コード例 #1
0
  private void loadBondedParams() {
    String fileName = "res/amber03/ffbonded.itp";
    List<String> fileAsList = FileReader.readFile(fileName);
    int bondtypes = fileAsList.indexOf("[ bondtypes ]");
    int constrainttypes = fileAsList.indexOf("[ constrainttypes ]");
    int angletypes = fileAsList.indexOf("[ angletypes ]");
    int improperDihedral = fileAsList.indexOf("[ dihedraltypes ]");
    int properDihedral = fileAsList.lastIndexOf("[ dihedraltypes ]");

    //		System.out.println(bondtypes);
    //		System.out.println(constrainttypes);
    //		System.out.println(angletypes);
    //		System.out.println(improperDihedral);
    //		System.out.println(properDihedral);

    loadBondParams(fileAsList.subList(bondtypes + 1, constrainttypes));
    loadAngleParams(fileAsList.subList(angletypes + 1, improperDihedral));
    loadImproperDihedralParams(fileAsList.subList(improperDihedral + 1, properDihedral));
    loadProperDihedralParams(fileAsList.subList(properDihedral + 1, fileAsList.size()));
  }
コード例 #2
0
 private void loadNonBondedParams() {
   String fileName = "res/amber03/ffnonbonded.itp";
   List<String> fileAsList = FileReader.readFile(fileName);
   int atomtypes = fileAsList.indexOf("[ atomtypes ]");
   loadVdParams(fileAsList.subList(atomtypes + 1, fileAsList.size()));
 }