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

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 SMILES,

Re: [Rdkit-discuss] cairo/png problem

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 getDrawingTex

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

> 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 Pau

Re: [Rdkit-discuss] chair vs boat detection

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? http:

Re: [Rdkit-discuss] explicit H atoms

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 https://lists

Re: [Rdkit-discuss] explicit H atoms

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

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(), atom.GetHybridizati

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

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 = Draw.MolsToGridImage([

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

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

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] Perceived bond orders of RNA PDB-files

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 p

Re: [Rdkit-discuss] Line recall/edit non-functional in Python 3.6.5 interpreter from miniconda3 RDKit install?

On 18/09/2018 19:45, Ian Tickle wrote: Hi all, I'm finding that the line recall/edit function is broken in the Python 3.6.5 interpreter from miniconda3 installation of RDKit, i.e. the arrow keys just type out the escape sequences. If I use miniconda2 instead it's fine.  Also line recall/edit wo

Re: [Rdkit-discuss] Atom mapping

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 c

Re: [Rdkit-discuss] Atom mapping

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 how

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

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: C1=CC=C(C=C1)[N+]2=CC=CC3=C2C4=C(C=CC

Re: [Rdkit-discuss] Issue with the latest RDKit DB build

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 newl

[Rdkit-discuss] Contrib code license

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, Slashdot.org

Re: [Rdkit-discuss] 3d descriptors generation

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

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

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 get

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

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] minGW fails to build rdkit

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 > -DCMAKE_INS

Re: [Rdkit-discuss] Stereochemistry

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 bon

Re: [Rdkit-discuss] Coot heading to Fedora

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 haven't

Re: [Rdkit-discuss] Coot heading to Fedora

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 sinc

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

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 Smarts?

[Rdkit-discuss] compiling with the RDKit with cairo on Fedora

Hi Greg and Gianluca (in particular), [meta: I think this is an RDKit issue rather than a Fedora one (I might be wrong)] I installed rdkit-2016.03.2-6.fc24.x86_64 and now am trying to compile my program with that. To do so, I include the flag -I/usr/include/rkdit When trying to use the inclu

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

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] Ring membership

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 id

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

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] off-topic: atom names in sdf files?

for an example. > > Atom names stored in this fashion are read in by the RDKit and can be > accessed as the > "molFileAlias" atom property; they can also be stored accordingly. See > > https://gist.github.com/ptosco/6e4468350f0fff183e4507ef24f092a1#file-pdb_atom_names

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

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] Error when building RdKit 2013_09_1

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

Re: [Rdkit-discuss] library name change?

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 libSmilesPa

Re: [Rdkit-discuss] library name change?

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. -- ___ Rdkit-

[Rdkit-discuss] library name change?

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 (a

Re: [Rdkit-discuss] Error compiling RDKit with MinGW on Windows

On 23/06/16 13:29, Anne wrote: > Hi everyone, > > I have been trying to compile RDKit (rdkit-Release_2016_03_2.tar.gz) > using CodeBlocks 16.01 with the MinGW (gcc 4.9) compiler on Win7. But I > keep getting the following error in the LocaleSwitcher.cpp: > > [] > > [ 1%] Building CXX object >

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

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", "copyright"

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

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 : > > /nas02/home/r/m/rmendez/Work/Software/miniconda/envs/my-rdkit-env/include/boost:/nas02/home/r/m/rmendez/Work/Software/miniconda/envs/my-rdkit-env/l

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

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 tha

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

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

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

On 19/02/2016 05:00, Greg Landrum wrote: On Fri, Feb 19, 2016 at 5:00 AM, Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: 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

Re: [Rdkit-discuss] Compiling git rdkit

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 wrote: >> >> >> Using: >> Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn) >> T

[Rdkit-discuss] Compiling git rdkit

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 o

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

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: > > > T

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

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, &conf); bool includeStereo = true;

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

ctfile.pdf 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 mailto:pems...@mrc-lmb.cam.a

[Rdkit-discuss] Atom Symbol Case in MolFile?

