[Rdkit-discuss] problem compiling RDKit_Q22010_1

2010-08-25 Thread Paul Emsley
Hi, I am trying to compile RDKit for the first time, ubuntu 10.04 x86_64 ... [ 82%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o [ 83%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o [ 83%] Building CXX object

Re: [Rdkit-discuss] problem compiling RDKit_Q22010_1

2010-08-25 Thread Paul Emsley
On 25/08/10 16:14, Greg Landrum wrote: Hi Paul, On Wed, Aug 25, 2010 at 7:26 AM, Paul Emsleypaul.ems...@bioch.ox.ac.uk wrote: Hi, I am trying to compile RDKit for the first time, ubuntu 10.04 x86_64 ... unsigned long)::s_data' can not be used when making a shared object;

[Rdkit-discuss] Generating 3D coordinates

2010-09-10 Thread Paul Emsley
Hi All, I've been tinkering a bit more with RDKit and having fun. I have hit a problem though. I am trying to reproduce Greg's Generating 3D coordinates in RDKit-overview.pdf in C++: This is what I have (mostly via cut 'n paste): int main(int argc, char **argv) { std::string

Re: [Rdkit-discuss] Generating 3D coordinates

2010-09-11 Thread Paul Emsley
It's kind of interesting (and encouraging) that the optimizer doesn't completely freak out when you hand it a 2D conformer. :-) Ah... :) What makes 3D coordinates? (I'm guessing it's a one-liner somewhere...) It is indeed a one-liner (two lines with a bit of error checking).

[Rdkit-discuss] compiling with -Wundef

2010-09-12 Thread Paul Emsley
Hi, If I try to compile using RDKit's Invariant.h using g++ with -Wundef: /home/paul/rdkit/svn/rdkit/trunk/Code/RDGeneral/Invariant.h:142:7: warning: INVARIANT_ASSERT_METHOD is not defined /home/paul/rdkit/svn/rdkit/trunk/Code/RDGeneral/Invariant.h:151:7: warning: INVARIANT_SILENT_METHOD is

Re: [Rdkit-discuss] Updates to the build system

2010-09-15 Thread Paul Emsley
On 15/09/10 05:38, Greg Landrum wrote: Dear all, Thanks to some really great help from Gianluca Sforna and Riccardo Vianello, the RDKit build system has been updated to make installing the software in standard locations (like /usr/local on linux machines) easier. The changes should also make

Re: [Rdkit-discuss] newbie help cleaning up sterochemistry in SMILES string

2010-09-18 Thread Paul Emsley
On 18/09/10 05:19, Greg Landrum wrote: On Sat, Sep 18, 2010 at 12:05 AM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: So now with the replace function in python I can easily remove sterochem information from the molecule. smiles_corrected = smiles_broken.replace(@,) Once I

[Rdkit-discuss] assignRadicals...

2010-09-19 Thread Paul Emsley
Hi, It seems to me that the declaration void assignRadicals(RWMol mol) needs to be added to MolOps.h Cheers, Paul. -- Start uncovering the many advantages of virtual appliances and start using them to simplify

Re: [Rdkit-discuss] svg export from rdkit messed up in Adobe Illustrator , but not in firefox / chrome: fixes?

2010-09-24 Thread Paul Emsley
As a hack, I suppose that you could add transform=scale(0.2) (or some such) to the attributes of the paths for the glyph symbols. i.e. replace path style=stroke:none; d=M 0.5 1.765625 L 0.5 -7.046875 L 5.5 -7.046875 L 5.5 1.765625 L 0.5 1.765625 Z M 1.0625 1.21875 L 4.9375 1.21875 L 4.9375

[Rdkit-discuss] kekulizing carbazole

2010-10-31 Thread Paul Emsley
Hi, I'm running into problems when I try to kekulize carbazole. The description I start with is that all the bonds are marked as Bond::AROMATIC and I do setIsAromatic(true) on all the atoms (which are all non-hydrogens). The explicitValence() for the N is 3. MolOps::Kekulize() fails in that

Re: [Rdkit-discuss] kekulizing carbazole

2010-11-01 Thread Paul Emsley
On 31/10/10 14:18, Greg Landrum wrote: Hi Paul, On Sun, Oct 31, 2010 at 12:09 PM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: I'm running into problems when I try to kekulize carbazole. The description I start with is that all the bonds are marked as Bond::AROMATIC and I do

[Rdkit-discuss] C++ documentation?

