mmff94basedparametersetreader.java

化学图形处理软件

/*  $RCSfile$
 *  $Author: egonw $
 *  $Date: 2007-01-04 18:46:10 +0100 (Thu, 04 Jan 2007) $
 *  $Revision: 7636 $
 *
 *  Copyright (C) 2004-2007  The Chemistry Development Kit (CDK) project
 *
 *  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.awt.Color;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Hashtable;
import java.util.StringTokenizer;
import java.util.Vector;

import org.openscience.cdk.AtomType;

/**
 * AtomType list configurator that uses the ParameterSet originally
 * defined in mmff94.prm from moe. This class was added to be able to port
 * mmff94 to CDK.
 *
 * @author         chhoppe
 * @cdk.created    2004-09-07
 * @cdk.module     forcefield
 * @cdk.keyword    atom type, mmff94
 */
public class MMFF94BasedParameterSetReader {

	private String configFile = "org/openscience/cdk/modeling/forcefield/data/mmff94.prm";
	private InputStream ins = null;
	private Hashtable parameterSet;
	private Vector atomTypes;
	private StringTokenizer st;
	private String key = "";
	private String sid;

	private String configFilevdW = "org/openscience/cdk/modeling/forcefield/data/mmffvdw.prm";
	private InputStream insvdW = null;
	private StringTokenizer stvdW;
	private String sidvdW;

	private String configFileDFSB = "org/openscience/cdk/modeling/forcefield/data/mmffdfsb.par";
	private InputStream insDFSB;
	private StringTokenizer stDFSB;

	/**
	 *Constructor for the MM2BasedParameterSetReader object
	 */
	public MMFF94BasedParameterSetReader() {
		parameterSet = new Hashtable();
		atomTypes = new Vector();
	}
	
	public Hashtable getParamterSet(){
		return parameterSet;
	}
	
	public Vector getAtomTypes(){
		return atomTypes;
	}
	/**
	 * Sets the file containing the config data
	 *
	 * @param  ins  The new inputStream type InputStream
	 */
	public void setInputStream(InputStream ins) {
		this.ins = ins;
	}
	
	/**
	 * Read a text based configuration file out of the force field mm2 file
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setAtomTypeData() throws Exception {
		
		key = "data" + sid;
		Vector data = new Vector();
		
		String sradius = st.nextToken();
		String swell = st.nextToken();
		String sapol=st.nextToken();
		String sNeff=st.nextToken();
		//st.nextToken();
		String sDA=st.nextToken();
		String sq0=st.nextToken();
		String spbci=st.nextToken();
		String sfcadj=st.nextToken();
		
		
		stvdW.nextToken();
		stvdW.nextToken();
		String sA = stvdW.nextToken();
		String sG = stvdW.nextToken();
		
		try {
			double well = new Double(swell).doubleValue();
			double apol = new Double(sapol).doubleValue();
			double Neff = new Double(sNeff).doubleValue();
			double fcadj = new Double(sfcadj).doubleValue();
			//double pbci = new Double(spbci).doubleValue();
			double a = new Double(sA).doubleValue();
			double g = new Double(sG).doubleValue();
			
			data.add(new Double(well));
			data.add(new Double(apol));
			data.add(new Double(Neff));
			data.add(new String(sDA));
			data.add(new Double(fcadj));
			data.add(new Double(spbci));
			data.add(new Double(a));
			data.add(new Double(g));
			
		} catch (NumberFormatException nfe) {
			throw new IOException("Data: Malformed Number due to:"+nfe);
		}
		
		//logger.debug("data : " + data);
		parameterSet.put(key, data);
		
		key="vdw"+sid;
		data = new Vector();
		try{
			double radius = new Double(sradius).doubleValue();
			data.add(new Double(radius));

