Re: [Open Babel] Chirality and winding

Same here, I'll be happy to give it a spin. Thanks! On 02/20/2015 09:08 AM, Nathan Pimental wrote: > Please, do, put a branch on GitHub, I'd be glad to test. > > On Thu, Feb 19, 2015 at 10:58 PM, Geoffrey Hutchison > > wrote: > > > We have an idea what to

Re: [Open Babel] Chirality and winding

Please, do, put a branch on GitHub, I'd be glad to test. On Thu, Feb 19, 2015 at 10:58 PM, Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > > We have an idea what to add to get around this (distance geometry), > > but no-one has done it yet. > > I'm fairly close, but I'm still doing testi

Re: [Open Babel] Chirality and winding

> We have an idea what to add to get around this (distance geometry), > but no-one has done it yet. I'm fairly close, but I'm still doing testing to make sure it's robust. If anyone would like to test, I can put a branch up on GitHub. -Geoff --

Re: [Open Babel] Chirality and winding

This limitation of the 3D builder is described in the docs and also flagged up by the warning message: https://open-babel.readthedocs.org/en/latest/3DStructureGen/SingleConformer.html#obbuilder We have an idea what to add to get around this (distance geometry), but no-one has done it yet. Regards

Re: [Open Babel] Chirality and winding

In fact, my mistake was to assume the config object would be build accordingly to Cahn-Ingold-Prelog rules, hence my misunderstanding when the winding showed up identical. I've read the documentation and tried with refs, and yes, it works as expected (same results as with the winding with less co

Re: [Open Babel] Chirality and winding

The config object represents the usual way chemists communicate stereochemistry in a diagram; looking either from/towards a particular atom, atoms X, Y and Z are arranged clockwise/anticlockwise. Your code is correctly inverting the stereo. If you invert the 'winding', and keep everything else the

Re: [Open Babel] Chirality and winding

Noel, thanks for the clarification. It makes sense now, but it means that I'm using the wrong tool for what I want to do. In a previous discussion[1] I was suggested to use this code to alter the chirality of a tetrahedral stereocenter, since OBTetrahedralStereo.Invert() doesn't seem to be ava

Re: [Open Babel] Chirality and winding

Hi, Hope you don't mind but... 1. Should GetId() not GetIdx()-1 2. Should be "HasTetrahedralStereo(idx)" Regarding the main question, the config objects are correct, but the stereo definition consist of three parts (see the API docs): view, winding and refs. You were just looking at the winding.

[Open Babel] Chirality and winding

Hi, I can't understand the way in which chiral winding is handled by OpenBabel. I wrote a small test script in Python (attached) to try to clarify the concept. The output is: ClC(I)Br -> WINDING [1->2] -> ClC(I)Br Cl[C@H](I)Br -> WINDING [1->2] -> Cl[C@@H](I)Br Cl[C@@H](I)Br -> WINDING [1->2]