mmpdb
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rdkit
A package to identify matched molecular pairs and use them to predict property changes.
I have large database 500K compounds and I am interested in finding only few transforms. Ideally I would like to give transform in the form of smirks. I understand that...
At this point the CSV output generated with `mmpdb index --out csv [...]` does not contain property information even if you specify a property file with `--properties`. If a property...
Most of the Cut-SMARTS currently cut bonds between aliphatic carbon and Halogens. This may not be desirable, since it leads to CF3 and OCF3 groups being split up. These splits...
When mmpdb transform is called, the algorithm currently fragments the input molecule and searches for replacements for all fragments in the DB. This can then be filtered by the substructure...
In Python 2.7 the built-in json module was significantly slower than the third-party ujson and cjson modules at parsing the fragment file. If one of the latter two is not...
Hello! I tried to run the command `mmpdb fragment tests/chembl_test.smi -o tests/chembl_test.fragments` with my own data - looks like this (if it matters): ``` c1cn(-c2ccc3c(-c4cc5cc(CN6CCCCC6)ccc5[nH]4)n[nH]c3c2)nn1 CN(C)C(=O)c1ccc2c(-c3cc4cc(CN5CCOCC5)ccc4[nH]3)n[nH]c2c1 c1cnn(-c2ccc3c(-c4cc5cc(CN6CCCCC6)ccc5[nH]4)n[nH]c3c2)c1 c1cc2[nH]c(-c3n[nH]c4cc(-c5cn[nH]c5)ccc34)cc2cc1CN1CCOCC1 c1ncc(-c2cnc(Nc3cc(N4CCNCC4)ccn3)s2)cn1 ```...
Just an idea for docs. It could be pretty helpful if there will be an installation guide in the README.md file.
The one indexed in PyPI is 2.1. It would be great if the latest version is also in PyPI. Thanks.
Hi! I am getting an unexpected generated molecule when using double cuts. The transformation, which in this case is the linker, is attached the wrong way around (details below). I...
Hi all, I recently found some unexpected outcomes when using "mmpdb transform" with or without the property flag. The mmpdb database was generated using ChEMBL database with calculated LogP as...
