[Rdkit-discuss] Using Gobbi_Pharm2D
Dear RDKitters,
within a given list of SMILES codes, I would like to get matches between
acidic functionalies and basic functionalities as well when I do a search
gainst a query SMILES code.
To be more precise: In the example given below, I would like to get all the
entries in the db_smiles list that bear an carboxylic acid functionality
(without the phenyl ring). Additionally, I would like to "jump" from one
acid to another - e.g. jump from an carboxylic acid to an hydroxyl group.
Of course, this is a much weaker acid.
In my understanding, 2 steps are necessary - not reflected in my snippet:
(1) Dump out the basic/acidic functionality of the query molecule
(2) Do the same task for each db_smile & find matches between the
pharmacophoric
features.
Here comes the snippet:
"
query_mol = Chem.MolFromSmiles('O=C(O)c1c1')
query_fp = Generate.Gen2DFingerprint(query_mol,Gobbi_Pharm2D.factory)
for db_smile in db_smiles:
db_mol = Chem.MolFromSmiles(db_smile)
db_mol_fp = Generate.Gen2DFingerprint(query_mol,Gobbi_Pharm2D.factory)
"
Cheers & Thanks,
Paul
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Re: [Rdkit-discuss] Python error after install
Dear Greg, Thanks, it works now. I had to go through the sequence cmake, make and make install again with all environment variables set. I'm pretty sure I did this in my previous attempt, could it be that the variables need to be set explicitly, eg PYTHONPATH=/path/to/rdbase rather that PYTHONPATH=$RDBASE ? In any case, these are the variables I set before I do 'cmake ..' , 'make','make install' from $RDBASE/build: BOOSTROOT=/path/to/boost_1_47_0 RDBASE=/path/to/RDKit_2011_09_1 PYTHONPATH=/path/to/RDKit_2011_09_1 LD_LIBRARY_PATH=/path/to/boost_1_47_0:/path/to/boost_1_47_0/stage/lib:/path/to/RDKit_2011_09_1/:path/to/RDKit_2011_09_1/build/lib/ Boost_INCLUDEDIR=/path/to/boost_1_47_0 The tests from 'ctest' all pass and I can do 'from rdkit import Chem' in the interactive python interpreter, so I guess I'm looking forward to doing some chemistry soon! Thanks again, Felix On 27 Oct 2011, at 04:40, Greg Landrum wrote: > Dear Felix, > > On Thu, Oct 27, 2011 at 12:41 AM, Felix Krueger > wrote: >> I tried building RDKit in a Ubuntu virtual machine. The output said the >> build was successful, ctest gave a number errors: >>3 - pyBV (Failed) > >> 76 - pythonTestDirChem (Failed) >> I think I know why these tests fail...when I try importing Chem, I get: >> from rdkit import Chem >> Traceback (most recent call last): >> File "", line 1, in >> File "/home/mo/Library/RDKit_2011_09_1/rdkit/Chem/__init__.py", line 18, >> in >> from rdkit import rdBase >> ImportError: cannot import name rdBase >> I see rdBase.so sitting in $RDBASE/build/rdkit and I've got it in my PATH, >> PYTHONPATH and LD_LIBRARY_PATH... >> Would anyone know, is this an issue of finding the module or is there a >> problem with the way it was built? > > Did you do a "make install" after you did the "make"? > rdBase.so should end up being put in $RDBASE/rdkit when you do this. > Then you need to be sure that $RDBASE is in your PYTHONPATH and that > $RDBASE/lib is in your LD_LIBRARY_PATH. > > -greg -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
