Re: [Rdkit-discuss] 3d descriptors generation
Thanks Greg and Paul for clarification . Hoping to get the release soon. Cheers, Abhik Seal Ph.D. (Cheminformatics) On Thu, Jul 13, 2017 at 1:10 PM, Greg Landrum <greg.land...@gmail.com> wrote: > To further elaborate on this: the new 3D descriptors are currently > available in github and will be in the next release, but they aren't in the > 2017.03 release. > > On Thu, Jul 13, 2017 at 7:43 PM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> > wrote: > >> 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 the code >> >> >> from rdkit import Chem >> from rdkit import rdBase >> from rdkit import RDConfig >> import os >> >> from rdkit.Chem import rdMolDescriptors as rdMD >> >> smi = 'CCC(C)CO' >> m = Chem.MolFromSmiles(smi) >> >> r= rdMD.CalcRDF(m)+rdMD.CalcMORSE(m) >> >> >> That version of RDKit does not have CalcRDF as an attribute of >> rdMolDescriptors. >> >> Paul. >> >> >> >> -- >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] 3d descriptors generation
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 the code from rdkit import Chem from rdkit import rdBase from rdkit import RDConfig import os from rdkit.Chem import rdMolDescriptors as rdMD smi = 'CCC(C)CO' m = Chem.MolFromSmiles(smi) r= rdMD.CalcRDF(m)+rdMD.CalcMORSE(m) print r Sincerely, Abhik Seal Ph.D. (Cheminformatics) -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Clustering
Hello all , How about doing some dimension reduction using pca or Tsne and then run clustering using some selected top components like top 20 and I think then the clustering would be fast . Thanks Abhik On Mon, Jun 5, 2017 at 6:11 AM David Cosgrove <davidacosgrov...@gmail.com> wrote: > Hi, > I have used this algorithm for many years clustering sets of several > millions of compounds. Indeed, I am old enough to know it as the Taylor > algorithm. It is slow but reliable. A crucial setting is the similarity > threshold for the clusters, which dictates the size of the neighbour lists > and hence the amount of RAM required. It also, of course, determines the > quality of the clusters. My implementation is at > https://github.com/OpenEye-Contrib/Flush.git. This repo has a number of > programs of relevance, the one you want is called cluster. I have just > confirmed that it compiles on ubuntu 16. It needs the fingerprints as > ascii bitstrings, I don't have code for turning RDKit fingerprints into > this format, but I would imagine it's quite straightforward. The program > runs in parallel using OpenMPI. That's valuable for two reasons. One is > speed, but the more important one is memory use. If you can spread the > slave processes over several machines you can cluster much larger sets of > molecules as you are effectively expanding the RAM of the machine. When I > wrote the original, 64MB was a lot of RAM, it is less of an issue these > days but still matters if clustering millions of fingerprints. Note that > the program cluster doesn't ever store the distance matrix, just the lists > of neighbours for each molecule within the threshold. This reduces the > memory footprint substantially if you have a tight-enough cluster threshold. > HTH, > Dave > > > > On Mon, Jun 5, 2017 at 11:22 AM, Nils Weskamp <nils.wesk...@gmail.com> > wrote: > >> Hi Michal, >> >> I have done this a couple of times for compound sets up to 10M+ using a >> simplified variant of the Taylor-Butina algorithm. The overall run time >> was in the range of hours to a few days (which could probably be >> optimized, but was fast enough for me). >> >> As you correctly mentioned, getting the (sparse) similarity matrix is >> fairly simple (and can be done in parallel on a cluster). Unfortunately, >> this matrix gets very large (even the sparse version). Most clustering >> algorithms require random access to the matrix, so you have to keep it >> in main memory (which then has to be huge) or calculate it on-the-fly >> (takes forever). >> >> My implementation (in C++, not sure if I can share it) assumes that the >> similarity matrix has been pre-calculated and is stored in one (or >> multiple) files. It reads these files sequentially and whenever a >> compound pair with a similarity beyond the threshold is found, it checks >> whether one of the cpds. is already a centroid (in which case the other >> is assigned to it). Otherwise, one of the compounds is randomly chosen >> as centroid and the other is assigned to it. >> >> This procedure is highly order-dependent and thus not optimal, but has >> to read the whole similarity matrix only once and has limited memory >> consumption (you only need to keep a list of centroids). If you still >> run into memory issues, you can start by clustering with a high >> similarity threshold and then re-cluster centroids and singletons on a >> lower threshold level. >> >> I also played around with DBSCAN for large compound databases, but (as >> previously mentioned by Samo) found it difficult to find the right >> parameters and ended up with a single huge cluster covering 90 percent >> of the database in many cases. >> >> Hope this helps, >> Nils >> >> Am 05.06.2017 um 11:02 schrieb Michał Nowotka: >> > Is there anyone who actually done this: clustered >2M compounds using >> > any well-known clustering algorithm and is willing to share a code and >> > some performance statistics? >> >> >> >> -- >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > > > > -- > David Cosgrove > Freelance computational chemistry and chemoinformatics developer > http://cozchemix.co
Re: [Rdkit-discuss] molecule standardization in cartridge search
Hi
Long time back I used PL python with RDKit cartridge inside postgres i have
made a blog post here is the link might be of help
http://data2quest.blogspot.com/2014/07/converting-inchi-to-mol-using-plpython.html
Abhik Seal
Indiana University Bloomington
School of Informatics and Computing
Cheminformatics and Chemgenomics group <http://registratio54.wix.com/ccrg>
abs...@indiana.edu
http://mypage.iu.edu/~abseal/index.htm
On Fri, Sep 25, 2015 at 1:37 PM, Jan Holst Jensen <j...@biochemfusion.com>
wrote:
> Hi Tim,
>
> A simple getting-started example is:
>
> CREATE FUNCTION smiles2molfile(smiles text) RETURNS text
> LANGUAGE plpythonu AS $$
> import rdkit
> from rdkit import Chem
>
> mol = Chem.MolFromSmiles(smiles)
> return Chem.MolToMolBlock(mol)
> $$;
>
>
> and you can then
>
> select smiles2molfile('CC');
>
> and get back a molfile.
