Re: [Rdkit-discuss] 2018.03.1 RDKit release

On Tue, Apr 24, 2018 at 7:03 PM, Andrew Dalke wrote: > > By the way, how do I install RDKit into a specified location? I usually > expect something like --prefix /usr/local, and there's a > CMAKE_INSTALL_PREFIX which defaults to "/usr/local" but "make install" puts >

Re: [Rdkit-discuss] RPM distros

apt install rpm should get you rpmbuild -David > On Nov 15, 2017, at 2:59 PM, Tim Dudgeon wrote: > > OK, makes sense, but I'm building on a Debian system. So neither 'yum install > rpm-build' nor 'apt-get install rpm-build' doesn't work. > > So (sorry for the stupid

Re: [Rdkit-discuss] Conformer generation

Hi Paul, Your reuse of the variable num_confs inside the loop is causing that monotonic decrease. So, if a molecule returns 190 conformers, the next iteration has you only asking for 190 conformers. And so on. Best, David On Wed, Oct 25, 2017 at 12:36 PM, Paul Hawkins

Re: [Rdkit-discuss] Using inchikey as entry

I believe InchiKey uses a 1 way hash (sha-256), so what you are asking for is basically impossible. That is, to go from InchiKey to molecule requires already having a table of molecules corresponding to the InchiKeys. There are various services online that have such lookup tables for a large

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

What happens if you do this instead? cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DPYTHON_EXECUTABLE=/usr/bin/python3.4 .. That seems to work for me on Ubuntu 14.04, also, delete your entire build directory and make it again before running the command. -David On Mon, Oct 3, 2016 at 11:05 AM, Philip

Re: [Rdkit-discuss] The RDKit and modern C++

I've used Red Hat's developer toolset for years on RHEL5 to be able to build stuff there using gcc 4.8 and that software has seemed to run fine when shipping to people running RHEL5 and RHEL6. I have "source /opt/rh/devtoolset-2/enable" in my bash profile and that sets all the environment

Re: [Rdkit-discuss] Problems after installing rdkit release 2016_03_1

what does os.environ["PYTHONPATH”] show when you are in IDLE? > On Jul 19, 2016, at 12:26 PM, Jessica Krause wrote: > > Dear All, > > I installed the new release of Rdkit in Ubunutu 16.04. I am not able to > import rdkit module in my IDLE and Spyder after installing

Re: [Rdkit-discuss] GetMol and GetMolFrags in C++

When I want to replicate one of RDKit’s python functions in C++, I go to the source. RDKit has very readable wrappers that make this a surprisingly nice approach (many other pieces of software have pretty ugly wrappers, so this is a major compliment to RDKit). For this, I think the source is:

Re: [Rdkit-discuss] cis/trans directional bond and smiles strings in python

That behavior appears to all be in python; as you’ve written it, your smiles string has a newline before rdkit ever sees it: >>> print 'C/C=C\n1nc(nn1)C' C/C=C 1nc(nn1)C >>> print 'C/C=C\\n1nc(nn1)C' C/C=C\n1nc(nn1)C > On Oct 12, 2015, at 4:37 PM, Michael Reutlinger wrote: >

Re: [Rdkit-discuss] NP-score and SA-score datas

This is the easiest way. python -c "import json,gzip,pickle; print json.dumps(pickle.load(gzip.open('publicnp.model.gz', 'rb')))" > publicnp.model.json Modify as appropriate for the other file. -David On Sun, Sep 6, 2015 at 11:48 AM, Guillaume GODIN < guillaume.go...@firmenich.com> wrote: >

Re: [Rdkit-discuss] Memory management during conformer generation

On Jun 27, 2015, at 6:05 AM, Dmitri Maziuk dmaz...@bmrb.wisc.edu wrote: On 6/26/2015 9:48 AM, az wrote: Thanks Jean-Paul You're right that I eat up a lot of memory with large files but I think its not the whole story. If it were, my memory should come back each time a new file is being