2011-10-20 Thread Paul Emsley
Hi, Is there a web presence for the C++ documentation that I am missing? The easy-to-find link: http://rdkit.org/C++_Docs seems empty. Thanks, Paul. -- The demand for IT networking professionals continues to grow,

[Rdkit-discuss] MolFileAtomLine() massDiff

2012-02-04 Thread Paul Emsley
Greg, Just a small FYI: According to ctfile.pdf, the mass difference on the atom line in the atom block should be clamped between -3 to 4 (inclusive). I discovered this because MolToMolFile() had written out a mol file with mass diffs of -11, -13, -15 :) (I had presumed that when I used

[Rdkit-discuss] MolChemicalFeature.h installed?

2012-02-06 Thread Paul Emsley
Hi Greg, Maybe I'm missing something... Is it possible for you to add an rdkit_headers for MolChemicalFeature.h and friends in Code/GraphMol/MolChemicalFeatures/CMakeLists.txt? Thanks, Paul. -- Try before you buy =

Re: [Rdkit-discuss] generate atom names?

2012-04-11 Thread Paul Emsley
On 10/04/12 12:01, Greg Landrum wrote: On Tue, Apr 10, 2012 at 11:07 AM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: (Just making sure I have not missed anything...) Is there a function that generates unique atom names (using at-setProp(name, name) presumably) for a given molecule? (I

[Rdkit-discuss] un-oneandahalfs

2012-04-12 Thread Paul Emsley
Hi all, (Sorry for another noob question) When creating a 2d depiction, or otherwise, is there a way to turn a carboxylate (with ONEANDAHALF bonds between the carbon and oxygens) into something with a carbonyl oxygen (DOUBLE) and a hydroxyl oxygen (SINGLE)? Cheers, Paul.

Re: [Rdkit-discuss] un-oneandahalfs

2012-04-15 Thread Paul Emsley
On 15/04/12 16:36, Paul Emsley wrote: On 14/04/12 06:14, Greg Landrum wrote: On Thu, Apr 12, 2012 at 1:05 PM, Paul Emsleypaul.ems...@bioch.ox.ac.uk wrote: When creating a 2d depiction, or otherwise, is there a way to turn a carboxylate (with ONEANDAHALF bonds between the carbon and oxygens

Re: [Rdkit-discuss] [Rdkit-devel] 2012.03 (Q1 2012) RDKit release

2012-04-16 Thread Paul Emsley
On 13/04/12 05:37, Greg Landrum wrote: I'm very happy to announce that the next version of the RDKit -- 2012.03 (a.k.a Q1 2012) -- is released. Cool - thanks. Compiling now. In the pages: http://sourceforge.net/projects/rdkit/files/rdkit/Q1_2012/ http://sourceforge.net/projects/rdkit/files/

[Rdkit-discuss] PyObject * - RDKit::ROMol *

2012-04-29 Thread Paul Emsley
Hi all, I am trying to write a C++ function to examine an RDKit::ROMol... but running it from a python script: m = Chem.MolFromSmilesString('Oc1c1') do_cool_stuff(m) my C++ (which gets swigged) is: PyObject *do_cool_stuff(PyObject *pyo) { RDKit::ROMol *mol = magic(pyo);

Re: [Rdkit-discuss] PyObject * - RDKit::ROMol *

2012-04-30 Thread Paul Emsley
On 30/04/12 08:39, Uwe Hoffmann wrote: Hi, Am 29.04.2012 16:19, schrieb Paul Emsley: I am trying to write a C++ function to examine an RDKit::ROMol... but running it from a python script: m = Chem.MolFromSmilesString('Oc1c1') do_cool_stuff(m) my C++ (which gets swigged

Re: [Rdkit-discuss] PIL - molecule depiction

2012-05-07 Thread Paul Emsley
On 07/05/12 12:49, paul.czodrow...@merckgroup.com wrote: Dear RDKitters, when typing in from rdkit.sping import PIL I end up in this error message Traceback (most recent call last): File stdin, line 1, inmodule File

Re: [Rdkit-discuss] speed of Tanimoto similarity calculations

2012-05-07 Thread Paul Emsley
On 07/05/12 15:13, Uwe Hoffmann wrote: hi, Am 07.05.2012 14:40, schrieb Gonzalo Colmenarejo-Sanchez: Hi, I'm using these compilation options: g++ -o tanird tanird.cpp -I$RDBASE/Code -I$RDBASE/Extern -L$RDBASE/lib -lChemReactions -lFileParsers -lSmilesParse -lDepictor -lSubstructMatch

Re: [Rdkit-discuss] Molecule with no atoms, so is it valid?