>
> For more advanced usage it is worth taking a look at the rdchord project
> that TJ has sent links to.
>
> Cheers
> -- Jan
>
>
> On 2015-09-25 15:54, Tim Dudgeon wrote:
>
> Jan,
>
> thanks for that. I'll give it a try.
> Are there any examples of writing RDKit functions and procedures for
> postgres in python?
> I see this general postgres docs:
> http://www.postgresql.org/docs/9.4/static/plpython.html
> but wondered if there are any RDKit specific examples anywhere?
>
> Tim
>
> On 25/09/2015 08:30, Jan Holst Jensen wrote:
>
> On 2015-09-24 16:22, Tim Dudgeon wrote:
>
> I'm trying to get to grips with using the RDKit cartridge, and so far
> its going well.
> One thing I'm concerned about is molecule standardization, along the
> lines of the ChemAxon Standardizer that allows substructure searches to
> be done is a way that is largely independent of the quirks of structure
> representation. The classic example would be how nitro groups are
> represented, so that it didn't matter which nitro representation was in
> the query or target structures, because both were converted to a
> canonical form.
>
> My initial thoughts are that this would be done by:
> 1. loading the "raw" structures into a source column that would never be
> changed
> 2. defining a function that performed the necessary transform to
> generate the canonical form of a molecule.
> 3. generating a "canonical" structure column that was the result of
> passing the raw structures through that function
> 4. building the SSS index on that canonical column
> 5. executing queries using that function to canonicalize the query
> structure
>
> The problem I'm finding is that there do not seem to be postgres
> functions defined for doing molecular transforms (essentially a reaction
> transform) and doing things like removing explicit hydrogens. At least
> not in the functions listed on this
> page:http://rdkit.org/docs/Cartridge.html#functions
>
> Am I missing something here, or might I be barking up completely the
> wrong tree?
>
> Tim
>
> Hi Tim,
>
> We have about the same situation and we're adding standardization
> (beyond what RDKit implicitly does when it sanitizes the molecule)
> through Python stored procedures. You will need to build and maintain
> a normal Python-enabled RDKit installation in parallel to the
> cartridge. The Python stored procedures can access the normal RDKit
> installation and then run whatever Python code is necessary to do
> additional molecule cleanup.
>
> You will need to tweak your Postgres environment so the Python stored
> procedures can load RDKit. This is what I have defined in an
> environment file on CentOS:
>
> RDBASE=/opt/rdkit
> LD_LIBRARY_PATH=/opt/rdkit/lib
> PYTHONPATH=/opt/rdkit
>
> On Ubuntu this would go into /etc/postgresql/9.x/main/environment (in
> a slightly different format where the values have to be single-quoted).
>
> Cheers
> -- Jan, Biochemfusion
>
>
>
>
> --
>
> ___
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>
>
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Re: [Rdkit-discuss] Ridiculously easy problem - capture RDKit's error messages
Hi JP,
I think you can use try and catch ,
try:
throws()
return 0
except Exception, err:
sys.stderr.write('ERROR: %s\n' % str(err))
return 1
Hope this helps.
Abhik Seal
Indiana University Bloomington
School of Informatics and Computing
Cheminformatics and Chemgenomics group http://registratio54.wix.com/ccrg
abs...@indiana.edu
http://mypage.iu.edu/~abseal/index.htm
On Fri, Jan 23, 2015 at 8:58 AM, JP jeanpaul.ebe...@inhibox.com wrote:
Yo RDKitters,
I am stuck on something so basic, its embarrassing. But for the life of
me I cannot figure it out on my own. This is probably more of a python
question than an RDKit one.
I want to capture the RDKit warning/error message from python. e.g.
import rdkit
from rdkit import Chem
Chem.MolFromSmiles('XXX')
[14:51:32] SMILES Parse Error: syntax error for input: XXX
I want to capture that error message (which in this case isn't very
informative, but if you read in a mol2 you can get something like
[14:25:46] 3ZGZ.A: warning - O.co2 with non C.2 or S.o2 neighbor. Which I
am also interested in). The big picture is that I built a web up where you
upload an sdf, mol, mol2 or smi file - and I want to show RDKit's error
message if there something funny in the query file.
I have tried the obvious (I think):
#!/usr/bin/env python
import sys
import rdkit
from rdkit import Chem
f = open(err.log, w)
original_stderr = sys.stderr
sys.stderr = f
Chem.MolFromSmiles('XXX')
sys.stderr = original_stderr
f.close()
This still shows the error message in the terminal and not in the file. I
tried the same for stdout, still no cigar.
