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
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