Class PharmacophoreQueryAtom

All Implemented Interfaces:
Serializable, Cloneable, IAtom, IAtomType, ICDKObject, IChemObject, IElement, IIsotope, IQueryAtom

public class PharmacophoreQueryAtom extends Atom implements IQueryAtom
Represents a query pharmacophore group. This class is meant to be used to construct pharmacophore queries in conjunction with PharmacophoreQueryBond and an QueryAtomContainer.
Author:
Rajarshi Guha
See Also:
Source code:
main
Belongs to CDK module:
pcore
Keywords:
pharmacophore, 3D isomorphism
  • Constructor Details

    • PharmacophoreQueryAtom

      public PharmacophoreQueryAtom(String symbol, String smarts)
      Creat a new query pharmacophore group
      Parameters:
      symbol - The symbol for the group
      smarts - The SMARTS pattern to be used for matching
  • Method Details

    • getSymbol

      public String getSymbol()
      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:
    • setSymbol

      public void setSymbol(String symbol)
      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:
    • getSmarts

      public String getSmarts()
      Get the SMARTS pattern for this pharmacophore group.
      Returns:
      The SMARTS pattern
    • matches

      public boolean matches(IAtom atom)
      Checks whether this query atom matches a target atom. Currently a query pharmacophore atom will match a target pharmacophore group if the symbols of the two groups match. This is based on the assumption that pharmacophore groups with the same symbol will have the same SMARTS pattern.
      Specified by:
      matches in interface IQueryAtom
      Parameters:
      atom - A target pharmacophore group
      Returns:
      true if the current query group has the same symbol as the target group
    • toString

      public String toString()
      String representation of this pharmacophore group.
      Specified by:
      toString in interface IChemObject
      Overrides:
      toString in class Atom
      Returns:
      String representation of this pharmacophore group