Examples of ParameterStore

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

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  }

  private static ParameterStore openAndReadGaffFile(String gaffFileName) {

    InputStream inputStream = null;
    ParameterStore gaffParameterStore = null;

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

    try {
      gaffParameterStore = new ParameterStore();
      gaffParameterStore.readParm(inputStream);
    } catch (IOException e) {
      System.out.println("Cannot parse ParameterStore file"
          + gaffFileName);
      e.printStackTrace();
    }

    LOG.debug(gaffParameterStore.getTitle());
    return gaffParameterStore;

  }
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Examples of name.mjw.jamber.IO.AMBER.ParameterStore

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    InputStream frcmodIs = OpenMMXMLWithMol2RitonavirTest.class.getClass()
        .getResourceAsStream(
            "/name/mjw/jamber/IO/OpenMM/ritonavir/ritonavir.frcmod");

    try {
      parameterStore = new ParameterStore();
      parameterStore.readParm(gaffIs);
      parameterStore.readFrcmod(frcmodIs);

    } catch (Exception e) {
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Examples of name.mjw.jamber.IO.AMBER.ParameterStore

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    InputStream parmIs = OpenMMXMLWithLibTest.class
        .getClass()
        .getResourceAsStream("/name/mjw/jamber/IO/AMBER/lib/parm99.dat");

    try {
      parameterStore = new ParameterStore();
      parameterStore.readParm(parmIs);

    } catch (IOException e) {

      e.printStackTrace();
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Examples of name.mjw.jamber.IO.AMBER.ParameterStore

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        .getClass()
        .getResourceAsStream(
            "/name/mjw/jamber/IO/OpenMM/bromoergocryptine/bromoergocryptine.frcmod");

    try {
      parameterStore = new ParameterStore();
      parameterStore.readParm(gaffIs);
      parameterStore.readFrcmod(frcmodIs);

    } catch (Exception e) {
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Examples of name.mjw.jamber.IO.AMBER.ParameterStore

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    InputStream parmLiteFrcmod = OpenMMXMLWithMol2CYPCPDITest.class
        .getClass().getResourceAsStream(
            "/name/mjw/jamber/IO/AMBER/CPDI/parm99_lite.dat");

    try {
      parameterStore = new ParameterStore();

      parameterStore.readParm(gaffIs);

      // TODO make consistent with other methods
      try {
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Examples of name.mjw.jamber.IO.AMBER.ParameterStore

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        .getClass()
        .getResourceAsStream(
            "/name/mjw/jamber/IO/OpenMM/erythromycin/erythromycin.frcmod");

    try {
      parameterStore = new ParameterStore();
      parameterStore.readParm(gaffIs);
      parameterStore.readFrcmod(frcmodIs);

    } catch (Exception e) {
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Examples of name.mjw.jamber.IO.AMBER.ParameterStore

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    InputStream gaffIs = OpenMMXMLWithMol2KetoconazoleTest.class.getClass()
        .getResourceAsStream("/name/mjw/jamber/IO/AMBER/lib/gaff.dat");

    try {
      parameterStore = new ParameterStore();
      parameterStore.readParm(gaffIs);

    } catch (IOException e) {

      e.printStackTrace();
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Examples of name.mjw.jamber.IO.AMBER.ParameterStore

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        .getResourceAsStream("/name/mjw/jamber/IO/AMBER/lib/gaff.dat");



    try {
      parameterStore = new ParameterStore();
      parameterStore.readParm(gaffIs);

    } catch (Exception e) {

      e.printStackTrace();
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Examples of name.mjw.jamber.IO.AMBER.ParameterStore

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        .getResourceAsStream("/name/mjw/jamber/IO/AMBER/lib/gaff.dat");



    try {
      parameterStore = new ParameterStore();
      parameterStore.readParm(gaffIs);

    } catch (Exception e) {

      e.printStackTrace();
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Examples of org.ocpsoft.rewrite.param.ParameterStore

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   private boolean handleBindings(final Rewrite event, final EvaluationContextImpl context,
            ParameterValueStore values)
   {
      boolean result = true;
      ParameterStore store = (ParameterStore) context.get(ParameterStore.class);

      for (Entry<String, Parameter<?>> entry : store) {
         Parameter<?> parameter = entry.getValue();
         String value = values.retrieve(parameter);
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