Package name.mjw.jamber.IO.AMBER

Examples of name.mjw.jamber.IO.AMBER.Lib

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    // Populate the internal state of the object as directed by the command
    // line options
    parseArguments(args);

    // Connectivity needs to be abstracted from the Mol2 file
    lib = new Lib(inputMol2);

    // Create the OpenMMXML object
    openMMXML = new OpenMMXML(parameterStore, lib);

    // Write the four bits of OpenMM XML
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    try {

      ritonavirMol2 = new Mol2(ritonavirMol2Stream);

      lib = new Lib(ritonavirMol2);

    } catch (IOException e) {

      e.printStackTrace();
    }
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    InputStream aminoct94Stream = OpenMMXMLWithLibTest.class.getClass()
        .getResourceAsStream(
            "/name/mjw/jamber/IO/AMBER/lib/all_aminoct94.lib");

    try {
      lib = new Lib(amino94Stream, aminont94Stream, aminoct94Stream);

    } catch (IOException e) {

      e.printStackTrace();
    }
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    try {

      bromoergocryptineMol2 = new Mol2(bromoergocryptineMol2Stream);

      lib = new Lib(bromoergocryptineMol2);

    } catch (IOException e) {

      e.printStackTrace();
    }
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    try {

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

      lib = new Lib(heme);

      /*
       * Set the HEM residue external connection bond by hand since Mol2
       * does not contain that information.
       */
 
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    try {

      erythromycinMol2 = new Mol2(erythromycinMol2Stream);

      lib = new Lib(erythromycinMol2);

    } catch (IOException e) {

      e.printStackTrace();
    }
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    try {

      ketoconazoleMol2 = new Mol2(ketoconazoleMol2Stream);

      lib = new Lib(ketoconazoleMol2);

    } catch (IOException e) {

      e.printStackTrace();
    }
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    try {

      benzeneMol2 = new Mol2(benzeneMol2Stream);

      lib = new Lib(benzeneMol2);

    } catch (IOException e) {

      e.printStackTrace();
    }
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    try {

      aceticAcidMol2 = new Mol2(aceticAcidMol2Stream);

      lib = new Lib(aceticAcidMol2);

    } catch (IOException e) {

      e.printStackTrace();
    }
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Related Classes of name.mjw.jamber.IO.AMBER.Lib

  • name.mjw.jamber.IO.OpenMM.AmberToOpenMM
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithLibTest
  • 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
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2KetoconazoleTest
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2RitonavirTest
  • java.io.InputStreamReader
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