[Rdkit-discuss] Matching Generalized Compounds

Hi All, I’m interested in having GetSubstructMatches return non-“null” results in the following example. The results should lead to a match where atom 1 maps to atom 11, 2 to 12, etc. m1 = Chem.MolFromSmiles('[*:1][CH2:2][C:3]([CH3:4])=[CH2:5]') m2 =

Re: [Rdkit-discuss] back tracking descriptor names from RandomForest feature_importance

Hi Shojiro, This might not be the most elegant and efficient way but it worked for what I wanted to do. I changed my apply function as below: allDescp=[name[0] for name in Descriptors._descList] for name in allDescp: temp=MoleculeDescriptors.MolecularDescriptorCalculator([name])

Re: [Rdkit-discuss] Alignment using LIgpargen file

Dear Phuong, it works for me with the latest RDKit release. I am wondering if you are using an older RDKit version where maybe the PDB parser was not assigning formal charges based on connectivity? Then you would have to manually set the formal charge of the protonated nitrogen atom (# 2 N)

Re: [Rdkit-discuss] Alignment using LIgpargen file

Hi Paolo, I got this new error when I tried with different chemicals: python 3DAlignmentwith3OAwithGRO.py CCNC\(N\)N_afterMD.pdb CC\[NH2\+\]CCN_Ligpargen.pdb [12:02:45] Explicit valence for atom # 2 N, 4, is greater than permitted Traceback (most recent call last): File