Re: [Rdkit-discuss] rdkit can not read sodium hexaflourophosphate molfile

See this commit if you want to know how it has been fixed in the development code. https://github.com/rdkit/rdkit/commit/672f8ea2008ca88ee4c9dc91eab74894916a https://github.com/rdkit/rdkit/commit/672f8ea2008ca88ee4c9dc91eab74894916a -David On May 21, 2015, at 4:26 AM, Contact

Re: [Rdkit-discuss] FYI: google code shutting down

well, presumably the documentation not in the wiki would continue to be online. http://rdkit.org/docs/index.html http://rdkit.org/docs/index.html http://rdkit.org/docs/api/index.html http://rdkit.org/docs/api/index.html http://rdkit.org/docs/cppapi/index.html

Re: [Rdkit-discuss] Chem.Draw darker colors

In [6]: opt.elemDict Out[6]: {0: (0.5, 0.5, 0.5), 1: (0.55, 0.55, 0.55), 7: (0, 0, 1), 8: (1, 0, 0), 9: (0.2, 0.8, 0.8), 15: (1, 0.5, 0), 16: (0.8, 0.8, 0), 17: (0, 0.8, 0), 35: (0.5, 0.3, 0.1)} presumably, you set fluorine and sulfur by changing the values of 9 and 16. -David On Feb

Re: [Rdkit-discuss] Errors while running CTest

Did you start a new bash shell to get those environment variables set? Just editing that file does not set them. -David On Sep 24, 2014, at 5:22 AM, Shantheya Balasupramaniam s.balasupraman...@tu-bs.de wrote: Dear Sir or Madam, i tried to install the RDKit on ubuntu 14.04 (64bit):

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

I haven't tried it, but I'm assuming that once Paolo's pull request is accepted, this will work out of the box. https://github.com/rdkit/rdkit/pull/261 -David On Fri, May 16, 2014 at 1:51 PM, Jan Domanski jan...@gmail.com wrote: The reply from Paolo was amazing and quick. I'm looking at this

Re: [Rdkit-discuss] structure to IUPAC name made on RDkit?

Certainly, RDKit can help, any cheminformatics toolkit with SMARTS/substructures to quickly classify something as a ketone, ester, ether, bond orders, ring finding, path finding, etc. can help. As for how hard it is, I think for drug discovery, most would start with the Nomenclature of Organic

Re: [Rdkit-discuss] rdkit.Chem.rdMolDescriptors._CalcMolWt()

/publications/pac/78/11/2051/ , I would argue that you are concerned with precision at a level beyond what is currently accepted. -- David Hall On Thursday, December 12, 2013 at 5:13 PM, Dimitri Maziuk wrote: Hi, what exactly does rdkit.Chem.rdMolDescriptors._CalcMolWt( mol ) do? : #!/usr

Re: [Rdkit-discuss] libc++ fix for RDKit_2013_06_1

FYI if you want to still use homebrew to install rdkit with the fixes applied: brew install --HEAD rdkit will pull from git head for the rdkit install and compiles on mavericks -David On Tue, Nov 5, 2013 at 11:26 AM, Hans De Winter h...@silicos-it.com wrote: Hi all, all errors are gone

Re: [Rdkit-discuss] RDkit, OS X 10.9 and clang++

I'm fairly confident this isn't a compiler problem, but a libc++ problem. CXXFLAGS=-stdlib=libstdc++ cmake .. gets you past the current problem. But if boost is built against libc++ , it doesn't link, so I also built boost against libstdc++ and everything built. Based on Greg's playing with

Re: [Rdkit-discuss] git build of RDKIT on Ubuntu 13.04 fails with message recompile with -fPIC

Have you tried using the shared library libpython2.7.so instead of the static libpython2.7.a ? On Sun, Sep 8, 2013 at 6:37 AM, hari jayaram hari...@gmail.com wrote: Hello all... I managed to solve part of the problem with the build using a modified version of FindPythonLibsNew.cmake based

Re: [Rdkit-discuss] Problem of install of RDkit in Ubuntu

Can you specify what other free tools you installed? Some tools have a tendency to install their own python, causing problems. A common culprit for this is autodock tools. Can you run `which python` and see what python you are running? If it is not /usr/bin/python , it probably was installed by