Re: [Rdkit-discuss] UFF atom type errors

2017-10-09 Thread Bennion, Brian
et> Subject: Re: [Rdkit-discuss] UFF atom type errors Yeah, those atom types that you are seeing are the names of the UFF atom types that the RDKit assigns. If an atom has a hybridization/charge-state that's not recognized, you'll get those parameterization errors. If you're aware of a be

Re: [Rdkit-discuss] UFF atom type errors

2017-10-06 Thread Greg Landrum
EUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8 > > > ------ > > *De :* Bennion, Brian <benni...@llnl.gov> > *Envoyé :* vendredi 6 octobre 2017 06:11 > *À :* RDKit Discuss (rdkit-discuss@lists.sourceforge.net) > *Objet :* [Rdkit-discuss] UFF atom type errors

Re: [Rdkit-discuss] UFF atom type errors

2017-10-06 Thread Bennion, Brian
Envoyé : vendredi 6 octobre 2017 06:11 À : RDKit Discuss (rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>) Objet : [Rdkit-discuss] UFF atom type errors Hello, As part of my workflow, I am attempting to generate a starting 3D structure from a 2D representation lo

Re: [Rdkit-discuss] UFF atom type errors

2017-10-06 Thread Guillaume GODIN
h SA RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8 De : Bennion, Brian <benni...@llnl.gov> Envoyé : vendredi 6 octobre 2017 06:11 À : RDKit Discuss (rdkit-discuss@lists.sourceforge.net) Objet : [Rdkit-discuss] UFF atom type errors Hello, As

[Rdkit-discuss] UFF atom type errors

2017-10-05 Thread Bennion, Brian
Hello, As part of my workflow, I am attempting to generate a starting 3D structure from a 2D representation loaded from an sdf file. On certain structures I receive the following UFF errors when attempting to minimize the structure. [20:50:43] UFFTYPER: Unrecognized atom type: He1 (0)