epam / epam/Indigo

`IndigoException: molecule: invalid connectivity given: -1` when ionizing ChEMBL SMILES

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#1,173 3 comments 0 reactions 1 assignee Claimed by @AliaksandrDziarkach View on GitHub
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Description

I was willing to play a bit with pKa models in Indigo when I found this issue.

**Steps to Reproduce**

```python
from indigo import Indigo

indigo = Indigo()

indigo.setOption("pKa-model", "advanced")
indigo.setOption("pKa-model-level", 5)
indigo.setOption("pKa-model-min-level", 2)
pH = 7.4
pH_toll = 0.5

# RDKit generated SMILES (aspirin from ChEMBL database)
smiles = "CC(=O)Oc1ccccc1C(=O)O"

mol = indigo.loadMolecule(smiles)
mol.ionize(pH, pH_toll)
```

```
IndigoException: molecule: invalid connectivity given: -1
```
Same happens for other SMILES like paracetamol `CC(=O)Nc1ccc(O)cc1`. I imagined there is some generalized issue.

**Expected behavior**
Molecule to be ionized.

**Actual behavior**
Indigo throwing a connectivity error.

**Indigo version**
Indigo built from: https://github.com/epam/Indigo/commit/2d696a21414e2c9cdb5952bcba21e0f7139a975f

**Additional context**
It would be also nice to have some extended documentation about the pKa models in Indigo. There is a lack of open source pKa calculators and having the ones in Indigo better documented I think it could bring some users.
I would be happy to compare the results with current ChEMBL pKa calcualted values.

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