Re: [Rdkit-discuss] Struggling with apache + rdkit + django

Dear Stéphane, I can run Python scripts import RDKit modules on CentOS 7 by putting the following rdkit.conf file in /etc/ld.so.conf.d: $ cat /etc/ld.so.conf.d/rdkit.conf /var/www/cgi-bin/rdkit/rdkit-Release_2016_03_1/lib and adding two SetEnv directives in the section of my Apache

Re: [Rdkit-discuss] GetSubstructMatch vs MMFFOptimize

Dear Robert, the reason of the failure is that MMFF uses its own aromaticity model (see http://www.rdkit.org/docs/GettingStartedInPython.html#working-with-3d-molecules). Therefore, after calling AllChem.MMFFOptimizeMolecule(mols[0]) you will need to add the following call:

Re: [Rdkit-discuss] depicting fragments

Dear Francesco, Check this: https://nbviewer.jupyter.org/gist/ptosco/1a02149fa0602c24c86cc557b0cfedef More information and examples in this RDKit blog post that Greg published some time ago: http://rdkit.blogspot.it/2015/02/new-drawing-code.html Best, Paolo > On 5 May 2016, at 17:01,

Re: [Rdkit-discuss] DLL load failed after from rdkit import rdBase in python

Dear Hans-Juergen, I'd make sure you have both %RDBASE%\lib and the folder containing Boost DLLs in your PATH. I'd also check that PYTHONPATH points to %RDBASE%, and that no Python 32-bit DLLs are your PATH. Best, Paolo > On 1 May 2016, at 10:47, Contact wrote: > > Hi,

Re: [Rdkit-discuss] sdf reading error between osx and windows

Dear Steven, did you try to open the file in binary mode on the Windows build ans see if it makes a difference? It does not make any difference on Linux and OS X, but it will change how newlines are handled on Windows. I suspect that's where the problem might be. Please get back to me, later

Re: [Rdkit-discuss] Protonation and deprotonation

Dear Mark, you may wish to have a look at the SetFormalCharge() method, which operates on Atom objects: http://www.rdkit.org/docs/api/rdkit.Chem.rdchem.Atom-class.html#SetFormalCharge E.g., to protonate a piperidine: import rdkit from rdkit import Chem # create molecule from SMILES mol =

Re: [Rdkit-discuss] conformation search and constraints

Dear Rafal, On 22/04/2016 17:15, Rafal Roszak wrote: > Hello, > > I want to find: > A) "global minimum" [*] for given compound(s) and > B) (for the same compound) minimum with constraint(s) (e.g. frozen > angle) > > For problem A) I tried folowing code: > > self.MOLEC=Chem.MolFromSmiles(SMILES)

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

04/2016 19:43, Paolo Tosco wrote: Dear Tim, did you check that the Boost libraries you linked the RDKit against are in the postgres user LD_LIBRARY_PATH? You might need to login as root, then su postgres, and echo "export LD_LIBRARY_PATH=" > ~/.bashrc. Then, as root, resta

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

Dear Tim, did you check that the Boost libraries you linked the RDKit against are in the postgres user LD_LIBRARY_PATH? You might need to login as root, then su postgres, and echo "export LD_LIBRARY_PATH=" > ~/.bashrc. Then, as root, restart the postgres service. That fixed the problem for

Re: [Rdkit-discuss] ring bond query

Dear Yingfeng, the reason why RingInfo is not initialized is that you are invoking SmilesToMol() with the sanitize flag set to false; setting that parameter to true in the SmilesToMol() call should fix your problem. Kind regards, Paolo On 4/13/2016 16:48, Yingfeng Wang wrote: This is my

Re: [Rdkit-discuss] DLL load failed error

alled by means of pip and should be Python 2.7 and 32bit versions. Hence there are plenty of things that could be getting in the way of the RDKit installation but I wondered if there was anything known regarding this DLL error. Would redoing the installations in a different order (ie RDKit be

Re: [Rdkit-discuss] UFF Angle Bend force constant

Dear Rafal, good catch: there was actually a bug in getUFFAngleBendParams(), where the theta0 value (in radians) was multiplied by the RAD2DEG conversion factor before being returned to the user (which is correct, since theta0 values in the UFF parameters are given in radians),but then,

