polymerist.rdutils.rdprops.atomprops

For assigning, transferring, and removing properties of RDKit Atoms

Attributes

`T`
`label_R_groups`

`atom_ids_with_prop`(→ list[int])	Returns list of indices of atoms which have a particular property assigned
`aggregate_atom_prop`(→ dict[int, T])	Collects the values of a given Prop across all atoms in an RDKit molecule
`clear_atom_props`(→ None)	Wipe properties of all atoms in a molecule
`annotate_atom_prop`(→ None)	Labels the desired Prop for all atoms in a Mol which have it
`annotate_atom_ids`(→ None)	Draws atom indices over their positions when displaying a Mol.
`clear_atom_annotations`(→ None)	Removes atom annotations over their positions when displaying a Mol
`label_linkers`(→ None)	Labels wild-type ("*") atoms in a Mol for display

polymerist.rdutils.rdprops.atomprops.atom_ids_with_prop(rdmol: rdkit.Chem.Mol, prop_name: str) → list[int][source]: Returns list of indices of atoms which have a particular property assigned

polymerist.rdutils.rdprops.atomprops.aggregate_atom_prop(rdmol: rdkit.Chem.Mol, prop: str, prop_type: T = str) → dict[int, T][source]: Collects the values of a given Prop across all atoms in an RDKit molecule

polymerist.rdutils.rdprops.atomprops.clear_atom_props(rdmol: rdkit.Chem.Mol) → None[source]: Wipe properties of all atoms in a molecule

polymerist.rdutils.rdprops.atomprops.annotate_atom_prop(rdmol: rdkit.Chem.Mol, prop: str, prop_type: T = str, annotate_precision: int | None = None) → None[source]: Labels the desired Prop for all atoms in a Mol which have it

polymerist.rdutils.rdprops.atomprops.annotate_atom_ids(rdmol: rdkit.Chem.Mol, atom_id_remap: dict[int, int] | None = None) → None[source]: Draws atom indices over their positions when displaying a Mol. Can optionally provide a dict mapping atom indices to some other integers

polymerist.rdutils.rdprops.atomprops.clear_atom_annotations(rdmol: rdkit.Chem.Mol) → None[source]: Removes atom annotations over their positions when displaying a Mol

polymerist.rdutils.rdprops.atomprops.label_linkers(rdmol: rdkit.Chem.Mol, label_props: Iterable[str] = None, naming_funct: Callable[[int], str] | None = None) → None[source]: Labels wild-type (“*”) atoms in a Mol for display