/**
* Constructor.
*
* @param atom1 - First protein atom to be connected by the virtual cross-linker.
* @param atom2 - Second protein atom to be connected by the virtual cross-linker.
*/
public CrossLink(final Atom atom1, final Atom atom2) {
this(
atom1,
atom2,
Math.abs(atom1.getRank() - atom2.getRank()),
Mathematics.distance(atom1.getXYZ(), atom2.getXYZ()));
}
/**
* Maps the hydrophobicity property of the protein on a list of atom. Note, that only atoms within
* mm.constants.Constants.PHYSICOCHEMICAL_INFLUENCE_RADIUS will be included in the potential
* calculation.
*
* @param sampleAtoms List of atoms on which potential will be calculated.
*/
public final void mapHydrophobicity(final AtomList sampleAtoms) {
float max = mm.constants.Constants.PHYSICOCHEMICAL_INFLUENCE_RADIUS;
for (Atom sampleAtom : sampleAtoms) {
for (Atom atom : this.polyPeptideComplex.getAllAtoms()) {
float dist = Mathematics.distance(atom.getXYZ(), sampleAtom.getXYZ());
if (dist <= max) {
float h = atom.getXlogP();
double s = Mathematics.sigmoidFunction(dist, max);
sampleAtom.setHes((float) (sampleAtom.getHes() + (h * s)));
}
}
}
}