public double getOverlapScore ( IAtomContainer ac , Vector overlappingAtoms , Vector overlappingBonds ) { double overlapScore = 0 ; overlapScore = getAtomOverlapScore ( ac , overlappingAtoms ) ; //overlapScore += getBondOverlapScore(ac, overlappingBonds); return overlapScore ; }
Calculates a score based on the overlap of atoms and intersection of bonds . The overlap is calculated by summing up the distances between all pairs of atoms if they are less than half the standard bondlength apart .