Re: [Rdkit-discuss] MolFromPDBBlock and heterocycles

Hi Steven, The PDB reader in the RDKit doesn’t determine any bond orders - everything is read as a single bond. In order to set the bond orders, you need to call the AssignBondOrdersFromTemplate() function using a reference molecule generated from SMILES (or SDF). Here is some example code from

Re: [Rdkit-discuss] MolFromPDBBlock and heterocycles

Hi Steven, The PDB reader in the RDKit doesn’t determine any bond orders - everything is read as a single bond. In order to set the bond orders, you need to call the AssignBondOrdersFromTemplate() function using a reference molecule generated from SMILES (or SDF). Here is some example code

[Rdkit-discuss] drawing code take 2

:( Here's one where AddHs() really breaks things. It is an unpleasant molecule to draw. So it looks like the issue is that - for CID 112084 call to AddHs() changed the layout (arguably not for the better), whereas - for CID 260719 it didn't change the layout/shorten the bonds when it really

[Rdkit-discuss] MolFromPDBBlock and heterocycles

Hello! I have a pdb block that I am working with, which is attached to this email. The ligand has aromatic ring structures in it; however, when it is read into RDKit and converted into a smiles string, the aromatic rings are converted into aliphatic rings. Any thoughts? Here is the python code:

Re: [Rdkit-discuss] MolWt of substructure hit?

Hi, Thanks for this, the clue that I needed was that there's a method: " matches = mol.GetSubstructMatches(pat) " This should work fine for what I need. Cheers, Steve. -Original Message- From: Andrew Dalke [mailto:da...@dalkescientific.com] Sent: 07 September 2016 12:10 To: Stephen

Re: [Rdkit-discuss] MolWt of substructure hit?

On Sep 7, 2016, at 11:53 AM, Stephen O'hagan wrote: > How would I find the molecular weight (fraction) of that substructure within > a compounds expressed as a SMILES string, e.g.: I don't know if a built-in function which does this. It's possible to write one. Here's a function which will

[Rdkit-discuss] MolWt of substructure hit?

Hi, Supposing I have identified a substructure as a SMARTS string, e.g. [#6](:,-[#6]:,-[#6](-[#6]):,-[#6]-[#6](:[#6]:[#7]):[#6]:[#6]):,-[#6]:,-[#6] - In general, this may have wild card atoms. How would I find the molecular weight (fraction) of that substructure within a compounds expressed