Re: [Rdkit-discuss] mmFF minimization in context of two ligands/binding pocket

Dear Steven, just to add up a small bit to Maciek's reply, you may find some examples how to use the RDKit MMFF94 C++ API in Code/ForceField/MMFF/testMMFFForceField.cpp and in Code/ForceField/MMFF/testMMFFHelpers.cpp. All of the constraints are available from C++, a search for "fixed atoms"

Re: [Rdkit-discuss] Suppress stdout and stderr in rdkit

Dear Gaetano, you may try the following: from rdkit import rdBase rdBase.DisableLog('rdApp.error') You may check the logging levels you wish to disable/enable in rdkit/RDLogger.py, or use a wildcard such as 'rdApp.*' to affect all levels at once. Best, Paolo On 17/02/2016 23:54, Gaetano

Re: [Rdkit-discuss] stereochemistry of S with degree 3

Dear Andrew, that functional group is a sulfoxide, and it is indeed chiral because has a lone pair on the sulfur, which is pyramidal; there is a short description here: https://en.wikipedia.org/wiki/Sulfoxide So it is the same (R,S) chirality you would have on a tetrahedral carbon. The carbon

Re: [Rdkit-discuss] stereochemistry of S with degree 3

Sorry for the noise, this is the same message as before, just with less typos and repetitions. I couldn't help re-sending it after reading what I had written! Dear Andrew, the reason why Chem.CanonSmiles("CN[S@@](=O)C1=CC=CC=C1") returns 'CN[S@@](=O)c1c1' and

Re: [Rdkit-discuss] stereochemistry of S with degree 3

Dear Andrew, the reason why Chem.CanonSmiles("CN[S@@](=O)C1=CC=CC=C1") returns 'CN[S@@](=O)c1c1' and Chem.CanonSmiles("CN1.[S@@]1(=O)C1=CC=CC=C1") returns 'CN[S@](=O)c1c1' is that there is a "ghost" atom involved in determining the sulfur chirality, which is a lone pair, which is the

Re: [Rdkit-discuss] enumation of conjugated pi system in a molecule

Dear Guillaume, please find attached a C++ snippet which exemplifies how to do what you need. For instance, if you issue the following: $ ./conjGrp c1c1Cc1c1CCc1c1 6 0,1 13 1 14 2 you get a printout of a list where the first column is the index of the heavy atom

Re: [Rdkit-discuss] Generation of stereo-isomers

Dear Soren, I have recently used the RDKit to enumerate stereocentres. The approach I followed was to generate a 3D structure for the molecule of interest (including hydrogens) using EmbedMolecule(), followed by MMFF optimization; do not pay attention to stereochemistry at this stage. Then I

Re: [Rdkit-discuss] rdkitjs test cases update + issues related to MMFFOptimizeMoleculeConfs

Dear Guillaume, would it be a lot of work to try to build against the current head? I have recently modified MMFFOptimizeMoleculeConfs() in the C++ layer to make it more efficient when running multithreaded: https://github.com/rdkit/rdkit/pull/534 So it would be interesting to know if the

Re: [Rdkit-discuss] raw RMSD matrix of docking poses

Dear Jose Manuel, I found a script on my hard disk which should do what you describe. Syntax is ./symmFit.py [-r] [-s] refFile.sdf prbFIle.sdf The -r option triggers the computation in place, i.e., without realigning poses. The -s option triggers consideration of symmetric atoms when doing

Re: [Rdkit-discuss] MMFF tunning

Dear Guillaume, I am afraid I can't reproduce what you describe. Please look at the enclosed Python script, which generates a molecule from your SMILES string, then it attempts to embed it multiple times, and for each embedding it carries out multiple minimizations. If you run it with:

Re: [Rdkit-discuss] licence type

Dear Guillaume, it looks like a forward declaration is missing there; try patching Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h as follows: *** ./Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h Wed May 13 09:32:12 2015 --- ./Code/GraphMol/ForceFieldHelpers/MMFF/Builder.hWed May 13

Re: [Rdkit-discuss] licence type

*De :* Paolo Tosco [paolo.to...@unito.it] *Envoyé :* mercredi, 13. mai 2015 10:35 *À :* Guillaume GODIN; Greg Landrum *Cc :* rdkit-discuss@lists.sourceforge.net *Objet :* Re: [Rdkit-discuss] licence type Dear Guillaume, it looks like a forward

Re: [Rdkit-discuss] How to get force field contributions?

