mm2basedparametersetreader.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) 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.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;
import org.openscience.cdk.tools.LoggingTool;

/**
 * AtomType list configurator that uses the ParameterSet originally
 * defined in mm2.prm from tinker. This class was added to be able to port
 * mm2 to CDK.
 *
 * @author         chhoppe
 * @cdk.created    2004-09-07
 * @cdk.module     forcefield
 * @cdk.keyword    atom type, MM2
 */
public class MM2BasedParameterSetReader {

//	private final LoggingTool logger = new LoggingTool(MM2BasedParameterSetReader.class);
	
	private String configFile = "org/openscience/cdk/modeling/forcefield/data/mm2.prm";
	private InputStream ins = null;
	private Hashtable parameterSet;
	private Vector atomTypes;
	private StringTokenizer st;
	private String key = "";

	/**
	 *Constructor for the MM2BasedParameterSetReader object
	 */
	public MM2BasedParameterSetReader() {
		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 setForceFieldDefinitions() throws Exception {
		String sid = st.nextToken();
		String svalue = st.nextToken();
		if (sid.equals(">bontunit")) {
			try {
				double value1 = new Double(svalue).doubleValue();
				key = sid.substring(1);
				parameterSet.put(key, new Double(value1));
			} catch (NumberFormatException nfe) {
				throw new IOException("VdWaalsTable.ReadvdWaals: " +
						"Malformed Number");
			}
		} else if (sid.equals(">bond-cubic")) {
			try {
				double value1 = new Double(svalue).doubleValue();
				key = sid.substring(1);
				//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
				parameterSet.put(key, new Double(value1));
			} catch (NumberFormatException nfe) {
				throw new IOException("VdWaalsTable.ReadvdWaals: " +
						"Malformed Number");
			}
		} else if (sid.equals(">bond-quartic")) {
			try {
				double value1 = new Double(svalue).doubleValue();
				key = sid.substring(1);
				//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
				parameterSet.put(key, new Double(value1));
			} catch (NumberFormatException nfe) {
				throw new IOException("VdWaalsTable.ReadvdWaals: " +
						"Malformed Number");
			}
		} else if (sid.equals(">angleunit")) {
			try {
				double value1 = new Double(svalue).doubleValue();
				key = sid.substring(1);
				//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
				parameterSet.put(key, new Double(value1));
			} catch (NumberFormatException nfe) {
				throw new IOException("VdWaalsTable.ReadvdWaals: " +
						"Malformed Number");
			}
		} else if (sid.equals(">angle-sextic")) {
			try {
				double value1 = new Double(svalue).doubleValue();
				key = sid.substring(1);
				//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
				parameterSet.put(key, new Double(value1));
			} catch (NumberFormatException nfe) {
				throw new IOException("VdWaalsTable.ReadvdWaals: " +
						"Malformed Number");
			}
		} else if (sid.equals(">strbndunit")) {
			try {
				double value1 = new Double(svalue).doubleValue();
				key = sid.substring(1);
				//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
				parameterSet.put(key, new Double(value1));
			} catch (NumberFormatException nfe) {
				throw new IOException("VdWaalsTable.ReadvdWaals: " +
						"Malformed Number");
			}
		} else if (sid.equals(">opbendunit")) {
			try {
				double value1 = new Double(svalue).doubleValue();
				key = sid.substring(1);
				//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
				parameterSet.put(key, new Double(value1));
			} catch (NumberFormatException nfe) {
				throw new IOException("VdWaalsTable.ReadvdWaals: " +
						"Malformed Number");
			}
		} else if (sid.equals(">torsionunit")) {
			try {
				double value1 = new Double(svalue).doubleValue();
				key = sid.substring(1);
				//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
				parameterSet.put(key, new Double(value1));
			} catch (NumberFormatException nfe) {
				throw new IOException("VdWaalsTable.ReadvdWaals: " +
						"Malformed Number");
			}
		} else if (sid.equals(">vdwtype")) {
			key = sid.substring(1);
			//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
			parameterSet.put(key, svalue);
		} else if (sid.equals(">radiusrule")) {
			key = sid.substring(1);
			//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
			parameterSet.put(key, svalue);
		} else if (sid.equals(">radiustype")) {
			key = sid.substring(1);
			//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
			parameterSet.put(key, svalue);
		} else if (sid.equals(">radiussize")) {
			key = sid.substring(1);
			//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
			parameterSet.put(key, svalue);
		} else if (sid.equals(">epsilonrule")) {
			key = sid.substring(1);
			//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
			parameterSet.put(key, svalue);
		} else if (sid.equals(">a-expterm")) {
			try {
				key = sid.substring(1);
				//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
				parameterSet.put(key, svalue);
			} catch (NumberFormatException nfe) {
				throw new IOException("VdWaalsTable.ReadvdWaals: " +
						"Malformed Number");
			}
		} else if (sid.equals("b-expterm")) {
			try {
				key = sid.substring(1);
				//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
				parameterSet.put(key, svalue);
			} catch (NumberFormatException nfe) {
				throw new IOException("VdWaalsTable.ReadvdWaals: " +
						"Malformed Number");
			}
		} else if (sid.equals(">c-expterm")) {
			try {
				double value1 = new Double(svalue).doubleValue();
				key = sid.substring(1);
				//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
				parameterSet.put(key, new Double(value1));
			} catch (NumberFormatException nfe) {
				throw new IOException("VdWaalsTable.ReadvdWaals: " +
						"Malformed Number");
			}
		} else if (sid.equals(">vdw-14-scale")) {
			try {
				double value1 = new Double(svalue).doubleValue();
				key = sid.substring(1);
				//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
				parameterSet.put(key, new Double(value1));
			} catch (NumberFormatException nfe) {
				throw new IOException("VdWaalsTable.ReadvdWaals: " +
						"Malformed Number");
			}
		} else if (sid.equals(">chg-14-scale")) {
			try {
				double value1 = new Double(svalue).doubleValue();
				key = sid.substring(1);
				//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
				parameterSet.put(key, new Double(value1));
			} catch (NumberFormatException nfe) {
				throw new IOException("VdWaalsTable.ReadvdWaals: " +
						"Malformed Number");
			}
		} else if (sid.equals(">dielectric")) {
			try {
				double value1 = new Double(svalue).doubleValue();
				key = sid.substring(1);
				//if (parameterSet.containsKey(key)){logger.debug("KeyError: hasKey "+key);}
				parameterSet.put(key, new Double(value1));
			} catch (NumberFormatException nfe) {
				throw new IOException("VdWaalsTable.ReadvdWaals: " +
						"Malformed Number");
			}
		} else {
		}
	}

