Standardizer gets stuck on a molecule

[adlvdl]

Hi, I have been trying your module to standardize molecules. However it gets stuck with molecule ZINC000100026244. By the stacktrace when I do a keyboard interruption, it seems to get stuck at the reionize step. Is there a way to set a timeout period so that if it gets stuck like this I can just disregard this molecule and continue?
I put below the bug example and the stacktrace:

from rdkit import Chem
import molvs
smi="CCOC(=O)C(=O)[CH-]C#N"
s = molvs.Standardizer()
mol=Chem.MolFromSmiles(smi)
mol = s.standardize(mol)

---

KeyboardInterrupt Traceback (most recent call last)
in ()
2 s = molvs.Standardizer()
3 mol=Chem.MolFromSmiles(smi)
----> 4 mol = s.standardize(mol)
5 print(Chem.MolToSmiles(mol, True))

C:\Software\Miniconda\lib\site-packages\molvs\standardize.py in standardize(self, mol)
97 mol = self.disconnect_metals(mol)
98 mol = self.normalize(mol)
---> 99 mol = self.reionize(mol)
100 Chem.AssignStereochemistry(mol, force=True, cleanIt=True)
101 # TODO: Check this removes symmetric stereocenters

C:\Software\Miniconda\lib\site-packages\molvs\charge.py in call(self, mol)
152 def call(self, mol):
153 """Calling a Reionizer instance like a function is the same as calling its reionize(mol) method."""
--> 154 return self.reionize(mol)
155
156 def reionize(self, mol):

C:\Software\Miniconda\lib\site-packages\molvs\charge.py in reionize(self, mol)
195
196 while True:
--> 197 ppos, poccur = self._strongest_protonated(mol)
198 ipos, ioccur = self._weakest_ionized(mol)
199 if ioccur and poccur and ppos < ipos:

C:\Software\Miniconda\lib\site-packages\molvs\charge.py in _strongest_protonated(self, mol)
211 def _strongest_protonated(self, mol):
212 for position, pair in enumerate(self.acid_base_pairs):
--> 213 for occurrence in mol.GetSubstructMatches(pair.acid):
214 return position, occurrence
215 return None, None

KeyboardInterrupt:

[mcs07]

Thanks for the bug report.

This should now be fixed - there was a bug in the patterns that are used to decide whether the ionised atom should be changed, resulting in an infinite loop.

Run pip install -U molvs to update to the latest version.

[adlvdl]

Yes, with the update the example now completes. However a new molecule (ZINC000060321958) that previously finished now is giving problems. Like before I paste the example and traceback.

smi="C[N+]1=C[CH-]N(C(=N)N)/C1=C/N+[O-]"
s = molvs.Standardizer()
mol=Chem.MolFromSmiles(smi)
mol = s.standardize(mol)

---

StandardizeError Traceback (most recent call last)
in ()
2 s = molvs.Standardizer()
3 mol=Chem.MolFromSmiles(smi)
----> 4 mol = s.standardize(mol)
5 print(Chem.MolToSmiles(mol, True))

C:\Software\Miniconda\lib\site-packages\molvs\standardize.py in standardize(self, mol)
97 mol = self.disconnect_metals(mol)
98 mol = self.normalize(mol)
---> 99 mol = self.reionize(mol)
100 Chem.AssignStereochemistry(mol, force=True, cleanIt=True)
101 # TODO: Check this removes symmetric stereocenters

C:\Software\Miniconda\lib\site-packages\molvs\charge.py in call(self, mol)
153 def call(self, mol):
154 """Calling a Reionizer instance like a function is the same as calling its reionize(mol) method."""
--> 155 return self.reionize(mol)
156
157 def reionize(self, mol):

C:\Software\Miniconda\lib\site-packages\molvs\charge.py in reionize(self, mol)
200 if ioccur and poccur and ppos < ipos:
201 if poccur[-1] == ioccur[-1]:
--> 202 raise StandardizeError('Reionizer entered an infinite loop! Please report as a MolVS bug.')
203 log.info('Moved proton from %s to %s', self.acid_base_pairs[ppos].name, self.acid_base_pairs[ipos].name)
204 patom = mol.GetAtomWithIdx(poccur[-1])

StandardizeError: Reionizer entered an infinite loop! Please report as a MolVS bug.

[mcs07]

Sorry for dropping this - I hope this is now fixed with v0.0.9.

Let me know if there are still any problems.