Greg Landrum

The current implementation of the way chirality is considered does not follow the algorithm in the ECFP paper. We should add an option to do this. Description of how to...

add an extra argument to toggle use of GetBestRMS()

Matching of stereochemistry queries from complex atomic SMARTS is wrong

2

**Description:** Here's a little demo: ``` In [5]: p = Chem.MolFromSmarts('[#6]-[#6,#7@](-[#17])(-[#35])-[#9]') In [6]: print(p.GetAtomWithIdx(1).DescribeQuery()) AtomOr AtomAtomicNum 6 = val AtomAnd AtomAtomicNum 7 = val AtomNull In [7]: ms = [Chem.MolFromSmiles(x)...

This is a container issue to track progress towards supporting non-tetrahedral atomic stereochemistry within the RDKit. I suspect it's going to be a long time before this whole thing is...

Consider adding normalization rule for azides

1

I was surprised to see this form of an azide in the database:  It's an odd form and I only find it once in ChEMBL26 (https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1652082/) in contrast to...

allow sanitization of the result molecules in standardize_mol()

3

In order to help prevent users from getting themselves into trouble, we should add a `standardize` argument to `standardize_mol()` that defaults to True. One argument against setting the default to...

This adds `c:`, `t:`, and `ctu:` to the CXSMILES readers and writers. These only apply to ring bonds. It also: - updates the documentation to include the newly supported CXSMILES...

**Describe the bug** Here's the demo: ``` In [26]: m = Chem.MolFromSmiles("OC1CCCN1") In [27]: Chem.MolToSmiles(m) Out[27]: 'OC1CCCN1' In [28]: m.GetProp("_smilesBondOutputOrder") Out[28]: '[0,1,5,2,3,4,]' In [29]: m.GetProp("_smilesAtomOutputOrder") Out[29]: '[0,1,2,3,4,5,]' ``` Given that...

When I added the global `{get,set}UseLegacyStereo` option I overlooked the possibly conflicting interaction between it and `SmilesParserParams.useLegacyStereo`, i.e. being explicit about which one takes precedence. This remedies that by having...