	/**
	 *  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;

		double mass = 0.0;
		st.nextToken();
		String sid = st.nextToken();
		rootType = st.nextToken();
		name = st.nextToken();
		String san = st.nextToken();
		String sam = st.nextToken();
		String smaxbond = st.nextToken();

		try {
			mass = new Double(sam).doubleValue();
			an = Integer.parseInt(san);
			maxbond = Integer.parseInt(smaxbond);

		} catch (NumberFormatException nfe) {
			throw new IOException("AtomTypeTable.ReadAtypes: " +
					"Malformed Number");
		}

		AtomType atomType = new AtomType(name, rootType);
		atomType.setAtomicNumber(an);
		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);
	}

	/**
	 *  Read vdw radius, stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setvdWaals() throws Exception {
		Vector data = new Vector();
		st.nextToken();
		String sid = st.nextToken();
		String sradius = st.nextToken();
		String sepsi = st.nextToken();
		try {
			double epsi = new Double(sepsi).doubleValue();
			double radius = new Double(sradius).doubleValue();
			data.add(new Double(radius));
			data.add(new Double(epsi));

		} catch (NumberFormatException nfe) {
			throw new IOException("VdWaalsTable.ReadvdWaals: " +
					"Malformed Number");
		}
		key = "vdw" + sid;
		//if (parameterSet.containsKey(key)){System.out.println("KeyError: hasKey "+key);}
		parameterSet.put(key, data);
	}

	/**
	 *  Read vdW pair radius,stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setvdWaalpr() throws Exception {
		Vector data = new Vector();
		st.nextToken();
		String sid1 = st.nextToken();
		String sid2 = st.nextToken();
		String value1 = st.nextToken();
		String value2 = st.nextToken();
		try {
			double va1 = new Double(value1).doubleValue();
			double va2 = new Double(value2).doubleValue();
			data.add(new Double(va1));
			data.add(new Double(va2));

		} catch (NumberFormatException nfe) {
			throw new IOException("VdWaalsTable.ReadvdWaalsPR:Malformed Number due to"+nfe.toString());
		}
		key = "vdwpr" + sid1 + ";" + sid2;
		parameterSet.put(key, data);
	}

	/**
	 *  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 sid1 = st.nextToken();
		String sid2 = st.nextToken();
		String value1 = st.nextToken();
		String value2 = st.nextToken();

		try {
			double va1 = new Double(value1).doubleValue();
			double va2 = new Double(value2).doubleValue();
			data.add(new Double(va1));
			data.add(new Double(va2));

		} catch (NumberFormatException nfe) {
			throw new IOException("setBond: Malformed Number");
		}
		key = "bond" + sid1 + ";" + sid2;
		parameterSet.put(key, data);
	}

	/**
	 *  Sets the bond3 attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setBond3() throws Exception {
		Vector data = new Vector();
		st.nextToken();
		String sid1 = st.nextToken();
		String sid2 = st.nextToken();
		String value1 = st.nextToken();
		String value2 = st.nextToken();

		try {
			double va1 = new Double(value1).doubleValue();
			double va2 = new Double(value2).doubleValue();
			data.add(new Double(va1));
			data.add(new Double(va2));

		} catch (NumberFormatException nfe) {
			throw new IOException("setBond3: Malformed Number");
		}
		key = "bond3_" + sid1 + ";" + sid2;
		parameterSet.put(key, data);
	}

	/**
	 *  Sets the bond4 attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setBond4() throws Exception {
		Vector data = new Vector();
		st.nextToken();
		String sid1 = st.nextToken();
		String sid2 = st.nextToken();
		String value1 = st.nextToken();
		String value2 = st.nextToken();

		try {
			double va1 = new Double(value1).doubleValue();
			double va2 = new Double(value2).doubleValue();
			data.add(new Double(va1));
			data.add(new Double(va2));

		} catch (NumberFormatException nfe) {
			throw new IOException("setBond4: Malformed Number");
		}
		key = "bond4_" + 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 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 {
			double va1 = new Double(value1).doubleValue();
			double va2 = new Double(value2).doubleValue();
			double va3 = new Double(value3).doubleValue();