Exemplo n.º 1
0
 /**
  * @param dssp
  * @return voronoi data reuced and decomposited by given pdbmodel no grid will be used!
  */
 public VoronoiData prepareSimple(DSSPEntry dssp) {
   VoronoiData data;
   data = new VoronoiData(dssp.getId());
   data.reduceDSSP(dssp);
   voro.decomposite(data);
   return data;
 }
Exemplo n.º 2
0
 /**
  * @param pdb
  * @param type
  * @return voronoi data reuced and decomposited by given pdbmodel no grid will be used
  */
 public VoronoiData prepareSimple(PDBEntry pdb, VoroPrepType type) {
   VoronoiData data;
   data = new VoronoiData(pdb.getId());
   data.reducePDB(type, pdb);
   voro.decomposite(data);
   return data;
 }
Exemplo n.º 3
0
 /**
  * voronoi data container for multiple sequence scoring on model will be initialized
  *
  * @param model
  * @return voronoi data reuced and decomposited by given pdbmodel grid will be used and generated
  */
 @Override
 public void prepareSequenceScoring(Object model) {
   PDBEntry entry = (PDBEntry) model;
   data = new VoronoiData(entry.getId());
   data.reducePDB(entry);
   data.fillGridWithoutClashes(gridExtend, gridDensity, gridClash);
   voro.decomposite(data);
   data.detectOuterGrid(minContact);
 }
Exemplo n.º 4
0
 /**
  * normal preparation of data in solvent
  *
  * @param dssp
  * @param gridExtend
  * @param gridDensity
  * @param gridClash
  * @param minContact
  * @return voronoi data reuced and decomposited by given pdbmodel grid will be generated and used
  */
 public VoronoiData prepareWithGrid(
     DSSPEntry dssp, double gridExtend, double gridDensity, double gridClash, double minContact) {
   VoronoiData data;
   data = new VoronoiData(dssp.getId());
   data.reduceDSSP(dssp);
   data.fillGridWithoutClashes(gridExtend, gridDensity, gridClash);
   voro.decomposite(data);
   data.detectOuterGrid(minContact);
   return data;
 }
Exemplo n.º 5
0
 /**
  * returns amino acid wise score of given sequence on model set previously by
  * prepareSquenceScoring no more decomposition will be made by calling this method
  */
 @Override
 public double[] getSequenceAminoScoring(AminoAcidName[] sequence) {
   VoronoiData data = this.data.clone();
   data.overrideAminoNames(sequence);
   return getAminoScores(data);
 }