Examples of appendExternalBond()

Examples of name.mjw.jamber.IO.AMBER.Residue.appendExternalBond()

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       * 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");
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Examples of name.mjw.jamber.IO.AMBER.Residue.appendExternalBond()

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      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) {
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Examples of name.mjw.jamber.IO.AMBER.Residue.appendExternalBond()

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      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.appendExternalBond()

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      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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