mmff94basedparametersetreader.java

化学图形处理软件

				data.add(new Double(va4));
			}
			parameterSet.put(key, data);

		} catch (NumberFormatException nfe) {
			throw new IOException("setAngle: Malformed Number due to:"+nfe);
		}
	}
	
	
	/**
	 *  Sets the strBnd attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setStrBnd() 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();
		
		try {
		    //int code=new Integer(scode).intValue();
			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("setStrBnd: Malformed Number due to:"+nfe);
		}
		key = "strbnd" + scode + ";" + sid1 + ";" + sid2 + ";" + sid3;
		//logger.debug("key =" + key);
		parameterSet.put(key, data);
	}
	
	/**
	 *  Sets the torsion attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setTorsion() throws Exception {
		Vector data = null;
		st.nextToken();
		String scode = st.nextToken(); // String scode
		String sid1 = st.nextToken();
		String sid2 = st.nextToken();
		String sid3 = st.nextToken();
		String sid4 = st.nextToken();
		String value1 = st.nextToken();
		String value2 = st.nextToken();
		String value3 = st.nextToken();
		String value4 = st.nextToken();
		String value5 = st.nextToken();
		
		try {
			double va1 = new Double(value1).doubleValue();
			double va2 = new Double(value2).doubleValue();
			double va3 = new Double(value3).doubleValue();
			double va4 = new Double(value4).doubleValue();
			double va5 = new Double(value5).doubleValue();

			key = "torsion" + scode + ";" + sid1 + ";" + sid2 + ";" + sid3 + ";" + sid4;
			//logger.debug("key = " + key);
			if (parameterSet.containsKey(key)) {
				data = (Vector) parameterSet.get(key);
				data.add(new Double(va1));
				data.add(new Double(va2));
				data.add(new Double(va3));
				data.add(new Double(va4));
				data.add(new Double(va5));
				//logger.debug("data = " + data);
			}
			else{
			    data = new Vector();
			    data.add(new Double(va1));
			    data.add(new Double(va2));
			    data.add(new Double(va3));
			    data.add(new Double(va4));
			    data.add(new Double(va5));
				//logger.debug("data = " + data);
			}

			parameterSet.put(key, data);

		} catch (NumberFormatException nfe) {
			throw new IOException("setTorsion: Malformed Number due to:"+nfe);
		}
	}
	
	/**
	 *  Sets the opBend attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setOpBend() throws Exception {
		Vector data = new Vector();
		st.nextToken();
		String sid1 = st.nextToken();
		String sid2 = st.nextToken();
		String sid3 = st.nextToken();
		String sid4 = st.nextToken();
		String value1 = st.nextToken();

		try {
			double va1 = new Double(value1).doubleValue();
			data.add(new Double(va1));
			key = "opbend" + sid1 + ";" + sid2 + ";" + sid3 + ";" + sid4;
			if (parameterSet.containsKey(key)) {
				data = (Vector) parameterSet.get(key);
				data.add(new Double(va1));
			}
			parameterSet.put(key, data);

		} catch (NumberFormatException nfe) {
			throw new IOException("setOpBend: Malformed Number due to:"+nfe);
		}
	}
	
	
	/**
	 *  Sets the Default Stretch-Bend Parameters into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setDefaultStrBnd() throws Exception {
		//logger.debug("Sets the Default Stretch-Bend Parameters");
		Vector data = new Vector();
		stDFSB.nextToken();
		String sIR = stDFSB.nextToken();
		String sJR = stDFSB.nextToken();
		String sKR = stDFSB.nextToken();
		String skbaIJK = stDFSB.nextToken();
		String skbaKJI = stDFSB.nextToken();

		try {
			key = "DFSB" + sIR + ";" + sJR + ";" + sKR;
			double kbaIJK = new Double(skbaIJK).doubleValue();
			double kbaKJI = new Double(skbaKJI).doubleValue();
			data.add(new Double(kbaIJK));
			data.add(new Double(kbaKJI));
			parameterSet.put(key, data);

		} catch (NumberFormatException nfe) {
			throw new IOException("setDFSB: Malformed Number due to:"+nfe);
		}
	}
	
