Examples of Residue

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

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

      Residue hemeResidue = lib.getResidueByName("HEM");
      Atom connectionAtom = hemeResidue.getAtoms().get(27);
      hemeResidue.appendExternalBond(connectionAtom);

      // Load CYP residue information
      lib.addFromMol2(cyp);

      Residue cypResidue = lib.getResidueByName("CYP");
      Atom connectionAtomN = cypResidue.getAtoms().get(0);
      Atom connectionAtomC = cypResidue.getAtoms().get(8);
      Atom connectionAtomS = cypResidue.getAtoms().get(7);
      cypResidue.appendExternalBond(connectionAtomN);
      cypResidue.appendExternalBond(connectionAtomC);
      cypResidue.appendExternalBond(connectionAtomS);

    } catch (IOException e) {

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

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    if (is == null) {
      throw new NullPointerException("Null argument: InputStream");
    }

    residue = new Residue("tmp");

    try {
      LOG.info("Reading Mol2 file");
      read(is);
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