epam / epam/Indigo

Unsure hydrogen count

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Dominant language
C++
Stars
406
Forks
134
Avg merge
2d 11h
Merged PRs (30d)
24

Description

```
from indigo import Indigo

indigo = Indigo()
mol = indigo.loadMolecule('CCN(C1=NC(=CS1)CC(=O)NC2=CC=C(C=C2)Cl)C(=O)CCC(=O)[O-]')
atom = mol.getAtom(0)
r = mol.addAtom('Ar')
r.addBond(atom, 1)
print(mol.canonicalSmiles())
```
The above code gives error "SMILES saver: unsure hydrogen count on atom #26"
The problem is the added atom is not recognized as a pseudo atom. How to solve this issue?

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reproducing the Python snippet using Indigo, especially the addAtom, addBond, and canonicalSmiles calls. Trace how the added Ar atom is represented before serialization; done means the snippet treats it as a pseudo atom and canonicalSmiles completes without the unsure hydrogen count error.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp, python
Domain
tooling
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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