[Rdkit-discuss] Generate depiction matching 2D structure

[Lukas P. <lp...@eb...>]

Dear all, 

 

I’ve just recently started using rdkit in python. Btw. A very nice piece of work. First, I’d like to generate 2D depiction of molecules I’m constructing from 3D coordinate data. I’m aware of methods such as GenerateDepictionMatching2DStructure(…) and GenerateDepictionMatching3DStructure(…). For most of the cases it works like a charm, however there are bits and pieces which need improving. That is why I wonder if there is a mean how to either a) provide multiple templates or b) to provide mapping between the model and the template on the atomic level. For instance, I have a molecule containing two copies of the template, just one of them gets correctly rendered, while the other is still a mess. The documentation says something about AtomPairsParameters (http://www.rdkit.org/Python_Docs/rdkit.Chem.rdMolDescriptors.AtomPairsParameters-class.html), but given the description I have no clue whether or how to use it.

 

The second question I have in mind is that I’m facing the same issues on macOS and python 3.6.x as described here: https://sourceforge.net/p/rdkit/mailman/message/36093960/ and here https://github.com/rdkit/rdkit/issues/1617 so I hope there will be a solution in the future, as I’d like to use python 3.6

 

My current setup is:

macOS High Siera

Conda: 4.3.25

Rdkit 2017.9.2

Python: 3.5.3

 

I look forward to an answer

All the best,
lukas