mm2basedparametersetreader.java

化学图形处理软件

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

		} catch (NumberFormatException nfe) {
			throw new IOException("setAngle: Malformed Number");
		}

	}

	/**
	 *  Sets the angle3 attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setAngle3() 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();
			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));

		} catch (NumberFormatException nfe) {
			throw new IOException("setAngle3: Malformed Number");
		}
		key = "angle3_" + sid1 + ";" + sid2 + ";" + sid3;
		parameterSet.put(key, data);
	}

	/**
	 *  Sets the angle4 attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setAngle4() 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();
			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));

		} catch (NumberFormatException nfe) {
			throw new IOException("setAngle4: Malformed Number");
		}
		key = "angle4_" + sid1 + ";" + sid2 + ";" + sid3;
		parameterSet.put(key, data);
	}

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

		try {
			double va1 = new Double(value1).doubleValue();
			data.add(new Double(va1));
		} catch (NumberFormatException nfe) {
			throw new IOException("setStrBnd: Malformed Number");
		}
		key = "strbnd" + sid1;
		parameterSet.put(key, data);
	}

	/**
	 *  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 value1 = st.nextToken();

		try {
			double va1 = new Double(value1).doubleValue();
			data.add(new Double(va1));
			key = "opbend" + sid1 + ";" + sid2;
			if (parameterSet.containsKey(key)) {
				//logger.debug("KeyError: hasKey "+key);
				data = (Vector) parameterSet.get(key);
				data.add(new Double(va1));
			}
			parameterSet.put(key, data);

		} catch (NumberFormatException nfe) {
			throw new IOException("setOpBend: Malformed Number");
		}

	}

	/**
	 *  Sets the torsion attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setTorsion() 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();
		st.nextToken();
		st.nextToken();
		String value2 = st.nextToken();
		st.nextToken();
		st.nextToken();
		String value3 = st.nextToken();
		st.nextToken();
		st.nextToken();

		try {
			double va1 = new Double(value1).doubleValue();
			double va2 = new Double(value2).doubleValue();
			double va3 = new Double(value3).doubleValue();
			data.add(new Double(va1));
			data.add(new Double(va2));
			data.add(new Double(va3));

			key = "torsion" + sid1 + ";" + sid2 + ";" + sid3 + ";" + sid4;
			if (parameterSet.containsKey(key)) {
				data = (Vector) parameterSet.get(key);
				data.add(new Double(va1));
				data.add(new Double(va2));
				data.add(new Double(va3));
			}
			parameterSet.put(key, data);
		} catch (NumberFormatException nfe) {
			throw new IOException("setTorsion: Malformed Number");
		}

	}

	/**
	 *  Sets the torsion4 attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setTorsion4() 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();
		st.nextToken();
		st.nextToken();
		String value2 = st.nextToken();
		st.nextToken();
		st.nextToken();
		String value3 = st.nextToken();
		st.nextToken();
		st.nextToken();

		try {
			double va1 = new Double(value1).doubleValue();
			double va2 = new Double(value2).doubleValue();
			double va3 = new Double(value3).doubleValue();
			data.add(new Double(va1));
			data.add(new Double(va2));
			data.add(new Double(va3));

		} catch (NumberFormatException nfe) {
			throw new IOException("setTorsion4: Malformed Number");
		}
		key = "torsion4_" + sid1 + ";" + sid2 + ";" + sid3 + ";" + sid4;
		parameterSet.put(key, data);
	}

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

		try {
			double va1 = new Double(value1).doubleValue();
			data.add(new Double(va1));
		} catch (NumberFormatException nfe) {
			throw new IOException("setCharge: Malformed Number due to "+nfe.toString());
		}
		key = "charge" + sid1;
		parameterSet.put(key, data);
	}

	/**
	 *  Sets the dipole attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setDipole() 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("setDipole: " +
					"Malformed Number");
		}
		key = "dipole" + sid1 + ";" + sid2;
		parameterSet.put(key, data);
	}

	/**
	 *  Sets the dipole3 attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setDipole3() 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("setDipole3: " +
					"Malformed Number");
		}
		key = "dipole3_" + sid1 + ";" + sid2;
		parameterSet.put(key, data);
	}

