Re: [Rdkit-discuss] setting valence of choice to S and P atoms in rdkit

(CC'ing the list as I hadn't in my original reply) Dear Janusz, this is what I would do: >>> from rdkit import Chem >>> mol = Chem.MolFromSmiles('SSC') >>> print Chem.MolToSmiles(mol) CSS >>> print Chem.MolToSmiles(mol, allHsExplicit=True) [CH3][S][SH] >>> a = mol.GetAtomWithIdx(1) >>> print

Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

Looks like it is finding the correct version of boost (and it is finding boost serialize). /opt/rdkit/rdkit-Release_2017_03_2/build$ cmake -D RDK_BUILD_INCHI_SUPPORT=ON -D BOOST_ROOT=/opt/boost_1_61_0/ -D Boost_NO_SYSTEM_PATHS=ON .. -- Could NOT find InChI in system locations (missing:

Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

Let's move this off the list for a bit until we get it resolved. Can you please do: "VERBOSE=1 make testReaction" and send the output just to me? Thanks, -greg On Wed, Jun 21, 2017 at 10:24 AM, JP wrote: > Looks like it is finding the correct version of boost

[Rdkit-discuss] RMSD value between two non-covalent molecular complexes

dear RDKit experts, is it possible to calculate RMSD value between two non-covalent molecular complexes? For instance: complex1: X(conformer1) + H2O complex2: X(conformer2) + H2O i tried GetBestRMS and GetO3A.Align but the program clearly neglects H2O and calculates the RMSD only between

Re: [Rdkit-discuss] RDKit Compile Issue

Hi Matthew, Let's keep this off the list until it is solved. Is your RDBASE environment variable correctly set? p. > On 21 Jun 2017, at 20:59, Matthew Lardy wrote: > > Hi Paolo, > > Here are the results from test #5: > > test 5 > Start 5: testMultiFPB > > 5: Test

[Rdkit-discuss] Is there a Ubuntu ppa or some repository with the latest rdkit release as .deb ?

Hello, I'd like to install rdkit system-wide. However, I'd like the install to use a regular system package since rdkit is available in my distro. I don't like system-wide install from sources. Because they tend to install things in different places than what the binary package does, and

[Rdkit-discuss] RDKit Compile Issue

Hi all, I'm trying to get a new build for any version of RDKit from 2016_4 to the most reccent release. Everything builds correctly, but when I perform the tests each version fails at the same place: Start 5: testMultiFPB 5/116 Test #5: testMultiFPB

Re: [Rdkit-discuss] setting valence of choice to S and P atoms in rdkit

Hi Ling (and Paolo earlier), Thank you very much for your answers, both work very well. All the best and happy coding! Dr Janusz Petkowski Research Fellow at MIT EAPS Tel: +1 (617) 258 - 6910

Re: [Rdkit-discuss] Reverse scale of svg coordinates to atom coordinates

Thank you for the fast reply, Greg and Yang,   GetDrawCoords seem to be exactly what I need to proceed. I'll get the bleeding edge version or try and patch the code :-) Esben Jannik Bjerrum cand.pharm, Ph.D /Sent from my Ubuntu Touch Phone Phone +45 2823 8009

Re: [Rdkit-discuss] RDKit Compile Issue

Hi Matthew, try running a couple of the failing tests in verbose mode: ctest -I 5,5 -V ctest -I 9,9 -V I'd also suggest to check that your Boost libraries are in your LD_LIBRARY_PATH, as you have built your own. Cheers, p. On 06/21/17 19:17, Matthew Lardy wrote: Hi all, I'm trying to get

Re: [Rdkit-discuss] RDKit Compile Issue

Hi Paolo, Here are the results from test #5: test 5 Start 5: testMultiFPB 5: Test command: /gne/research/workspace/lardym/rdkit-Release_2017_03_2/build/Code/DataStructs/testMultiFPB 5: Test timeout computed to be: 9.99988e+06 5: [12:58:03] --- 5: Testing MultiFPBReader

Re: [Rdkit-discuss] RMSD value between two non-covalent molecular complexes

Hi Gosia, you may want to look at the CombineMols() function in the rdmolops module. If you make a single molecule out of the two fragments, then you should manage to get what you are looking for. Cheers, p. On 06/21/17 14:47, gosia olejniczak wrote: dear RDKit experts, is it possible to

Re: [Rdkit-discuss] Reverse scale of svg coordinates to atom coordinates

Hi Esben, The call you are looking for is drawer.GetDrawCoords(atomIdx). This was, unfortunately, missing from the last release. It will be in the next one: In [14]: mol = Chem.MolFromSmiles('CC') ...: mc = rdMolDraw2D.PrepareMolForDrawing(mol) ...: drawer =

Re: [Rdkit-discuss] Reverse scale of svg coordinates to atom coordinates

Hi, Esben Jannik Bjerrum,     I have studied how to do it, though it may not be the best way. In `rdMolDraw` there are `getAtomCoords` and `getDrawCoords` in C++ APIs     http://www.rdkit.org/docs/cppapi/classRDKit_1_1MolDraw2D.html#abd327050dfa838543103d1f2c5f28f23      But these APIs are

Re: [Rdkit-discuss] Definition of HBA differs from pipeline pilot

Hi, Chris, ? ? Thank you very much for the suggestion. But I tend to tell my fellows to use?Lipinski' HBA in PP :). ? ? (BTW,?http://www.macinchem.org?is pretty good. I like the website and thanks for the "advertisement") Cheers, Hongbin Yang? ?From:?Chris

[Rdkit-discuss] Reverse scale of svg coordinates to atom coordinates

Hi RDkitters,   I'm experimenting a bit with an application with some user interactivity. I get the SVG coordinates from the Mol SVG drawing from the user interaction and need to get back to the atom coordinates with the goal of identifying the atom nearest the selected coordinates (or is there