/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2004-2008 Rajarshi Guha <rajarshi.guha@gmail.com>
*
* Contact: cdk-devel@lists.sourceforge.net
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.openscience.cdk.pharmacophore;
import org.openscience.cdk.Bond;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.isomorphism.matchers.IQueryBond;
/**
* Represents a pharmacophore query angle constraint.
*
* @author Rajarshi Guha
* @cdk.module pcore
* @cdk.githash
* @cdk.keyword pharmacophore
* @cdk.keyword 3D isomorphism
* @see PharmacophoreQueryAtom
* @see PharmacophoreMatcher
* @see org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
*/
@TestClass("org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBondTest")
public class PharmacophoreQueryAngleBond extends Bond implements IQueryBond {
private double upper;
private double lower;
public PharmacophoreQueryAngleBond() {
}
/**
* Create a query angle constraint between three query groups.
* <p/>
* Note that the angle is only considered upto 2 decimal places.
*
* @param atom1 The first pharmacophore group
* @param atom2 The second pharmacophore group
* @param atom3 The third pharmacophore group
* @param lower The lower bound of the angle between the three groups
* @param upper The upper bound of the angle between the three groups
*/
public PharmacophoreQueryAngleBond(PharmacophoreQueryAtom atom1,
PharmacophoreQueryAtom atom2,
PharmacophoreQueryAtom atom3,
double lower, double upper) {
super(new IAtom[]{atom1, atom2, atom3});
this.upper = round(upper, 2);
this.lower = round(lower, 2);
}
/**
* Create a query angle constraint between three query groups.
* <p/>
* 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).
* <p/>
* Note that the angle is only considered upto 2 decimal places.
*
* @param atom1 The first pharmacophore group
* @param atom2 The second pharmacophore group
* @param atom3 The third pharmacophore group
* @param angle The exact angle between the two groups
*/
public PharmacophoreQueryAngleBond(PharmacophoreQueryAtom atom1,
PharmacophoreQueryAtom atom2,
PharmacophoreQueryAtom atom3,
double angle) {
super(new PharmacophoreQueryAtom[]{atom1, atom2, atom3});
this.upper = round(angle, 2);
this.lower = round(angle, 2);
}
/**
* Checks whether the query angle constraint matches a target distance.
* <p/>
* This method checks whether a query constraint is satisfied by an observed
* angle (represented by a {@link org.openscience.cdk.pharmacophore.PharmacophoreAngleBond} in the target molecule.
* Note that angles are compared upto 2 decimal places.
*
* @param bond The angle relationship in a target molecule
* @return true if the target angle lies within the range of the query constraint
*/
@TestMethod("testMatches")
public boolean matches(IBond bond) {
if (bond instanceof PharmacophoreAngleBond) {
PharmacophoreAngleBond pbond = (PharmacophoreAngleBond) bond;
double bondLength = round(pbond.getBondLength(), 2);
return bondLength >= lower && bondLength <= upper;
} else return false;
}
@TestMethod("testUpper")
public double getUpper() {
return upper;
}
@TestMethod("testLower")
public double getLower() {
return lower;
}
private double round(double val, int places) {
long factor = (long) Math.pow(10, places);
val = val * factor;
long tmp = Math.round(val);
return (double) tmp / factor;
}
/**
* String representation of an angle constraint.
*
* @return String representation of and angle constraint
*/
@TestMethod("testToString")
public String toString() {
StringBuffer sb = new StringBuffer();
sb.append("AC::").append(getAtom(0)).append("::").append(getAtom(1)).append("::").append(getAtom(2));
sb.append("::[").append(getLower()).append(" - ").append(getUpper()).append("] ");
return sb.toString();
}
}