[Rdkit-discuss] InChI to Mol to InChi

2018-12-17 Thread JEAN-MARC NUZILLARD
Dear all, I tried to transform an InChI into a Mol and back to InChi. The following code: inchi1 = "InChI=1S/C20H26O4/c1-12(2)17-11-18(22)14(4)7-5-6-13(3)8-16(21)9-15-10-19(17)24-20(15)23/h6-7,10,12,17,19H,5,8-9,11H2,1-4H3/b13-6-,14-7+/t17-,19-/m1/s1" m = Chem.MolFromInchi(inchi1) m = Chem.Ad

Re: [Rdkit-discuss] InChI to Mol to InChi

2018-12-17 Thread Jason Biggs
Is this the same issue as https://github.com/rdkit/rdkit/issues/1852? where the input string specifies a trans double bond in a ring but EmbedMolecule returns a cis configuration? I get different SMILES string before and after embedding, C/C1=C/C/C=C(\C)C(=O)C[C@H](C(C)C)[C@H]2C=C(CC(=O)C1)C(=O)O

Re: [Rdkit-discuss] InChI to Mol to InChi

2018-12-17 Thread Yingfeng Wang
Jason, I can see the image :-) Yingfeng On Mon, Dec 17, 2018 at 10:01 AM Jason Biggs wrote: > Is this the same issue as https://github.com/rdkit/rdkit/issues/1852? > where the input string specifies a trans double bond in a ring but > EmbedMolecule returns a cis configuration? I get different

Re: [Rdkit-discuss] InChI to Mol to InChi

2018-12-17 Thread Dmitri Maziuk via Rdkit-discuss
On Mon, 17 Dec 2018 14:23:32 +0100 JEAN-MARC NUZILLARD wrote: ... > returns DIFFERENT. > > Removing the EmbedMolecule step returns EQUAL. > > How could I change that? You could try generating multiple conformers instead and checking if one of them returns EQUAL. -- Dmitri Maziuk __

Re: [Rdkit-discuss] [**SPAM** ? (26%)] Re: InChI to Mol to InChi

2018-12-17 Thread JEAN-MARC NUZILLARD
Is there any more deterministic procedure than the one of trying until success is obtained? How do I determine the InChI string of a conformer obtained after multiple embedding? I know how to do it for a molecule, so, how do I make a molecule from a conformer? All the best, Jean-Marc Le

Re: [Rdkit-discuss] InChI to Mol to InChi

2018-12-17 Thread Dimitri Maziuk via Rdkit-discuss
On 12/17/18 4:50 PM, JEAN-MARC NUZILLARD wrote: > Is there any more deterministic procedure than the one of trying until > success is obtained? > > How do I determine the InChI string of a conformer obtained after > multiple embedding? This representation keeps 3D config: http://alatis.nmrfam.wis