2012-05-25 Thread Paul Emsley
On 23/05/12 13:24, JP wrote: The generator is going to give me an empty (third) molecule? So I have to always dirty my code with m.GetNumAtoms() 0 in that loop. What is the empty molecule is at the end of the file (ouch)? I'm curious about this point in particular. I don't know the

[Rdkit-discuss] python/c++ interface again...

2012-06-01 Thread Paul Emsley
Hi, I've been trying to read boost python docs and I am lost... I'd like to return a PyObject *. I have a RDKit::RWMol, say - or a pointer to a new one if need be... // return a regularized molecule (copy of input with coordinates replaced) PyObject * coot::regularize(PyObject *mol_in_py) {

Re: [Rdkit-discuss] python/c++ interface again...

2012-06-02 Thread Paul Emsley
On 02/06/12 04:44, Greg Landrum wrote: On Fri, Jun 1, 2012 at 1:41 PM, Paul Emsleypaul.ems...@bioch.ox.ac.uk wrote: I'd like to return a PyObject *. I have a RDKit::RWMol, say - or a pointer to a new one if need be... If you are using a boost.python interface, and your function is

[Rdkit-discuss] Fwd: Re: RDKit-based implementation of QED (quantitative estimation of drug-likeness)

2012-06-11 Thread Paul Emsley
seems to have got stuck - trying again... Original Message Subject: Re: [Rdkit-discuss] RDKit-based implementation of QED (quantitative estimation of drug-likeness) Date: Mon, 11 Jun 2012 06:57:28 +0100 From: Paul Emsley paul.ems...@bioch.ox.ac.uk To: rdkit-discuss

Re: [Rdkit-discuss] Building on CentOS 5.8: Python-related tests fail

2012-06-23 Thread Paul Emsley
On 23/06/12 14:05, Paul Emsley wrote: if you do encounter such, your solution may be somewhat simpler. Ooops, I meant: if you do *not* encounter such ... -- Live Security Virtual Conference Exclusive live event

Re: [Rdkit-discuss] Announcement: 1st RDKit User Group Meeting scheduled

2012-07-06 Thread Paul Emsley
On 06/07/12 10:06, JP wrote: I just noticed that this is a user meeting and not a dev one - so perhaps such a topic is out of scope... What's the difference? A user uses python and a dev uses python, boost.python and c++? Anyway, I too (AFAICS ATM) would be interested in your suggestion

Re: [Rdkit-discuss] Detecting rings and bond types from PDB HETATM record

2012-07-06 Thread Paul Emsley
On 06/07/12 10:27, JP wrote: Steifl -- that is a really crafty and less painful way how to go about it. The SMILES is in fact, a wget call away - since I am processing PDB deposited structures. http://www.rcsb.org/pdb/rest/describeHet?chemicalID=NAG It is not clear to me how the SMILES

Re: [Rdkit-discuss] RDKIT installation issue on Centos 5.6

2012-07-19 Thread Paul Emsley
On 19/07/12 13:28, Fabian Dey wrote: Dear all, I am having difficulties installing RDKIT on a Centos 5.6 (with python bindings). I compiled and installed the latest numpy, boost and cmake version from their sources (I had also tried using the versions available through yum - which are

Re: [Rdkit-discuss] problems with RDKit and Mountain Lion

2012-10-09 Thread Paul Emsley
homebrew is using the old svn repo? On 09/10/12 22:33, James Swetnam wrote: George- My templating fix was submitted as 2155, and HEAD in SVN is at 2234. I'm not terribly familiar with homebrew, or why it thinks 2148 is HEAD James On Tue, Oct 9, 2012 at 2:27 PM, George Papadatos

