forcefieldconfigurator.java

化学图形处理软件

/*  $Revision: 8313 $ $Author: egonw $ $Date: 2007-05-08 13:48:40 +0200 (Tue, 08 May 2007) $
 *
 *  Copyright (C) 2004-2007  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 org.openscience.cdk.CDKConstants;
import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.exception.NoSuchAtomTypeException;
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.ringsearch.SSSRFinder;
import org.openscience.cdk.tools.HOSECodeGenerator;
import org.openscience.cdk.tools.manipulator.RingSetManipulator;

import java.io.InputStream;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.Vector;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

/**
 *  Reads in a force field configuration file, set the atom types into a vector, and the data into a hashtable
 *  Therfore it uses the class MM2BasedParamterSetReader
 *  private Hashtable parameterSet;
 *  key=nameofdatafield+atomid1+;atomid2;atomxid
 *  
 *  <p>MM2 and MMFF94 force field are implemented 
 *  With force field data it configures the cdk atom (assign atomtype, van der Waals radius, charge...)
 *
 * @author     chhoppe
 * @cdk.created    2004-09-07
 * @cdk.module     forcefield
 */
public class ForceFieldConfigurator {

	private String ffName = "mmff94";
	private Vector atomTypes;
	private Hashtable parameterSet=null;
	private MM2BasedParameterSetReader mm2 = null;
	private MMFF94BasedParameterSetReader mmff94= null;
	private InputStream ins = null;
	private String[] fftypes = {"mm2","mmff94"};
	
	/**
	 *Constructor for the ForceFieldConfigurator object
	 */
	public ForceFieldConfigurator() { }

	/**
	 *  Sets the inputStream attribute of the ForceFieldConfigurator object
	 *
	 * @param  ins  The new inputStream value
	 */
	public void setInputStream(InputStream ins) {
		this.ins = ins;
	}
  
  
	/**
	 *  gives a list of possible force field types
	 *
	 *@return                the list
	 */
  public String[] getFfTypes(){
    return fftypes;
  }

	/**
	 *  Sets the forceFieldType attribute of the ForceFieldConfigurator object
	 *
	 * @param  ffname  The new forceFieldType name
	 */
	public boolean checkForceFieldType(String ffname) {
		boolean check=false;
		for (int i = 0; i <= fftypes.length; i++) {
			if (fftypes[i].equals(ffname)) {
				check=true;
				break;
			} 
		}
		if (!check) {
//			logger.debug("FFError:checkForceFieldType> Unknown forcefield:" + ffname + "Take default:"+ffName);
			return false;
		}
		return true;
	}

	/**
	 *Constructor for the ForceFieldConfigurator object
	 *
	 * @param  ffname  name of the force field data file
	 */
	public void setForceFieldConfigurator(String ffname) throws CDKException {
		ffname=ffname.toLowerCase();
		boolean check=false;
		
		if (ffname==ffName && parameterSet!=null){
		}else{
			check=this.checkForceFieldType(ffname);
			ffName=ffname;
			if (ffName.equals("mm2")) {
				//logger.debug("ForceFieldConfigurator: open Force Field mm2");
				//f = new File(mm2File);
				//readFile(f);
				ins = this.getClass().getClassLoader().getResourceAsStream("org/openscience/cdk/modeling/forcefield/data/mm2.prm");
				//logger.debug("ForceFieldConfigurator: open Force Field mm2 ... READY");
				mm2 = new MM2BasedParameterSetReader();
				mm2.setInputStream(ins);
				//logger.debug("ForceFieldConfigurator: mm2 set input stream ... READY");
				try{
					this.setMM2Parameters();
				}catch (Exception ex1){
					throw new CDKException("Problems with set MM2Parameters due to "+ex1.toString(), ex1);	
				}
			}else if (ffName.equals("mmff94") || !check) {
				//logger.debug("ForceFieldConfigurator: open Force Field mmff94");
				//f = new File(mmff94File);
				//readFile(f);
				ins = this.getClass().getClassLoader().getResourceAsStream("org/openscience/cdk/modeling/forcefield/data/mmff94.prm");
				mmff94= new MMFF94BasedParameterSetReader();
				
				mmff94.setInputStream(ins);
				try{
					this.setMMFF94Parameters();
				}catch (Exception ex2){
					throw new CDKException("Problems with set MM2Parameters due to"+ex2.toString(), ex2);	
				}
			}
		}
		//throw new CDKException("Data file for "+ffName+" force field could not be found");
	}


