/** * 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))); } } } }
/** * 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())); }