Dear Joseph, please find attached a commented Python script which illustrates how to achieve what you describe. You can do the same from C++. In the C++/Python API documentation you may also find that accessor functions are available to retrieve force constants/equilibrium values for the

Re: [Rdkit-discuss] SDF tags and -

Dear all, Indeed, as Riccardo mentions, according to the specifications in CTfile.pdf a property should be truncated after the first blank line. This is also what other SDF parsers I have tried actually do. What I noticed is that other SDF parsers are tolerant of spurious lines not starting

Re: [Rdkit-discuss] out-of-plane bends

Dear Michal, please find attached a small script which accomplishes what you describe by a different approach, i.e. it minimizes only the methyl group in 2-methylthiophene while keeping the rest fixed, effectively pushing it back in plane. Would that work for you? Best, Paolo On 04/15/2015

Re: [Rdkit-discuss] Problem building recent revisions on Windows

Hi James, Greg, I just submitted a pull request which fixes: - one actual build failure on Windows (missing library dependency in Code/GraphMol/CMakeLists.txt) - one test failure on Windows (this was a CR+LF fix included in a previous pull request of mine which seems not to have been merged

Re: [Rdkit-discuss] tests failed on Cygwin

: - 13: Unit tests for copying UFF ForceFields. 13: done 13/85 Test #13: testUFFForceField Passed0.35 sec Best wishes, Michal On 17 March 2015 at 23:27, Paolo Tosco paolo.to...@unito.it wrote: Hi Michal, regarding test 13, would you mind trying to change

Re: [Rdkit-discuss] tests failed on Cygwin

Hi Michal, regarding test 13, would you mind trying to change line 1400 in /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp from TEST_ASSERT((int)MolTransforms::getDihedralDeg(mol-getConformer(), 1, 3, 6, 8) == -10); to std::cout

Re: [Rdkit-discuss] Tests failing on Windows: more info

Hi James, investigating what is going wrong in the Windows build is on my to-do list for 21-22 Feb; I'll let you know if I manage to find something. Kind regards, Paolo On 02/10/2015 06:14 PM, James Davidson wrote: Hi Paolo, Greg, et al. I have also been having some problems recently

Re: [Rdkit-discuss] Tests failing on Windows: more info

usual visual studio 2010 setup. On Fri, Jan 23, 2015 at 7:11 PM, Paolo Tosco paolo.to...@unito.it wrote: Dear Igor, Thank for your suggestion. Indeed, all of my environment variables are correctly set. I have just verified that I can build the latest released version 2014_09_2 with MSVC

[Rdkit-discuss] Tests failing on Windows: more info

Dear Igor, Thank for your suggestion. Indeed, all of my environment variables are correctly set. I have just verified that I can build the latest released version 2014_09_2 with MSVC 2013 without issues, all tests are passed. Instead, with the development version, The following tests FAILED:

Re: [Rdkit-discuss] RDkit library path

Dear Nicolas, the x86_64 RPM package installs all C++ RDKit libraries in /usr/lib64, so the path required by R should be /usr/lib64. If instead the Python path is required, you might try /usr/lib64/python2.6/site-packages/rdkit or alternatively /usr/lib64/python2.6/site-packages. HTH, kind

Re: [Rdkit-discuss] GetSubstructMatches() and resonance structures

] atom equivalence for substructure ma... Skip to site navigation (Press enter) View on www.mail-archive.com Preview by Yahoo From: Paolo Tosco paolo.to...@unito.it To: rdkit-discuss@lists.sourceforge.net rdkit-discuss@lists.sourceforge.net Sent: Thursday, October 30, 2014 4:26 PM Subject

[Rdkit-discuss] GetSubstructMatches() and resonance structures

Dear all, The following code snippet compares two resonance structures of formate anion: import rdkit from rdkit import Chem mol1=Chem.MolFromSmiles('C([O-])=O') mol2=Chem.MolFromSmiles('C(=O)[O-]') mol1.GetSubstructMatches(mol2, uniquify = False) ((0, 2, 1),) mol1.GetSubstructMatches(mol1,

Re: [Rdkit-discuss] how to retrieve force field angles and bond lengths values?

