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

name.mjw.jamber.IO.AMBER.Atom
Abstraction of an Atom that is found within a residue an AMBER Lib file. @author mw529

       * 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) {

View Full Code Here

      LOG.debug(tokens[1]
          + "-->"
          + ChemicalSymbol.chemicalSymbolToZ(ChemicalSymbol
              .amberAtomTypeToChemicalSymbol(tokens[5])));


      Atom atom = new Atom(tokens[1], tokens[5],
          ChemicalSymbol.chemicalSymbolToZ(ChemicalSymbol
              .amberAtomTypeToChemicalSymbol(tokens[5])),
          Double.parseDouble(tokens[8]));


      residue.setName(tokens[7]);

View Full Code Here

       */


      Integer OffsettedIndexOfAtomA = Integer.parseInt((tokens[1])) - 1;
      Integer OffsettedIndexOfAtomB = Integer.parseInt((tokens[2])) - 1;


      Atom a = residue.getAtoms().get(OffsettedIndexOfAtomA);
      Atom b = residue.getAtoms().get(OffsettedIndexOfAtomB);


      a.setIndexWithinCurrentResidue(OffsettedIndexOfAtomA);
      b.setIndexWithinCurrentResidue(OffsettedIndexOfAtomB);


      Connection connection = new Connection(a, b);
      residue.addConnection(connection);


    }

View Full Code Here

    // <Atom type="1960" charge="1.0" sigma="0.526699322165"
    // epsilon="0.00071128"/>


    for (int i = 0; i < lib.getAtoms().size(); i++) {


      Atom atom = lib.getAtomByIndex(i);


      Element AtomElement = new Element("Atom");


      Attribute NonbondedForceElementTypeAttribute = new Attribute(
          "type", uid + Integer.toString(i));
      AtomElement.addAttribute(NonbondedForceElementTypeAttribute);


      DecimalFormat df = new DecimalFormat("#.####");
      Attribute NonbondedForceElementChargeAttribute = new Attribute(
          "charge", df.format(atom.getCharge()));


      AtomElement.addAttribute(NonbondedForceElementChargeAttribute);


      // Now look up the atomtype from the parm file
      AtomType atomType = parameterStore.getAtomByType(atom.getType());


      /*
       * Convert values; getVdwRadius is in the form of r_min and in
       * Angstroms, this needs to be converted to sigma and into nm.
       *

View Full Code Here

    DecimalFormat df = new DecimalFormat("#.####");


    for (int i = 0; i < lib.getAtoms().size(); i++) {
      Element AtomElement = new Element("Atom");


      Atom atom = lib.getAtomByIndex(i);


      Attribute GBSAOBCTypeAttribute = new Attribute("type", uid
          + Integer.toString(i));


      Attribute GBSAOBCChargeAttribute = new Attribute("charge",
          df.format(atom.getCharge()));


      Attribute GBSAOBCRadiusAttribute = new Attribute("radius",
          df.format(getGBSAOBCIIRadius(atom)));


      Attribute GBSAOBCScaleAttribute = new Attribute("scale",

View Full Code Here

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Related Classes of name.mjw.jamber.IO.AMBER.Atom

name.mjw.jamber.IO.Mol2

name.mjw.jamber.IO.OpenMM.OpenMMXML

name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2CYPCPDITest

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