forcefieldconfigurator.java

化学图形处理软件

		if (ffName.equals("mm2")){
			return configureMM2BasedAtom(atom, hoseCode,_boolean);
		}else if (ffName.equals("mmff94")){
			return configureMMFF94BasedAtom(atom, hoseCode,_boolean);
		}
		return atom;
	}
	
	/**
	 *  Configures an atom to a mm2 based atom type
	 *
	 * @param  atom              atom to be configured
	 * @param  hoseCode          the 4 sphere hose code of the atom
	 * @return                   atom
	 * @exception  CDKException  Description of the Exception
	 */
	public org.openscience.cdk.interfaces.IAtom configureMM2BasedAtom(org.openscience.cdk.interfaces.IAtom atom, String hoseCode,boolean hetRing) throws Exception {
		//logger.debug("CONFIGURE MM2 ATOM");
		Vector atomTypePattern = null;
		MM2BasedAtomTypePattern atp = new MM2BasedAtomTypePattern();
		atomTypePattern = atp.getAtomTypePatterns();
		Double d_tmp = null;
		Pattern p = null;
		String ID = "";
		boolean atomTypeFlag = false;
		
		if (atom instanceof IPseudoAtom) {
			return atom;
		}
		
		hoseCode=removeAromaticityFlagsFromHoseCode(hoseCode);
		
		String [] ids={"C","Csp2","C=","Csp","HC","O","O=","N","Nsp2","Nsp",
				"F","CL","BR","I","S","S+",">SN","SO2","SI","LP","HO",
				"CR3R","HN","HOCO","P","B","BTET","HN2","C.","C+","GE",
				"SN","PB","SE","TE","D","NPYD","CE3R","N+","NPYL","Oar",
				"Sthi","N2OX","HS","=N=","NO3","OM","HN+","OR","Car","HE",
				"NE","AR","KR","XE","","","","MG","PTET","FE","FE","NI","NI","CO","CO",
				"","","OX","OK","C++","N=C","NPD+","N+=","N2OX"
		};
		
		for (int j = 0; j < atomTypePattern.size(); j++) {
			p = (Pattern) atomTypePattern.elementAt(j);
			Matcher mat = p.matcher(hoseCode);
			if (mat.matches()) {
				ID = ids[j];
				//CHECK Rings 1,2,8,9? Thiole 44? AZO 9? Radical - ? Amid 23/enol 21?
				if (j == 0) {
					//csp3
					if (atom.getFlag(CDKConstants.ISINRING)) {
						if (atom.getProperty("RING_SIZE").equals(new Integer(3))) {
							ID=ids[21];
						}else if (atom.getProperty("RING_SIZE").equals(new Integer(6)) & atom.getFlag(CDKConstants.ISAROMATIC)) {
							ID=ids[1];
						}else if (atom.getFlag(CDKConstants.ISAROMATIC)){
							ID=ids[1];
						}
					}
				} else if (j == 1) {
					//csp2
					if (atom.getFlag(CDKConstants.ISINRING)) {
						if (atom.getProperty("RING_SIZE").equals(new Integer(6)) & atom.getFlag(CDKConstants.ISAROMATIC)) {
						}else if (atom.getProperty("RING_SIZE").equals(new Integer(3))) {
							ID=ids[37];
						}else{
							ID=ids[1];
							}
					}
					p = (Pattern) atomTypePattern.elementAt(2);
					//COOH
					mat = p.matcher(hoseCode);
					if (mat.matches() & !atom.getFlag(CDKConstants.ISINRING)) {
						ID=ids[2];
					}
						