	/**
	 *  Sets the piAtom attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setPiAtom() throws Exception {
		Vector data = new Vector();
		st.nextToken();
		String sid1 = st.nextToken();
		String value1 = st.nextToken();
		String value2 = st.nextToken();
		String value3 = st.nextToken();

		try {
			double va1 = new Double(value1).doubleValue();
			double va2 = new Double(value2).doubleValue();
			double va3 = new Double(value3).doubleValue();
			data.add(new Double(va1));
			data.add(new Double(va2));
			data.add(new Double(va3));

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

	/**
	 *  Sets the piBond attribute stored into the parameter set
	 *
	 * @exception  Exception  Description of the Exception
	 */
	private void setPiBond() 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("setPiBond: " +
					"Malformed Number");
		}
		key = "pibond" + sid1 + ";" + sid2;
		parameterSet.put(key, data);
	}

	/**
	 * The main method which parses through the force field configuration file
	 *
	 * @exception  Exception  Description of the Exception
	 */
	public void readParameterSets() throws Exception {
		//vdW,vdWp,bond,bond4,bond3,angle,angle4,angle3,
		//strbond,opbend,torsion,torsion4,charge,dipole,
		//dipole3,piatom,pibond,dipole3
		//logger.debug("------ ReadParameterSets ------");

		if (ins == null) {
			ins = getClass().getResourceAsStream(configFile);
		}
		if (ins == null) {
			throw new IOException("There was a problem getting the default stream: " + configFile);
		}

		// read the contents from file
		BufferedReader r = new BufferedReader(new InputStreamReader(ins), 1024);
		String s;
		int[] a = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
		try {
			while (true) {
				s = r.readLine();
				if (s == null) {
					break;
				}
				st = new StringTokenizer(s, "\t ;");
				int nt = st.countTokens();
				if (s.startsWith(">") & nt > 1) {
					setForceFieldDefinitions();
					a[0]++;
				} else if (s.startsWith("atom") & nt <= 8) {
					a[0]++;
					setAtomTypes();
				} else if (s.startsWith("vdw ") & nt <= 5) {
					setvdWaals();
					a[1]++;
				} else if (s.startsWith("vdwpr ") & nt <= 6) {
					setvdWaalpr();
					a[2]++;
				} else if (s.startsWith("bond ") & nt <= 7) {
					setBond();
					a[3]++;
				} else if (s.startsWith("bond4 ") & nt == 5) {
					setBond4();
					a[4]++;
				} else if (s.startsWith("bond3 ") & nt == 5) {
					setBond3();
					a[5]++;
				} else if (s.startsWith("angle ") & nt == 8) {
					setAngle();
					a[6]++;
				} else if (s.startsWith("angle4 ") & nt == 8) {
					setAngle4();
					a[17]++;
				} else if (s.startsWith("angle3 ") & nt == 8) {
					setAngle3();
					a[7]++;
				} else if (s.startsWith("strbnd ") & nt == 5) {
					setStrBnd();
					a[8]++;
				} else if (s.startsWith("opbend ") & nt == 4) {
					setOpBend();
					a[9]++;
				} else if (s.startsWith("torsion ") & nt == 14) {
					setTorsion();
					a[10]++;
				} else if (s.startsWith("torsion4 ") & nt == 14) {
					setTorsion4();
					a[11]++;
				} else if (s.startsWith("charge ") & nt == 3) {
					setCharge();
					a[12]++;
				} else if (s.startsWith("dipole ") & nt == 5) {
					setDipole();
					a[13]++;
				} else if (s.startsWith("dipole3 ") & nt == 5) {
					setDipole3();
					a[14]++;
				} else if (s.startsWith("piatom ") & nt == 5) {
					setPiAtom();
					a[15]++;
				} else if (s.startsWith("pibond ") & nt == 5) {
					setPiBond();
					a[16]++;
				} 
			}// end while
			ins.close();
		} catch (IOException e) {
			throw new IOException("There was a problem parsing the mm2 forcefield due to:"+e.toString());
		}
	}
}