John Mayfield
John Mayfield
Currently providing a query molecule to this function leaves the expressions intact, it should perhaps strip back the expressions or we provide an option to decided what to do. Example...
Follow on from #938 and #920. We can do better with the MOLfile, need a bit more tweaking to get a non-query molecule out from the dative bond example
#### Reference Issue Extends on from: #6730 #### What does this implement/fix? Explain your changes. Treat any implicit/missing neighbours in SMARTS and SMILES as being attached to the central (chiral)...
#### Reference Issue n/a #### What does this implement/fix? Explain your changes. - add a ``getMaxNbors(tag)`` utility function to avoid repeated logic in multiple places - tweak ``getChiralPermutation()`` for handling...
Some salt names use a semi-colon to indicate the salt. OPSIN supports this is but only as ``"; "`` Example name ``(2S,4R)-1-[(2S)-2-amino-3,3-dimethyl-butanoyl]-4-hydroxy-N-[[4-(4-methylthiazol-5-yl)phenyl]methyl]pyrrolidine-2-carboxamide;hydrochloride``
The recent addition of ``SANITIZE_CLEANUP_ORGANOMETALLICS`` (https://github.com/rdkit/rdkit/pull/6357) means many ``->`` and ``>> Chem.MolToSmiles(Chem.MolFromSmiles('[NH3][Pt][NH3]')) 'N->[Pt]
``` M V30 COUNTS 0 1 M V30 BEGIN REACTANT M V30 END REACTANT M V30 BEGIN PRODUCT M V30 BEGIN CTAB ``` 0 reactants but still has a REACTANT...
Wrote this 10+ years ago for my PhD... about time I clean it up and merge it in. I think the 2018 was a rebase. Some minor work needed
Andrew Dalke has noted that the EState FP and substructure patterns FP have different outputs depending on the whether implicit/explicit hydrogens are used. We should documented this behaviour and recommend...
**Summary** AAM timeout seems to hang on moderate size smiles even with a small timeout. **Steps to Reproduce** 1. Indigo via Java (and likely C code), 1.14.0 - 1.20.0 ```java...