@Deprecated public class OverlapResolver extends Object
Modifier and Type  Class and Description 

class 
OverlapResolver.OverlapPair
Deprecated.
A little helper class to store pairs of overlapping atoms.

Constructor and Description 

OverlapResolver()
Deprecated.

Modifier and Type  Method and Description 

boolean 
areIntersected(IBond bond1,
IBond bond2)
Deprecated.
Checks if two bonds cross each other.

double 
displace(IAtomContainer ac,
Vector overlappingAtoms,
Vector overlappingBonds)
Deprecated.
Makes a small displacement to some atoms or rings in the given
atomcontainer.

double 
getAtomOverlapScore(IAtomContainer ac,
Vector overlappingAtoms)
Deprecated.
Calculates a score based on the overlap of atoms.

double 
getBondOverlapScore(IAtomContainer ac,
Vector overlappingBonds)
Deprecated.
Calculates a score based on the intersection of bonds.

double 
getOverlapScore(IAtomContainer ac,
Vector overlappingAtoms,
Vector overlappingBonds)
Deprecated.
Calculates a score based on the overlap of atoms and intersection of bonds.

double 
resolveOverlap(IAtomContainer ac,
IRingSet sssr)
Deprecated.
Main method to be called to resolve overlap situations.

public double resolveOverlap(IAtomContainer ac, IRingSet sssr)
ac
 The atomcontainer in which the atom or bond overlap existssssr
 A ring set for this atom container if one exists, otherwhise nullpublic double displace(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds)
ac
 The AtomContainer to work onoverlappingAtoms
 Description of the ParameteroverlappingBonds
 Description of the Parameterpublic double getOverlapScore(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds)
ac
 The Atomcontainer to work onoverlappingAtoms
 Description of the ParameteroverlappingBonds
 Description of the Parameterpublic double getAtomOverlapScore(IAtomContainer ac, Vector overlappingAtoms)
ac
 The Atomcontainer to work onoverlappingAtoms
 Description of the Parameterpublic double getBondOverlapScore(IAtomContainer ac, Vector overlappingBonds)
ac
 The Atomcontainer to work onoverlappingBonds
 Description of the ParameterCopyright © 2017. All Rights Reserved.