Re: [Rdkit-discuss] another request for feedback on a new python API documentation format

2018-05-10 Thread Greg Landrum
Hi Maciek, The old docs are all still online. Since there aren't links, you just need to know the URL scheme: http://rdkit.org/RDKit_Docs.2017_09_1.tgz http://rdkit.org/RDKit_Docs.2016_03_1.tgz note that there are almost always only the "_1.tgz" version available; the patch releases don't

Re: [Rdkit-discuss] Atom mapping

2018-05-10 Thread Paul Emsley
On 10/05/2018 10:39, carlo del moro wrote: I put an example for better explain my problem. starting from a PDB representing HPE, I use RDKIT/obabel for calculate the relative SMILES. The three-letter-code (chemical component id) in a PDB file has meaning - it is a pointer to chemistry. The

Re: [Rdkit-discuss] Atom mapping

2018-05-10 Thread Maciek Wójcikowski
Hi, The smiles atom order is saved in a private property '_smilesAtomOutputOrder', see discussion on Github: https://github.com/rdkit/rdkit/issues/794 The order of atoms in PDB is the same as in RDKit's Mol object, thus it's fairly easy to find such mapping. Pozdrawiam, | Best regards,

Re: [Rdkit-discuss] Atom mapping

2018-05-10 Thread carlo del moro
Thanks to all for the replies, I put an example for better explain my problem. starting from a PDB representing HPE, I use RDKIT/obabel for calculate the relative SMILES. Next, using a RDKIT's function I fragment the smiles in substructure like this "CC(=O)O"; now I need to remap this