com.actelion.research.chem.properties.fractaldimension.FractalDimensionMoleculeMain Maven / Gradle / Ivy
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/*
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package com.actelion.research.chem.properties.fractaldimension;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.SmilesParser;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.util.CommandLineParser;
import com.actelion.research.util.IO;
import java.io.*;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;
/**
* FractalDimensionMoleculeMain
* Modest v. Korff
*
* Created by korffmo1 on 27.08.18.
*/
public class FractalDimensionMoleculeMain {
public static final String PREFIX_OUTPUT = "fractalDimensionMoleculeResult";
public static final int TOTAL_CAPACITY = (int)(30*Math.pow(10,6));
private static final String USAGE =
"FractalDimensionMoleculeMain.\n" +
"Modest von Korff, Thomas Sander.\n" +
"2018.\n" +
"Calculates the fractal dimension for molecules. The " +
"application is memory demanding. 1 GB RAM should be " +
"assigned. Input is a file with a list of SMILES strings. Output is a tab separated file with a header " +
"line. One line is produced for each SMILES string in the result file. \n" +
"-h this help text.\n" +
"-i String path to SMILES input file. Text file with with SMILES, separated by newline.\n" +
"-w String path to output directory.\n" +
"[-c] integer maximum capacity times 1000 for fragments, default is " + TOTAL_CAPACITY + " .\n" +
"[-D] boolean elusive output" + ".\n" +
"\n";
public static void main(String[] args) throws Throwable {
CommandLineParser clp = new CommandLineParser();
clp.parse(args);
if (clp.getNumArguments()==0 || clp.help()) {
System.out.println(USAGE);
System.exit(0);
}
clp.checkCommandWithValue("-i");
File fiMolecule = new File(clp.get("-i"));
if (!fiMolecule.isFile()) {
System.err.println("Not a file " + fiMolecule.getAbsolutePath() + ".");
System.out.println(USAGE);
System.exit(0);
}
clp.checkCommandWithValue("-w");
File workdir = new File(clp.get("-w"));
if (!workdir.isDirectory()) {
System.err.println("Not a directory '" + workdir.getAbsolutePath() + "'.");
System.out.println(USAGE);
System.exit(0);
}
File fiOutTbl = new File(workdir, PREFIX_OUTPUT + ".txt");
fiOutTbl.createNewFile();
if(!fiOutTbl.canWrite()){
throw new IOException("No permission to write output file " + fiOutTbl.getAbsolutePath() + ".");
}
List liSMILES = IO.readLines2List(fiMolecule);
List liMolecule = new ArrayList();
SmilesParser smilesParser = new SmilesParser();
System.out.println("Parsing SMILES");
for (int i = 0; i < liSMILES.size(); i++) {
String smile = liSMILES.get(i);
try {
StereoMolecule mol = new StereoMolecule();
smilesParser.parse(mol, smile);
mol.ensureHelperArrays(Molecule.cHelperRings);
InputObjectFracDimCalc inputObjectFracDimCalc = new InputObjectFracDimCalc(mol, i, smile);
liMolecule.add(inputObjectFracDimCalc);
} catch (Exception e) {
System.err.println("SMILES parsing error in line " + i + " for " + smile);
e.printStackTrace();
}
}
System.out.println("Parsed " + liSMILES.size() + " SMILES. Succeeded for " + liMolecule.size() + ".");
int totalCapacity = TOTAL_CAPACITY;
if (clp.contains("-c")) {
String s = clp.get("-c");
if(s==null){
System.err.println("No capacity value given for -c.");
} else {
totalCapacity = Integer.parseInt(s) * 1000;
}
}
System.out.println("Total capacity " + totalCapacity);
boolean elusive = false;
if(clp.contains("-D")){
elusive = true;
System.out.println("Elusive output.");
}
FractalDimensionMolecule fractalDimensionMolecule = new FractalDimensionMolecule(totalCapacity, elusive);
BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(fiOutTbl), StandardCharsets.UTF_8));
ResultFracDimCalcHeaderTags resultFracDimCalcHeaderTags = new ResultFracDimCalcHeaderTags();
bw.write(resultFracDimCalcHeaderTags.toStringHeader());
for (InputObjectFracDimCalc inputObjectFracDimCalc : liMolecule) {
ResultFracDimCalc result = fractalDimensionMolecule.process(inputObjectFracDimCalc);
bw.write("\n");
bw.write(result.toString());
bw.flush();
}
bw.close();
fractalDimensionMolecule.finalizeThreads();
System.out.println("Wrote output into " + fiOutTbl.getAbsolutePath() + ".");
System.out.println("Finished");
}
}