		}catch (NumberFormatException nfe2) {
//			logger.debug("vdwError: Malformed Number due to:"+nfe2);
		  }
		parameterSet.put(key, data);

		key="charge"+sid;
		data = new Vector();
		try{
			double q0 = new Double(sq0).doubleValue();
			data.add(new Double(q0));
		}catch (NumberFormatException nfe3) {
			System.out.println("Charge: Malformed Number due to:"+nfe3);
		}
		parameterSet.put(key, data);
	}
	
	/**
	 *  Read and stores the atom types in a vector
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setAtomTypes() throws Exception {
		String name = "";
		String rootType = "";
		//int an = 0;
		int rl = 255;
		int gl = 20;
		int bl = 147;
		int maxbond = 0;
		int atomNr=0;
		
		double mass = 0.0;
		st.nextToken();
		String sid = st.nextToken();
		rootType = st.nextToken();
		String smaxbond = st.nextToken();
		String satomNr=st.nextToken();
		String smass=st.nextToken();
		name = st.nextToken();
		
		
		try {
			maxbond = Integer.parseInt(smaxbond);
			mass= Double.parseDouble(smass);
			atomNr=Integer.parseInt(satomNr);
		
		} catch (NumberFormatException nfe) {
			throw new IOException("AtomTypeTable.ReadAtypes: " +
					"Malformed Number");
		}
		
		AtomType atomType = new AtomType(name, rootType);
		atomType.setAtomicNumber(atomNr);
		atomType.setExactMass(mass);
		atomType.setFormalNeighbourCount(maxbond);
		atomType.setSymbol(rootType);
		Color co = new Color(rl, gl, bl);
		atomType.setProperty("org.openscience.cdk.renderer.color", co);
		atomType.setAtomTypeName(sid);
		atomTypes.addElement(atomType);
	}
	
	
	/**
	 *  Sets the bond attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setBond() throws Exception {
		Vector data = new Vector();
		st.nextToken();
		String scode = st.nextToken();
		String sid1 = st.nextToken();
		String sid2 = st.nextToken();
		String slen = st.nextToken();
		String sk2 = st.nextToken();
		String sk3 = st.nextToken();
		String sk4 = st.nextToken();
		String sbci = st.nextToken();
		
		try {
			double len = new Double(slen).doubleValue();
			double k2 = new Double(sk2).doubleValue();
			double k3 = new Double(sk3).doubleValue();
			double k4 = new Double(sk4).doubleValue();
			double bci = new Double(sbci).doubleValue();
			data.add(new Double(len));
			data.add(new Double(k2));
			data.add(new Double(k3));
			data.add(new Double(k4));
			data.add(new Double(bci));
			
		} catch (NumberFormatException nfe) {
			throw new IOException("setBond: Malformed Number due to:"+nfe);
		}
		key = "bond" + scode + ";" + sid1 + ";" + sid2;
		parameterSet.put(key, data);
	}
	
	/**
	 *  Sets the angle attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setAngle() throws Exception {
		Vector data = new Vector();
		st.nextToken();
		String scode = st.nextToken(); // String scode
		String sid1 = st.nextToken();
		String sid2 = st.nextToken();
		String sid3 = st.nextToken();
		String value1 = st.nextToken();
		String value2 = st.nextToken();
		String value3 = st.nextToken();
		String value4 = st.nextToken();
		
		try {
		    //int code=new Integer(scode).intValue();
			double va1 = new Double(value1).doubleValue();
			double va2 = new Double(value2).doubleValue();
			double va3 = new Double(value3).doubleValue();
			double va4 = new Double(value4).doubleValue();
			data.add(new Double(va1));
			data.add(new Double(va2));
			data.add(new Double(va3));
			data.add(new Double(va4));
			
			key = "angle" + scode + ";" + sid1 + ";" + sid2 + ";" + sid3;
			if (parameterSet.containsKey(key)) {
				data = (Vector) parameterSet.get(key);
				data.add(new Double(va1));
				data.add(new Double(va2));
				data.add(new Double(va3));