	/**
	 *  Sets the atomTypes attribute of the ForceFieldConfigurator object
	 *
	 * @param  atomtypes  The new atomTypes 
	 */
	public void setAtomTypes(Vector atomtypes) {
		atomTypes = atomtypes;
	}

	/**
	 *  Sets the parameters attribute of the ForceFieldConfigurator object
	 *
	 * @param  parameterset  The new parameter values
	 */
	public void setParameters(Hashtable parameterset) {
		parameterSet = parameterset;
	}

	/**
	 *  Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force field
	 */
	public void setMM2Parameters() throws CDKException{
		try{
			mm2.readParameterSets();
		}catch(Exception ex1){
			throw new CDKException("Problem within readParameterSets due to:"+ex1.toString(), ex1);
		}
		parameterSet = mm2.getParamterSet();
		atomTypes = mm2.getAtomTypes();
  }
	
	public void setMMFF94Parameters() throws Exception{
		mmff94.readParameterSets();
		parameterSet = mmff94.getParamterSet();
		atomTypes = mmff94.getAtomTypes();
	}
	
	/**
	 *  Gets the atomTypes attribute of the ForceFieldConfigurator object
	 *
	 * @return    The atomTypes vector
	 */
	public Vector getAtomTypes() {
		return atomTypes;
	}

	/**
	 *  Gets the parameterSet attribute of the ForceFieldConfigurator object
	 *
	 * @return    The parameterSet hashtable
	 */
	public Hashtable getParameterSet() {
		return this.parameterSet;
	}

	/**
	 *  Find the atomType for a id
	 *
	 * @param  ID                           Atomtype id of the forcefield
	 * @return                              The atomType 
	 * @exception  NoSuchAtomTypeException  atomType is not known
	 */
	private IAtomType getAtomType(String ID) throws NoSuchAtomTypeException {
		IAtomType at = null;
    		for (int i = 0; i < atomTypes.size(); i++) {
			at = (IAtomType) atomTypes.get(i);
			if (at.getAtomTypeName().equals(ID)) {
				return at;
			}
		}
		throw new NoSuchAtomTypeException("AtomType " + ID + " could not be found");
	}

	
	/**
	 *  Method assigns atom types to atoms (calculates sssr and aromaticity)
	 *
	 *@return                sssrf set
	 *@exception  Exception  Description of the Exception
	 */
	public IRingSet assignAtomTyps(IMolecule molecule) throws Exception {
		org.openscience.cdk.interfaces.IAtom atom = null;
		String hoseCode = "";
		HOSECodeGenerator hcg = new HOSECodeGenerator();
		int NumberOfRingAtoms = 0;
		IRingSet ringSetA = null;
		IRingSet ringSetMolecule = new SSSRFinder(molecule).findSSSR();
		boolean isInHeteroRing = false;
		try {
			HueckelAromaticityDetector.detectAromaticity(molecule);
		} catch (Exception cdk1) {
			System.out.println("AROMATICITYError: Cannot determine aromaticity due to: " + cdk1.toString());
		}

		for (int i = 0; i < molecule.getAtomCount(); i++) {
			atom = molecule.getAtom(i);
			if (ringSetMolecule.contains(atom)) {
				NumberOfRingAtoms = NumberOfRingAtoms + 1;
				atom.setFlag(CDKConstants.ISINRING, true);
				atom.setFlag(CDKConstants.ISALIPHATIC, false);
				ringSetA = ringSetMolecule.getRings(atom);
				RingSetManipulator.sort(ringSetA);
				IRing sring = (IRing) ringSetA.getAtomContainer(ringSetA.getAtomContainerCount()-1);
				atom.setProperty("RING_SIZE", new Integer(sring.getRingSize()));
				isInHeteroRing = false;
				Iterator containers = RingSetManipulator.getAllAtomContainers(ringSetA).iterator();
				while (!isInHeteroRing && containers.hasNext()) {
					isInHeteroRing = isHeteroRingSystem((IAtomContainer) containers.next());
				}
			} else {
				atom.setFlag(CDKConstants.ISALIPHATIC, true);
				atom.setFlag(CDKConstants.ISINRING, false);
				isInHeteroRing = false;
			}
			atom.setProperty("MAX_BOND_ORDER", new Double(molecule.getMaximumBondOrder(atom)));

