Class OverlapResolver

java.lang.Object
org.openscience.cdk.layout.OverlapResolver

@Deprecated public class OverlapResolver extends Object
Deprecated.
does not resolve overlaps correctly
Helper class for Structure Diagram Generation. Resolves atom or bond overlaps after the actual SDG was done
Author:
steinbeck
Source code:
main
Belongs to CDK module:
sdg
Keywords:
layout, 2D-coordinates
Created on:
2003-09-4
  • Constructor Details

    • OverlapResolver

      public OverlapResolver()
      Deprecated.
  • Method Details

    • 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