Brian Kelley b6e5bdd111 Fix/rgroup sdf isotope (#2449) ...

* update version of japanese docs

* Remove external labels from cores

* Fix syntax errors

* Add better autodetection of labels, add dummyatom label, don't fall back to indexes when onlyMatchAtRgroups are set

* Add better autodetection of labels, add dummyatom label, don't fall back to indexes when onlyMatchAtRgroups are set

* Move autodetection before alignment, fix final core labelling

* Fix stupid bit twiddling mistake

* None of the original mol's should actually match the cores with onlyMatchAtRgroups

* Convert PRECONDITION to CHECK_INVARIANT

* Run clang-format

* use nullptr instead of 0 for pointers

* Handle cases where molecules don't have anything for an R-group properly.

Here's the python demo of the bug:

```
In [14]: scaffold2 = Chem.MolFromSmiles('c1c([*:1])cncn1')

In [15]: scaffold = Chem.MolFromSmiles('c1c([*:1])cccn1')

In [19]: mols2 = [Chem.MolFromSmiles(smi) for smi in 'c1c(F)cc(O)cn1 c1c(F)cncn1 c1c(Cl)cc(O)cn1'.split()]

In [20]: print(rdRGroupDecomposition.RGroupDecompose([scaffold,scaffold2],mols2,asSmiles=True,asRows=False))
({'Core': ['c1ncc([*:2])cc1[*:1]', 'c1ncc([*:1])cn1', 'c1ncc([*:2])cc1[*:1]'], 'R1': ['F[*:1]', 'F[*:1]', 'Cl[*:1]'], 'R2': ['[H]O[*:2]', '[H]O[*:2]', '']}, [])
```

* Fixes #2471

2019-06-04 15:41:20 +02:00

21 KiB

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