Any ideas ?
THANKS!
JP
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[Rdkit-discuss] Error in reading sdf format
Hi RDkiters,
I have a sdf file attached(2 molecules only) and when i want to do simple
printing of the mol using code below i am getting an error not sure what is
wrong with the file
from rdkit import Chem
suppl = Chem.SDMolSupplier('data.sdf')
for mol in suppl:
... print mol
...
[21:15:14] ERROR: Cannot convert to int on line 4
[21:15:14] ERROR: moving to the begining of the next molecule
None
[21:15:14] ERROR: Cannot convert to int on line 106
[21:15:14] ERROR: moving to the begining of the next molecule
Any help on this problem ?
Abhik Seal
Indiana University Bloomington
School of Informatics and Computing
Cheminformatics and Chemgenomics group http://registratio54.wix.com/ccrg
abs...@indiana.edu
http://mypage.iu.edu/~abseal/index.htm
data.sdf
Description: Binary data
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Re: [Rdkit-discuss] Error in reading sdf format
Thanks for pointing me to that missing blank like Andrew and JP
Abhik Seal
Indiana University Bloomington
School of Informatics and Computing
Cheminformatics and Chemgenomics group http://registratio54.wix.com/ccrg
abs...@indiana.edu
http://mypage.iu.edu/~abseal/index.htm
On Wed, Jul 23, 2014 at 10:21 PM, JP jeanpaul.ebe...@inhibox.com wrote:
The problem is in the data file -- I added an example, benzene, from
wikipedia, and fixed the first one of your molecules for you (attached).
Amongst other things - the first three lines are header lines (
http://en.wikipedia.org/wiki/Chemical_table_file), you only have two of
those.
I find the specification very useful when I hit these kind of problems.
Here it is: http://c4.cabrillo.edu/404/ctfile.pdf
On 23 July 2014 22:26, Abhik Seal abhik1...@gmail.com wrote:
Hi RDkiters,
I have a sdf file attached(2 molecules only) and when i want to do simple
printing of the mol using code below i am getting an error not sure what is
wrong with the file
from rdkit import Chem
suppl = Chem.SDMolSupplier('data.sdf')
for mol in suppl:
... print mol
...
[21:15:14] ERROR: Cannot convert to int on line 4
[21:15:14] ERROR: moving to the begining of the next molecule
None
[21:15:14] ERROR: Cannot convert to int on line 106
[21:15:14] ERROR: moving to the begining of the next molecule
Any help on this problem ?
Abhik Seal
Indiana University Bloomington
School of Informatics and Computing
Cheminformatics and Chemgenomics group
http://registratio54.wix.com/ccrg
abs...@indiana.edu
http://mypage.iu.edu/~abseal/index.htm
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[Rdkit-discuss] Feature generation in postgres cartridge
Hi Greg,
I was using postgres cartridge i found there are several implementations
for chemical features. Some of them i tried like maccs, morganbv_fp i found
they generate hexadecimal values. So when i convert hexadecimal to binary i
found maccs has 168 values and for morganvbv_fp it has 512 binary values.
I may be wrong in understading but just to make sure if i am correct or
not. If i am correct then how can I generate 1024 binary values or it is
restricted to 512? I found the binary values are different using two
different radius which is what i expect. Can this binary values be extended
to 1024 bits or so on. So if this is the case doesnt it cause error in
similarity calculation ?
using radius 4
chembl_18=#select
morganbv_fp('Cc1ccc2nc(-c3ccc(NC(C4N(C(c5cccs5)=O)CCC4)=O)cc3)sc2c1',4);
\x104008800230218340002440c540250700100c4843840200400c000846208005008188a00082084802411e0820a481400860a80408404241000441006008
Using radius 6
chembl_18=# select
morganbv_fp('Cc1ccc2nc(-c3ccc(NC(C4N(C(c5cccs5)=O)CCC4)=O)cc3)sc2c1',6);
\x104408800230218340003c42c540250700100c4843840200400c00084e20c005008188a000c2884802415e0820a481400862a8042842424102044100600c
Thanks
Abhik
Abhik Seal
Indiana University Bloomington
School of Informatics and Computing
Cheminformatics and Chemgenomics group http://registratio54.wix.com/ccrg
abs...@indiana.edu
http://mypage.iu.edu/~abseal/index.htm
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[Rdkit-discuss] Fwd: Error in installation of RDkit from source on Mac OSx 10.9.1
Hi All, I tried to install via homebrew but after running it cannot move to stage of rdkit installation on Mac 10.9.1 brew install --HEAD rdkit ==* Installing rdkit dependency: *boost *==** Downloading http://downloads.sourceforge.net/project/boost/boost/1.49.0/boos http://downloads.sourceforge.net/project/boost/boost/1.49.0/boos* Already downloaded: /Library/Caches/Homebrew/boost-1.49.0.tar.bz2 *==** ./bootstrap.sh --prefix=/usr/local/Cellar/boost/1.49.0 --libdir=/usr/local/C* *==** ./bjam --prefix=/usr/local/Cellar/boost/1.49.0 --libdir=/usr/local/Cellar/bo* When i was trying to build from source then i am having some types.cpp error .Attached is the log of error msg. Then i tried to install RDkit from source with Boost and all dependencies.I was able to install Boost1.49 but the problem with rdkit cmake is that it is throwing an error at make[2]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o] Error 1 make[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error My command was cmake -D PYTHON_LIBRARY=/usr/lib/python2.7/config/libpython2.7.a -D PYTHON_INCLUDE_DIR=/usr/include/python2.7 -D PYTHON_EXECUTABLE=/usr/bin/python -DBOOST_ROOT=/usr/local/boost_1_49_0 Then i also changed the boost version to 1.55 again i found the same error Anyone came across this type of error ? Attached is my error log. Can anyone guide me through whats going wrong. Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm -- Forwarded message -- From: Abhik Seal abhik1...@gmail.com Date: Mon, Feb 24, 2014 at 11:25 PM Subject: Error in installation of RDkit from source on Mac OSx 10.9.1 To: Rdkit-discuss@lists.sourceforge.net rdkit-discuss@lists.sourceforge.net Hi All, I tried to install via homebrew but after running it cannot move to stage of rdkit installation on Mac 10.9.1 brew install --HEAD rdkit ==* Installing rdkit dependency: *boost *==** Downloading http://downloads.sourceforge.net/project/boost/boost/1.49.0/boos http://downloads.sourceforge.net/project/boost/boost/1.49.0/boos* Already downloaded: /Library/Caches/Homebrew/boost-1.49.0.tar.bz2 *==** ./bootstrap.sh --prefix=/usr/local/Cellar/boost/1.49.0 --libdir=/usr/local/C* *==** ./bjam --prefix=/usr/local/Cellar/boost/1.49.0 --libdir=/usr/local/Cellar/bo* When i was trying to build from source then i am having some types.cpp error .Attached is the log of error msg. Then i tried to install RDkit from source with Boost and all dependencies.I was able to install Boost1.49 but the problem with rdkit cmake is that it is throwing an error at make[2]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o] Error 1 make[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error My command was cmake -D PYTHON_LIBRARY=/usr/lib/python2.7/config/libpython2.7.a -D PYTHON_INCLUDE_DIR=/usr/include/python2.7 -D PYTHON_EXECUTABLE=/usr/bin/python -DBOOST_ROOT=/usr/local/boost_1_49_0 Then i also changed the boost version to 1.55 again i found the same error Anyone came across this type of error ? Attached is my error log. Can anyone guide me through whats going wrong. Thanks Abhik Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm abhikseal/usr/local/src/RDKit_2013_09_1/build$cmake .. -- Boost version: 1.55.0 -- Found the following Boost libraries: -- python -- Boost version: 1.55.0 -- Found the following Boost libraries: -- regex -- Configuring done -- Generating done -- Build files have been written to: /usr/local/src/RDKit_2013_09_1/build abhikseal/usr/local/src/RDKit_2013_09_1/build$make [ 1%] Built target fastentropy [ 1%] Built target inchi_support Scanning dependencies of target RDGeneral [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o In file included from /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/types.cpp:15: In file included from /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/types.h:20: In file included from /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Invariant.h:15: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:434: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/algorithm:593: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/utility:255:15: error: no viable overloaded '=' first = __p.first; ~ ^ ~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tree:1246:35: note: in instantiation of member function 'std::__1::pairconst std::__1
[Rdkit-discuss] Error in installation of RDkit from source on Mac OSx 10.9.1
Hi All, Apologies for multiple postings, ignore my last posting. I tried to install rdkit via homebrew but after running it cannot move to stage of rdkit installation on Mac 10.9.1 brew install --HEAD rdkit ==* Installing rdkit dependency: *boost *==** Downloading http://downloads.sourceforge.net/project/boost/boost/1.49.0/boos http://downloads.sourceforge.net/project/boost/boost/1.49.0/boos* Already downloaded: /Library/Caches/Homebrew/boost-1.49.0.tar.bz2 *==** ./bootstrap.sh --prefix=/usr/local/Cellar/boost/1.49.0 --libdir=/usr/local/C* *==** ./bjam --prefix=/usr/local/Cellar/boost/1.49.0 --libdir=/usr/local/Cellar/bo* When i was trying to build from source then i am having some types.cpp error .Attached is the log of error msg. Then i tried to install RDkit from source with Boost and all dependencies.I was able to install Boost1.49 but the problem with rdkit cmake is that it is throwing an error at make[2]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o] Error 1 make[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error My command was cmake -D PYTHON_LIBRARY=/usr/lib/python2.7/config/libpython2.7.a -D PYTHON_INCLUDE_DIR=/usr/include/python2.7 -D PYTHON_EXECUTABLE=/usr/bin/python -DBOOST_ROOT=/usr/local/boost_1_49_0 Then i also changed the boost version to 1.55 again i found the same error Anyone came across this type of error ? Attached is my error log. Can anyone guide me through what's going wrong ? Thanks Abhik Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm abhikseal/usr/local/src/RDKit_2013_09_1/build$cmake .. -- Boost version: 1.55.0 -- Found the following Boost libraries: -- python -- Boost version: 1.55.0 -- Found the following Boost libraries: -- regex -- Configuring done -- Generating done -- Build files have been written to: /usr/local/src/RDKit_2013_09_1/build abhikseal/usr/local/src/RDKit_2013_09_1/build$make [ 1%] Built target fastentropy [ 1%] Built target inchi_support Scanning dependencies of target RDGeneral [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o In file included from /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/types.cpp:15: In file included from /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/types.h:20: In file included from /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Invariant.h:15: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:434: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/algorithm:593: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/utility:255:15: error: no viable overloaded '=' first = __p.first; ~ ^ ~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tree:1246:35: note: in instantiation of member function 'std::__1::pairconst std::__1::basic_stringchar, boost::any::operator=' requested here __cache-__value_ = *__first; ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tree:1187:9: note: in instantiation of function template specialization 'std::__1::__treestd::__1::pairconst std::__1::basic_stringchar, boost::any, std::__1::__map_value_compareconst std::__1::basic_stringchar, boost::any, std::__1::lessconst std::__1::basic_stringchar , true, std::__1::allocatorstd::__1::pairconst std::__1::basic_stringchar, boost::any ::__assign_multistd::__1::__tree_const_iteratorstd::__1::pairconst std::__1::basic_stringchar, boost::any, const std::__1::__tree_nodestd::__1::pairconst std::__1::basic_stringchar, boost::any, void * *, long ' requested here __assign_multi(__t.begin(), __t.end()); ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/map:766:21: note: in instantiation of member function 'std::__1::__treestd::__1::pairconst std::__1::basic_stringchar, boost::any, std::__1::__map_value_compareconst std::__1::basic_stringchar, boost::any, std::__1::lessconst std::__1::basic_stringchar , true, std::__1::allocatorstd::__1::pairconst std::__1::basic_stringchar, boost::any ::operator=' requested here __tree_ = __m.__tree_; ^ /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Dict.h:41:13: note: in instantiation of member function 'std::__1::mapconst std::__1::basic_stringchar, boost::any, std::__1::lessconst std::__1::basic_stringchar , std::__1::allocatorstd::__1::pairconst std::__1
[Rdkit-discuss] Error in installation of RDkit from source on Mac OSx 10.9.1
Hi All, I tried to install via homebrew but after running it cannot move to stage of rdkit installation on Mac 10.9.1 brew install --HEAD rdkit ==* Installing rdkit dependency: *boost *==** Downloading http://downloads.sourceforge.net/project/boost/boost/1.49.0/boos http://downloads.sourceforge.net/project/boost/boost/1.49.0/boos* Already downloaded: /Library/Caches/Homebrew/boost-1.49.0.tar.bz2 *==** ./bootstrap.sh --prefix=/usr/local/Cellar/boost/1.49.0 --libdir=/usr/local/C* *==** ./bjam --prefix=/usr/local/Cellar/boost/1.49.0 --libdir=/usr/local/Cellar/bo* When i was trying to build from source then i am having some types.cpp error .Attached is the log of error msg. Then i tried to install RDkit from source with Boost and all dependencies.I was able to install Boost1.49 but the problem with rdkit cmake is that it is throwing an error at make[2]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o] Error 1 make[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error My command was cmake -D PYTHON_LIBRARY=/usr/lib/python2.7/config/libpython2.7.a -D PYTHON_INCLUDE_DIR=/usr/include/python2.7 -D PYTHON_EXECUTABLE=/usr/bin/python -DBOOST_ROOT=/usr/local/boost_1_49_0 Then i also changed the boost version to 1.55 again i found the same error Anyone came across this type of error ? Attached is my error log. Can anyone guide me through whats going wrong. Thanks Abhik Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm abhikseal/usr/local/src/RDKit_2013_09_1/build$cmake .. -- Boost version: 1.55.0 -- Found the following Boost libraries: -- python -- Boost version: 1.55.0 -- Found the following Boost libraries: -- regex -- Configuring done -- Generating done -- Build files have been written to: /usr/local/src/RDKit_2013_09_1/build abhikseal/usr/local/src/RDKit_2013_09_1/build$make [ 1%] Built target fastentropy [ 1%] Built target inchi_support Scanning dependencies of target RDGeneral [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o In file included from /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/types.cpp:15: In file included from /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/types.h:20: In file included from /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Invariant.h:15: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:434: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/algorithm:593: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/utility:255:15: error: no viable overloaded '=' first = __p.first; ~ ^ ~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tree:1246:35: note: in instantiation of member function 'std::__1::pairconst std::__1::basic_stringchar, boost::any::operator=' requested here __cache-__value_ = *__first; ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tree:1187:9: note: in instantiation of function template specialization 'std::__1::__treestd::__1::pairconst std::__1::basic_stringchar, boost::any, std::__1::__map_value_compareconst std::__1::basic_stringchar, boost::any, std::__1::lessconst std::__1::basic_stringchar , true, std::__1::allocatorstd::__1::pairconst std::__1::basic_stringchar, boost::any ::__assign_multistd::__1::__tree_const_iteratorstd::__1::pairconst std::__1::basic_stringchar, boost::any, const std::__1::__tree_nodestd::__1::pairconst std::__1::basic_stringchar, boost::any, void * *, long ' requested here __assign_multi(__t.begin(), __t.end()); ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/map:766:21: note: in instantiation of member function 'std::__1::__treestd::__1::pairconst std::__1::basic_stringchar, boost::any, std::__1::__map_value_compareconst std::__1::basic_stringchar, boost::any, std::__1::lessconst std::__1::basic_stringchar , true, std::__1::allocatorstd::__1::pairconst std::__1::basic_stringchar, boost::any ::operator=' requested here __tree_ = __m.__tree_; ^ /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Dict.h:41:13: note: in instantiation of member function 'std::__1::mapconst std::__1::basic_stringchar, boost::any, std::__1::lessconst std::__1::basic_stringchar , std::__1::allocatorstd::__1::pairconst std::__1::basic_stringchar, boost::any ::operator=' requested here
