Re: [Rdkit-discuss] Setting custom coordinates for new atoms

: Thursday, August 29, 2019 2:31:37 AM To: Illimar Hugo Rekand; rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Setting custom coordinates for new atoms Hi Illimar, The problem here is that you are adding atoms to your RWMol, but the Conformer object that you are trying to access

Re: [Rdkit-discuss] Setting custom coordinates for new atoms

r.cpp Failed Expression: dp_mol->getNumAtoms() == d_positions.size() RDKIT: 2019.09.1dev1 BOOST: 1_67 Hoping to hear from you soon! Illimar Rekand Ph.D. candidate, Brenk-lab, Haug-lab Department of Biomedicine Department of Chemistry University of Bergen _

Re: [Rdkit-discuss] Setting custom coordinates for new atoms

itions.size() RDKIT: 2019.09.1dev1 BOOST: 1_67 Hoping to hear from you soon! Illimar Rekand Ph.D. candidate, Brenk-lab, Haug-lab Department of Biomedicine Department of Chemistry University of Bergen From: Paolo Tosco Sent: Thursday, August 22, 2019 11:

Re: [Rdkit-discuss] Setting custom coordinates for new atoms

Hi Illimar, AddAtom() will return the index i of the added atom, then you can call SetAtomPosition on that index on the molecule conformer and pass a Point3D with the desired coordinates: conf.SetAtomPosition(i, Point3D(x, y, z)) Cheers, p. On 08/22/19 09:24, Illimar Hugo Rekand wrote:

[Rdkit-discuss] Setting custom coordinates for new atoms

Hello, everyone I'm wondering whether there is a way to set custom coordinates to an atom in a conformer? In particular I'm interested in using the AddAtom() function in the RWMol class to place a new dummy atom in a PDB-file. Illimar Rekand Ph.D. candidate, Brenk-lab, Haug-lab Department