search

ci-lab-cz / pharmd

MD pharmacophores and virtual screening
BSD 3-Clause "New" or "Revised" License
31 stars 17 forks source link

updated to new CGRtools #1

Closed stsouko closed 3 years ago

stsouko commented 3 years ago

fixes. but I found problem with new sssr algorithm implemented in CGRtools. I need some time for fixing it.

stsouko commented 3 years ago

жизнь боль. старый алгоритм совка был быстр, но пролетал порой. новый протелает крайне редко, но зараза имеет сложность N^3 (N - число атомов) а не ~N+M как старый (M - число связей) короче говоря все ой как плохо если атомов больше пары сотен

DrrDom commented 3 years ago

Thank you! So we will wait for a final version. I would like to point out that MetalComplex features were not added to pmapper master and may cause issues. I also noticed HalogenDonor/Acceptor, but these features are not supported by pmapper. You may keep these three features if they will not cause issues or please remove them from the final version.

stsouko commented 3 years ago

now sssr algorithm fixed in CGRtools. also updated aromatic rings detection (new in CGRtools). molecule class monkey patching changed to new api of file parsers.

stsouko commented 3 years ago

Thank you! So we will wait for a final version. I would like to point out that MetalComplex features were not added to pmapper master and may cause issues. I also noticed HalogenDonor/Acceptor, but these features are not supported by pmapper. You may keep these three features if they will not cause issues or please remove them from the final version.

no. these types of interactions disabled.