	
	/**
	 * The main method which parses through the force field configuration file
	 *
	 * @exception  Exception  Description of the Exception
	 */
	public void readParameterSets() throws Exception {
		//vdW,bond,angle,strbond,opbend,torsion,data
		//logger.debug("------ Read MMFF94 ParameterSets ------");

		if (ins == null) {
            ClassLoader loader = this.getClass().getClassLoader();
            System.out.println("loader.getClassName:" + loader.getClass().getName());
			ins = loader.getResourceAsStream(configFile);
		}
		if (ins == null) {
			throw new IOException("There was a problem getting the default stream: " + configFile);
		}
		
		BufferedReader r = new BufferedReader(new InputStreamReader(ins), 1024);
		String s;
		int[] a = {0, 0, 0, 0, 0, 0, 0, 0};
		
		if (insvdW == null) {
			insvdW = this.getClass().getClassLoader().getResourceAsStream(configFilevdW);
		}
		if (insvdW == null) {
			throw new IOException("There was a problem getting the default stream: " + configFilevdW);
		}
		
		BufferedReader rvdW = new BufferedReader(new InputStreamReader(insvdW), 1024);
		String svdW;
		int ntvdW;
				
		if (insDFSB == null) {
			insDFSB = this.getClass().getClassLoader().getResourceAsStream(configFileDFSB);
		}
		if (insDFSB == null) {
			throw new IOException("There was a problem getting the default stream: " + configFileDFSB);
		}
		
		BufferedReader rDFSB = new BufferedReader(new InputStreamReader(insDFSB), 1024);
		String sDFSB;
		int ntDFSB;
				
		try {
			while (true) {
				s = r.readLine();
				if (s == null) {
					break;
				}
				st = new StringTokenizer(s,"\t; ");
				int nt = st.countTokens();
				if (s.startsWith("atom") & nt <= 8) {
					setAtomTypes();
					a[0]++;
				} else if (s.startsWith("bond") & nt == 9) {
					setBond();
					a[1]++;
				} else if (s.startsWith("angle") & nt <= 10) {
					setAngle();
					a[2]++;
				} else if (s.startsWith("strbnd") & nt == 7) {
					setStrBnd();
					a[3]++;
				} else if (s.startsWith("torsion") & nt == 11) {
					setTorsion();
					a[4]++;					
				} else if (s.startsWith("opbend") & nt == 6) {
					setOpBend();
					a[5]++;
				} else if (s.startsWith("data") & nt == 10) {
					readatmmffvdw:
						while (true) {
							svdW = rvdW.readLine();
							if (svdW == null) {
								break;
							}
							stvdW = new StringTokenizer(svdW,"\t; ");
							ntvdW = stvdW.countTokens();
							//logger.debug("ntvdW : " + ntvdW);
							if (svdW.startsWith("vdw") & ntvdW == 9) {
								st.nextToken();
								sid = st.nextToken();
								stvdW.nextToken();
								sidvdW = stvdW.nextToken();
								if (sid.equals(sidvdW)) {
									setAtomTypeData();
									a[6]++;
								}
								break readatmmffvdw;
							}
						}// end while
				}
			}// end while

			ins.close();
			insvdW.close();
		} catch (IOException e) {
			System.err.println(e.toString());
			throw new IOException("There was a problem parsing the mmff94 forcefield");
		}

		try {
			//logger.debug("Parses the Default Stretch-Bend Parameters");
			while (true) {
				sDFSB = rDFSB.readLine();
				//logger.debug("sDFSB = " + sDFSB);
				if (sDFSB == null) {
					//logger.debug("sDFSB == null, break");
					break;
				}
				stDFSB = new StringTokenizer(sDFSB,"\t; ");
				ntDFSB = stDFSB.countTokens();
				//logger.debug("ntDFSB : " + ntDFSB);
				if (sDFSB.startsWith("DFSB") & ntDFSB == 6) {
					setDefaultStrBnd();
				}
			}
			insDFSB.close();
			//logger.debug("insDFSB closed");
		} catch (IOException e) {
			System.err.println(e.toString());
			throw new IOException("There was a problem parsing the Default Stretch-Bend Parameters (mmffdfsb.par)");
		}
	}

}