Pavel

Hi! It depends what is the context of "speed up". 1. I tried to make it fast but there is definitely space for improvement. However, each next improvement of speed...

I have to profile code to remember all details and pitfalls. I'll post those results here to enable a more objective discussion. What I remember is that I implemented a...

I put here results of tests and some conclusions. I currently do not consider speed up as a priority issue because we use relatively slow scorings and structure generation is...

Investigating issue with duplicates I found and fixed the bug of generation of duplicated fragments before their mutation. All fragments with 1 or 2 attachment points were duplicated, thus twice...

Yes, this should speed up on 30-40%, but there will be about 20-25% (in average) of duplicated molecules in the output. If you are ok with them you may remove...

I do not know you may try to measure performance. But fingerprints have collisions and thus some molecules will be falsely identified as duplicates. So some compounds will be erroneously...

Pymol can visualize pharmacophore features in xyz-files as spheres. Not always convenient but currently this is the only way. If you failed to generate xyz-file please provide a reproducible example....

You may click on spheres to look at the "atom" name. A - acceptor, D - donor, a - aromatic, H - hydrophobic, P- positive, N - negative. Features which...

Yes, this makes sense, we do the same if we want to visualize pharmacophores.

Hi Vito, there are few options: 1) Use our psearch software from this branch of the repo https://github.com/meddwl/psearch/tree/dev2. You will need to generate a database of conformers and pharmacophores for...