pmpreader.java

化学图形处理软件

//                                bondids.put(new Integer(id), new Integer(molecule.getAtomCount()));
//                                molecule.addBond((IBond)chemObject);
                            } else {
                                logger.error("chemObject is not initialized or of bad class type");
                            }
                            // logger.debug(molecule.toString());
                        }
                        line = readLine();
                    }
                    if (line.startsWith("%%Model End")) {
                    	// during the Model Start, all bonds are cached as PMP files might
                    	// define bonds *before* the involved atoms :(
                    	// the next lines dump the cache into the atom container

//                  	bondids.put(new Integer(id), new Integer(molecule.getAtomCount()));
//                  	molecule.addBond((IBond)chemObject);
                    	int bondsFound = bondids.size();
                    	logger.debug("Found #bonds: ", bondsFound);
                    	logger.debug("#atom ones: ", bondAtomOnes.size());
                    	logger.debug("#atom twos: ", bondAtomTwos.size());
                    	logger.debug("#orders: ", bondOrders.size());
                    	Iterator bonds = bondids.keySet().iterator();
                    	while (bonds.hasNext()) {
                    		Integer index = (Integer)bonds.next();
                    		double order = (bondOrders.get(index) != null ? ((Double)bondOrders.get(index)).doubleValue() : 1.0);
                    		logger.debug("index: ", index);
                    		logger.debug("ones: ", bondAtomOnes.get(index));
                    		IAtom atom1 = modelStructure.getAtom(
                    			((Integer)atomids.get(
                    				(Integer)bondAtomOnes.get(index)
                    			)).intValue()
                    		);
                    		IAtom atom2 = modelStructure.getAtom(
                        		((Integer)atomids.get(
                        			(Integer)bondAtomTwos.get(index)
                        		)).intValue()
                        	);
                    		IBond bond = modelStructure.getBuilder().newBond(atom1, atom2, order);
                    		modelStructure.addBond(bond);
                    	}
                    }
                } else if (line.startsWith("%%Traj Start")) {
                    chemSequence = chemFile.getBuilder().newChemSequence();
                    double energyFragment = 0.0;
                    double energyTotal = 0.0;
                    int Z = 1;
                    while (input.ready() && line != null && !(line.startsWith("%%Traj End"))) {
                        if (line.startsWith("%%Start Frame")) {
                            chemModel = chemFile.getBuilder().newChemModel();
                            crystal = chemFile.getBuilder().newCrystal();
                            while (input.ready() && line != null && !(line.startsWith("%%End Frame"))) {
                                // process frame data
                            	if (line.startsWith("%%Atom Coords")) {
                                	// calculate Z: as it is not explicitely given, try to derive it from the
                                	// energy per fragment and the total energy
                                	if (energyFragment != 0.0 && energyTotal != 0.0) {
                                		Z = (int)Math.round(energyTotal/energyFragment);
                                		logger.debug("Z derived from energies: ", Z);
                                	}
                                    // add atomC as atoms to crystal
                                    int expatoms = modelStructure.getAtomCount();
                                    for (int molCount = 1; molCount<=Z; molCount++) {
                                    	IAtomContainer clone = modelStructure.getBuilder().newAtomContainer();
                                    	for (int i=0; i < expatoms; i++) {
                                    		line = readLine();
                                    		IAtom a = clone.getBuilder().newAtom();
                                    		StringTokenizer st = new StringTokenizer(line, " ");
                                    		a.setPoint3d(
                                    			new Point3d(
                                    				Double.parseDouble(st.nextToken()),
                                    				Double.parseDouble(st.nextToken()),
                                    				Double.parseDouble(st.nextToken())
                                    			)
                                    		);
                                    		a.setCovalentRadius(0.6);
                                    		IAtom modelAtom = modelStructure.getAtom(((Integer)atomids.get(atomGivenIds.get(new Integer(i+1)))).intValue());
                                    		a.setSymbol(modelAtom.getSymbol());
                                    		clone.addAtom(a);
                                    	}
                                    	rebonder.rebond(clone);
                                    	crystal.add(clone);
                                    }
                                } else if (line.startsWith("%%E/Frag")) {
                                	line = readLine().trim();
                                	energyFragment = Double.parseDouble(line);
                                } else if (line.startsWith("%%Tot E")) {
                                	line = readLine().trim();
                                	energyTotal = Double.parseDouble(line);
                                } else if (line.startsWith("%%Lat Vects")) {
                                    StringTokenizer st;
                                    line = readLine();
                                    st = new StringTokenizer(line, " ");
                                    crystal.setA(new Vector3d(
                                        Double.parseDouble(st.nextToken()),
                                        Double.parseDouble(st.nextToken()),
                                        Double.parseDouble(st.nextToken())
                                    ));
                                    line = readLine();
                                    st = new StringTokenizer(line, " ");
                                    crystal.setB(new Vector3d(
                                        Double.parseDouble(st.nextToken()),
                                        Double.parseDouble(st.nextToken()),
                                        Double.parseDouble(st.nextToken())
                                    ));
                                    line = readLine();
                                    st = new StringTokenizer(line, " ");
                                    crystal.setC(new Vector3d(
                                        Double.parseDouble(st.nextToken()),
                                        Double.parseDouble(st.nextToken()),
                                        Double.parseDouble(st.nextToken())
                                    ));
                                } else if (line.startsWith("%%Space Group")) {
                                    line = readLine().trim();
                                    /* standardize space group name.
                                       See Crystal.setSpaceGroup() */
                                    if ("P 21 21 21 (1)".equals(line)) {
                                        crystal.setSpaceGroup("P 2_1 2_1 2_1");
                                    } else {
                                        crystal.setSpaceGroup("P1");
                                    }
                                } else {
                                }
                                line = readLine();
                            }
                            chemModel.setCrystal(crystal);
                            chemSequence.addChemModel(chemModel);
                        }
                        line = readLine();
                    }
                    chemFile.addChemSequence(chemSequence);
                } else {
                    // disregard line
                }
                // read next line
                line = readLine();
            }
        } catch (IOException e) {
            logger.error("An IOException happened: ", e.getMessage());
            logger.debug(e);
            chemFile = null;
        } catch (CDKException e) {
            logger.error("An CDKException happened: ", e.getMessage());
            logger.debug(e);
            chemFile = null;
		}