Re: [Rdkit-discuss] non-smallest rings

2013-01-22 Thread Paul Emsley
On 22/01/13 05:40, Greg Landrum wrote: Hi Paul, On Mon, Jan 21, 2013 at 4:13 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote: I am making heavy weather of the following problem - and am wondering if I am missing something (such as a useful RDKit function). I am working on this beasty

Re: [Rdkit-discuss] Building rdkit on Ubuntu 12.10

2013-04-25 Thread Paul Emsley
On 25/04/13 23:43, hari jayaram wrote: Hi I did a export RDBASE=/home/hari/RDKit_2012_09_1 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib Then cd into the build directory Run cmake .. Then run make At around 24% I get the following error ( see below) I installed the Ubuntu blessed

Re: [Rdkit-discuss] ROMol getConformer returning the copy of a conformer

2013-09-03 Thread Paul Emsley
On 03/09/13 20:21, Jan Domanski wrote: Hi, I'm trying to trivially modify the coordinates of the 0th atom of the 0th conformer in a (3D) ROMol called m. To do that I need to get the conformer: RDKit::ROMol m = ...; RDKit::Conformer conf = m.getConformer(-1); guessing somewhat, that

[Rdkit-discuss] RDKit UGM 2013 - a few pictures

2013-10-14 Thread Paul Emsley
https://www.dropbox.com/sh/a3s55kmxa37yx7e/vLC5uea1xP Paul. -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced

Re: [Rdkit-discuss] Beta of Q3 2013 release available

2013-10-25 Thread Paul Emsley
On 25/10/13 08:09, James Davidson wrote: Hi Roger, Thanks for the response The use of an integer file format flavor argument allows the caller to customize the behavior of the readers and writers. The semantics is that a reasonable default is zero (for all bits), but that new features may

Re: [Rdkit-discuss] PDB reader and bond perception

2014-01-13 Thread Paul Emsley
On 13/01/14 17:54, JP wrote: RDKitters! Finally back on the mailing list! I am sure we've been through this at the UGM (my mind must have wandered off!), but a quick question about the PDB reader and bond perception. Is this supported with the current PDB reader? I remember that

Re: [Rdkit-discuss] An ultimate way to compute 3D coordinates?

2014-04-05 Thread Paul Emsley
On 05/04/14 19:04, Michal Krompiec wrote: For example, it does not work well for long conjugated oligomers - sometimes it produces molecular knots instead of straight strands, and is quite slow for large systems. Can you expand on that? What sort of long conjugated oligomers were you

[Rdkit-discuss] chirality doxygen tweak

2014-07-01 Thread Paul Emsley
Hi Greg, I don't know if you care about this sort of thing, but if you do, then you should escape - i.e. \@ - (at least) one of the @s here (in Atom.h) //! tetrahedral: clockwise rotation (SMILES @@) So that the output html makes more sense. Currently see

[Rdkit-discuss] A case of the jaggies

2014-07-21 Thread Paul Emsley
Hi, Why are the structure images in the RDKit documentation nice and smooth but mine have the jaggies? What do I have to do to my PIL (or something?) for such smoothness? Thanks, Paul. -- Want fast and easy access

Re: [Rdkit-discuss] A case of the jaggies

2014-07-21 Thread Paul Emsley
On 21/07/14 17:22, Greg Landrum wrote: Hi Paul, On Mon, Jul 21, 2014 at 3:36 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk mailto:pems...@mrc-lmb.cam.ac.uk wrote: Why are the structure images in the RDKit documentation nice and smooth but mine have the jaggies? The jagged lines

Re: [Rdkit-discuss] Write mol/sdf files

2014-08-26 Thread Paul Emsley
On 26/08/14 10:42, acanada wrote: What is the best approach to write mol/sdf files for a compound which I already have chebi, inChi? m=Chem.MolFromInchi('InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3') print file('foo.mol','w+'),Chem.MolToMolBlock(m)

Re: [Rdkit-discuss] PandasTools on Windows iPython notebook

2014-09-25 Thread Paul Emsley
On 25/09/14 18:06, paul.czodrow...@merckgroup.com wrote: Dear RDKitter, on my new Windows laptop, I run into this issue: import pandas as pd import rdkit.Chem as Chem from rdkit.Chem import PandasTools = ValueError Traceback (most recent call last) ipython-input-6-52de9e808c94in

