org.openscience.cdk.layout

Class OverlapResolver

java.lang.Object

org.openscience.cdk.layout.OverlapResolver

Deprecated.

does not resolve overlaps correctly

@Deprecated
public class OverlapResolver
extends Object

Helper class for Structure Diagram Generation. Resolves atom or bond overlaps after the actual SDG was done

Author:

steinbeck

Source code:

master

Belongs to CDK module:

sdg

Keywords:

layout, 2D-coordinates

Created on:

2003-09-4

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	OverlapResolver.OverlapPair Deprecated. A little helper class to store pairs of overlapping atoms.

Constructor Summary

Constructors

Constructor and Description
OverlapResolver() Deprecated.

Method Summary

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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OverlapResolver

public OverlapResolver()

Deprecated.

Method Detail

resolveOverlap

public double resolveOverlap(IAtomContainer ac,
                             IRingSet sssr)

Deprecated.

Main method to be called to resolve overlap situations.

Parameters:

ac - The atomcontainer in which the atom or bond overlap exists

sssr - A ring set for this atom container if one exists, otherwhise null

displace

public double displace(IAtomContainer ac,
                       Vector overlappingAtoms,
                       Vector overlappingBonds)

Deprecated.

Makes a small displacement to some atoms or rings in the given atomcontainer.

Parameters:

ac - The AtomContainer to work on

overlappingAtoms - Description of the Parameter

overlappingBonds - Description of the Parameter

getOverlapScore

public double getOverlapScore(IAtomContainer ac,
                              Vector overlappingAtoms,
                              Vector overlappingBonds)

Deprecated.

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.

Parameters:

ac - The Atomcontainer to work on

overlappingAtoms - Description of the Parameter

overlappingBonds - Description of the Parameter

Returns:

The overlapScore value

getAtomOverlapScore

public double getAtomOverlapScore(IAtomContainer ac,
                                  Vector overlappingAtoms)

Deprecated.

Calculates a score based on the overlap of atoms. The overlap is calculated by summing up the distances between all pairs of atoms, if they are less than half the standard bondlength apart.

Parameters:

ac - The Atomcontainer to work on

overlappingAtoms - Description of the Parameter

Returns:

The overlapScore value

getBondOverlapScore

public double getBondOverlapScore(IAtomContainer ac,
                                  Vector overlappingBonds)

Deprecated.

Calculates a score based on the intersection of bonds.

Parameters:

ac - The Atomcontainer to work on

overlappingBonds - Description of the Parameter

Returns:

The overlapScore value

areIntersected

public boolean areIntersected(IBond bond1,
                              IBond bond2)

Deprecated.

Checks if two bonds cross each other.

Parameters:

bond1 - Description of the Parameter

bond2 - Description of the Parameter

Returns:

Description of the Return Value