# HG changeset patch # User bgruening # Date 1367083268 14400 # Node ID 0275ed8268903a03bfcf08a89452047b6177b96a # Parent c7f8a12d8176e93cf8fb5aedbd351527f0835a4d Uploaded diff -r c7f8a12d8176 -r 0275ed826890 rdkit_descriptors.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdkit_descriptors.py Sat Apr 27 13:21:08 2013 -0400 @@ -0,0 +1,77 @@ +#!/usr/bin/env python + +from rdkit.Chem import Descriptors +from rdkit import Chem +import sys, os, re +import argparse +import inspect + +def get_supplier( infile, format = 'smiles' ): + """ + Returns a generator over a SMILES or InChI file. Every element is of RDKit + molecule and has its original string as _Name property. + """ + with open(infile) as handle: + for line in handle: + line = line.strip() + if format == 'smiles': + mol = Chem.MolFromSmiles( line, sanitize=True ) + elif format == 'inchi': + mol = Chem.inchi.MolFromInchi( line, sanitize=True, removeHs=True, logLevel=None, treatWarningAsError=False ) + if mol is None: + yield False + else: + mol.SetProp( '_Name', line.split('\t')[0] ) + yield mol + + +def get_rdkit_descriptor_functions(): + """ + Returns all descriptor functions under the Chem.Descriptors Module as tuple of (name, function) + """ + ret = [ (name, f) for name, f in inspect.getmembers( Descriptors ) if inspect.isfunction( f ) and not name.startswith( '_' ) ] + ret.sort() + return ret + + +def descriptors( mol, functions ): + """ + Calculates the descriptors of a given molecule. + """ + for name, function in functions: + yield (name, function( mol )) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument('-i', '--infile', required=True, help='Path to the input file.') + parser.add_argument("--iformat", help="Specify the input file format.") + + parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'), + default=sys.stdout, help="path to the result file, default it sdtout") + + parser.add_argument("--header", dest="header", action="store_true", + default=False, + help="Write header line.") + + args = parser.parse_args() + + if args.iformat == 'sdf': + supplier = Chem.SDMolSupplier( args.infile ) + elif args.iformat =='smi': + supplier = get_supplier( args.infile, format = 'smiles' ) + elif args.iformat == 'inchi': + supplier = get_supplier( args.infile, format = 'inchi' ) + + functions = get_rdkit_descriptor_functions() + + if args.header: + args.outfile.write( '%s\n' % '\t'.join( [name for name, f in functions] ) ) + + for mol in supplier: + if not mol: + continue + descs = descriptors( mol, functions ) + molecule_id = mol.GetProp("_Name") + args.outfile.write( "%s\n" % '\t'.join( [molecule_id]+ [str(res) for name, res in descs] ) ) + diff -r c7f8a12d8176 -r 0275ed826890 rdkit_descriptors.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdkit_descriptors.xml Sat Apr 27 13:21:08 2013 -0400 @@ -0,0 +1,49 @@ + + calculated with RDKit + + + rdkit + + rdkit_descriptors.py -i "${infile}" --iformat "${infile.ext}" -o "${outfile}" $header 2>&1 + + + + + + + + + + + +.. class:: infomark + +**TIP:** If your data is not in SD- or SMILES format, use the pencil icon on your dataset to convert your data + +----- + +**Example** + +- Input file:: + + - SD-Format (http://en.wikipedia.org/wiki/Chemical_table_file) + - SMILES Format (http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification) + +- Result:: + + +http://code.google.com/p/rdkit/wiki/DescriptorsInTheRDKit +http://rdkit.org/Python_Docs/rdkit.Chem.Descriptors-module.html + + +----- + + +**Cite** + +Greg Landrum +[1] RDKit: Open-source cheminformatics; http://www.rdkit.org + + + + diff -r c7f8a12d8176 -r 0275ed826890 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Sat Apr 27 13:21:08 2013 -0400 @@ -0,0 +1,4 @@ + + + + diff -r c7f8a12d8176 -r 0275ed826890 tool_dependencies.xml --- a/tool_dependencies.xml Sat Apr 27 13:09:10 2013 -0400 +++ b/tool_dependencies.xml Sat Apr 27 13:21:08 2013 -0400 @@ -1,45 +1,5 @@ - - - - - - - - - - - - http://rdkit.googlecode.com/files/RDKit_2013_03_1.tgz - - - - - - - - - - - - - - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`pwd`/lib/ && - export PYTHONPATH=$PYTHONPATH:`pwd`/ && - mkdir build && - cd build && - cmake .. -DBOOST_ROOT=$BOOST_ROOT_DIR -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/rdkit/ -DRDK_INSTALL_INTREE=OFF - cd ./build && make - cd ./build && make install - - - $INSTALL_DIR/rdkit - $INSTALL_DIR/rdkit - $INSTALL_DIR/rdkit/bin - $INSTALL_DIR/rdkit/lib/ - - - - Compiling rdkit requires cmake, python headers, sqlite3, flex and bison. + +