Dear Jose Manuel, I'll look into exposing that functionality more conveniently in both the C++ and Python layers. You'll have to wait until the next weekend, though... :-) The repository on SourceForge is very outdated; all source code has been moved to Github long ago:

Re: [Rdkit-discuss] missing function for measuring angles

Dear José-Manuel, I have just updated to the latest RDKit development version and the modules listed in rdMolTransforms include the Get.../Set... functions you wish to use: import rdkit from rdkit import Chem from rdkit.Chem import rdMolTransforms dir(rdMolTransforms)

Re: [Rdkit-discuss] MMFF bond parameters

___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- == Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel

Re: [Rdkit-discuss] Minimizing a Boron containing molecule with MMFF94 ... surprising

Dear Jean-Paul, unfortunately there are no parameters for boron in the original MMFF94 formulation. OpenEye has developed extensions to MMFF94 to include divalent selenium and boron, but those parameters have not been published. Cheers, p. On 03/07/14 18:14, JP wrote: When I have a Boron

Re: [Rdkit-discuss] 3D alignment in Python: align conformers of 2 molecules

Dear Thomas, if you wish to align two structures by their MCS, O3A is probably not the tool for you. O3A is meant for unsupervised alignment, and it will attempt to align two structures matching the most similar pairs of atoms between the two. Similarity is defined by the closeness of their

Re: [Rdkit-discuss] DihedralConstraint in MMFF minimize - keeping amides planar

work out of the box? On 11 May 2014 23:08, Jan Domanski jan...@gmail.com wrote: Awesome, this was lightning speed Paolo – many thanks! - Jan On 10 May 2014 20:47, Paolo Tosco paolo.to...@unito.it wrote: Dear Jan, the reason why your restraint was seemingly not applied

Re: [Rdkit-discuss] DihedralConstraint in MMFF minimize - keeping amides planar

Jan, Greg gave the exact reply that I would have given if I didn't have to turn off the phone before takeoff. You may imagine a number of cases where a special rule might appear to fix things - while probably breaking a number of others. MMFF94 is one of the best force-fields for small

Re: [Rdkit-discuss] DihedralConstraint in MMFF minimize - keeping amides planar

://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- == Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: paolo.to

Re: [Rdkit-discuss] MMFF94 atom typing OHs connected to aromatic heterocycles.

. Download your free book today! http://p.sf.net/sfu/NeoTech ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- == Paolo

[Rdkit-discuss] UFF/MMFF constraints

Python: check Code/ForceField/Wrap/testConstraints.py Regards, Paolo -- == Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670

Re: [Rdkit-discuss] Minimising bits of molecules?

-- == Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it http://open3dqsar.org | http://open3dalign.org

Re: [Rdkit-discuss] UFF/MMFF atom types

some new parameters (as for UFF, adding Python support) and fall back to a related atom type (sulfur, in this case) for the missing ones. I'll look into that during the next days and let you know. Best, p. -- == Paolo Tosco, Ph.D. Department

Re: [Rdkit-discuss] bug in rdMolTransforms.SetDihedralDeg?

Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- == Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348

Re: [Rdkit-discuss] Append to SD file with SDWriter

-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- == Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011

Re: [Rdkit-discuss] SanitizeMMFFMol Error

-- == Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it http://open3dqsar.org | http

Re: [Rdkit-discuss] MMFF Problem

-discuss -- == Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it http

Re: [Rdkit-discuss] failed tests for github master version on ubuntu

/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- == Paolo Tosco, Ph.D. Department of Drug Science

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