/**
* @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;
}
/**
* @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;
}
/**
* 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);
}
/**
* 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;
}
/**
* 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);
}