Hi Taka,
So this bug is fix thanks.
Now I have two others issues:
1. This cell gives also an error:
dataset = rg.GetRGroupsAsColumns()
core = Chem.RemoveHs(dataset["Core"][0])
RDKit ERROR: [12:59:27] Explicit valence for atom # 6 N, 5, is greater than
permitted
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-23-487b32336f27> in <module>
1 dataset = rg.GetRGroupsAsColumns()
----> 2 core = Chem.RemoveHs(dataset["Core"][0])
ValueError: Sanitization error: Explicit valence for atom # 6 N, 5, is greater
than permitted
2. and after second issue when I’m running this cell:
res = enumeratemol(core,rg)
---------------------------------------------------------------------------
UnboundLocalError Traceback (most recent call last)
<ipython-input-25-04a5f3b3662f> in <module>
----> 1 res = enumeratemol(core,rg)
<ipython-input-4-8458dbd4277f> in enumeratemol(core, rg, maxmol)
11 mol = core
12 for idx,j in enumerate(i):
---> 13 mol = makebond(mol, rgs[idx][j])
14 AllChem.Compute2DCoords(mol)
15 mol = Chem.RemoveHs(mol)
<ipython-input-3-45dfd4e95811> in makebond(target, chain)
14 nbr2 = [x.GetOtherAtom(newmol.GetAtomWithIdx(atm2)) for x
in newmol.GetAtomWithIdx(atm2).GetBonds()][0]
15 nbr2.SetAtomMapNum(idx)
---> 16 newmol.AddBond(nbr1.GetIdx(), nbr2.GetIdx(),
order=Chem.rdchem.BondType.SINGLE)
17 nbr1.SetAtomMapNum(0)
18 nbr2.SetAtomMapNum(0)
UnboundLocalError: local variable 'nbr1' referenced before assignment
Thanks for helping
Guillaume
De : Taka Seri <[email protected]>
Date : mercredi, 20 novembre 2019 à 14:02
À : Guillaume GODIN <[email protected]>
Cc : "[email protected]" <[email protected]>
Objet : [*External*] Re: [Rdkit-discuss] Try to reproduce a code working in
January
Hi Guillaume,
I confirmed the issue.
RemoveHs does not work to invalid molecule.
So I updated my code example and uploaded gist.
Could you please check new version of my code?
https://gist.github.com/iwatobipen/77269b8a10eafe0e0cba8de5c1cae6ec
Any comments or suggestions will be appreciated.
Thanks,
Taka
2019年11月20日(水) 14:46 Guillaume GODIN
<[email protected]<mailto:[email protected]>>:
Dear community,
I try to reproduce this code
https://iwatobipen.wordpress.com/2019/01/18/generate-possible-molecules-from-a-dataset-chemoinformatics-rdkit/
but got an error un panda / rdkit during generation:
frame = frame[["ROMol", "Smiles", "Core", "R1", "R2", "R3"]]
frame['Core']=frame['Core'].apply(Chem.RemoveHs)
frame.head(2)
RDKit ERROR: [05:02:02]
RDKit ERROR:
RDKit ERROR: ****
RDKit ERROR: Pre-condition Violation
RDKit ERROR: getExplicitValence() called without call to calcExplicitValence()
RDKit ERROR: Violation occurred on line 161 in file
/opt/conda/conda-bld/rdkit_1561471048963/work/Code/GraphMol/Atom.cpp
RDKit ERROR: Failed Expression: d_explicitValence > -1
RDKit ERROR: ****
RDKit ERROR:
RDKit ERROR: [05:05:04] Explicit valence for atom # 6 N, 5, is greater than
permitted
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-74-d2864fc13f85> in <module>
1 frame = frame[["ROMol", "Smiles", "Core", "R1", "R2", "R3"]]
----> 2 frame['Core']=frame['Core'].apply(Chem.RemoveHs)
3 frame.head(2)
~/miniconda/envs/py37/lib/python3.7/site-packages/pandas/core/series.py in
apply(self, func, convert_dtype, args, **kwds)
3589 else:
3590 values = self.astype(object).values
-> 3591 mapped = lib.map_infer(values, f, convert=convert_dtype)
3592
3593 if len(mapped) and isinstance(mapped[0], Series):
pandas/_libs/lib.pyx in pandas._libs.lib.map_infer()
ValueError: Sanitization error: Explicit valence for atom # 6 N, 5, is greater
than permitted
Any idea why ?
BR
Guillaume
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