[Rdkit-discuss] Question on how to create mol from fragmented mol

2017-10-05 Thread Lingtjien hong
I want to implement the following algorithm using RDkit - given an atom - break the bonds between this atom and its neighbor(s) - create new mol types/variables from the neighboring fragments example: R1-C-R2 - given atom C - return two mol types/variables R1 and R2 (not C) How can I achieve

Re: [Rdkit-discuss] nitrogen valence issues

2017-10-05 Thread Chris Earnshaw
Hi Be aware that there is a problem with one of the azide groups in CHEMBL592333 - in SMILES it's '-N=[NH+]-[NH-]' rather than '-N=[N+]=[N-]. This doesn't render the structure chemically invalid but it's probably wrong. What's the provenance of your SD file? It isn't the same as as a fresh

[Rdkit-discuss] UFF atom type errors

2017-10-05 Thread Bennion, Brian
Hello, As part of my workflow, I am attempting to generate a starting 3D structure from a 2D representation loaded from an sdf file. On certain structures I receive the following UFF errors when attempting to minimize the structure. [20:50:43] UFFTYPER: Unrecognized atom type: He1 (0)

Re: [Rdkit-discuss] Question on how to create mol from fragmented mol

2017-10-05 Thread Paolo Tosco
Dear Ling, This Jupyter notebook shows two possible different approaches to accomplish this: https://gist.github.com/ptosco/f60d7fc122001c7f72e99bc66748c47b HTH, cheers p. On 10/05/17 11:12, Lingtjien hong wrote: I want to implement the following algorithm using RDkit - given an atom -

Re: [Rdkit-discuss] nitrogen valence issues

2017-10-05 Thread Chris Earnshaw
Hi Some interesting differences in behaviour compared with my RDkit installation. Using the ChEMBL SMILES (freshly downloaded now) -

Re: [Rdkit-discuss] Implicit Hydrogens On Aromatic Hetereoatoms

2017-10-05 Thread Greg Landrum
Hi Chris, There's an additional step performed during sanitization that recognizes that the implicit H needs to be on the N. The steps of a normal full molecular sanitization operation are documented here: http://www.rdkit.org/docs/RDKit_Book.html#molecular-sanitization The adjustHs() function

[Rdkit-discuss] Implicit Hydrogens On Aromatic Hetereoatoms

2017-10-05 Thread Chris Murphy
Hi! I'm running at an issue with implicit hydrogens on aromatic heteroatoms. I am feeding the following sdf into a mol object: Mrv16c5 10021719092D 28 31 0 0 0 0999 V2000 -2.90000.20760. C 0 0 0 0 0 0 0 0 0 0 0 0 -2.18710.62280. N