rajarshi

 @Test public void foo() throws Exception {

        IsotopeFactory ifac = Isotopes.getInstance();
        IIsotope c = ifac.getMajorIsotope("C");
        IIsotope h = ifac.getMajorIsotope("H");
        IIsotope o = ifac.getMajorIsotope("O");
        IIsotope br79 = ifac.getMajorIsotope("Br");
        IIsotope br81 = ifac.getIsotope("Br", 81);

        MolecularFormulaRange mfRange = new MolecularFormulaRange();

rajarshi

import chemaxon.struc.Molecule;
import chemaxon.util.MolHandler;
import gov.nih.ncgc.algo.graph.VFLib2;
import gov.nih.ncgc.descriptor.MolecularFramework;
import gov.nih.ncgc.util.ChemUtil;
import gov.nih.ncgc.util.MolStandardizer;
import org.apache.commons.dbcp2.BasicDataSource;

import java.io.BufferedReader;
import java.io.FileReader;

rajarshi

import chemaxon.struc.Molecule;
import chemaxon.util.MolHandler;
import gov.nih.ncgc.algo.graph.VFLib2;
import gov.nih.ncgc.descriptor.MolecularFramework;
import gov.nih.ncgc.util.ChemUtil;
import gov.nih.ncgc.util.MolStandardizer;
import org.apache.commons.dbcp2.BasicDataSource;

import java.io.BufferedReader;
import java.io.FileReader;

rajarshi

library(dplyr)
library(rcdk)
all_form <- expand.grid(C=1:5, N=0:5, O=0:5, H=0:50)
all_form <- all_form %>%
    mutate(formula = paste0('C',C,'N',N,'O',O,'H',H)) 
system.time(valid <- sapply(all_form$formula, function(x) isvalid.formula(get.formula(x))))
table(valid)

rajarshi

function setjdk() {
  if [ $# -ne 0 ]; then
   removeFromPath '/System/Library/Frameworks/JavaVM.framework/Home/bin'
   if [ -n "${JAVA_HOME+x}" ]; then
    removeFromPath $JAVA_HOME
   fi
   export JAVA_HOME=`/usr/libexec/java_home -v $@`
   export PATH=$JAVA_HOME/bin:$PATH
  fi
 }

rajarshi

    public void testSA() throws FileNotFoundException, CDKException {
        FileInputStream fis = new FileInputStream("/Users/guhar/tmp/after_alignment.sdf");
        MDLV2000Reader reader = new MDLV2000Reader(fis, Mode.STRICT);
        IAtomContainer after = reader.read(new AtomContainer());
        fis = new FileInputStream("/Users/guhar/tmp/before_alignment.sdf");
        reader = new MDLV2000Reader(fis, Mode.STRICT);
        IAtomContainer before = reader.read(new AtomContainer());

        System.out.println(before.getProperty(CDKConstants.TITLE));
        System.out.println(after.getProperty(CDKConstants.TITLE));

rajarshi

byte[] molbytes = su.getFile(new ObjectId(oid));
        ByteArrayInputStream bais = new ByteArrayInputStream(molbytes);
        try {
            MolImporter importer = new MolImporter(bais);
            List<Molecule> mols = new ArrayList<Molecule>();
            while (true) {
                Molecule m = importer.read();
                if (m == null) break;
                m.setProperty("uuid", sub.getUserUuid());
                m.setProperty("pi_name", sub.getPiName());

rajarshi

library(ncgchts)
library(ggplot2)
library(RColorBrewer)
library(stringr)
data(sample.info)
con <- get.connection('hts', 'ncgc', 'probedb')
curve.order <- c(-1.1, -1.2, -2.1, -2.2, -1.3, -2.3, -1.4, -2.4,  1.1, 1.2, 2.1, 2.2, 1.3, 2.3, 1.4, 2.4, -3.0, 3.0, 4.0, 5.0)

protos <- c('s-levens-topo-HCT116-1', 's-levens-topo-mutant-1')
curves <- lapply(protos, function(p) {

rajarshi

"","C01","C02","C03","C04","C05","C06"
"1071",86.38420065,79.07808678,29.7117183,103.41587423,111.10614753,8.63011858
"10800",44.29501369,6.54247662,68.01638855,66.75177262,3.54032541,68.38830847
"10919",57.126174675,5.58139873,82.08353185,31.667684375,7.363592625,92.422583695
"11200",46.98399506,7.95712996,112.22964622,31.28326229,4.60511211,129.60868594
"1268",33.44880143,5.153618,79.30898798,29.60511291,32.73451976,94.67177589
"1352",19.37561449,0.17288331,78.88568485,9.14411316,24.0009678,78.18529926
"148",3.33528891,1.60941952,78.13779848,3.15238557,4.96052261,71.51730085
"1636",12.37098707,0.907317765,88.355246405,10.96153091,4.049607285,78.91513506
"1644",97.88520438,32.16221987,80.88268546,99.14777684,29.55725639,90.61186379

rajarshi