Re: [Rdkit-discuss] Problems homebrewing RDKit
Hi Nathan, I have used this formula http://silicos-it.com/cookbook/configuring_osx_for_chemoinformatics/configuring_osx_for_chemoinformatics.html for my 3 month new MACBOOK Pro OSX 10.8 Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Mon, Oct 21, 2013 at 12:07 PM, Nathan Brown nathan.br...@icr.ac.ukwrote: Hi All, I'm having some trouble installing RDKit using Eddie's brew on my new MacBook Pro. I've attached the reported errors below. Has anyone seen these before or have any idea how complete the installation? Cheers, Nath 104876CTHLT:Library nbrown$ brew doctor Your system is ready to brew. 104876CTHLT:Library nbrown$ brew install --HEAD rdkit == Cloning https://github.com/rdkit/rdkit.git Updating /Library/Caches/Homebrew/rdkit--git == cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/HEAD' -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DPYTHON_LIBRARY='/Syste used as include directory in directory /tmp/rdkit-oc3C/Code/ChemicalFeatures/Wrap -- Configuring incomplete, errors occurred! See also /tmp/rdkit-oc3C/CMakeFiles/CMakeOutput.log. See also /tmp/rdkit-oc3C/CMakeFiles/CMakeError.log. READ THIS: https://github.com/mxcl/homebrew/wiki/troubleshooting The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135031iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135031iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Error while building Postgresql cartridge in Mac Lion 10.8
Hi Nikolas, Now i am running into this error abhikseal/usr/local/Cellar/RDKit_2013_03_2/Code/PgSQL/rdkit$make c++ -arch x86_64 -pipe -Os -g -Wall -Wno-deprecated-declarations -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wformat-security -fno-strict-aliasing -fwrapv -bundle -multiply_defined suppress -o rdkit.so rdkit_io.o mol_op.o bfp_op.o sfp_op.o rdkit_gist.o low_gist.o guc.o cache.o adapter.o -L/usr/lib -arch x86_64 -pipe -Os -g -Wall -Wno-deprecated-declarations -Wl,-dead_strip_dylibs -L/usr/local/Cellar/RDKit_2013_03_2/lib -Wl,-rpath,'/usr/local/Cellar/RDKit_2013_03_2/lib' -lChemTransforms -lFileParsers -lSmilesParse -lFingerprints -lSubgraphs -lSubstructMatch -lDescriptors -lPartialCharges -lGraphMol -lDataStructs -lRDGeometryLib -lRDGeneral -pthread -bundle_loader /usr/bin/postgres clang: warning: argument unused during compilation: '-pthread' ld: file not found: /usr/bin/postgres clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [rdkit.so] Error 1 Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Wed, Jul 17, 2013 at 2:25 AM, Nikolas Fechner niko...@fechner.cc wrote: ** Dear Abhik, the error you see is probably related to Apple changing the path names for mountain lion. At several places a simple workaround is suggested (e.g. http://code.google.com/p/modwsgi/issues/detail?id=298), which is to create a symbolic link to use the default xctoolchain instead. sudo ln -s /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/ /Applications/Xcode.app/Contents/Developer/Toolchains/OSX10.8.xctoolchain Maybe that helps. Kind regards, Nikolas On July 17, 2013 at 1:33 AM Abhik Seal abhik1...@gmail.com wrote: Hi All, I have installed Rdkit using homebrew and after installing it i was trying to install the Postgresql cartridge in Mac and now it is throwing an unique error related to Xcode tools . Is any libraries missing. usr/local/Cellar/RDKit_2013_03_2/Code/PgSQL/rdkit$make /Applications/Xcode.app/Contents/Developer/Toolchains/OSX10.8.xctoolchain/usr/bin/cc -I/usr/local/Cellar/boost/1.53.0/ -I/usr/local/Cellar/RDKit_2013_03_2/Code -DRDKITVER='007000' -I. -I. -I/usr/include/postgresql/server -I/usr/include/postgresql/internal -I/usr/include/libxml2 -fPIC -c -o rdkit_io.o rdkit_io.c make: /Applications/Xcode.app/Contents/Developer/Toolchains/OSX10.8.xctoolchain/usr/bin/cc: No such file or directory make: *** [rdkit_io.o] Error 1 Any help on this ? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Error while building Postgresql cartridge in Mac Lion 10.8
Hi All, I have installed Rdkit using homebrew and after installing it i was trying to install the Postgresql cartridge in Mac and now it is throwing an unique error related to Xcode tools . Is any libraries missing. usr/local/Cellar/RDKit_2013_03_2/Code/PgSQL/rdkit$make /Applications/Xcode.app/Contents/Developer/Toolchains/OSX10.8.xctoolchain/usr/bin/cc -I/usr/local/Cellar/boost/1.53.0/ -I/usr/local/Cellar/RDKit_2013_03_2/Code -DRDKITVER='007000' -I. -I. -I/usr/include/postgresql/server -I/usr/include/postgresql/internal -I/usr/include/libxml2 -fPIC -c -o rdkit_io.o rdkit_io.c make: /Applications/Xcode.app/Contents/Developer/Toolchains/OSX10.8.xctoolchain/usr/bin/cc: No such file or directory make: *** [rdkit_io.o] Error 1 Any help on this ? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit ctest failed
