epam / epam/Indigo

Substructure matcher finds implicit hydrogens as atoms

Open
#1,872 0 comments 0 reactions 0 assignees View on GitHub
Hydrogens Priority: Medium
Dominant language
C++
Stars
406
Forks
134
Avg merge
2d 11h
Merged PRs (30d)
24

Description

**Steps to Reproduce**

```
smiles = "C";
smarts = "[!#6]";
Indigo indigo = new Indigo();
IndigoObject pattern = indigo.loadSmarts(smarts);
IndigoObject molecule = indigo.loadMolecule(smiles);
IndigoObject match = indigo.substructureMatcher(molecule).match(pattern);
if (match !=null) // a match is produced here. Working correctly for version 1.12.
```

**Actual behavior**
Match returns non-zero result for implicit hydrogens

**Expected behavior**
There should be no match for implicit hydrogens

**Environment details:**
- 1.18

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reproducing the issue with the provided Indigo, loadSmarts, loadMolecule, and substructureMatcher calls using molecule "C" and pattern "[!#6]". Locate the substructure-matching entry point and verify that implicit hydrogens are not returned as atom matches; add or update a regression test if the project has one for this behavior.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp, java
Domain
tooling
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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