Re: [Rdkit-discuss] Submol: bond vs atom indicies

FYI: If anybody needs the code which gets all residues as separate Molecules, here it is. prot = Chem.MolFromPDBFile('10gs/10gs_protein_rdkit.pdb', flavor=1) residues = [] aa = Chem.MolFromSmarts('NCC(=O)N') for res in Chem.SplitMolByPDBResidues(prot).values(): for frag in

Re: [Rdkit-discuss] Submol: bond vs atom indicies

I correct myself, all residue types are available from Chem.SplitMolByPDBResidues(). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-03-22 9:50 GMT+01:00 Maciek Wójcikowski : > Hi Greg, > 2016-03-22 6:28 GMT+01:00 Greg Landrum

Re: [Rdkit-discuss] Submol: bond vs atom indicies

Hi Greg, 2016-03-22 6:28 GMT+01:00 Greg Landrum : > > Hi Maciek, > > > On Mon, Mar 21, 2016 at 8:33 PM, Maciek Wójcikowski wrote: >> >> >> I came across one problem with RDKit today, namely Chem.PathToSubmol() function. Does the "path" mean atom or

Re: [Rdkit-discuss] Submol: bond vs atom indicies

Hi Maciek, On Mon, Mar 21, 2016 at 8:33 PM, Maciek Wójcikowski wrote: > > I came across one problem with RDKit today, namely Chem.PathToSubmol() > function. Does the "path" mean atom or bond indices? On this very list I > fount the examples showing usage with atom idx [

[Rdkit-discuss] Submol: bond vs atom indicies

Hi all, I came across one problem with RDKit today, namely Chem.PathToSubmol() function. Does the "path" mean atom or bond indices? On this very list I fount the examples showing usage with atom idx [ https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg03966.html], while the