				} else if (j == 5) {
					//OH/Ether
					if (atom.getFlag(CDKConstants.ISINRING)) {
						if (atom.getProperty("RING_SIZE").equals(new Integer(3))) {
							ID=ids[48];
							//EPOXY
						}else if (atom.getProperty("RING_SIZE").equals(new Integer(5)) & atom.getFlag(CDKConstants.ISAROMATIC)){
							ID=ids[40];
						}else{
							ID=ids[5];
						}
					}
				} else if (j == 7) {
					//n sp3
					if (atom.getFlag(CDKConstants.ISINRING) & atom.getFlag(CDKConstants.ISAROMATIC)) {
						if (atom.getProperty("RING_SIZE").equals(new Integer(5))) {
							ID=ids[39];
						}
					}
					//Amid
					p = (Pattern) atomTypePattern.elementAt(77);
					mat = p.matcher(hoseCode);
					if (mat.matches() & !atom.getFlag(CDKConstants.ISINRING)) {
						ID=ids[8];
					}
				} else if (j == 8) {
					//nsp2
					if (atom.getFlag(CDKConstants.ISINRING)) {
						if (atom.getProperty("RING_SIZE").equals(new Integer(6))) {
							ID=ids[36];
						}
					}
					p = (Pattern) atomTypePattern.elementAt(36);
					//AZO
					mat = p.matcher(hoseCode);
					if (mat.matches() & !atom.getFlag(CDKConstants.ISINRING)) {
						ID=ids[36];
					}
						
				} else if (j == 43) {
					//h thiol
					d_tmp = (Double) atom.getProperty("MAX_BOND_ORDER");
					if (d_tmp.doubleValue() > 1) {
						ID=ids[4];
					}
				} else if (j == 20) {
					//h alcohol,ether
					p = (Pattern) atomTypePattern.elementAt(76);
					//Enol
					mat = p.matcher(hoseCode);
					if (mat.matches() & !atom.getFlag(CDKConstants.ISINRING)) {
						ID=ids[27];
					}
					p = (Pattern) atomTypePattern.elementAt(23);
					//COOH
					mat = p.matcher(hoseCode);
					if (mat.matches() & !atom.getFlag(CDKConstants.ISINRING)) {
						ID=ids[23];
					}
				} else if (j == 22) {
					p = (Pattern) atomTypePattern.elementAt(75);
					//Amid
					mat = p.matcher(hoseCode);
					if (mat.matches()) {
						ID=ids[27];
					}
				} 

				atomTypeFlag = true;
				//logger.debug("Atom Symbol:" + atom.getSymbol() + " MATCH AtomType> " + ID + " HoseCode>" + hoseCode + " ");
				break;
			}//IF
		}//for end
		if (atomTypeFlag) {
			atomTypeFlag = false;
			return setAtom(atom, ID);
		} else {
			throw new NoSuchAtomTypeException("Atom is unkown: Symbol:" + atom.getSymbol() + " does not MATCH AtomType. HoseCode:" + hoseCode);
		}
	}
	
	public String removeAromaticityFlagsFromHoseCode(String hoseCode){
		String hosecode="";
		for (int i=0;i<hoseCode.length();i++){
			if (hoseCode.charAt(i)!= '*'){
				hosecode=hosecode+hoseCode.charAt(i);
			}
		}
		return hosecode;
	}
	
	/**
	 *  Configures an atom to a mmff94 based atom type
	 *
	 * @param  atom              atom to be configured
	 * @param  hoseCode          the 4 sphere hose code of the atom
	 * @return                   atom
	 * @exception  CDKException  Description of the Exception
	 */
	public org.openscience.cdk.interfaces.IAtom configureMMFF94BasedAtom(org.openscience.cdk.interfaces.IAtom atom, String hoseCode, boolean isInHetRing) throws Exception {
		//logger.debug("****** Configure MMFF94 AtomType ******");
		Vector atomTypePattern = null;
		MMFF94BasedAtomTypePattern atp = new MMFF94BasedAtomTypePattern();
		atomTypePattern = atp.getAtomTypePatterns();
		Pattern p = null;
		Pattern p2 = null;
		String ID = "";
		boolean atomTypeFlag = false;
		Matcher mat=null;
		Matcher mat2=null;
		hoseCode=removeAromaticityFlagsFromHoseCode(hoseCode);
		