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 into

Re: [Rdkit-discuss] KeyError on png from pythonTestDirChem

On 02/06/15 23:11, Bharath Ramsundar wrote: > As a quick update, I verified that I'm able to load and save png files > using PIL from ipython. > Are you able to save png files using the same python as you use for RDKit? import rdkit from PIL import Image im = Image.open('test.png') im.save('out.

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

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. -

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

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, return_v

Re: [Rdkit-discuss] MMFF bond parameters

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] MMFF bond parameters

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] PandasTools on Windows iPython notebook

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) in () 1importpandas aspd

Re: [Rdkit-discuss] Help needed with rdkit and apache

On 18/09/14 17:57, Grégori Gerebtzoff wrote: > > Now on the apache server, I added the same three lines to the > /etc/apache2/envvars file: > export RDBASE=/opt/RDKit_2014_03_1 > export LD_LIBRARY_PATH=$RDBASE/lib > export PYTHONPATH=$RDBASE:$PYTHONPATH > > Importing rdkit gives me the "ImportError

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

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] A case of the jaggies

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

[Rdkit-discuss] A case of the jaggies

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] aromatic flavin

On 08/07/14 15:40, Greg Landrum wrote: Hi Paul, On Tue, Jul 8, 2014 at 2:55 PM, Paul Emsley <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: I'm struggling to understand aromatic bond assignment. Are the rings of flavin aromatic? I think that the answer to that is pro

[Rdkit-discuss] aromatic flavin

Hi all, I'm struggling to understand aromatic bond assignment. Are the rings of flavin aromatic? I think that the answer to that is probably yes, but what does that mean? I thought that a 6-membered ring was considered aromatic if all of the bonds of the ring were aromatic. Is this correct

[Rdkit-discuss] chirality doxygen tweak

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 http://rdkit.org/C++_Docs/classRDKit

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

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 look

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

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 tha

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

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 fe

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

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 profilin

Re: [Rdkit-discuss] ambiguous detail

On 03/10/13 05:29, Greg Landrum wrote: > Hi Paul, > > This is just a guess, but do you by any chance have a "using namespace > boost::python" somewhere in your code? > > Yes (sheepish grin) Paul -- October Webinars: C

[Rdkit-discuss] ambiguous detail

Hi, I am trying to use RDKit from github (rather than the tarballs as I usually do). RDKit seemed to download and install without incident. However, when I try to build my program using the newly installed RDKit, I get: /home/paule/autobuild/build-with-rdkit/include/rdkit/GraphMol/Atom.h: In

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

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, th

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

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 Ubu

Re: [Rdkit-discuss] non-smallest rings

On 22/01/13 05:40, Greg Landrum wrote: > Hi Paul, > > On Mon, Jan 21, 2013 at 4:13 PM, Paul Emsley > 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 w

Re: [Rdkit-discuss] non-smallest rings

Hi Nik, Thanks for your speedy reply. On 21/01/13 17:19, Stiefl, Nikolaus wrote: > do you just have to check if an atom is in a 6-membered ring? If so then > > > In [8]: m = > Chem.MolFromSmiles('COc1ccc(cc1O[C@H]1C[C@@H]2CC[C@H]1C2)C1CNC(=O)NC1') > > In [9]: [a.IsInRingSize(6) for a in m.GetAto

[Rdkit-discuss] non-smallest rings

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 (as an example): http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=0CP COc1ccc(cc1O[C@H]1C[C@@H]2CC[C@H]1C2)C1CNC(=O)NC1 which h

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

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] Faulty valence for nitrogen in aromatic ring

On 14/08/12 18:06, Michael Palmer wrote: > Hi, > > it seems that nitrogen atoms in aromatic rings are being assigned > faulty valences... [snip] > > > I've seen this with several other compounds as well; I'm not exactly > sure that the error is strictly associated with aromaticity though. > Sorry i

Re: [Rdkit-discuss] SmilesToMol runtime error

On 02/08/12 14:48, Gonzalo Colmenarejo-Sanchez wrote: Hi, I have a c++ code that uses SmilesToMol. As soon as there is one SMILES that the program fails to sanitize I get an error message like this: /[13:46:35] Explicit valence for atom # 15 N, 5, is greater than permitted/ /terminate ca

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

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" - wh

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

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 SMIL

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

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 suggesti

Re: [Rdkit-discuss] problem with overlap in drawing.

