Hi,
I am trying to convert small CSV file (SMILES and associated property)
as SD File using CDK 1.2.0.
I am using parseSmiles -> StructureDiagramGenerator -> setSdFields ->
MDLWriter sequence.
Am getting following error:
(1) cannot find symbol in class
org.openscience.cdk.io.MDLWriter.mw.setSdFields(map);
(2) When I comment mw.setSdFields(map) line, I get the structure (no
SD tag) printed out with following null pointer Exception
Reason: null java.lang.NullPointerException
at java.io.Reader.<init>(Reader.java:61)
at java.io.InputStreamReader.<init>(InputStreamReader.java:55)
at
org.openscience.cdk.layout.TemplateHandler.loadTemplates(TemplateHandler.java:98)
at
org.openscience.cdk.layout.TemplateHandler.<init>(TemplateHandler.java:83)
at
org.openscience.cdk.layout.StructureDiagramGenerator.setMolecule(StructureDiagramGenerator.java:131)
at
org.openscience.cdk.layout.StructureDiagramGenerator.setMolecule(StructureDiagramGenerator.java:221)
at Smile2Str.GetStr(csv2sdf.java:47)
at csv2sdf.main(csv2sdf.java:102)
Attached is code and data file
Any help will be appreciated.
Thanks
om
Bioinformatics Center
University of Pune
Pune-411007
India
//-----------------------------------------------------------//
// Code written based on CDK for CSV to SDF file conversion //
// ompan...@gmail.com //
// date: 28/05/09 //
// ----------------------------------------------------------//
import org.openscience.cdk.*;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.io.MDLWriter;
import org.openscience.cdk.io.iterator.*;
import org.openscience.cdk.smiles.*;
import java.io.*;
import java.util.*;
import java.lang.*;
import java.util.HashMap;
import java.util.regex.*;
import java.io.StringWriter;
import java.io.FileWriter;
import java.io.File;
import java.sql.*;
class Smile2Str
{
IMolecule mol = null;
HashMap<String, Object> map = new HashMap<String, Object>();
//private HashMap sd_tags = new HashMap();
public void GetStr (String smi, int ID, double MIC) // constructor
{
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
StringWriter w = new StringWriter();
try
{
mol = sp.parseSmiles(smi);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
try
{
sdg.setMolecule(mol);
sdg.generateCoordinates();
mol = sdg.getMolecule();
//mol.setProperty("NIAID", ID);
map.put("NIAID", ID);
try
{
MDLWriter mw = new MDLWriter(w);
mw.setSdFields(map);
mw.writeMolecule(mol);
mw.close();
} catch (Exception e) {System.out.println(e.toString());}
System.out.println(w.toString());
}
catch (Exception exc) { exc.printStackTrace();}
}
catch (CDKException cdke) { cdke.printStackTrace();}
} // method
} // class
class csv2sdf
{
public static void main(String[] args) throws CDKException
{
int i, j, k=0;
String [] myArr = null;
String strLine;
int NIAID = 0;
double MIC = 0.00;
String SMILES;
String colname;
//Read File Line By Line
try
{
FileInputStream fstream = new FileInputStream("NIAID.csv");
//FileWriter w1 = new FileWriter (new File ("molecule.sdf")) ;
Smile2Str smi2str = new Smile2Str ();
DataInputStream in = new DataInputStream(fstream);
BufferedReader br = new BufferedReader(new InputStreamReader(in));
strLine = br.readLine();
if (strLine != null)
{
System.out.println ("Col name:" +strLine);
while ((strLine = br.readLine()) != null)
{
// "NIAID ID","MIC original","MIC original unit","MIC (uM)","TB dataset ID","Smiles"
// 180691,0.000003,"uM",0.000003,2767,"o1c2c(nc1C)c(OC(=O)COC)c1c(cccc1)c2OC(=O)COC"
strLine=strLine.replaceAll("\n","");
myArr = strLine.split (",");
NIAID=Integer.valueOf(myArr[0]);
MIC=Double.valueOf(myArr[3]);
SMILES=myArr[5];
SMILES=SMILES.replaceAll("\"", ""); // remove the quotes from SMILES
smi2str.GetStr(SMILES, NIAID, MIC);
//System.out.println (SMILES + NIAID + MIC);
}
}
//Close the input stream
in.close();
}
catch (Exception fe){System.err.println("Error: " + fe.getMessage());}
}
}//class
"NIAID ID","MIC original","MIC original unit","MIC (uM)","TB dataset ID","Smiles"
180691,0.000003,"uM",0.000003,2767,"o1c2c(nc1C)c(OC(=O)COC)c1c(cccc1)c2OC(=O)COC"
180690,0.000010,"uM",0.000010,2766,"o1c2c(nc1-c1ccccc1)C(=O)c1c(cccc1)C2=O"
180689,0.000010,"uM",0.000010,2765,"o1c2c(nc1C)C(=O)c1c(cccc1)C2=O"
180692,0.000020,"uM",0.000020,2768,"s1c2c(nc1C)C(=O)c1c(cccc1)C2=O"
185726,0.000100,"ug/ml",0.000113,2807,"O1c2c3c4c(c([O-])c2C)c([O-])c(NC(=O)/C(=C/C=C\C(C)C(O)C(C)C(O)C(C)C(OC(=O)C)C(C)C(OC)\C=C/OC1(C)C3=O)/C)c(N1CC[NH+](CC1)Cc1ccc(cc1)C)c4O"
2516,0.000100,"ug/ml",0.000119,28,"O1c2c3c4c(c([O-])c2C)c([O-])c(NC(=O)/C(=C/C=C\C(C)C(O)C(C)C(O)C(C)C(OC(=O)C)C(C)C(OC)\C=C/OC1(C)C3=O)/C)c(N1CC[NH+](CC1)CC(C)C)c4O"
113916,0.000100,"ug/ml",0.000124,2317,"s1cccc1\C=N/c1c2NC(=O)/C(=C\C=C\C(C)C(O)C(C)C(O)C(C)C(OC(=O)C)C(C)C(OC)\C=C/OC3(Oc4c(c(c(c([O-])c4C)c2[O-])c1O)C3=O)C)/C"
113800,0.000150,"ug/ml",0.000174,2248,"O1c2c3c4c(c([O-])c2C)C(=O)C(NC(=O)/C(=C/C=C\C(C)C(O)C(C)C(O)C(C)C(OC(=O)C)C(C)C(OC)\C=C/OC1(C)C3=O)/C)=C1NC2(N=C14)CC[NH+](CC2)CCC(C)C"
185729,0.000300,"ug/ml",0.000326,2810,"O1c2c3c4c(c([O-])c2C)c([O-])c(NC(=O)/C(=C/C=C\C(C)C(O)C(C)C(O)C(C)C(OC(=O)C)C(C)C(OC)\C=C/OC1(C)C3=O)/C)c(N1CC[NH+](CC1)Cc1c2c(ccc1)cccc2)c4O"
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