Package name.mjw.jamber.IO

Examples of name.mjw.jamber.IO.Mol2

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  @Test
  public void testLibFromMol2() {

    Lib lib2;
    Mol2 mol2 = null;

    InputStream mol2Stream = LibTest.class.getClass().getResourceAsStream(
        "/name/mjw/jamber/IO/AMBER/CPDI/HEM.mol2");

    try {
      mol2 = new Mol2(mol2Stream);

    } catch (IOException e) {

      e.printStackTrace();
    }
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  }

  private static Mol2 openAndReadMol2File(String mol2FileName) {

    InputStream inputStream = null;
    Mol2 mol2 = null;

    try {
      inputStream = new FileInputStream(mol2FileName);
    } catch (FileNotFoundException e) {
      System.out.println("Cannot open file" + mol2FileName);
      e.printStackTrace();
    }

    try {
      mol2 = new Mol2(inputStream);
    } catch (IOException e) {
      System.out.println("Cannot parse mol2 file" + mol2FileName);
      e.printStackTrace();
    }

    LOG.debug(mol2.getMolName());
    return mol2;
  }
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        .getClass().getResourceAsStream(
            "/name/mjw/jamber/IO/OpenMM/ritonavir/ritonavir.mol2");

    try {

      ritonavirMol2 = new Mol2(ritonavirMol2Stream);

      lib = new Lib(ritonavirMol2);

    } catch (IOException e) {
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        .getResourceAsStream(
            "/name/mjw/jamber/IO/OpenMM/bromoergocryptine/bromoergocryptine.mol2");

    try {

      bromoergocryptineMol2 = new Mol2(bromoergocryptineMol2Stream);

      lib = new Lib(bromoergocryptineMol2);

    } catch (IOException e) {
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        .getClass().getResourceAsStream(
            "/name/mjw/jamber/IO/AMBER/CYP/CYP.mol2");

    try {

      heme = new Mol2(hemeMol2Stream);
      cyp = new Mol2(cypMol2Stream);

      lib = new Lib(heme);

      /*
       * Set the HEM residue external connection bond by hand since Mol2
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        .getResourceAsStream(
            "/name/mjw/jamber/IO/OpenMM/erythromycin/erythromycin.mol2");

    try {

      erythromycinMol2 = new Mol2(erythromycinMol2Stream);

      lib = new Lib(erythromycinMol2);

    } catch (IOException e) {
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        .getResourceAsStream(
            "/name/mjw/jamber/IO/OpenMM/ketoconazole/ketoconazole.mol2");

    try {

      ketoconazoleMol2 = new Mol2(ketoconazoleMol2Stream);

      lib = new Lib(ketoconazoleMol2);

    } catch (IOException e) {
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        .getClass().getResourceAsStream(
            "/name/mjw/jamber/IO/OpenMM/benzene/benzene.mol2");

    try {

      benzeneMol2 = new Mol2(benzeneMol2Stream);

      lib = new Lib(benzeneMol2);

    } catch (IOException e) {
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        .getClass().getResourceAsStream(
            "/name/mjw/jamber/IO/AMBER/aceticAcid/acetic_acid.mol2");

    try {

      aceticAcidMol2 = new Mol2(aceticAcidMol2Stream);

      lib = new Lib(aceticAcidMol2);

    } catch (IOException e) {
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Related Classes of name.mjw.jamber.IO.Mol2

  • name.mjw.jamber.IO.AMBER.Atom
  • name.mjw.jamber.IO.AMBER.Connection
  • name.mjw.jamber.IO.AMBER.LibTest
  • name.mjw.jamber.IO.AMBER.Residue
  • name.mjw.jamber.IO.OpenMM.AmberToOpenMM
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2AceticAcidTest
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2BenzeneTest
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2BromoergocryptineTest
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2CYPCPDITest
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2ErythromycinTest
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