			try {
				hoseCode = hcg.getHOSECode(molecule, atom, 3);
				//logger.debug("HOSECODE GENERATION: ATOM "+i+" HoseCode: "+hoseCode+" ");
			} catch (CDKException ex1) {
				System.out.println("Could not build HOSECode from atom " + i + " due to " + ex1.toString());
				throw new CDKException("Could not build HOSECode from atom "+ i + " due to " + ex1.toString(), ex1);
			}
			try {
				configureAtom(atom, hoseCode, isInHeteroRing);
			} catch (CDKException ex2) {
				System.out.println("Could not final configure atom " + i + " due to " + ex2.toString());
				throw new Exception("Could not final configure atom due to problems with force field", ex2);
			}
		}
		
//		IBond[] bond = molecule.getBonds();
		String bondType;
        Iterator bonds = molecule.bonds();
        while (bonds.hasNext()) {
            IBond bond = (IBond) bonds.next();

			//logger.debug("bond[" + i + "] properties : " + molecule.getBond(i).getProperties());
			bondType = "0";
			if (bond.getOrder() == 1) {
				if ((bond.getAtom(0).getAtomTypeName().equals("Csp2")) &
					((bond.getAtom(1).getAtomTypeName().equals("Csp2")) | (bond.getAtom(1).getAtomTypeName().equals("C=")))) {
					bondType = "1";
				}
					
				if ((bond.getAtom(0).getAtomTypeName().equals("C=")) &
					((bond.getAtom(1).getAtomTypeName().equals("Csp2")) | (bond.getAtom(1).getAtomTypeName().equals("C=")))) {
					bondType = "1";}
					
				if ((bond.getAtom(0).getAtomTypeName().equals("Csp")) &
					(bond.getAtom(1).getAtomTypeName().equals("Csp"))) {
					bondType = "1";}
			}
//			molecule.getBond(i).setProperty("MMFF94 bond type", bondType);
            bond.setProperty("MMFF94 bond type", bondType);
            //logger.debug("bond[" + i + "] properties : " + molecule.getBond(i).getProperties());
		}

		return ringSetMolecule;
	}
	

	/**
	 *  Returns true if atom is in hetero ring system
	 *
	 *@param  ac  AtomContainer
	 *@return     true/false
	 */
	private boolean isHeteroRingSystem(IAtomContainer ac) {
		if (ac != null) {
			for (int i = 0; i < ac.getAtomCount(); i++) {
				if (!(ac.getAtom(i).getSymbol()).equals("H") && !(ac.getAtom(i).getSymbol()).equals("C")) {
					return true;
				}
			}
		}
		return false;
	}

	
	/**
	 *  Assigns an atom type to an atom
	 *
	 * @param  atom  The atom to be aasigned
	 * @param  ID    the atom type id
	 * @return       the assigned atom
	 */
	private org.openscience.cdk.interfaces.IAtom setAtom(org.openscience.cdk.interfaces.IAtom atom, String ID) throws Exception {
		IAtomType at = null;
		String key = "";
		Vector data = null;
		Double value = null;
		
		at = getAtomType(ID);
		if (atom.getSymbol()==null){
			atom.setSymbol(at.getSymbol());
		}
		atom.setAtomTypeName(at.getAtomTypeName());
		atom.setFormalNeighbourCount(at.getFormalNeighbourCount());
		key = "vdw" + ID;
		data = (Vector) parameterSet.get(key);
		value = (Double) data.firstElement();
		atom.setVanderwaalsRadius(value.doubleValue());
		key = "charge" + ID;
		if (parameterSet.containsKey(key)) {
			data = (Vector) parameterSet.get(key);
			value = (Double) data.firstElement();
			atom.setCharge(value.doubleValue());
		}
		Object color = at.getProperty("org.openscience.cdk.renderer.color");
		if (color != null) {
			atom.setProperty("org.openscience.cdk.renderer.color", color);
		}
		if (at.getAtomicNumber() != 0) {
			atom.setAtomicNumber(at.getAtomicNumber());
		} 
		if (at.getExactMass() > 0.0) {
			atom.setExactMass(at.getExactMass());
		} 
		return atom;
	}
	
	public org.openscience.cdk.interfaces.IAtom configureAtom(org.openscience.cdk.interfaces.IAtom atom, String hoseCode, boolean _boolean) throws Exception {