Re: [Rdkit-discuss] adding fragment to existing molecule

2017-08-07 Thread Stiefl, Nikolaus
Hi Per Just by looking at your code I would assume you have a sanitization issue. You create your pentane molecule and then add H’s. This will saturate each single carbon. When you then add a bond between the two fragments your atom 3 will have a valence of 5 and this causes issues. Maybe do the

Re: [Rdkit-discuss] adding fragment to existing molecule

2017-08-07 Thread Per Jr. Greisen
Hi Nikolaus and Ling, Thanks for your help (the atom numbe shouldnt be 43 but it still gives the error I will clarify)- yes Nikolaus you are right it is a sanitization issue and in this case I am trying to use it as a molecular editor to build a model molecule (a transition state model to be exact

[Rdkit-discuss] using rdkit to read in chembl23 1.7 million compounds

2017-08-07 Thread Bennion, Brian
Hello, This might be a nit picky question. I am attempting to read in the smiles string for the 1.7 million non-biological compounds in the latest chembl23 release. As it turns out 382 compounds fail to be read by RDkit. The errors are either kekulization failure or valence errors. Has anyone

Re: [Rdkit-discuss] using rdkit to read in chembl23 1.7 million compounds

2017-08-07 Thread Greg Landrum
Hi Brian, It's not that surprising. The RDKit is stricter about allowing unreasonable chemistry that the tool the ChEMBL group uses to produce SMILES or mol blocks. There are always some molecules that the RDKit just won't process. If you are concerned and see any in that group of failures that y

[Rdkit-discuss] FW: using rdkit to read in chembl23 1.7 million compounds

2017-08-07 Thread Bennion, Brian
From: Bennion, Brian Sent: Monday, August 07, 2017 11:39 To: 'Konrad Koehler' Subject: RE: [Rdkit-discuss] using rdkit to read in chembl23 1.7 million compounds Hello Konrad, Thank you for your response. For the handful of compounds i looked at: multiple ringed compounds that had %11 up to %14

Re: [Rdkit-discuss] FW: using rdkit to read in chembl23 1.7 million compounds

2017-08-07 Thread Maciek Wójcikowski
Hi Brian, Konrad, Just a sidenote - It's not a crash. Python/Boost is just complaining, that the first argument is in fact None and it should be RDKit Mol instance. Instead of filtering all lowercase s from smiles, you should check if mol is None in your for loop, and skip those which are. P

[Rdkit-discuss] . Re: using rdkit to read in chembl23 1.7 million compounds

2017-08-07 Thread Chris Swain
I've not tried to read in ChEMBL but I have tried to process other large datasets e.g. ZINC. My impression was that problems arose with small heterocyclic systems, particularly if fused or containing multiple different heteroatoms. I did wonder if the different aromaticity models might be the i

Re: [Rdkit-discuss] . Re: using rdkit to read in chembl23 1.7 million compounds

2017-08-07 Thread Bennion, Brian
The carbocations are in small heterocyclic molecules. see CHEMBL3815233 Brian From: Chris Swain Sent: Monday, August 7, 2017 11:46:30 AM To: rdkit-discuss@lists.sourceforge.net Subject: [Rdkit-discuss] . Re: using rdkit to read in chembl23 1.7 million compounds

Re: [Rdkit-discuss] . Re: using rdkit to read in chembl23 1.7 million compounds

2017-08-07 Thread Peter S. Shenkin
That molecule's SMILES is correctly rendered by RDKit, or at least by the version of RDKit behind Slack: [image: Inline image 1] -P. On Mon, Aug 7, 2017 at 3:54 PM, Bennion, Brian wrote: > The carbocations are in small heterocyclic molecules. see CHEMBL3815233 > > Brian > > >

Re: [Rdkit-discuss] . Re: using rdkit to read in chembl23 1.7 million compounds

2017-08-07 Thread Bennion, Brian
Hello Peter, Great, that just made me realize that I was not using my most recent conda environment version of RDkit. I reread the 2D sdf file with the latest rdkit version and now only 31 molecules are tossed out by the SDMolsupplier in RDKit. 51 compounds had errors when reading in the smiles

Re: [Rdkit-discuss] adding fragment to existing molecule

2017-08-07 Thread Christos Kannas
Hi Per, I can think of 2 approaches to solve this. The 1st is to have fragments of molecules that have an explicit connection point, i.e. OH[*] and C[*], and use RDKit's functionality of combining fragments. The 2nd is to use define a reaction for this using SMIRKS or Reaction SMILES, i.e. [O

Re: [Rdkit-discuss] problem with AssignAtomChiralTagsFromStructure

2017-08-07 Thread Greg Landrum
I don't think I understand the question. The Conformer object is normally attached to/associated with a mol object. -greg On Sun, Aug 6, 2017 at 11:41 AM, Per Jr. Greisen wrote: > Thanks - worked perfectly if I was to do this conformers is there an easy > way to transform between conformer obj

Re: [Rdkit-discuss] adding fragment to existing molecule

2017-08-07 Thread Greg Landrum
The other answers on this thread have been right on point with the exception of neglecting to explicitly encourage you to call Chem.SanitizeMol() on your joined molecule before you do anything else with it. In your case you'd call: Chem.SanitizeMol(back) This will lead to the error that Nik explain