pdbreader.java

化学图形处理软件

						if (isProteinStructure) {
							if (oBP.getAtomCount() > 0) {
								// save the model
								oSet.addAtomContainer(oBP);
								oModel.setMoleculeSet(oSet);
								oSeq.addChemModel(oModel);
								// setup a new one
								oBP = new PDBPolymer();
								oModel = oFile.getBuilder().newChemModel();
								oSet = oFile.getBuilder().newMoleculeSet();						
							}
						} else {
							if (molecularStructure.getAtomCount() > 0) {
//								 save the model
								oSet.addAtomContainer(molecularStructure);
								oModel.setMoleculeSet(oSet);
								oSeq.addChemModel(oModel);
								// setup a new one
								molecularStructure = oFile.getBuilder().newMolecule();
								oModel = oFile.getBuilder().newChemModel();
								oSet = oFile.getBuilder().newMoleculeSet();		
							}
						}
					} else if ("REMARK".equalsIgnoreCase(cCol)) {						
						Object comment = oFile.getProperty(CDKConstants.COMMENT);
                        if (comment == null) {
                        	comment = "";
                        }
                        if (lineLength >12) {
                        	comment = comment.toString() + cRead.substring(11).trim() + "\n";
                        	oFile.setProperty(CDKConstants.COMMENT, comment);
                        } else {
                        	logger.warn("REMARK line found without any comment!");
                        }
					} else if ("COMPND".equalsIgnoreCase(cCol)) {						
                        String title = cRead.substring(10).trim();
                        oFile.setProperty(CDKConstants.TITLE, title);
					} 
					
					/*************************************************************
					 * Read connectivity information from CONECT records.
					 * Only covalent bonds are dealt with. Perhaps salt bridges
					 * should be dealt with in the same way..?
					 */
					else if (readConnect.isSet() && "CONECT".equalsIgnoreCase(cCol))	{
						cRead.trim();
						if (cRead.length() < 16) {
							logger.debug("Skipping unexpected empty CONECT line! : ", cRead);
						} else {
						
							String bondAtom = cRead.substring(7, 11).trim();
							int bondAtomNo = Integer.parseInt(bondAtom);
							String bondedAtom = cRead.substring(12, 16).trim();
							int bondedAtomNo = -1;
							
							try	{bondedAtomNo = Integer.parseInt(bondedAtom);}
							catch(Exception e)	{bondedAtomNo = -1;}
							
							if(bondedAtomNo != -1)	{
								addBond(oBP, bondAtomNo, bondedAtomNo);
								logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
							}
							
							if(cRead.length() > 17)	{
								bondedAtom = cRead.substring(17, 21);
								bondedAtom = bondedAtom.trim();
								try	{bondedAtomNo = Integer.parseInt(bondedAtom);}
								catch(Exception e)	{bondedAtomNo = -1;}
								
								if(bondedAtomNo != -1)	{
									addBond(oBP, bondAtomNo, bondedAtomNo);
									logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
								}
							}
							
							if(cRead.length() > 22)	{
								bondedAtom = cRead.substring(22, 26);
								bondedAtom = bondedAtom.trim();
								try	{bondedAtomNo = Integer.parseInt(bondedAtom);}
								catch(Exception e)	{bondedAtomNo = -1;}
								
								if(bondedAtomNo != -1)	{
									addBond(oBP, bondAtomNo, bondedAtomNo);
									logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
								}
							}
							
							if(cRead.length() > 27)	{
								bondedAtom = cRead.substring(27, 31);
								bondedAtom = bondedAtom.trim();
								try	{bondedAtomNo = Integer.parseInt(bondedAtom);}
								catch(Exception e)	{bondedAtomNo = -1;}
								
								if(bondedAtomNo != -1)	{
									addBond(oBP, bondAtomNo, bondedAtomNo);
									logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
								}
							}
						}
					}
					/*************************************************************/
					
