Paolo Tosco

JS test_legacy_stereochem() fails on master

1

The assertion that fails is the one I commented out below: ```javascript RDKitModule.use_legacy_stereo_perception(false); mol = RDKitModule.get_mol("C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2"); assert.equal(mol.is_valid(),1); //assert.equal(mol.get_smiles(),"CC1CC2(CC[C@H](C)CC2)CC[C@@H]1C"); ``` The reason why it fails is that the new stereo code...

I noticed a warning during compilation caused by a spurious `\c` tag in a Python docstring. This PR removes it.

Expose reaction drawing and additional FPs in MinimalLib

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- exposed reaction drawing in MinimalLib - fixed a typo in the error message "JSON doesn't contain 'atoms' field, or it is not an array" - replaced RapidJson `HasMember()` with...

CanonicalizeMol may generate the mirror image of the starting coordinates

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### Discussed in https://github.com/rdkit/rdkit/discussions/5292 Originally posted by **petrucci86** May 15, 2022 It was found that `CanonicalizeMol()` may generate the mirror image of the starting coordinates. Here's a reproducible: ``` from...

Random crashes while running smiTestCatch

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**Describe the bug** I am getting random crashes while running `Code/GraphMol/SmilesParse/smiTestCatch`; I wonder if this has to do with this recently merged PR: #5251. **To Reproduce** I am running `Code/GraphMol/SmilesParse/smiTestCatch`...

Improve MCS performance when CompleteRingsOnly is set

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This PR stems from the observation that MCS runs on medium size molecules can take a very long time when `CompleteRingsOnly` is set to `true`. For example, this pair of...

Small PR just to update the AvalonTools version (and make future updates easier).

Small fix to avoid incurring into division by zero, e.g., when coordinates of the molecule are all zero.

**Describe the bug** Attempting to carry out R-group decomposition with cores containing query atoms may result in unexpected failures to decompose molecules that do match the core. **To Reproduce** ```...

Regression in the way aldehydes are drawn in current master

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See below for a reproducible. What happens is that the formyl double bond is drawn as if it were in a ring, so the oxygen looks misplaced. ``` from IPython.display...