        return chemFile;
    }

    private void processModelCommand(String object, String command, String format, String field) {
        logger.debug(object + "->" + command + " (" + format + "): " + field);
        if ("Model".equals(object)) {
            logger.warn("Unkown PMP Model command: " + command);
        } else if ("Atom".equals(object)) {
            if ("ACL".equals(command)) {
                Matcher atomTypeMatcher = atomTypePattern.matcher(field);
                if (atomTypeMatcher.matches()) {
                    int atomicnum = Integer.parseInt(atomTypeMatcher.group(1));
                    String type = atomTypeMatcher.group(2);
                    ((IAtom)chemObject).setAtomicNumber(atomicnum);
                    ((IAtom)chemObject).setSymbol(type);
                } else {
                    logger.error("Incorrectly formated field value: " + field + ".");
                }
            } else if ("Charge".equals(command)) {
                try {
                    double charge = Double.parseDouble(field);
                    ((IAtom)chemObject).setCharge(charge);
                } catch (NumberFormatException e) {
                    logger.error("Incorrectly formated float field: " + field + ".");
                }
            } else if ("CMAPPINGS".equals(command)) {
            } else if ("FFType".equals(command)) {
            } else if ("Id".equals(command)) {
            	// ok, should take this into account too
            	chemObject.setProperty(PMP_ID, field);
            } else if ("Mass".equals(command)) {
            } else if ("XYZ".equals(command)) {
            } else if ("ZOrder".equals(command)) {
            	// ok, should take this into account too
            	chemObject.setProperty(PMP_ZORDER, field);
            } else {
                logger.warn("Unkown PMP Atom command: " + command);
            }
        } else if ("Bond".equals(object)) {
            if ("Atom1".equals(command)) {
                int atomid = Integer.parseInt(field);
                // this assumes that the atoms involved in this bond are
                // already added, which seems the case in the PMP files
                bondAtomOnes.put(new Integer(bondCounter), new Integer(atomid));
//                IAtom a = molecule.getAtom(realatomid);
//                ((IBond)chemObject).setAtomAt(a, 0);
            } else if ("Atom2".equals(command)) {
                int atomid = Integer.parseInt(field);
                // this assumes that the atoms involved in this bond are
                // already added, which seems the case in the PMP files
                logger.debug("atomids: " + atomids);
                logger.debug("atomid: " + atomid);
                bondAtomTwos.put(new Integer(bondCounter), new Integer(atomid));
//                IAtom a = molecule.getAtom(realatomid);
//                ((IBond)chemObject).setAtomAt(a, 1);
            } else if ("Order".equals(command)) {
                double order = Double.parseDouble(field);
                bondOrders.put(new Integer(bondCounter), new Double(order));
//                ((IBond)chemObject).setOrder(order);
            } else if ("Id".equals(command)) {
            	int bondid = Integer.parseInt(field);
            	bondids.put(new Integer(bondCounter), new Integer(bondid));
            } else if ("Label".equals(command)) {
            } else if ("3DGridOrigin".equals(command)) {
            } else if ("3DGridMatrix".equals(command)) {
            } else if ("3DGridDivision".equals(command)) {
            } else {
                logger.warn("Unkown PMP Bond command: " + command);
            }
        } else {
            logger.warn("Unkown PMP object: " + object);
        }
    }
    
    private void constructObject(IChemObjectBuilder builder, String object) {
        if ("Atom".equals(object)) {
            chemObject = builder.newAtom("C");
        } else if ("Bond".equals(object)) {
        	bondCounter++;
            chemObject = builder.newBond();
        } else if ("Model".equals(object)) {
            modelStructure = builder.newAtomContainer();
        } else {
            logger.error("Cannot construct PMP object type: " + object);
        }
    };

    public void close() throws IOException {
        input.close();
    }
}