atomtetrahedralligandplacer3d.java

化学图形处理软件

/*  $RCSfile$
 *  $Author: egonw $
 *  $Date: 2007-04-16 10:40:19 +0200 (Mon, 16 Apr 2007) $
 *  $Revision: 8201 $
 *
 *  Copyright (C) 2005-2007  Christian Hoppe <[e-mail]>
 *
 *  Contact: [e-mail]
 *
 *  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.
 *  All we ask is that proper credit is given for our work, which includes
 *  - but is not limited to - adding the above copyright notice to the beginning
 *  of your source code files, and to any copyright notice that you may distribute
 *  with programs based on this work.
 *
 *  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.modeling.builder3d;

import java.io.IOException;
import java.util.Hashtable;
import java.util.Vector;

import javax.vecmath.AxisAngle4d;
import javax.vecmath.Matrix3d;
import javax.vecmath.Point3d;
import javax.vecmath.Vector3d;

import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.CDKConstants;

/**
 *  A set of static utility classes for geometric calculations on Atoms.
 *
 *@author         Peter Murray-Rust,chhoppe,egonw
 *@cdk.created    2003-??-??
 * @cdk.module    builder3d
 */
public class AtomTetrahedralLigandPlacer3D {

	private Hashtable pSet = null;
	private final double DEFAULT_BOND_LENGTH_H = 1.0;
	//private final double DEFAULT_BOND_LENGTH_HA = 1.3;

	public final double TETRAHEDRAL_ANGLE =
			2.0 * Math.acos(1.0 / Math.sqrt(3.0));

	private final double SP2_ANGLE = 120 * Math.PI / 180;
	private final double SP_ANGLE = Math.PI;

	final static Vector3d XV = new Vector3d(1.0, 0.0, 0.0);
	final static Vector3d YV = new Vector3d(0.0, 1.0, 0.0);


	/**
	 *  Constructor for the AtomTetrahedralLigandPlacer3D object
	 */
	AtomTetrahedralLigandPlacer3D() { }


	/**
	 *  Constructor for the setParameterSet object
	 *
	 *@param  moleculeParameter  Description of the Parameter
	 */
	public void setParameterSet(Hashtable moleculeParameter) {
		pSet = moleculeParameter;
	}


	/**
	 *  Generate coordinates for all atoms which are singly bonded and have no
	 *  coordinates. This is useful when hydrogens are present but have no coords.
	 *  It knows about C, O, N, S only and will give tetrahedral or trigonal
	 *  geometry elsewhere. Bond lengths are computed from covalent radii or taken
	 *  out of a paramter set if available. Angles are tetrahedral or trigonal
	 *
	 *@param  atomContainer  the set of atoms involved
	 *@exception  Exception  Description of the Exception
	 *@cdk.keyword           coordinate calculation
	 *@cdk.keyword           3D model
	 */
	public void add3DCoordinatesForSinglyBondedLigands(IAtomContainer atomContainer) throws Exception {
		IAtomContainer noCoords = new org.openscience.cdk.AtomContainer();
		IAtomContainer withCoords = new org.openscience.cdk.AtomContainer();
		IAtom refAtom = null;
		IAtom atomC = null;
		int nwanted = 0;
		for (int i = 0; i < atomContainer.getAtomCount(); i++) {
			refAtom = atomContainer.getAtom(i);
			if (!refAtom.getSymbol().equals("H") && hasUnsetNeighbour(refAtom, atomContainer)) {
				noCoords = getUnsetAtomsInAtomContainer(refAtom, atomContainer);
				withCoords = getPlacedAtomsInAtomContainer(refAtom, atomContainer);
				if (withCoords.getAtomCount() > 0) {
					atomC = getPlacedHeavyAtomInAtomContainer(withCoords.getAtom(0), refAtom, atomContainer);
				}
				if (refAtom.getFormalNeighbourCount() == 0 && refAtom.getSymbol().equals("C")) {
					nwanted = noCoords.getAtomCount();
				} else if (refAtom.getFormalNeighbourCount() == 0 && !refAtom.getSymbol().equals("C")) {
					nwanted = 4;
				} else {
					nwanted = refAtom.getFormalNeighbourCount() - withCoords.getAtomCount();
				}
				Point3d[] newPoints = get3DCoordinatesForLigands(refAtom,
						noCoords, withCoords, atomC, nwanted, DEFAULT_BOND_LENGTH_H, -1);
				for (int j = 0; j < noCoords.getAtomCount(); j++) {
					IAtom ligand = noCoords.getAtom(j);
					Point3d newPoint = rescaleBondLength(refAtom, ligand, newPoints[j]);
					ligand.setPoint3d(newPoint);
					ligand.setFlag(CDKConstants.ISPLACED, true);
				}