Dear Vladimir, Check the python path . RDBASE must have the python path. Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Fri, Aug 17, 2012 at 8:29 PM, Vladimir Chupakhin chu...@gmail.comwrote: Dear colleagues, after compiling and installing last RDKit under Ubuntu12.04 (64bit) I have following test failed. The following tests FAILED: 3 - pyBV (Failed) 8 - testPyGeometry (Failed) 35 - pyChemReactions (Failed) 42 - pyMolDescriptors (Failed) 61 - pyGraphMolWrap (SEGFAULT) 69 - pyFeatures (Failed) 76 - pythonTestDirChem (Failed) I can't find the source of mistakes and errors. Can you please suggest me any solutions? RDBASE is provided in .bashrc, boost and openbabel library are installed in default Ubuntu paths. Thank you, -- Vladimir Chupakhin, Boston, MA, USA LinkedIN: http://www.linkedin.com/in/chupvl *Info from the log file* 3/76 Testing: pyBV 3/76 Test: pyBV Command: /usr/bin/python /home/chupvl/scisoft/rdkit/Code/DataStructs/Wrap/testBV.py Directory: /home/chupvl/scisoft/rdkit/build/Code/DataStructs/Wrap pyBV start time: Aug 17 10:38 EDT Output: -- ...EE == ERROR: test7FPS (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/DataStructs/Wrap/testBV.py, line 153, in test7FPS self.failUnlessEqual(DataStructs.BitVectToFPSText(bv),03008280) AttributeError: 'module' object has no attribute 'BitVectToFPSText' 8/76 Testing: testPyGeometry 8/76 Test: testPyGeometry Command: /usr/bin/python /home/chupvl/scisoft/rdkit/Code/Geometry/Wrap/testGeometry.py Directory: /home/chupvl/scisoft/rdkit/build/Code/Geometry/Wrap testPyGeometry start time: Aug 17 10:38 EDT Output: -- ..E.. == ERROR: test6Dihedrals (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/Geometry/Wrap/testGeometry.py, line 350, in test6Dihedrals ang = geom.ComputeDihedralAngle(p1,p2,p3,p4) AttributeError: 'module' object has no attribute 'ComputeDihedralAngle' -- Ran 9 tests in 0.023s FAILED (errors=1) Testing Geometry wrapper end of output Test time = 0.08 sec -- Test Failed. testPyGeometry end time: Aug 17 10:38 EDT testPyGeometry time elapsed: 00:00:00 -- 35/76 Testing: pyChemReactions 35/76 Test: pyChemReactions Command: /usr/bin/python /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py Directory: /home/chupvl/scisoft/rdkit/build/Code/GraphMol/ChemReactions/Wrap pyChemReactions start time: Aug 17 10:38 EDT Output: -- ..E...[10:38:56] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q [10:38:56] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q .[10:38:56] reactant atom-mapping number 1 found multiple times. [10:38:56] product atom-mapping number 2 not found in reactants. F.E. == ERROR: test16GetReactingAtoms (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py, line 399, in test16GetReactingAtoms rAs = rxn.GetReactingAtoms() AttributeError: 'ChemicalReaction' object has no attribute 'GetReactingAtoms' == ERROR: test8Properties (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py, line 286, in test8Properties self.failUnlessEqual(ps[0][0].GetAtomWithIdx(1).GetIsotope(),3); AttributeError: 'Atom' object has no attribute 'GetIsotope' == FAIL: test5Validation (__main__.TestCase) -- Traceback (most recent call last): File /home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py, line 250, in test5Validation self.failUnless(rxn.Validate()==(1,1)) AssertionError: False is not true
Re: [Rdkit-discuss] Problem of install of RDkit in Ubuntu
Dear Markus, Yes it is not their its lost. Will install again and see. Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 8:46 PM, Abhik Seal abhik1...@gmail.com wrote: Dear Greg, The error is no module named rdkit Well i am using the windows installer of ubuntu.I guess it should be problem of that. If had been path problem then should the rdkit runned and passed all test? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 8:34 PM, Markus Sitzmann sitzm...@helix.nih.govwrote: Hi Abhik, are you maybe doing this on a virtual machine and/or are you booting Ubuntu just from an ISO image? Markus On 7/24/2012 9:32 AM, Abhik Seal wrote: Dear All, I have a peculiar problem of RDKit installation I installed RDKit in ubuntu 11.06 with all the 76 test passed and also i started working in it. But it happened three times to me that when i use RDkit after 2-3 days later then i found that it cannot recognise the command in python from rdkit import Chem showing error Which means that i again have to install RDkit ? It happened three times to me . I didn't upgraded my ubuntu but i installed some other free tools. Did anybody found this problem? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Markus Sitzmann, Ph.D. Chemical Biology Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 (office) 301-846-6033 (fax) sitzm...@helix.nih.gov http://www.linkedin.com/pub/1/7b8/342 http://www.xing.com/profile/Markus_Sitzmann -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Problem of install of RDkit in Ubuntu
Dear All, I have a peculiar problem of RDKit installation I installed RDKit in ubuntu 11.06 with all the 76 test passed and also i started working in it. But it happened three times to me that when i use RDkit after 2-3 days later then i found that it cannot recognise the command in python from rdkit import Chem showing error Which means that i again have to install RDkit ? It happened three times to me . I didn't upgraded my ubuntu but i installed some other free tools. Did anybody found this problem? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problem of install of RDkit in Ubuntu