					else if ("HELIX ".equalsIgnoreCase(cCol)) {
//						HELIX    1 H1A CYS A   11  LYS A   18  1 RESIDUE 18 HAS POSITIVE PHI    1D66  72
//						          1         2         3         4         5         6         7
//						01234567890123456789012345678901234567890123456789012345678901234567890123456789
						PDBStructure structure = new PDBStructure();
						structure.setStructureType(PDBStructure.HELIX);
					    structure.setStartChainID(cRead.charAt(19));
					    structure.setStartSequenceNumber(Integer.parseInt(cRead.substring(21, 25).trim()));
					    structure.setStartInsertionCode(cRead.charAt(25));
					    structure.setEndChainID(cRead.charAt(31));
					    structure.setEndSequenceNumber(Integer.parseInt(cRead.substring(33, 37).trim()));
					    structure.setEndInsertionCode(cRead.charAt(37));
					    oBP.addStructure(structure);
					} else if ("SHEET ".equalsIgnoreCase(cCol)) {
						PDBStructure structure = new PDBStructure();
						structure.setStructureType(PDBStructure.SHEET);
					    structure.setStartChainID(cRead.charAt(21));
					    structure.setStartSequenceNumber(Integer.parseInt(cRead.substring(22, 26).trim()));
					    structure.setStartInsertionCode(cRead.charAt(26));
					    structure.setEndChainID(cRead.charAt(32));
					    structure.setEndSequenceNumber(Integer.parseInt(cRead.substring(33, 37).trim()));
					    structure.setEndInsertionCode(cRead.charAt(37));
					    oBP.addStructure(structure);
					} else if ("TURN  ".equalsIgnoreCase(cCol)) {
						PDBStructure structure = new PDBStructure();
						structure.setStructureType(PDBStructure.TURN);
					    structure.setStartChainID(cRead.charAt(19));
					    structure.setStartSequenceNumber(Integer.parseInt(cRead.substring(20, 24).trim()));
					    structure.setStartInsertionCode(cRead.charAt(24));
					    structure.setEndChainID(cRead.charAt(30));
					    structure.setEndSequenceNumber(Integer.parseInt(cRead.substring(31, 35).trim()));
					    structure.setEndInsertionCode(cRead.charAt(35));
					    oBP.addStructure(structure);
					} // ignore all other commands
				}
			} while (_oInput.ready() && (cRead != null));
		} catch (Exception e) {
			logger.error("Found a problem at line:\n");
			logger.error(cRead);
			logger.error("01234567890123456789012345678901234567890123456789012345678901234567890123456789");
			logger.error("          1         2         3         4         5         6         7         ");
			logger.error("  error: " + e.getMessage());
			logger.debug(e);
		}
		
		// try to close the Input
		try {
			_oInput.close();
		} catch (Exception e) {
			logger.debug(e);
		}
		
		// Set all the dependencies
		oModel.setMoleculeSet(oSet);
		oSeq.addChemModel(oModel);
		oFile.addChemSequence(oSeq);
		
		return oFile;
	}
	
	private void addBond(PDBPolymer obp, int bondAtomNo, int bondedAtomNo) {
		IAtom firstAtom = (PDBAtom)atomNumberMap.get(new Integer(bondAtomNo));
		IAtom secondAtom = (PDBAtom)atomNumberMap.get(new Integer(bondedAtomNo));
		if (firstAtom == null) {
			logger.error("Could not find bond start atom in map with serial id: ", bondAtomNo);
		}
		if (secondAtom == null) {
			logger.error("Could not find bond target atom in map with serial id: ", bondAtomNo);
		}
		obp.addBond(firstAtom.getBuilder().newBond(firstAtom, secondAtom, 1));
	}

	private boolean createBondsWithRebondTool(IBioPolymer pol){
		RebondTool tool = new RebondTool(2.0, 0.5, 0.5);
		try {
//			 configure atoms
		      AtomTypeFactory factory = AtomTypeFactory.getInstance("org/openscience/cdk/config/data/jmol_atomtypes.txt", 
		    	  pol.getBuilder());
		      java.util.Iterator atoms = pol.atoms();
		      while (atoms.hasNext()) {
		    	  IAtom atom = (IAtom)atoms.next();
		        try {
		        	IAtomType[] types = factory.getAtomTypes(atom.getSymbol());
		        	if (types.length > 0) {
		        		// just pick the first one
		        		AtomTypeManipulator.configure(atom, types[0]);
		        	} else {
		        		logger.warn("Could not configure atom with symbol: "+ atom.getSymbol());
		        	}
				} catch (Exception e) {
					logger.warn("Could not configure atom (but don't care): " + e.getMessage());
					logger.debug(e);
				}
		      }
			tool.rebond(pol);
		} catch (Exception e) {
			logger.error("Could not rebond the polymer: " + e.getMessage());
			logger.debug(e);
		}
		return true;
	}