				noCoords.removeAllElements();
				withCoords.removeAllElements();
			}
		}
	}


	/**
	 *  Rescales Point2 so that length 1-2 is sum of covalent radii. 
	 *  If covalent radii cannot be found, use bond length of 1.0
	 *
	 *@param  atom1          stationary atom
	 *@param  atom2          moveable atom
	 *@param  point2         coordinates for atom 2
	 *@return                new coords for atom 2
	 *@exception  Exception  Description of the Exception
	 */
	public Point3d rescaleBondLength(IAtom atom1, IAtom atom2, Point3d point2) throws Exception {
		Point3d point1 = atom1.getPoint3d();
		double d1 = atom1.getCovalentRadius();
		double d2 = atom2.getCovalentRadius();
		// in case we have no covalent radii, set to 1.0
		double distance = (d1 < 0.1 || d2 < 0.1) ? 1.0 :
				atom1.getCovalentRadius() + atom2.getCovalentRadius();
		if (pSet != null) {
			distance = getDistanceValue(atom1.getAtomTypeName(), atom2.getAtomTypeName());
		}
		Vector3d vect = new Vector3d(point2);
		vect.sub(point1);
		vect.normalize();
		vect.scale(distance);
		Point3d newPoint = new Point3d(point1);
		newPoint.add(vect);
		return newPoint;
	}


	/**
	 *  Adds 3D coordinates for singly-bonded ligands of a reference atom (A).
	 *  Initially designed for hydrogens. The ligands of refAtom are identified and
	 *  those with 3D coordinates used to generate the new points. (This allows
	 *  strucures with partially known 3D coordinates to be used, as when groups
	 *  are added.) "Bent" and "non-planar" groups can be formed by taking a subset
	 *  of the calculated points. Thus R-NH2 could use 2 of the 3 points calculated
	 *  from (1,iii) nomenclature: A is point to which new ones are "attached". A
	 *  may have ligands B, C... B may have ligands J, K.. points X1, X2... are
	 *  returned The cases (see individual routines, which use idealised geometry
	 *  by default): (0) zero ligands of refAtom. The resultant points are randomly
	 *  oriented: (i) 1 points required; +x,0,0 (ii) 2 points: use +x,0,0 and
	 *  -x,0,0 (iii) 3 points: equilateral triangle in xy plane (iv) 4 points
	 *  x,x,x, x,-x,-x, -x,x,-x, -x,-x,x (1a) 1 ligand(B) of refAtom which itself
	 *  has a ligand (J) (i) 1 points required; vector along AB vector (ii) 2
	 *  points: 2 vectors in ABJ plane, staggered and eclipsed wrt J (iii) 3
	 *  points: 1 staggered wrt J, the others +- gauche wrt J (1b) 1 ligand(B) of
	 *  refAtom which has no other ligands. A random J is generated and (1a)
	 *  applied (2) 2 ligands(B, C) of refAtom A (i) 1 points required; vector in
	 *  ABC plane bisecting AB, AC. If ABC is linear, no points (ii) 2 points: 2
	 *  vectors at angle ang, whose resultant is 2i (3) 3 ligands(B, C, D) of
	 *  refAtom A (i) 1 points required; if A, B, C, D coplanar, no points. else
	 *  vector is resultant of BA, CA, DA fails if atom itself has no coordinates
	 *  or >4 ligands
	 *
	 *@param  refAtom        (A) to which new ligands coordinates could be added
	 *@param  length         A-X length
	 *@param  angle          B-A-X angle (used in certain cases)
	 *@param  nwanted        Description of the Parameter
	 *@param  noCoords       Description of the Parameter
	 *@param  withCoords     Description of the Parameter
	 *@param  atomC          Description of the Parameter
	 *@return                Point3D[] points calculated. If request could not be
	 *      fulfilled (e.g. too many atoms, or strange geometry, returns empty
	 *      array (zero length, not null)
	 *@exception  Exception  Description of the Exception
	 *@cdk.keyword           coordinate generation
	 */

	public Point3d[] get3DCoordinatesForLigands(IAtom refAtom,
			IAtomContainer noCoords, IAtomContainer withCoords, IAtom atomC, int nwanted, double length, double angle) throws Exception {
		Point3d newPoints[] = new Point3d[1];

		if (noCoords.getAtomCount() == 0 && withCoords.getAtomCount() == 0) {
			return newPoints;
		}