[Rdkit-discuss] MMFF bond parameters

2014-09-29 Thread Paul Emsley
Dear Paolo (I presume :-), I'd like to get the ro values for the bonds in an MMFF. I have the following so far: void mmff_bonds(RDKit::ROMol mol_in) { RDKit::MMFF::MMFFMolProperties *mmffMolProperties = new RDKit::MMFF::MMFFMolProperties(mol_in); ForceFields::ForceField *field = new

Re: [Rdkit-discuss] MMFF bond parameters

2014-09-29 Thread Paul Emsley
On 30/09/14 00:15, Paolo Tosco wrote: I'm afraid currently there is no public method to get r0 and kb from ForceField contribs. I have attached a C++ sample program which shows how to get the information you need from a ROMol. Ah! - His eyes opened! Thanks very much. P.

[Rdkit-discuss] Python argument types did not match C++ signature

2014-10-14 Thread Paul Emsley
Hi RDKitters, I'm a bit lost with boost::python/RDKit/MacOSX. I have a boost::python function: RDKit::ROMol *hydrogen_transformations(const RDKit::ROMol r); which is exposed like this: BOOST_PYTHON_MODULE(pyrogen) { def(hydrogen_transformations, hydrogen_transformations,

Re: [Rdkit-discuss] https://sourceforge.net

2015-03-23 Thread Paul Emsley
On 21/03/15 04:48, Greg Landrum wrote: Does anyone see a problem with me doing a commit there that removes all the code and just leaves a look in github readme? I would have found this useful :-) Paul. -- Dive

[Rdkit-discuss] Atom Symbol Case in MolFile?

2016-01-18 Thread Paul Emsley
Dear RDKitters, Is is clear what the case of the second character of an atom symbol in the atom block of a MolFile should be? i.e. "CL", "Cl" or either? Thanks, Paul. -- Site24x7 APM Insight: Get Deep Visibility

Re: [Rdkit-discuss] Compiling git RDKit on Mac OS X

2016-02-24 Thread Paul Emsley
Moving on... Now I get the message (see below). What's the difference? In the Release-based link.txt we have: -install_name /Users/pemsley/autobuild/b-e-l/rdkit-Release_2015_03_1/build/lib/libSLNParse.1.dylib In the git-based link.txt we have: -install_name @rpath/libSLNParse.1.dylib Is

Re: [Rdkit-discuss] Compiling git RDKit on Mac OS X (was: Atoms with strange positions/bonds when drawer makes PNG)

2016-02-23 Thread Paul Emsley
On 23/02/2016 15:52, Greg Landrum wrote: On Tue, Feb 23, 2016 at 3:50 PM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: This seems to be the relevant difference in the cmake output: [ 3%] Linking CXX shared libra

[Rdkit-discuss] Compiling git rdkit

2016-02-23 Thread Paul Emsley
Using: Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn) Target: x86_64-apple-darwin14.5.0 and boost_1_54_0: Scanning dependencies of target testMatCalc [ 29%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o [ 30%] Building CXX

Re: [Rdkit-discuss] Compiling git rdkit

2016-02-23 Thread Paul Emsley
Yes, but not for boost. On 23/02/2016 13:19, Giuseppe Marco Randazzo wrote: > Are you using homebrew? > >> On 23 Feb 2016, at 14:17, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: >> >> >> Using: >> Apple LLVM version 6.1.0 (clang-602.0.49) (based

Re: [Rdkit-discuss] Atom Symbol Case in MolFile?

2016-01-19 Thread Paul Emsley
says: "entry in periodic table" I interpret this to mean "Cl", since that's what one finds in the typical periodic table. The RDKit, curiously, agrees with me. ;-) :-) -greg On Mon, Jan 18, 2016 at 8:45 AM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk <mailto:pems...

[Rdkit-discuss] Atoms with strange positions/bonds when drawer makes PNG

2016-02-16 Thread Paul Emsley
Dear RDKitters, I have the following test code: std::string smiles="Clc1c1"; RDKit::ROMol *m_local = RDKit::SmilesToMol(smiles); RDDepict::compute2DCoords(*m_local); RDKit::Conformer conf = m_local->getConformer(); WedgeMolBonds(*m_local, ); bool includeStereo = true;

