content: /*
  * Copyright (c) 1997 - 2016
  * Actelion Pharmaceuticals Ltd.
  * Gewerbestrasse 16
  * CH-4123 Allschwil, Switzerland
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  * modification, are permitted provided that the following conditions are met:
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  * 1. Redistributions of source code must retain the above copyright notice, this
  *    list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
  * 3. Neither the name of the the copyright holder nor the
  *    names of its contributors may be used to endorse or promote products
  *    derived from this software without specific prior written permission.
  *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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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
   * <p>Modest v. Korff</p>
   * <p>
   * 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<String> liSMILES = IO.readLines2List(fiMolecule);
  
          List<InputObjectFracDimCalc> liMolecule = new ArrayList<InputObjectFracDimCalc>();
  
          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");
  
      }
  
  
  
  
  }