content: /*
   * Copyright (c) 1997 - 2016
   * Actelion Pharmaceuticals Ltd.
   * Gewerbestrasse 16
   * CH-4123 Allschwil, Switzerland
   *
   * All rights reserved.
   *
   * Redistribution and use in source and binary forms, with or without
   * modification, are permitted provided that the following conditions are met:
   *
   * 1. Redistributions of source code must retain the above copyright notice, this
   *    list of conditions and the following disclaimer.
   * 2. Redistributions in binary form must reproduce the above copyright notice,
   *    this list of conditions and the following disclaimer in the documentation
   *    and/or other materials provided with the distribution.
   * 3. Neither the name of the the copyright holder nor the
   *    names of its contributors may be used to endorse or promote products
   *    derived from this software without specific prior written permission.
   *
   * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
   * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
   * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
   * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
   * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
   * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
   * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
   * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
   * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
   * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
   *
   * @author Joel Freyss
   */
  
  package com.actelion.research.chem.io.pdb.calc;
  
  import com.actelion.research.chem.Coordinates;
  import com.actelion.research.chem.StereoMolecule;
  
  
  /**
   * Utility class to perform 3D geometry calculations on molecules
   */
  public class GeometryCalculator {
  	
  	public final static Coordinates getCoordinates(StereoMolecule mol, int atm) {
  		return new Coordinates(mol.getAtomX(atm), mol.getAtomY(atm), mol.getAtomZ(atm));
  	}
  
  	
  	/**
  	 * Gets the Angle between 3 atoms
  	 * @param mol
  	 * @param a1
  	 * @param a2
  	 * @param a3
  	 * @return the angle
  	 */
  	public final static double getAngle(StereoMolecule mol, int a1, int a2, int a3) {
  		Coordinates c1 = mol.getAtomCoordinates(a1);
  		Coordinates c2 = mol.getAtomCoordinates(a2);
  		Coordinates c3 = mol.getAtomCoordinates(a3);
  
  		return c1.subC(c2).getAngle(c3.subC(c2));
  	}
  	
  	public final static double getAngle(Coordinates c1, Coordinates c2, Coordinates c3) {
  		return c1.subC(c2).getAngle(c3.subC(c2));
  	}
  	
    	/**
  	 * Gets the Dihedral Angle between 4 atoms
  	 * @param mol
       * @param a1
       * @param a2
       * @param a3
  	 * @param a4
  	 * @return the angle
  	 */
  	public final static double getDihedral(StereoMolecule mol, int a1, int a2, int a3, int a4) {
  		Coordinates c1 = mol.getAtomCoordinates(a1);
  		Coordinates c2 = mol.getAtomCoordinates(a2);
  		Coordinates c3 = mol.getAtomCoordinates(a3);
  		Coordinates c4 = mol.getAtomCoordinates(a4);
  		return c1.getDihedral(c2, c3, c4);
  	}
  		
  	/**
  	 * Gets the center of Gravity of a molecule
  	 * @param mol
  	 * @return
  	 */
  	public final static Coordinates getCenterGravity(StereoMolecule mol) {
  		Coordinates c = new Coordinates();
  		for(int i=0; i<mol.getAllAtoms(); i++) {
  			c.x += mol.getAtomX(i); 
  			c.y += mol.getAtomY(i); 
  			c.z += mol.getAtomZ(i); 
  		}
  		c.x /= mol.getAllAtoms();
  		c.y /= mol.getAllAtoms();
  		c.z /= mol.getAllAtoms();
  		
  		return c;
  	}
  	
  	/**
  	 * Gets the Bounds of a molecule
  	 * @param molecule
  	 * @return an Array of Coordinares [lowerBounds, upperbounds]
  	 */
  	public final static Coordinates[] getBounds(StereoMolecule molecule) {
  		if(molecule.getAllAtoms()==0) return new Coordinates[]{new Coordinates(0, 0, 0), new Coordinates(0, 0, 0)};
  		Coordinates[] coords = new Coordinates[]{new Coordinates(Float.MAX_VALUE, Float.MAX_VALUE, Float.MAX_VALUE), new Coordinates(-Float.MAX_VALUE, -Float.MAX_VALUE, -Float.MAX_VALUE)};
  		for(int i=0; i<molecule.getAllAtoms(); i++) {
  			coords[0].x = Math.min(coords[0].x, molecule.getAtomX(i)); 
  			coords[0].y = Math.min(coords[0].y, molecule.getAtomY(i)); 
  			coords[0].z = Math.min(coords[0].z, molecule.getAtomZ(i)); 
  
  			coords[1].x = Math.max(coords[1].x, molecule.getAtomX(i)); 
  			coords[1].y = Math.max(coords[1].y, molecule.getAtomY(i)); 
  			coords[1].z = Math.max(coords[1].z, molecule.getAtomZ(i)); 
  		}
  		return coords;
  	}		
  
  	/**
  	 * Translate a Molecule
  	 * @param molecule
  	 * @param c
  	 */
  	public final static void translate(StereoMolecule molecule, Coordinates c) {
  		for(int i=0; i<molecule.getAllAtoms(); i++) {
  			molecule.setAtomX(i, molecule.getAtomX(i)+c.x);
  			molecule.setAtomY(i, molecule.getAtomY(i)+c.y);
  			molecule.setAtomZ(i, molecule.getAtomZ(i)+c.z);
  		}
  	}
  	
  }
  