[Rdkit-discuss] cartridge: successful build on Cygwin 64-bit
Dear All, In case this may be useful to anybody in the future: RDKit (current github version) builds nicely on Cygwin 64-bit without any modifications (GCC 4.9.2, boost 1.55). The following tests fail: 13 - testUFFForceField (SEGFAULT) - rounding error 15 - pyForceFieldConstraints (Failed) - rounding error 65 - pyMolDraw2D (SEGFAULT) 66 - testFMCS (SEGFAULT) 67 - pyFMCS (SEGFAULT) 85 - pythonTestDirChem (Failed) More importantly, the postgres cartridge builds without any problems (postgresql 9.4.1), without modification of the makefile, and passes all tests. Perhaps not everybody knows that Cygwin can be installed without admin rights (invoke the setup application from command line with --no-admin), so this solution will work in almost every Windows environment and is almost equivalent to a portable app. Unfortunately, 32-bit Cygwin does not behave so nicely, as I have written before. Best wishes, Michal -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Hall Kier descriptors and three/four membered rings
FYI: this should now be fixed. The problem was an error in the way rings were handled. This will change the value of ChiNv/ChiNn for any system where there's a ring of size N or smaller. -greg On Wed, Mar 25, 2015 at 6:00 AM, Greg Landrum wrote: > That looks like a bug. Here's the github issue: > https://github.com/rdkit/rdkit/issues/463 > > I'll take a look and see if I can find/fix it. > > -greg > > On Tue, Mar 24, 2015 at 4:49 PM, Michael wrote: > >> Dear all, >> >> I noticed a discrepancy for the Hall Kier desciptors with molecules >> containing three/four membered rings (e.g. lactams) depending on the actual >> atom number ordering of the molecule. >> >> Here are two example molecules: >> >> O=C(Nc1nccs1)NC(C1CC1)C >> Chi3v: 2.9071859893 >> after reordering atoms using Chem.RenumberAtoms: >> Chi3v: 2.94464346787 >> >> CC1(C)SC2C(N)C(=O)N2C1C(=O)O >> Chi4n: 2.01009790787 >> after reordering: >> Chi4n: 2.0043325592 >> >> I attached a notebook with the code for the examples. >> >> I know, the differences are small, but it still surprises me that there >> is a difference at all. I always assumed that the atom order shouldn't make >> a difference. >> >> Best, >> Michael >> >> >> -- >> Dive into the World of Parallel Programming The Go Parallel Website, >> sponsored >> by Intel and developed in partnership with Slashdot Media, is your hub >> for all >> things parallel software development, from weekly thought leadership >> blogs to >> news, videos, case studies, tutorials and more. Take a look and join the >> conversation now. http://goparallel.sourceforge.net/ >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> > -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] RDKit on cygwin32: python silently crashes
Dear All,
I know that building on Cygwin is not a popular topic here, but perhaps
someone will have some ideas. I'm trying to build on 32-bit Cygwin under
Windows 7 32-bit. The build seems successful and C tests are passed, but
importing the python bindings causes python to crash silently:
$ python
Python 2.7.8 (default, Jul 28 2014, 01:34:03)
[GCC 4.8.3] on cygwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit import Chem
$ python -v -c 'from rdkit import Chem'
[cut]
import rdkit.Chem.PeriodicTable # precompiled from
/home/M/RDKit/rdkit/Chem/PeriodicTable.pyc
dlopen("/home/M/RDKit/rdkit/Chem/rdchem.dll", 2);
import rdkit.Chem.rdchem # dynamically loaded from
/home/M/RDKit/rdkit/Chem/rdchem.dll
dlopen("/home/M/RDKit/rdkit/Chem/rdmolfiles.dll", 2);
import rdkit.Chem.rdmolfiles # dynamically loaded from
/home/M/RDKit/rdkit/Chem/rdmolfiles.dll
dlopen("/home/M/RDKit/rdkit/Chem/rdmolops.dll", 2);
$
Any ideas on how to investigate this?
It seems that this problem is related to 32-bit Cygwin, as under Cygwin64
everything works just fine (thanks to Jan Holst Jensen for verifying this).
Best wishes,
Michal
--
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/___
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