Re: [Rdkit-discuss] Get distances between two atoms in different molecules
Thanks, this worked like a charm! I was wondering on another thing: I wanted to calculate the bond angle between three atoms in the two conformers (essentially looking for possible hydrogen bonding). Again, rdMolTransforms.GetAngleDeg() inputs only one conformer, while the Point3D angle functions inputs either two or four atom indices. Is there some function I've either misunderstood/missed or is it better to retrieve this angle from vector calculations? Illimar Rekand Ph.D. candidate, Brenk-lab, Haug-lab Department of Biomedicine Department of Chemistry University of Bergen From: Paolo Tosco Sent: Friday, August 16, 2019 4:33:36 PM To: Illimar Hugo Rekand Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Get distances between two atoms in different molecules Hi Illimar, You may use Point3D.Distance: conf_a.GetAtomPosition(i).Distance(conf_b.GetAtomPosition(j)) Cheers, p. > On 16 Aug 2019, at 16:01, Illimar Hugo Rekand wrote: > > Hello everyone, > > > I see that GetBondDistance() is a useful tool for calculating the distances > between atoms, whether bonded or nonbonded. However, I am unsure on how to > implement this function to calculate distances between atoms in different > molecule, as the functions requires a conformer as an argument. > > > Would I need to generate a conformer containing both molecules in order to > use this function for calculating the intermolecular atom distances? > > > Illimar Rekand > Ph.D. candidate, > Brenk-lab, Haug-lab > Department of Biomedicine > Department of Chemistry > University of Bergen > > > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Get distances between two atoms in different molecules
Hi Illimar, You may use Point3D.Distance: conf_a.GetAtomPosition(i).Distance(conf_b.GetAtomPosition(j)) Cheers, p. > On 16 Aug 2019, at 16:01, Illimar Hugo Rekand wrote: > > Hello everyone, > > > I see that GetBondDistance() is a useful tool for calculating the distances > between atoms, whether bonded or nonbonded. However, I am unsure on how to > implement this function to calculate distances between atoms in different > molecule, as the functions requires a conformer as an argument. > > > Would I need to generate a conformer containing both molecules in order to > use this function for calculating the intermolecular atom distances? > > > Illimar Rekand > Ph.D. candidate, > Brenk-lab, Haug-lab > Department of Biomedicine > Department of Chemistry > University of Bergen > > > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Get distances between two atoms in different molecules
Hello everyone, I see that GetBondDistance() is a useful tool for calculating the distances between atoms, whether bonded or nonbonded. However, I am unsure on how to implement this function to calculate distances between atoms in different molecule, as the functions requires a conformer as an argument. Would I need to generate a conformer containing both molecules in order to use this function for calculating the intermolecular atom distances? Illimar Rekand Ph.D. candidate, Brenk-lab, Haug-lab Department of Biomedicine Department of Chemistry University of Bergen ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