Re: [Rdkit-discuss] Atoms with strange positions/bonds when drawer makes PNG

2016-02-18 Thread Paul Emsley
Hi Greg, I tried to investigate this further with github rdkit but I am as yet unable to configure/cmake it yet on this Mac (something related to boost python has changed) :-/ :-) - will keep poking at it and/or abstracting it... Thanks, Paul. On 19/02/2016 09:19, Greg Landrum wrote: > > >

Re: [Rdkit-discuss] Problems with building RDKit on Linux

2016-03-19 Thread Paul Emsley
On 18/03/2016 19:23, Mendez Giraldez, Raul wrote: > Yes, I think so Paul. my $LD_LIBRARY_PATH points towards the installed boost > (by conda) is : > >

Re: [Rdkit-discuss] Problems with building RDKit on Linux

2016-03-19 Thread Paul Emsley
On 17/03/2016 18:00, Mendez Giraldez, Raul wrote: > Hi everybody, > > I'm trying to build RDKit on Red Hat Enterprise Linux Server release > 5.11 and I get the following problem after trying to import rdkit libraries: > > > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 > Type "help",

[Rdkit-discuss] library name change?

2016-08-19 Thread Paul Emsley
Greg, RDKit is becoming increasingly popular and is getting picked up by third parties, including the Linux distros. It seems to me that several RDKit library names are too generic (and hence confusing) for such an environment: I have in mind libs such as Alignment, Catalog, FileParsers

Re: [Rdkit-discuss] library name change?

2016-08-19 Thread Paul Emsley
On 19/08/2016 12:52, Greg Landrum wrote: > > It seems logical to me, though I would probably go with RDKit instead of RD > as the prefix. OK, that's clearer yet. -- ___

Re: [Rdkit-discuss] library name change?

2016-08-19 Thread Paul Emsley
I'd like to pick apart this comment: On 19/08/2016 15:45, Igor Filippov wrote: > It is sometimes a bit of a pain to collect the list of the dependencies. Do you mean that (for example) if you wanted to link with libMolChemicalFeatures, you also have to add libSubstructureMatch and

Re: [Rdkit-discuss] Error when building RdKit 2013_09_1

2016-09-05 Thread Paul Emsley
On 05/09/16 17:27, ??? wrote: Hi, Menaka, An easy way I suggest is to install boost via package manager, for example: $ sudo apt-get install libboost-devlibboost-system-devlibboost-thread-devlibboost-serialization-devlibboost-python-devlibboost-regex-dev and if you're on fedora you can

[Rdkit-discuss] off-topic: atom names in sdf files?

2016-09-10 Thread Paul Emsley
Hi RDKiters, Is it possible to store (PDB) atom names in sdf files? If so, how is this done? (It was not clear to me after reading CTFile.pdf.) (I hope that this question is allowed.) Thanks, Paul. --

Re: [Rdkit-discuss] Ring membership

2016-09-29 Thread Paul Emsley
On 29/09/16 15:12, Marco Stenta wrote: > Dear Colleagues, > I am working on intramolecular hydrogen bonds, formed between > donor-acceptors separated by 2,3,4 atoms, as described in the Roche paper: > Kuhn, B.; Mohr, P.; Stahl, M. J. Med. Chem. 2010, 53, 2601. > > I will use SMARTS and RDKIT to

Re: [Rdkit-discuss] error while calculating rms and shape tanimoto

2016-09-22 Thread Paul Emsley
Files 1.pdb and 2.pdb do not contain CONECT records (so missing bond orders?). File 1.pdb contains an atom with name BR43. Maybe the PDB parser can't parse that (seems valid to me, FWTW). Paul On 22/09/16 11:15, Amit singh wrote: Hi Files a.pdb and b.pdb are from RDKit test data (working

Re: [Rdkit-discuss] Find out if a molecuole object was generated from smiles or smarts

2016-11-07 Thread Paul Emsley
On 07/11/2016 12:37, Axel Pahl wrote: > > amongst other options, I can generate an RDKit mol object by one of > these two ways: > > mol1 = Chem.MolFromSmiles() > mol2 = Chem.MolFromSmarts() > > Is there a possibility to detect for a given mol object whether it was > generated from Smiles or

Re: [Rdkit-discuss] Coot heading to Fedora

2016-11-18 Thread Paul Emsley
On 18/11/2016 18:35, Gianluca Sforna wrote: > I just wanted to mention that coot (crystallographic macromolecular > building toolkit)[1] is the first package (at least, that I know of) > requiring rdkit as a dependency under review [2] to enter Fedora > repositories. I've been cheering you on

