Re: [Rdkit-discuss] about SMILES
Hi Jean-Marc, The question about atom data was answered elsewhere by Nils, but on atom ordering: On Mon, Jun 13, 2022 at 2:50 PM Jean-Marc Nuzillard < jm.nuzill...@univ-reims.fr> wrote: > > About mol = Chem.MolFromSmiles(smi), I would like to know > whether the atoms indexes in mol follow always exactly the apparition > order of > the atoms in smi. > The RDKit preserves the atom ordering. The only exception to this is that by default any hydrogens which are present in the SMILES will be removed (you can turn this off), so 'FC(O[H])Br' ends up being a four atom molecule with indices 0:F, 1:C, 2:O, 3:Br -greg ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] about SMILES
Dear Nils, thank you for pointing out the existence CXSMILES. In CXSMILES, the SMILES is written first and is followed by atom data. This is not what I had in mind first but this is ok for me. The good point is that the ad hoc reader and writer are already available through rdkit. Best regards, Jean-Marc Le 13/06/2022 à 17:04, Nils Weskamp a écrit : Dear Jean-Marc, I am not entirely sure I understand what you mean with "insert atom data inside of a chain". There are a number of proprietary extensions of smiles, such as e.g. CXSMILES https://docs.chemaxon.com/display/docs/chemaxon-extended-smiles-and-smarts-cxsmiles-and-cxsmarts.md that offer various additional options. To some extent, CXSMILES are supported by RDKit: https://www.rdkit.org/docs/RDKit_Book.html#cxsmiles-cxsmarts-extensions Hope ths helps, Nils Am 13.06.2022 um 14:30 schrieb Jean-Marc Nuzillard: Dear all, About mol = Chem.MolFromSmiles(smi), I would like to know whether the atoms indexes in mol follow always exactly the apparition order of the atoms in smi. Are there extensions of the SMILES format that would allow one to insert atom data inside of a chain? If yes, where could I find details about these extensions? Best, Jean-Marc Nuzillard -- Jean-Marc Nuzillard Directeur de Recherches au CNRS Institut de Chimie Moléculaire de Reims CNRS UMR 7312 Moulin de la Housse CPCBAI, Bâtiment 18 BP 1039 51687 REIMS Cedex 2 France ORCID : -0002-5120-2556 Tel : +33 (0)3 26 91 82 10 http://www.univ-reims.fr/icmr http://eos.univ-reims.fr/LSD/CSNteam.html https://nuzillard.github.io/PyLSD http://eos.univ-reims.fr/LSD/JmnSoft ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] about SMILES
Dear Jean-Marc, I am not entirely sure I understand what you mean with "insert atom data inside of a chain". There are a number of proprietary extensions of smiles, such as e.g. CXSMILES https://docs.chemaxon.com/display/docs/chemaxon-extended-smiles-and-smarts-cxsmiles-and-cxsmarts.md that offer various additional options. To some extent, CXSMILES are supported by RDKit: https://www.rdkit.org/docs/RDKit_Book.html#cxsmiles-cxsmarts-extensions Hope ths helps, Nils Am 13.06.2022 um 14:30 schrieb Jean-Marc Nuzillard: Dear all, About mol = Chem.MolFromSmiles(smi), I would like to know whether the atoms indexes in mol follow always exactly the apparition order of the atoms in smi. Are there extensions of the SMILES format that would allow one to insert atom data inside of a chain? If yes, where could I find details about these extensions? Best, Jean-Marc Nuzillard ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] about SMILES
Dear all, About mol = Chem.MolFromSmiles(smi), I would like to know whether the atoms indexes in mol follow always exactly the apparition order of the atoms in smi. Are there extensions of the SMILES format that would allow one to insert atom data inside of a chain? If yes, where could I find details about these extensions? Best, Jean-Marc Nuzillard -- Jean-Marc Nuzillard Directeur de Recherches au CNRS Institut de Chimie Moléculaire de Reims CNRS UMR 7312 Moulin de la Housse CPCBAI, Bâtiment 18 BP 1039 51687 REIMS Cedex 2 France ORCID : -0002-5120-2556 Tel : +33 (0)3 26 91 82 10 http://www.univ-reims.fr/icmr http://eos.univ-reims.fr/LSD/CSNteam.html https://nuzillard.github.io/PyLSD http://eos.univ-reims.fr/LSD/JmnSoft ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