		String [] ids={"C","Csp2","C=","Csp","CO2M","CNN+","C%","CIM+","CR4R",
				"CR3R","CE4R","Car","C5A","C5B","C5","HC","HO","HN","HOCO",
				"HN=C","HN2","HOCC","HOH","HOS","HN+","HO+","HO=+","HP","O","O=",
				"OX","OM","O+","O=+","OH2","Oar","N","N=C","NC=C","NSP","=N=","NAZT",
				"N+","N2OX","N3OX","NC#N","NO3","N=O","NC=O","NSO","N+=","NCN+","NGD+","NR%",
				"NM","N5M","NPYD","NPYL","NPD+","N5A","N5B","NPOX","N5OX","N5+","N5","S",
				"S=C",">SN","SO2","SX","SO2M","=SO","Sthi","PTET","P","-P=C","F","CL","BR",
				"I","SI","CL04","FE+2","FE+3","F-","CL-","BR-","LI+","NA+","K+","ZN+2","CA+2","CU+1",
				"CU+2","MG+2","Du"
		};
		
		if (atom instanceof IPseudoAtom) {
			return atom;
		}
		
		for (int j = 0; j < atomTypePattern.size(); j++) {
			p = (Pattern) atomTypePattern.elementAt(j);
			mat = p.matcher(hoseCode);
			if (mat.matches()) {
				ID = ids[j];
				if (j == 0) {//csp3
					if (atom.getFlag(CDKConstants.ISINRING)) {
						p = (Pattern) atomTypePattern.elementAt(13);//c beta heteroaromatic ring
						mat = p.matcher(hoseCode);
						p2 = (Pattern) atomTypePattern.elementAt(12);//c alpha heteroaromatic ring
						mat2 = p2.matcher(hoseCode);
						if (mat.matches() && isInHetRing && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(5))){
							ID = ids[13];
						}else if (mat2.matches() && isInHetRing && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(5))){
							ID = ids[12];
						}else if (atom.getProperty("RING_SIZE").equals(new Integer(3))& !atom.getFlag(CDKConstants.ISAROMATIC)) {
							ID = ids[9];//sp3 3mem rings
						}else if (atom.getProperty("RING_SIZE").equals(new Integer(4)) & !atom.getFlag(CDKConstants.ISAROMATIC)) {
							ID = ids[8];//sp3 4mem rings
						}else if (atom.getFlag(CDKConstants.ISAROMATIC) && isInHetRing && atom.getProperty("RING_SIZE").equals(new Integer(5))) {
							ID = ids[14];//C in het 5 ring
						}else if (atom.getFlag(CDKConstants.ISAROMATIC)) {
							ID = ids[11];//C in benzene, pyroll
						}
					}else{
						p = (Pattern) atomTypePattern.elementAt(66);//S=C
						mat = p.matcher(hoseCode);
						if (mat.matches()){
							ID = ids[66];
						}
					}
				} else if (j == 1) {//csp2
					if (atom.getFlag(CDKConstants.ISINRING)) {
						if (atom.getProperty("RING_SIZE").equals(new Integer(4)) & !atom.getFlag(CDKConstants.ISAROMATIC) && !isInHetRing) {
							ID = ids[29];//C= in 4 ring
						}
					}
					
				} else if (j == 2) {//csp2 C=Hetatom
					if (atom.getFlag(CDKConstants.ISINRING) && isInHetRing && atom.getFlag(CDKConstants.ISAROMATIC)) {
						ID = ids[12];
					}
				
				} else if (j == 36) {//n sp3
					//Amid
					p = (Pattern) atomTypePattern.elementAt(48);
					mat = p.matcher(hoseCode);
					if (mat.matches() & !atom.getFlag(CDKConstants.ISINRING)) {
						ID = ids[48];
					}
					
					p = (Pattern) atomTypePattern.elementAt(44);//sp3 n-oxide
					mat = p.matcher(hoseCode);
					if (mat.matches()){
						ID = ids[44];
					}
					
					p = (Pattern) atomTypePattern.elementAt(56);//npyd
					mat = p.matcher(hoseCode);
					
					if (atom.getFlag(CDKConstants.ISAROMATIC)){//id in pyridin, pyrol etc...						if (mat.matches() && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(5))){
						if(atom.getProperty("RING_SIZE").equals(new Integer(6)) && mat.matches()){
							ID = ids[56];
						}else if(atom.getProperty("RING_SIZE").equals(new Integer(5)) && mat.matches()){
							ID = ids[57];
						}else{
							ID=ids[64];
						}
					}
					
					p = (Pattern) atomTypePattern.elementAt(61);//npyd
					mat = p.matcher(hoseCode);
					if (atom.getFlag(CDKConstants.ISAROMATIC)){//id in pyridin, pyrol etc...						if (mat.matches() && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(5))){
						if(atom.getProperty("RING_SIZE").equals(new Integer(6)) && mat.matches()){
							ID = ids[61];
						}else if(atom.getProperty("RING_SIZE").equals(new Integer(5)) && mat.matches()){
							ID = ids[62];
						}else{
							ID=ids[43];
						}
					}
					
					p = (Pattern) atomTypePattern.elementAt(45);//NC#N
					mat = p.matcher(hoseCode);
					if (mat.matches()){
						ID = ids[45];
					}
				
