Re: [Rdkit-discuss] How to center atom labels vertically?

2020-10-21 Thread theozh
Hi Greg, in the meantime, I updated to RDKit2020.03 via Anaconda and also tried Draw.MolToImage(), but I'm running into new problems. I believe that I need a QPixmap for a PyQt5 QTableWideget, hence, I need to convert the PIL image into a QPixmap. The lines: from PyQt5.QtGui import

[Rdkit-discuss] Descriptors and organometallics

2020-10-21 Thread Stefan Kuhn
Hi all, is RDKit able to handle arganometallics (dative bonds) in its descriptor calculations? Sorry if this is in the doc, but I couldn't find it. For my understanding, dative bonds are part of RDKit, but I am not sure if the descriptors calculate something useful with them. Sorry again if this

Re: [Rdkit-discuss] How to preserve undefined stereochemistry?

2020-10-21 Thread Paolo Tosco
Hi Adelene, Greg, I have updated my gist fixing my gross vocabulary mistake ("undefined" to "unspecified") and I have also added an example of the crossed bond depiction by changing the BondStereo attribute to STEREOANY. @Adelene: I think you touched an interesting point here. There are indeed

Re: [Rdkit-discuss] How to center atom labels vertically?

2020-10-21 Thread Norwid Behrnd via Rdkit-discuss
Dear theoz, thanks for reminding about release 2020.09.1.0, less than a day old.[1] Assuming you refer currently using release 2019.03.6 I added to conda by the instruction of conda install -c conda-forge rdkit I would wait a little for an update because a) the relevant repository for

Re: [Rdkit-discuss] How to center atom labels vertically?

2020-10-21 Thread theozh
Dear Greg and David, thank you for your responses. Sorry, for not being incomplete with information. I'm using RDKit2019.03 under Windows using Anaconda3. I haven't found out yet how to update to the latest RDKit (2020.09?) version. In a PyQt Application I want to list structures as images in a

Re: [Rdkit-discuss] How to preserve undefined stereochemistry?

2020-10-21 Thread Adelene LAI
Hi Greg, Hi Paolo, @Paolo - thanks for the updated gist! @Greg - thanks for this detailed explanation. I think it makes sense to equate unspecified with unknown stereochem. I can't think of any obvious caveats to this convention change for now (but maybe others in the community can?). When