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 *********************************************************************************** DISCLAIMER This email and any files transmitted with it, including replies and forwarded copies (which may contain alterations) subsequently transmitted from Firmenich, are confidential and solely for the use of the intended recipient. The contents do not represent the opinion of Firmenich except to the extent that it relates to their official business. ***********************************************************************************
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