Brian Kelley

descriptastorus support

1

Hi Eric! It's been a while. I've stolen your pyjanitor ides for the descriptastorus for chemistry related descriptors: https://github.com/bp-kelley/descriptastorus ``` df = pandas.DataFrame(dict(smiles=smiles)) df2 = descriptastorus.descriptors.create_descriptors( df, mols_column_name="smiles", generator_names=["Morgan3Counts","RDKit2D"]) ```...

cdxml parser

4

This is the bones for a working CDXML parser. There are a few things left, cis/trans stereo, grabbing the coordinates and parsing into ChemReactions, making proper query atoms for reactions...

Add osx pthread_barrier so osx gets the LeadPicker optimizations

8

Adds a BSD-2 pthread_barrier from: https://github.com/ademakov/DarwinPthreadBarrier.git So osx can get the optimizations for the LeadPicker.

[WIP] Add rgroup decomposition option for molzip

6

This is code that allows mol zip to zip up some odd rgroup decompositions such as splitting rings. This is modeled after the following Python code: ``` def molzip_smi(smiles): """Fix...

Enhance molzip to properly handle RGroupDecompositions

1

This adds a new molzip that works correctly on RGroupRow. Example: ``` >>> from rdkit import Chem >>> from rdkit.Chem import rdRGroupDecomposition as rgd >>> core = Chem.MolFromSmiles('CO') >>> mols...

EnumerateStereoisomers generates different isomers with legacy and new stereo code

6

Example of the issue: ``` Chem.SetUseLegacyStereoPerception(False) smi = "NC(F)C(I)C(F)N" print("SMI:", smi) m = Chem.MolFromSmiles(smi) print(f"stereo: {[x.type for x in Chem.FindPotentialStereo(m)]}") isomers = list(EnumerateStereoisomers(m)) print("new stereo num isomers", len(isomers)) for ism...

py-boost runtime should be = not >=

2

https://github.com/rdkit/conda-rdkit/blob/92017d1ddfd5651410a9f162aa6254992ba51262/rdkit/meta.yaml#L37 This pulls the wrong rdkit version at runtime if a new one exists.

postgressql95

1

I think the meta.yaml is incorrect ``` fn: https://ftp.postgresql.org/pub/source/v9.5.2/postgresql-9.5.2.tar.bz2 url: https://ftp.postgresql.org/pub/source/v9.5.2/postgresql-9.5.2.tar.bz2 ``` should probably be ``` fn: postgresql-9.5.2.tar.bz2 url: https://ftp.postgresql.org/pub/source/v9.5.2/postgresql-9.5.2.tar.bz2 ``` That got it to work for me at least.

Add python Conformer.SetPositions wrapper

1

This took a bit longer than it should have. Usage ``` array = mol.GetConformer(0).GetPositions() mol.GetConformer(0).SetPositions(array) ```

Speed up boost vector iterators

9

Fixes #7639 Boost Iterators are amazingly slow for iteration, but accessing by index is very fast. This converts the __iter__ protocol to use the __getitem__ protocol and results in a...