groups(→ set[tuple[int, int]])	Get set of bonds matching an atom being bonded to a amino group
amino_group_grid(→ dict[None])	Returns Dictionary mapping bonds to amino groups to their dihedral grid
find_t_butyl_groups(→ set[tuple[int, int]])	Get set of bonds matching the R-C bond in t-butyl groups
t_butyl_groups_grid(→ dict[None])	Returns Dictionary mapping bonds to t-butyl groups to their dihedral grid
find_iso_propyl_groups(→ set[dict[int, int]])	Get set of bonds matching the R-C bond in isopropyl groups
iso_propyl_groups_grid(→ dict[None])	Returns Dictionary mapping bonds to iso-propyl groups to their dihedral grid
find_alkane_bonds(→ set[tuple[int, int]])	Get set of bonds matching the simple C-C bond
simple_alkanes_grid(→ dict[None])	Returns Dictionary mapping alkane bonds to iso-propyl groups to their dihedral grid

Module Contents

tqchem.functional_groups.match_atomic_numbers(molecule_node: dict[str, int], subgraph_node: dict[str, int | collections.abc.Iterable[int]])

Determine if a node in the molecule matches a node in the subgraph

Required for checking isomorphisms of graphs. We check the atomic numbers and assume that an atomic number of -1 means an unspecified residue. The subgraph node can also have a list of atomic numbers and the graphs match the molecule_node’s atomic number is in the list.

tqchem.functional_groups.match_bond_order_range(molecule_edge: dict[str, int], subgraph_edge: dict[str, int | collections.abc.Iterable[int]])

Determine if the bond order of the molecule is inside a range defined for the subgraph

Required for checking isomorphisms of graphs.

tqchem.functional_groups.bonds_from_isomorphism_mappings(mappings: collections.abc.Iterable[dict[int, int]], subgraph_bonds: list[tuple[int, int]]) → set[tuple[int, int]]

Converts bonds defined on the subgraph to bonds on the graph

Parameters:

• mapping (list[dict[int, int]]) – Mappings for nodes on the graph to nodes on the subgraph

• subgraph_bonds (list[tuple[int, int]]) – list of bonds defined for the subgraph nodes

Returns:

bonds – set of bonds defined on the graph

Return type:

set[tuple[int, int]]

tqchem.functional_groups.find_methyl_groups(graph: networkx.Graph) → set[tuple[int, int]]

Get set of bonds matching an atom being bonded to a methyl group

tqchem.functional_groups.find_single_bonded_chalcogen(graph: networkx.Graph) → set[tuple[int, int]]

Get set of bonds matching R-O-R or R-S-R bonds

tqchem.functional_groups.single_bonded_chalcogens_grid(graph: networkx.Graph, grid: numpy.ndarray) → dict[None]

Returns Dictionary mapping chalcogen single bonds to their grid

tqchem.functional_groups.find_amide_groups(graph: networkx.Graph) → set[tuple[int, int]]

Get set of bonds matching the C-N bond in amide groups

tqchem.functional_groups.amide_bonds_grid(graph: networkx.Graph, grid: numpy.ndarray) → dict[None]

Returns Dictionary mapping amide bonds to their dihedral grid

tqchem.functional_groups.find_amino_groups(graph: networkx.Graph) → set[tuple[int, int]]

Get set of bonds matching an atom being bonded to a amino group

tqchem.functional_groups.amino_group_grid(graph: networkx.Graph, grid: numpy.ndarray) → dict[None]

Returns Dictionary mapping bonds to amino groups to their dihedral grid

tqchem.functional_groups.find_t_butyl_groups(graph: networkx.Graph) → set[tuple[int, int]]

Get set of bonds matching the R-C bond in t-butyl groups

tqchem.functional_groups.t_butyl_groups_grid(graph: networkx.Graph, grid: numpy.ndarray) → dict[None]

Returns Dictionary mapping bonds to t-butyl groups to their dihedral grid

tqchem.functional_groups.find_iso_propyl_groups(graph: networkx.Graph) → set[dict[int, int]]

Get set of bonds matching the R-C bond in isopropyl groups

tqchem.functional_groups.iso_propyl_groups_grid(graph: networkx.Graph, grid: numpy.ndarray) → dict[None]

Returns Dictionary mapping bonds to iso-propyl groups to their dihedral grid

tqchem.functional_groups.find_alkane_bonds(graph: networkx.Graph) → set[tuple[int, int]]

Get set of bonds matching the simple C-C bond

tqchem.functional_groups.simple_alkanes_grid(graph: networkx.Graph, grid: numpy.ndarray) → dict[None]

Returns Dictionary mapping alkane bonds to iso-propyl groups to their dihedral grid