		// too many ligands at present
		if (withCoords.getAtomCount() > 3) {
			return newPoints;
		}

		if (refAtom.getFormalNeighbourCount() == 1 || refAtom.getMaxBondOrder() > 4) {
		} else if (refAtom.getFormalNeighbourCount() == 2 || refAtom.getMaxBondOrder() == 3) {
			//sp
			if (angle == -1){
				angle=SP_ANGLE;
			}
			newPoints[0] = get3DCoordinatesForSPLigands(refAtom, withCoords, length, angle);
		} else if (refAtom.getFormalNeighbourCount() == 3 || (refAtom.getMaxBondOrder() > 1 && refAtom.getMaxBondOrder() < 3)) {
			//sp2
			if (angle == -1){
				angle=SP2_ANGLE;
			}
			try {
				newPoints = get3DCoordinatesForSP2Ligands(refAtom, noCoords, withCoords, atomC, length, angle);
			} catch (Exception ex1) {
//				logger.debug("Get3DCoordinatesForLigandsERROR: Cannot place SP2 Ligands due to:" + ex1.toString());
				throw new IOException("Cannot place sp2 substituents");
			}

		} else {
			//sp3
			try {
				newPoints = get3DCoordinatesForSP3Ligands(refAtom, noCoords, withCoords, atomC, nwanted, length, angle);
			} catch (Exception ex1) {
//				logger.debug("Get3DCoordinatesForLigandsERROR: Cannot place SP3 Ligands due to:" + ex1.toString());
				throw new IOException("Cannot place sp3 substituents");
			}
		}
		//logger.debug("...Ready "+newPoints.length+" "+newPoints[0].toString());
		return newPoints;
	}

	public Point3d get3DCoordinatesForSPLigands(IAtom refAtom, IAtomContainer withCoords, double length, double angle) {
		//logger.debug(" SP Ligands start "+refAtom.getPoint3d()+" "+(withCoords.getAtomAt(0)).getPoint3d());
		Vector3d ca = new Vector3d(refAtom.getPoint3d());
		ca.sub((withCoords.getAtom(0)).getPoint3d());
		ca.normalize();
		ca.scale(length);
		Point3d newPoint = new Point3d(refAtom.getPoint3d());
		newPoint.add(ca);
		return newPoint;
	}


	/**
	 *  Main method for the calculation of the ligand coordinates for sp2 atoms.
	 *  Decides if one or two coordinates should be created
	 *
	 *@param  refAtom            central atom (Atom)
	 *@param  noCoords           Description of the Parameter
	 *@param  withCoords         Description of the Parameter
	 *@param  atomC              Description of the Parameter
	 *@param  length             Description of the Parameter
	 *@param  angle              Description of the Parameter
	 *@return                    coordinates as Points3d []
	 */
	public Point3d[] get3DCoordinatesForSP2Ligands(IAtom refAtom, IAtomContainer noCoords, IAtomContainer withCoords, IAtom atomC, double length, double angle) {
		//logger.debug(" SP2 Ligands start");
		Point3d newPoints[] = new Point3d[1];
		if (angle < 0) {
			angle = SP2_ANGLE;
		}
		if (withCoords.getAtomCount() >= 2) {
			//logger.debug("Wanted:1 "+noCoords.getAtomCount());
			newPoints[0] = calculate3DCoordinatesSP2_1(refAtom.getPoint3d(), (withCoords.getAtom(0)).getPoint3d(),
					(withCoords.getAtom(1)).getPoint3d(), length, -1 * angle);

		} else if (withCoords.getAtomCount() <= 1) {
			//logger.debug("NoCoords 2:"+noCoords.getAtomCount());
			newPoints = calculate3DCoordinatesSP2_2(refAtom.getPoint3d(), (withCoords.getAtom(0)).getPoint3d(),
					(atomC != null) ? atomC.getPoint3d() : null, length, angle);
		}
		//logger.debug("Ready SP2");
		return newPoints;
	}


	/**
	 *  Main method for the calculation of the ligand coordinates for sp3 atoms.
	 *  Decides how many coordinates should be created
	 *
	 *@param  refAtom            central atom (Atom)
	 *@param  nwanted            how many ligands should be created
	 *@param  length             bond length
	 *@param  angle              angle in a B-A-(X) system; a=central atom;
	 *      x=ligand with unknown coordinates
	 *@param  noCoords           Description of the Parameter
	 *@param  withCoords         Description of the Parameter
	 *@param  atomC              Description of the Parameter
	 *@return                    Description of the Return Value
	 */