For the record, there's little added complexity compiling from the svn repo than using the release tar file. On 02/07/12 11:48, Adrian Jasiński wrote: > Thanks for that, I hope it will help. I will wait for next release and > check other structures drawing. > Unfortunately I can't publish all s

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

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

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

On 23/06/12 04:39, Greg Landrum wrote: > On Fri, Jun 22, 2012 at 5:46 PM, Leonardo Trabuco wrote: >> Thanks for following up. Below is the output you asked for. Looks like an >> import error in the boost library. Any ideas? > Based on what I've been able to find on the 'net, the error is typical >

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

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 To: rdkit-discuss@lists.sourceforge.net

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

On 30/03/12 15:27, Hans De Winter wrote: Hi - A RDKit-based implementation of the QED measure as described by Richard Bickerton (Nature Chemistry, 2012, 4, 90-98) has been implemented and made available for download from our website ( www.silicos-it.com > Biscu-it

Re: [Rdkit-discuss] Kekulization Problems

On 06/06/12 14:06, Nicholas Firth wrote: Well I'm not quite sure what the issue is to be honest (also not very sure if this fix will even work, so thought it best to ask). The work round is: ROMol *tempMol= static_cast(new RWMol(mol)); tempMol = MolOps::addHs(*tempMol); mol = s

Re: [Rdkit-discuss] Kekulization Problems

On 06/06/12 13:37, Paul Emsley wrote: On 06/06/12 12:27, Nicholas Firth wrote: Hi All, I'm having some issues with getting some more 'interesting' ring systems to kekulize. I'm creating the molecule in RDKit by individually adding all the atoms and bonds from a graph. H

Re: [Rdkit-discuss] Kekulization Problems

On 06/06/12 12:27, Nicholas Firth wrote: Hi All, I'm having some issues with getting some more 'interesting' ring systems to kekulize. I'm creating the molecule in RDKit by individually adding all the atoms and bonds from a graph. However I have found similar issue when trying to initialise a

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

On 02/06/12 04:44, Greg Landrum wrote: > > On Fri, Jun 1, 2012 at 1:41 PM, Paul Emsley > 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 func

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

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] Molecule with no atoms, so is it valid?

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

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

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 -lSubstruct

Re: [Rdkit-discuss] PIL - molecule depiction

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 "", line 1, in >File > "/SW/python/x86_64/2.6/lib/python2.6/site-packages/rdkit/sping

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

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') &

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

On 30/04/12 01:03, Eddie Cao wrote: > Hi Andrew, > > I also prefer #2. #1 is not quite sensible because many readers like > MolFromSmiles will return None on failure and it will be hard to distinguish > bad input from an empty one if we choose to do #1. Semantically, in many > RDKit use cases, N

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

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); inner_coo

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

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/

Re: [Rdkit-discuss] un-oneandahalfs

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 >> Emsley wrote: >>> >>> When creating a 2d depiction, or otherwise, is there a way to turn a >>> carboxylate (with ONEANDAHALF bonds

[Rdkit-discuss] un-oneandahalfs

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] generate atom names?

On 10/04/12 12:01, Greg Landrum wrote: > On Tue, Apr 10, 2012 at 11:07 AM, Paul Emsley > wrote: >> (Just making sure I have not missed anything...) >> >> Is there a function that generates unique atom names (using >> at->setProp("name", name) pre

[Rdkit-discuss] generate atom names?

Hi All, (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 don't see such a thing). Cheers, Paul. --

[Rdkit-discuss] MolChemicalFeature.h installed?

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 =

[Rdkit-discuss] MolFileAtomLine() massDiff

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 atom->

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