Class PharmacophoreQueryBond

All Implemented Interfaces:
Serializable, Cloneable, IBond, ICDKObject, IChemObject, IElectronContainer, IQueryBond

public class PharmacophoreQueryBond extends Bond implements IQueryBond
Represents a pharmacophore query distance constraint.
Author:
Rajarshi Guha
See Also:
Source code:
main
Belongs to CDK module:
pcore
Keywords:
pharmacophore, 3D isomorphism
  • Constructor Details

    • PharmacophoreQueryBond

      public PharmacophoreQueryBond()
    • PharmacophoreQueryBond

      public PharmacophoreQueryBond(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, double lower, double upper)
      Create a query distance constraint between two query groups. Note that the distance is only considered upto 2 decimal places.
      Parameters:
      atom1 - The first pharmacophore group
      atom2 - The second pharmacophore group
      lower - The lower bound of the distance between the two groups
      upper - The upper bound of the distance between the two groups
      See Also:
    • PharmacophoreQueryBond

      public PharmacophoreQueryBond(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, double distance)
      Create a query distance constraint between two query groups. This constructor allows you to define a query distance constraint such that the distance between the two query groups is exact (i.e., not a range). Note that the distance is only considered upto 2 decimal places.
      Parameters:
      atom1 - The first pharmacophore group
      atom2 - The second pharmacophore group
      distance - The exact distance between the two groups
      See Also:
  • Method Details

    • matches

      public boolean matches(IBond bond)
      Checks whether the query distance constraint matches a target distance. This method checks whether a query constraint is satisfied by an observed distance (represented by a PharmacophoreBond in the target molecule. Note that distance are compared upto 2 decimal places.
      Specified by:
      matches in interface IQueryBond
      Parameters:
      bond - The distance relationship in a target molecule
      Returns:
      true if the target distance lies within the range of the query constraint
    • getUpper

      public double getUpper()
    • getLower

      public double getLower()
    • toString

      public String toString()
      String representation of a distance constraint.
      Specified by:
      toString in interface IChemObject
      Overrides:
      toString in class Bond
      Returns:
      String representation of a distance constraint