gmol.base.data.mmcif.smiles

Classes

MmcifRefLigand(atoms, bonds)
RefLigandInput(smiles, atom_ids)

Functions

convert_chem_comp(ccd)	Convert CCD to smiles and atom indexes.
input_from_reference(ref_ligand)
mol_from_chem_comp(atoms, bonds)	Return a RDKit molecule from a list of atoms and bonds.
reference_from_mmcif(res_cc[, extra_bonds])
unique_atom_id(residue_id, atom_id)

class RefLigandInput(smiles: str, atom_ids: list[str])

smiles: str

atom_ids: list[str]

class MmcifRefLigand(atoms: list[ChemCompAtom], bonds: list[ChemCompBond])

atoms: list[ChemCompAtom]

bonds: list[ChemCompBond]

mol_from_chem_comp(atoms: list[ChemCompAtom], bonds: list[ChemCompBond]) → Mol

Return a RDKit molecule from a list of atoms and bonds.

Parameters:

• atoms – list of atoms.

• bonds – list of bonds.

Returns:

A molecule with correct atom id (GetProp("atom_id"), stereochemistry (GetProp("absolute_config")) and aromaticity. All hydrogens are removed.

unique_atom_id(residue_id: ResidueId, atom_id: str) → str

reference_from_mmcif(res_cc: list[tuple[ResidueId, ChemComp]], extra_bonds: list[Branch] | None = None) → MmcifRefLigand

input_from_reference(ref_ligand: MmcifRefLigand) → RefLigandInput

convert_chem_comp(ccd: dict[str, ChemComp]) → tuple[list[str], dict[str, ndarray[tuple[Any, ...], dtype[str_]]]]

Convert CCD to smiles and atom indexes.

Parameters:

ccd – Dictionary of ccd code to ChemComp object.