rdchiral

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There are some (corner) cases in template_extractor.py which would return None instead of a dict. This introduces some inconsistencies, and possibly AttributeError in downstream processing (e.g. for models that only...

zhengkaitu

- Manually add isotope labels to atoms whenever they are used for matching - Fix chirality around unmapped rings - Improve definition of fragment around tetrahedral centers for determining if...

itai-levin

template_extractor

2

Good morning, unpon installing the pip package pip install rdchiral the version 1.0.0 ins installed among the installed modules I miss template_extractor.py I see that there is a commit where...

acquaregia

Pre-condition Violation: attempt to add self-bond

1

With the following code: `from rdchiral import main as rdc` `reaction = rdc.rdchiralReaction('[C:1]-[N;H0;D3;+0:2](-[C:3])-[O;H0;D2;+0:6]-[C:5]=[O;D1;H0:4]>>[C:1]-[NH;D2;+0:2]-[C:3].[O;D1;H0:4]=[C:5]-[O;H0;D2;+0:6]-[O;H0;D2;+0:6]-[C:5]=[O;D1;H0:4]')` `rct = rdc.rdchiralReactants('O=C(ON1C(=O)CCC1=O)c1ccc2c(c1)OCO2')` `reactants = rdc.rdchiralRun(reaction, rct)` I get the following error: Traceback (most recent call last):...

robertdavidburbidgephd

The new rdkit 2020.03 has stricter bond checks (maybe incorrect) and [the code to merge molecules](https://github.com/connorcoley/rdchiral/blob/246e17133f70565b851fa3fbb10152dc2afa884a/rdchiral/main.py#L259) fails and gives the following error. A temporary workaround is to use ReplaceBond() instead...

ljn917

Chiral centers more than one bond away from reaction centers

1

This testing was done with commit 246e171 (current master head), python 3.8 and rdkit 2020.03.4 (conda-forge). Below is a reaction from USPTO, PatentNumber US03956392. The current code may produce inconsistent...

ljn917

Rule not applied when I think it should be.

4

Hi, Nice project. I've got quite a simple rule I'd like to apply which has no chirality specified. `[#6:4][#8:6][#6:2](=[O:3])[#6:1] >> [#6:4][#6:2](=[O:3])[#6:1]` This works fine in most cases, but not for...

willfinnigan

unexpected template extracted

2

Hi I have a strange case where the template extractor gives unexpected results. I am cleaning up my reaction database and use the template extractor to spot low quality data....

acquaregia