Dear Greg, The error is no module named rdkit Well i am using the windows installer of ubuntu.I guess it should be problem of that. If had been path problem then should the rdkit runned and passed all test? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 8:34 PM, Markus Sitzmann sitzm...@helix.nih.govwrote: Hi Abhik, are you maybe doing this on a virtual machine and/or are you booting Ubuntu just from an ISO image? Markus On 7/24/2012 9:32 AM, Abhik Seal wrote: Dear All, I have a peculiar problem of RDKit installation I installed RDKit in ubuntu 11.06 with all the 76 test passed and also i started working in it. But it happened three times to me that when i use RDkit after 2-3 days later then i found that it cannot recognise the command in python from rdkit import Chem showing error Which means that i again have to install RDkit ? It happened three times to me . I didn't upgraded my ubuntu but i installed some other free tools. Did anybody found this problem? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Markus Sitzmann, Ph.D. Chemical Biology Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 (office) 301-846-6033 (fax) sitzm...@helix.nih.gov http://www.linkedin.com/pub/1/7b8/342 http://www.xing.com/profile/Markus_Sitzmann -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problem of install of RDkit in Ubuntu
Dear Markus, Well i agree then but what about other tools like cdk,open babel they are working well Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 9:31 PM, Markus Sitzmann sitzm...@helix.nih.govwrote: Hi Abhik, I am not entirely sure how this windows installer of ubuntu works, but probably you have to make sure that you install RDkit in the right place (a directory that is actually written to the disk). Your problem is probably that you install RDKit only virtually, i.e. in a part of the directory tree that is coming from the ISO image underlying your Ubuntu installation, so RDKit is gone after each reboot (it is only present as long as your Ubuntu installation is not rebooted). Markus On 7/24/2012 11:16 AM, Abhik Seal wrote: Dear Greg, The error is no module named rdkit Well i am using the windows installer of ubuntu.I guess it should be problem of that. If had been path problem then should the rdkit runned and passed all test? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 8:34 PM, Markus Sitzmann sitzm...@helix.nih.gov mailto:sitzm...@helix.nih.gov wrote: Hi Abhik, are you maybe doing this on a virtual machine and/or are you booting Ubuntu just from an ISO image? Markus On 7/24/2012 9:32 AM, Abhik Seal wrote: Dear All, I have a peculiar problem of RDKit installation I installed RDKit in ubuntu 11.06 with all the 76 test passed and also i started working in it. But it happened three times to me that when i use RDkit after 2-3 days later then i found that it cannot recognise the command in python from rdkit import Chem showing error Which means that i again have to install RDkit ? It happened three times to me . I didn't upgraded my ubuntu but i installed some other free tools. Did anybody found this problem? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu mailto:abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 tel:%2B18123699097 http://mypage.iu.edu/~abseal/index.htm -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net mailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Markus Sitzmann, Ph.D. Chemical Biology Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 tel:301-846-5974 (office) 301-846-6033 tel:301-846-6033 (fax) sitzm...@helix.nih.gov mailto:sitzm...@helix.nih.gov http://www.linkedin.com/pub/1/7b8/342 http://www.xing.com/profile/Markus_Sitzmann -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net mailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263
[Rdkit-discuss] Problem Installing RDkit on Windows
I was just trying my hands on rdkit and installed the package and when i tried to use it just a simple program: from rdkit import Chem from rdkit import rdbase m = Chem.MolFromSmiles(Cc1cc1) print mol.GetNumAtoms() I get an error like Traceback (most recent call last): File C:\Python27\rd1.py, line 1, in module from rdkit import Chem File C:\Python27\lib\site-packages\rdkit\Chem\__init__.py, line 18, in module from rdkit import rdBase ImportError: DLL load failed: The specified module could not be found. i using the recent version of rdkit and installed the package dont know whats wrong . Can you suggest something Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problem Installing RDkit on Windows
I have a python path set so do i need to just add this text ;C:\Rdkit\lib I did that still not wokring. Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Sun, Apr 1, 2012 at 7:13 PM, Greg Landrum greg.land...@gmail.com wrote: Dear Abhik, On Mon, Apr 2, 2012 at 12:56 AM, Abhik Seal abhik1...@gmail.com wrote: I was just trying my hands on rdkit and installed the package and when i tried to use it just a simple program: from rdkit import Chem from rdkit import rdbase m = Chem.MolFromSmiles(Cc1cc1) print mol.GetNumAtoms() I get an error like Traceback (most recent call last): File C:\Python27\rd1.py, line 1, in module from rdkit import Chem File C:\Python27\lib\site-packages\rdkit\Chem\__init__.py, line 18, in module from rdkit import rdBase ImportError: DLL load failed: The specified module could not be found. i using the recent version of rdkit and installed the package dont know whats wrong . Can you suggest something You need to make sure that the RDKit lib directory (it was part of the zip file) is in your PATH. This is most likely the cause of the problem. Best, -greg -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
