rajarshi

var data = new google.visualization.DataTable();
data.addColumn(’string’, ‘Solvent’);
data.addColumn(’number’, ‘Conc (M)’);
data.addRows(5);
data.setValue(0, 0, ‘thf’);
data.setValue(0, 1, 1.23);
data.setValue(1, 0, ‘acetonitrile’);
data.setValue(1, 1, 2.34);

rajarshi

 @Test
    public void testBug2784343() throws InvalidSmilesException {
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        String smiles = "C1(C)=C(C)CC(C)C2CC21";
        IMolecule mol1 = sp.parseSmiles(smiles);
        SmilesGenerator smilesGenerator = new SmilesGenerator();
        smilesGenerator.setUseAromaticityFlag(true);
        String gensmiles1 = smilesGenerator.createSMILES(mol1);

        smiles = "CC1(C)C2C(C)=CCC1C2(C)C";

rajarshi

 @Test
    public void testBug2784343() throws InvalidSmilesException {
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        String smiles = "C1(C)=C(C)CC(C)C2CC21";
        IMolecule mol1 = sp.parseSmiles(smiles);
        SmilesGenerator smilesGenerator = new SmilesGenerator();
        smilesGenerator.setUseAromaticityFlag(true);
        String gensmiles1 = smilesGenerator.createSMILES(mol1);

        smiles = "CC1(C)C2C(C)=CCC1C2(C)C";

rajarshi

package net.rguha.dc;

import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.InputSplit;
import org.apache.hadoop.mapreduce.RecordReader;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.mapreduce.lib.input.TextInputFormat;

/**

rajarshi

package net.rguha.dc;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.DataOutputBuffer;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.InputSplit;

rajarshi

PREFIX  chembl:  <http://rdf.farmbio.uu.se/chembl/onto/#>
SELECT DISTINCT ?x ?pmid ?desc WHERE { 
?protein chembl:hasKeyword "Isomerase" .
?x chembl:hasTarget ?protein .
?x chembl:organism "Mus musculus" .
?x chembl:hasDescription ?desc .
?x chembl:extractedFrom ?resource .
?resource <http://purl.org/ontology/bibo/pmid> ?pmid .
}

rajarshi

package gov.nih.ncgc;

import chemaxon.formats.MolImporter;
import chemaxon.sss.search.MCS;
import chemaxon.struc.Molecule;

import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

rajarshi

library(rcdk)

## Compare methods to convert Java BitSet -> R vector

mol <- parse.smiles("O=C(OC)C(c1ccccc1)C2NCCCC2")
fp <- .jnew('org/openscience/cdk/fingerprint/Fingerprinter',
            as.integer(1024),
            as.integer(6))
bitset <- .jcall(fp, "Ljava/util/BitSet;", "getFingerprint", mol)

rajarshi

package gov.nih.ncgc;

import org.openscience.cdk.ChemFile;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.io.Mol2Reader;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

rajarshi

running install
running build
running build_py
copying openbabel.py -> build/lib.macosx-10.5-universal-2.6
copying pybel.py -> build/lib.macosx-10.5-universal-2.6
running build_ext
building '_openbabel' extension
g++ -arch i386 -arch ppc -arch ppc64 -arch x86_64 -isysroot / -bundle -undefined dynamic_lookup build/temp.macosx-10.5-universal-2.6/Users/guhar/src/openbabel/scripts/python/openbabel-python.o -L../lib -lopenbabel -o build/lib.macosx-10.5-universal-2.6/_openbabel.so
ld warning: in ../lib/libopenbabel.dylib, file is not of required architecture
ld warning: in ../lib/libopenbabel.dylib, file is not of required architecture