Examples of Lib

name.mjw.jamber.IO.AMBER.Lib
md.org/doc/OFF_file_format.txt">format.
Residue information may also be added from Mol2 files, since AnteChamber prefers to encapsulate such information in this format rather than the lib/OFF format. @author mw529

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

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


    try {


      ritonavirMol2 = new Mol2(ritonavirMol2Stream);


      lib = new Lib(ritonavirMol2);


    } catch (IOException e) {


      e.printStackTrace();
    }

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

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


    try {


      bromoergocryptineMol2 = new Mol2(bromoergocryptineMol2Stream);


      lib = new Lib(bromoergocryptineMol2);


    } catch (IOException e) {


      e.printStackTrace();
    }

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

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


    try {


      erythromycinMol2 = new Mol2(erythromycinMol2Stream);


      lib = new Lib(erythromycinMol2);


    } catch (IOException e) {


      e.printStackTrace();
    }

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


    try {


      ketoconazoleMol2 = new Mol2(ketoconazoleMol2Stream);


      lib = new Lib(ketoconazoleMol2);


    } catch (IOException e) {


      e.printStackTrace();
    }

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


    try {


      benzeneMol2 = new Mol2(benzeneMol2Stream);


      lib = new Lib(benzeneMol2);


    } catch (IOException e) {


      e.printStackTrace();
    }

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


    try {


      aceticAcidMol2 = new Mol2(aceticAcidMol2Stream);


      lib = new Lib(aceticAcidMol2);


    } catch (IOException e) {


      e.printStackTrace();
    }

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