Re: [Rdkit-discuss] Coot heading to Fedora

2016-11-18 Thread Paul Emsley
On 18/11/2016 23:47, Greg Landrum wrote: > Hopefully you know that there is already a Cairo-based renderer in C++ and are > modifying/improving that? Oh. Either I didn't know about that or I'd forgotten about it. My code was well under-way before I heard about David's contribution and I

Re: [Rdkit-discuss] How to find the idx of hydrogens bonded to a specific atom

2016-10-13 Thread Paul Emsley
On 13/10/2016 05:04, Bin Song wrote: > Hello everyone, > > A new user of Rdkit and new subscriber of the mailing list reporting here. > > I have a question to ask, as stated in the subject. I have googled and > consulted the > documentation of rdkit, but found no answer. Basically, I want to run

Re: [Rdkit-discuss] Stereochemistry

2016-12-19 Thread Paul Emsley
On 19/12/2016 10:42, Jean-Marc Nuzillard wrote: > Thank you all! > > One more point: > > How do I get the bond indexes for which the E/Z configuration has been set? > I seems there are no "magic" properties for bonds and no HasProp() function > for bonds. Iterate through the bond list and use

Re: [Rdkit-discuss] minGW fails to build rdkit

2016-12-20 Thread Paul Emsley
On 20/12/16 15:13, Yingfeng Wang wrote: > Paolo, > > Thanks. I figure out this problem. The new cmake command is > > cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ > -DMSVC_RUNTIME_DLL=C:/Windows/System32/msvcr100.dll > -DRDK_USE_BOOST_SERIALIZATION=OFF -DBOOST_ROOT=C:/boost >

Re: [Rdkit-discuss] 3d descriptors generation

2017-07-13 Thread Paul Emsley
On 13/07/17 18:19, Abhik Seal wrote: Hello I am trying to generate 3d descriptors like RDF/MORSE using with 2017.03.01 release of rdkit and i am getting an error like module' object has no attribute 'CalcRDF' . I have Eigen3 installed as well. Any point outs what can be the issue ? Here is

[Rdkit-discuss] Contrib code license

2017-07-24 Thread Paul Emsley
Dear Greg, What license(s) will you allow for Contrib code? Is the Mozilla Public License acceptable? Thanks, Paul. -- Check out the vibrant tech community on one of the world's most engaging tech sites,

Re: [Rdkit-discuss] Which package should be used to improve the drawing quality in win64

2017-05-09 Thread Paul Emsley
On 09/05/2017 05:27, Hongbin Yang wrote: > Hi, all, > > By default, rdkit uses pillow to render images when using > rdkit.Chem.DrawMolecule. But > the quality is not good enough, like this: The effect you discuss is called aliasing. You want anti-aliasing. > If memory does not fail me,

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

2017-06-16 Thread Paul Emsley
On 16/06/2017 12:08, JP wrote: Hi Folks, Must have been eons ago last time I posted to this mailing list. The italians have a saying "chi non muore si rivede". I am trying to install the RDKit (release 2017_03_2) from source, without conda, and I thought this will be a breeze. But I am

Re: [Rdkit-discuss] Atom mapping

2018-05-09 Thread Paul Emsley
On 09/05/2018 16:27, carlo del moro wrote: we would like to know if it is possible to map the atom's ID of a SMILES represented substructure to the atom sequence of a ligand contained in a pdb file. This in order to get the spatial coordinates related to such substructure. Depending on

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] Issue with the latest RDKit DB build

2017-12-29 Thread Paul Emsley
On 29/12/2017 19:01, Drew Gibson via Rdkit-discuss wrote: Hello, and compliments of the season to you, RDKitters :) I'm having trouble getting the conda build of the DB package (rdkit-postgresql95) working. The issue I'm having occurs when trying to initialise the rdkit DB extension on a

Re: [Rdkit-discuss] postgres cartridge not parsing a SMILES

2018-01-13 Thread Paul Emsley
On 13/01/2018 18:52, Rajarshi Guha wrote: Hi, I'm using RDKit 2017.09 with Postgres 9.5 and a substructure query is failing when the query SMILES is C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3 Within [] the formal charge must be specified:

