Package org.openscience.cdk.pharmacophore

Class PharmacophoreAtom

java.lang.Object
org.openscience.cdk.ChemObject
org.openscience.cdk.Element
org.openscience.cdk.Isotope
org.openscience.cdk.AtomType
org.openscience.cdk.Atom
org.openscience.cdk.pharmacophore.PharmacophoreAtom
All Implemented Interfaces:
Serializable, Cloneable, IAtom, IAtomType, ICDKObject, IChemObject, IElement, IIsotope
public class PharmacophoreAtom extends Atom
A representation of a pharmacophore group. In general this class is used internally for pharmacophore matchin and does not be instantiated by the user. However after a successful match the user will get access to objects of this class which match parts of a query. The main features of a pharmacophore group are the SMARTS pattern defining what the group is meant to identify and the atoms of a molecule that correspond to the SMARTS pattern.
Author:
Rajarshi Guha
See Also:
Keywords:
pharmacophore, 3D isomorphism

  • Constructor Details

    • PharmacophoreAtom

      public PharmacophoreAtom(String smarts, String symbol, javax.vecmath.Point3d coordinates)
      Create a pharmacophore group.
      Parameters:
      smarts - The SMARTS pattern for the group
      symbol - The label for this group.
      coordinates - The coordinates for the group. Note that since a pharmacophore group may match multiple atoms (say a c1ccccc1 group), the coordinates for the group are the effective coordinates of all the atoms for the group. In effect this means that for multi-atom groups, the coordinate is simply the mean of the coordinates of the individual atoms for the group.

    • PharmacophoreAtom

      public PharmacophoreAtom(PharmacophoreAtom pharmacophoreAtom)
      Create a pharmacophore group.
      Parameters:
      pharmacophoreAtom - A previously created pharmacophore group

  • Method Details

    • get

      public static PharmacophoreAtom get(IAtom atom)

    • setSmarts

      public void setSmarts(String smarts)
      Set the SMARTS for the group.
      Parameters:
      smarts - The SMARTS pattern

    • getSmarts

      public String getSmarts()
      Get the SMARTS for the group.
      Returns:
      The SMARTS pattern
      See Also:

    • setSymbol

      public void setSymbol(String symbol)
      Description copied from class: Element
      Sets the element symbol of this element.
      Specified by:
      setSymbol in interface IElement
      Overrides:
      setSymbol in class Element
      Parameters:
      symbol - The element symbol to be assigned to this atom
      See Also:

    • getSymbol

      public String getSymbol()
      Description copied from class: Element
      Returns the element symbol of this element.
      Specified by:
      getSymbol in interface IElement
      Overrides:
      getSymbol in class Element
      Returns:
      The element symbol of this element. Null if unset.
      See Also:

    • setMatchingAtoms

      public void setMatchingAtoms(int[] atomIndices)
      Set the atoms of a target molecule that correspond to this group. This method is generally only useful in the context of pharmacophore matching
      Parameters:
      atomIndices - The indicies of the atoms in a molecule that match the pattern for this group.
      See Also:

    • getMatchingAtoms

      public int[] getMatchingAtoms()
      Get the atoms of a target molecule that correspond to this group. This method is generally only useful in the context of pharmacophore matching
      Returns:
      The indices of the atoms, in a molecule, that match the pattern for this group.
      See Also:

    • hashCode

      public int hashCode()
      Description copied from class: Atom
      Overrides:
      hashCode in class Atom

    • equals

      public boolean equals(Object o)
      Description copied from class: Atom
      Overrides:
      equals in class Atom