Class PharmacophoreQueryAngleBond

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

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

    • PharmacophoreQueryAngleBond

      public PharmacophoreQueryAngleBond()
    • PharmacophoreQueryAngleBond

      public PharmacophoreQueryAngleBond(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, PharmacophoreQueryAtom atom3, double lower, double upper)
      Create a query angle constraint between three query groups. Note that the angle is only considered upto 2 decimal places.
      Parameters:
      atom1 - The first pharmacophore group
      atom2 - The second pharmacophore group
      atom3 - The third pharmacophore group
      lower - The lower bound of the angle between the three groups
      upper - The upper bound of the angle between the three groups
    • PharmacophoreQueryAngleBond

      public PharmacophoreQueryAngleBond(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, PharmacophoreQueryAtom atom3, double angle)
      Create a query angle constraint between three query groups. This constructor allows you to define a query angle constraint such that the angle between the three query groups is exact (i.e., not a range). Note that the angle is only considered upto 2 decimal places.
      Parameters:
      atom1 - The first pharmacophore group
      atom2 - The second pharmacophore group
      atom3 - The third pharmacophore group
      angle - The exact angle between the two groups
  • Method Details

    • matches

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

      public double getUpper()
    • getLower

      public double getLower()
    • toString

      public String toString()
      String representation of an angle constraint.
      Specified by:
      toString in interface IChemObject
      Overrides:
      toString in class Bond
      Returns:
      String representation of and angle constraint