				}else if (j == 37) {//N=C n in imine
					p = (Pattern) atomTypePattern.elementAt(59);//n beta heteroaromatic ring
					mat = p.matcher(hoseCode);
					if (atom.getFlag(CDKConstants.ISINRING)) {
						if (mat.matches() && isInHetRing && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(5))){
							ID = ids[59];
						}else if( atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(6))){
							ID = ids[56];
						}else if( atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(5))){
							ID = ids[57];
						}
					}
					
					p = (Pattern) atomTypePattern.elementAt(43);//N2OX
					mat = p.matcher(hoseCode);
					if (mat.matches()){
						if (atom.getFlag(CDKConstants.ISAROMATIC)&& atom.getProperty("RING_SIZE").equals(new Integer(6))){
							ID = ids[61];//npox
						}else if (mat.matches() && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(5))){
							ID = ids[62];//n5ox
						}else{
							ID = ids[43];
						}
					}
				
				}else if (j==43){//sp2 n oxide
					if (atom.getFlag(CDKConstants.ISINRING) && atom.getFlag(CDKConstants.ISAROMATIC)
						&& atom.getProperty("RING_SIZE").equals(new Integer(5))){
						ID = ids[62];
					}else if (atom.getFlag(CDKConstants.ISINRING) && atom.getFlag(CDKConstants.ISAROMATIC)
						&& atom.getProperty("RING_SIZE").equals(new Integer(6))){
						ID = ids[61];
					}
				}else if (j==40 || j==41){//n in c=n=n or terminal n in azido
					if (atom.getFlag(CDKConstants.ISINRING) && atom.getFlag(CDKConstants.ISAROMATIC)
						&& atom.getProperty("RING_SIZE").equals(new Integer(5))){
						ID = ids[59];//aromatic N 5R alpha
					}
				}else if (j==50){//n+= 
					if (atom.getFlag(CDKConstants.ISINRING) && atom.getFlag(CDKConstants.ISAROMATIC)
						&& atom.getProperty("RING_SIZE").equals(new Integer(5))){
						ID = ids[63];//n5+
					}else if (atom.getFlag(CDKConstants.ISINRING) && atom.getFlag(CDKConstants.ISAROMATIC)
						&& atom.getProperty("RING_SIZE").equals(new Integer(6))){
						ID = ids[58];//npd+
					}
				}else if (j==28){//O ->furan
					if (atom.getFlag(CDKConstants.ISINRING) && atom.getFlag(CDKConstants.ISAROMATIC)
						&& atom.getProperty("RING_SIZE").equals(new Integer(5))){
							ID = ids[35];
					}
				}else if (j==16){//H-Object-> enol
					p = (Pattern) atomTypePattern.elementAt(21);//enol
					mat = p.matcher(hoseCode);
					if (mat.matches()){
						ID = ids[21];
					}
					p = (Pattern) atomTypePattern.elementAt(18);//enol
					mat = p.matcher(hoseCode);
					if (mat.matches()){
						ID = ids[18];
					}
					
				}else if (j==74){//P
					p = (Pattern) atomTypePattern.elementAt(75);//-P=C
					mat = p.matcher(hoseCode);
					if (mat.matches()){
						ID = ids[75];
					}
				}
				
				atomTypeFlag = true;
				//logger.debug("Atom Symbol:" + atom.getSymbol() + " MATCH AtomType> " + ID + " HoseCode>" + hoseCode + " ");
				break;
			}//IF
		}//for end
		if (atomTypeFlag) {
			atomTypeFlag = false;
			return setAtom(atom, ID);
		} else {
			throw new NoSuchAtomTypeException("Atom is unkown: Symbol:" + atom.getSymbol() + " does not MATCH AtomType. HoseCode:" + hoseCode);
		}
	}
}