Yeah, that's it. Thanks!
On Thu, Nov 22, 2018 at 9:57 PM Yutong Zhao <[email protected]> wrote: > assignID -> assignId > > On Thu, Nov 22, 2018 at 9:39 PM Chaya Stern <[email protected]> > wrote: > >> Hello, >> >> I am trying to create a molecule from a connectivity table and xyz >> coordinates, however, when I try to do that I get an Argument Error: >> >> ArgumentError: Python argument types in >> Mol.AddConformer(Mol, Conformer) >> did not match C++ signature: >> AddConformer(RDKit::ROMol {lvalue} self, RDKit::Conformer* conf, bool >> assignId=False) >> >> >> Below is what I did: >> >> >> from rdkit import Chem >> import numpy as np >> from rdkit.Geometry.rdGeometry import Point3D >> >> >> hooh = { >> 'symbols': ['H', 'O', 'O', 'H'], >> 'geometry': [ >> 1.84719633, 1.47046223, 0.80987166, >> 1.3126021, -0.13023157, -0.0513322, >> -1.31320906, 0.13130216, -0.05020593, >> -1.83756335, -1.48745318, 0.80161212 >> ], >> 'name': 'HOOH', >> 'connectivity': [[0, 1, 1], [1, 2, 1], [2, 3, 1]], >> } >> >> _atomic_number = {'H': 1, 'O':8} >> bond_types = {1:Chem.BondType.SINGLE, 2:Chem.BondType.DOUBLE, >> 3:Chem.BondType.TRIPLE} >> BOHR_2_ANGSTROM = 0.529177210 >> symbols = hooh['symbols'] >> geometry = np.array(hooh['geometry'], >> dtype=float).reshape(int(len(hooh['geometry'])/3), 3)*BOHR_2_ANGSTROM >> connectivity = hooh['connectivity'] >> >> molecule = Chem.Mol() >> editable_mol = Chem.RWMol(molecule) >> conformer = Chem.Conformer(len(symbols)) >> for i, s in enumerate(symbols): >> atom = editable_mol.AddAtom(Chem.Atom(_atomic_number[s])) >> atom_position = Point3D(geometry[i][0], geometry[i][1], >> geometry[i][2]) >> conformer.SetAtomPosition(atom, atom_position) >> >> # Add connectivity >> for bond in connectivity: >> bond_type = bond_types[bond[-1]] >> editable_mol.AddBond(bond[0], bond[1], bond_type) >> mol = editable_mol.GetMol() >> Chem.SanitizeMol(mol) >> initial_conformer = mol.AddConformer(conformer, assignID=True) >> >> I am using rdkit version 2018.09.1 on OSX. I am not sure what I am doing >> wrong. Any help will be appreciated. >> >> Thank you, >> Chaya >> -- >> Chaya D Stern >> Memorial Sloan Kettering Cancer Center >> Tri-Institutional Chemical Biology Program >> _______________________________________________ >> Rdkit-discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > > > -- > Yutong Zhao > -- Chaya D Stern Memorial Sloan Kettering Cancer Center Tri-Institutional Chemical Biology Program
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