	/**
	 * Creates an <code>Atom</code> and sets properties to their values from
	 * the ATOM record. If the line is shorter than 80 characters, the information
	 * past 59 characters is treated as optional. If the line is shorter than 59
	 * characters, a <code>RuntimeException</code> is thrown.
	 *
	 * @param cLine  the PDB ATOM record.
	 * @return the <code>Atom</code> created from the record.
	 * @throws RuntimeException if the line is too short (less than 59 characters).
	 */
	private PDBAtom readAtom(String cLine, int lineLength) {
		// a line looks like:
		// 01234567890123456789012345678901234567890123456789012345678901234567890123456789
		// ATOM      1  O5*   C A   1      20.662  36.632  23.475  1.00 10.00      114D  45
  		// ATOM   1186 1H   ALA     1      10.105   5.945  -6.630  1.00  0.00      1ALE1288

		if (lineLength < 59) {
			throw new RuntimeException("PDBReader error during readAtom(): line too short");
		}
		String elementSymbol = cLine.substring(12, 14).trim();
		
		if (elementSymbol.length() == 2) {
			// ensure that the second char is lower case
			elementSymbol = elementSymbol.charAt(0) + elementSymbol.substring(1).toLowerCase();
		}
		String rawAtomName = cLine.substring(12, 16).trim();
		String resName = cLine.substring(17, 20).trim();
		try {
			IAtomType type = pdbFactory.getAtomType(resName+"."+rawAtomName);
			elementSymbol = type.getSymbol();
		} catch (NoSuchAtomTypeException e) {
			logger.error("Did not recognize PDB atom type: " + resName+"."+rawAtomName);
		}
		PDBAtom oAtom = new PDBAtom(elementSymbol, 
			new Point3d(Double.parseDouble(cLine.substring(30, 38)),
			            Double.parseDouble(cLine.substring(38, 46)),
			            Double.parseDouble(cLine.substring(46, 54))
			)
		);
		
        oAtom.setRecord(cLine);
        oAtom.setSerial(Integer.parseInt(cLine.substring(6, 11).trim()));
        oAtom.setName(rawAtomName.trim());
        oAtom.setAltLoc(cLine.substring(16, 17).trim());
        oAtom.setResName(resName);
        oAtom.setChainID(cLine.substring(21, 22).trim());
        oAtom.setResSeq(cLine.substring(22, 26).trim());
        oAtom.setICode(cLine.substring(26, 27).trim());
        oAtom.setAtomTypeName(oAtom.getResName()+"."+rawAtomName);
		if (lineLength >= 59) {
            String frag = cLine.substring(54, 60).trim();
            if (frag.length() > 0) {
                oAtom.setOccupancy(Double.parseDouble(frag));
            }
		}
		if (lineLength >= 65) {
            String frag = cLine.substring(60, 66).trim();
            if (frag.length() > 0) {
                oAtom.setTempFactor(Double.parseDouble(frag));
            }
		}
		if (lineLength >= 75) {
            oAtom.setSegID(cLine.substring(72, 76).trim());
		}
//		if (lineLength >= 78) {
//            oAtom.setSymbol((new String(cLine.substring(76, 78))).trim());
//		}
		if (lineLength >= 79) {
            String frag = cLine.substring(78, 80).trim();
            if (frag.length() > 0) {
                oAtom.setCharge(Double.parseDouble(frag));
            }
		}
		
		/*************************************************************************************
		 * It sets a flag in the property content of an atom,
		 * which is used when bonds are created to check if the atom is an OXT-record => needs
		 * special treatment.
		 */
		String oxt = cLine.substring(13, 16).trim();
		
		if(oxt.equals("OXT"))	{
			oAtom.setOxt(true);
		}
		else	{
			oAtom.setOxt(false);
		}
		/*************************************************************************************/
		
		return oAtom;
	}
	
	public void close() throws IOException {
		_oInput.close();
	}

    private void initIOSettings() {
    	useRebondTool = new BooleanIOSetting("UseRebondTool", IOSetting.LOW,
          "Should the PDBReader deduce bonding patterns?", 
          "false");
        readConnect = new BooleanIOSetting("ReadConnectSection", IOSetting.LOW,
          "Should the CONECT be read?",
          "true");
    }
    
    public void customizeJob() {
        fireIOSettingQuestion(useRebondTool);
        fireIOSettingQuestion(readConnect);
    }

    public IOSetting[] getIOSettings() {
        IOSetting[] settings = new IOSetting[2];
        settings[0] = useRebondTool;
        settings[1] = readConnect;
        return settings;
    }

}