Re: [Rdkit-discuss] Perceived bond orders of RNA PDB-files

2019-12-04 Thread Paul Emsley
On 04/12/2019 08:28, Illimar Hugo Rekand wrote: Hello, everyone I was wondering if there is any reason for why aromaticity and perceived bond orders are not set properly when using the MolFromPDB-function for RNA PDB files, while it works perfectly for protein PDB files? You shouldn't be

Re: [Rdkit-discuss] c++ atomic lifetime

2020-08-27 Thread Paul Emsley
On 27/08/2020 20:15, Jason Biggs wrote: Everything I know about C++ I learned just so that I can write a link between an interpreted language and the rdkit, so there are definitely some gaps in my knowledge. What I'm trying to understand right now is the expected lifetime of an Atom pointer

Re: [Rdkit-discuss] mol2 file with atom type that is suitable for amber

2020-08-07 Thread Paul Emsley
On 05/08/2020 19:44, Nikhil Maroli wrote: I wanted to add atom types in mol2 file which is readable for amber/leap. Is it possible with rdkit? I did some work on CCP4 and Amber atom types a few years ago and then converted to parm@Frosst (which I found to be a lot harder) but not to the

Re: [Rdkit-discuss] Problem with Drawing a molecule

2020-11-16 Thread Paul Emsley
On 16/11/2020 21:28, Navid Shervani-Tabar wrote: Dear RDKit users, I'm trying to plot a single molecule using RDKit. I use the following code from rdkit.Chemimport Draw from rdkitimport Chem mol = Chem.MolFromSmiles('C1#CN2C1C2') Chem.rdmolops.SanitizeMol(mol) img =

Re: [Rdkit-discuss] chair vs boat detection

2021-03-12 Thread Paul Emsley
On 12/03/2021 05:11, Ling Chan wrote: Just wonder if there is any function to distinguish between a chair ring and a boat ring? Don't worry if there is no such utility. I can write my own geometry detection. Just that I don't want to reinvent the wheel. Isn't this Cremer Pople?

Re: [Rdkit-discuss] explicit H atoms

2021-03-09 Thread Paul Emsley
On 09/03/2021 09:01, Jean-Marc Nuzillard wrote: Sure, testosterone may be drawn as [snip] OK :-) That's a top quality rendering by the way. How did you make it? Paul. ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net

Re: [Rdkit-discuss] explicit H atoms

2021-03-08 Thread Paul Emsley
On 08/03/2021 13:55, Jean-Marc Nuzillard wrote: Is it always possible to represent an organic molecule in 2D with all necessary configuration hints (bond wedges pointing to the front or to the back) without introducing any explicit hydrogen atom? No. Testosterone.

Re: [Rdkit-discuss] hybridization of nitrogen in beta-lactam

2021-02-13 Thread Paul Emsley
On 13/02/2021 18:15, Peter St. John wrote: Is there any reason why RDKit says the nitrogen in beta-lactam is SP2-hybridized? I would have assumed it should be SP3. It doesn't seem to be the ring structure, 'C1NC1' lists all the atoms as being SP3. >>> [(atom.GetSymbol(),

Re: [Rdkit-discuss] Parsing a PDB file with atoms that are too close, causing bad bond

2021-09-28 Thread Paul Emsley
> PDB files have no bond information, This is not true. The chemistry is specified in the Chemical Component Dictionary using the residue identifier (so it's a reference to a chemical description, it's not embedded). https://www.wwpdb.org/data/ccd https://github.com/pdbeurope/ccdutils

Re: [Rdkit-discuss] cairo/png problem

2022-12-14 Thread Paul Emsley
On 13/12/2022 23:39, Thiessen, Paul (NIH/NLM/NCBI) [E] via Rdkit-discuss wrote: Hi folks, I’m trying to use the MolDraw2DCairo class to generate PNG images. But no matter what I’ve tried, including setting the ‘noFreetype’ param to true in the c’tor, I get an empty string from

Re: [Rdkit-discuss] Get original SMILES from molecule

2022-12-14 Thread Paul Emsley
On 14/12/2022 17:37, Thomas wrote: Is there a way to get the SMILES used to generate the molecule (NOT the canonical one)? Not as far as I know. If I generate a molecule from a SMILES, a call to GetAtoms() returns the atoms in the order of the input SMILES. I'd like to retrieve that