cmlcoremodule.java

化学图形处理软件

                    elsym.add(value);
                } // this is supported in CML 2.0 
                else if (att.equals("title")) {
                    eltitles.add(value);
                } // this is supported in CML 2.0 
                else if (att.equals("x2")) {
                    x2.add(value);
                } // this is supported in CML 2.0 
                else if (att.equals("xy2")) {
                    StringTokenizer tokenizer = new StringTokenizer(value);
                    x2.add(tokenizer.nextToken());
                    y2.add(tokenizer.nextToken());
                } // this is supported in CML 2.0 
                else if (att.equals("xyzFract")) {
                    StringTokenizer tokenizer = new StringTokenizer(value);
                    xfract.add(tokenizer.nextToken());
                    yfract.add(tokenizer.nextToken());
                    zfract.add(tokenizer.nextToken());
                } // this is supported in CML 2.0 
                else if (att.equals("xyz3")) {
                    StringTokenizer tokenizer = new StringTokenizer(value);
                    x3.add(tokenizer.nextToken());
                    y3.add(tokenizer.nextToken());
                    z3.add(tokenizer.nextToken());
                } // this is supported in CML 2.0 
                else if (att.equals("y2")) {
                    y2.add(value);
                } // this is supported in CML 2.0 
                else if (att.equals("x3")) {
                    x3.add(value);
                } // this is supported in CML 2.0 
                else if (att.equals("y3")) {
                    y3.add(value);
                } // this is supported in CML 2.0 
                else if (att.equals("z3")) {
                    z3.add(value);
                } // this is supported in CML 2.0 
                else if (att.equals("xFract")) {
                    xfract.add(value);
                } // this is supported in CML 2.0 
                else if (att.equals("yFract")) {
                    yfract.add(value);
                } // this is supported in CML 2.0 
                else if (att.equals("zFract")) {
                    zfract.add(value);
                } // this is supported in CML 2.0 
                else if (att.equals("formalCharge")) {
                    formalCharges.add(value);
                } // this is supported in CML 2.0 
                else if (att.equals("hydrogenCount")) {
                    hCounts.add(value);
                }
                else if (att.equals("isotope")) {
                    isotope.add(value);
                }
                else if (att.equals("dictRef")) {                	
                    logger.debug("ocupaccy: "+value);
                    atomDictRefs.add(value);
                } 
                else if (att.equals("spinMultiplicity")) {
                    spinMultiplicities.add(value);
                }
                else if (att.equals("occupancy")) {
                    occupancies.add(value);
                } 
                 
                else {
                    logger.warn("Unparsed attribute: " + att);
                }
            }
        } else if ("atomArray".equals(name) &&
        		   !xpath.endsWith("formula", "atomArray")) {
            boolean atomsCounted = false;
            for (int i = 0; i < atts.getLength(); i++) {
                String att = atts.getQName(i);
                int count = 0;
                if (att.equals("atomID")) {
                    count = addArrayElementsTo(elid, atts.getValue(i));
                } else if (att.equals("elementType")) {
                    count = addArrayElementsTo(elsym, atts.getValue(i));
                } else if (att.equals("x2")) {
                    count = addArrayElementsTo(x2, atts.getValue(i));
                } else if (att.equals("y2")) {
                    count = addArrayElementsTo(y2, atts.getValue(i));
                } else if (att.equals("x3")) {
                    count = addArrayElementsTo(x3, atts.getValue(i));
                } else if (att.equals("y3")) {
                    count = addArrayElementsTo(y3, atts.getValue(i));
                } else if (att.equals("z3")) {
                    count = addArrayElementsTo(z3, atts.getValue(i));
                } else if (att.equals("xFract")) {
                    count = addArrayElementsTo(xfract, atts.getValue(i));
                } else if (att.equals("yFract")) {
                    count = addArrayElementsTo(yfract, atts.getValue(i));
                } else if (att.equals("zFract")) {
                    count = addArrayElementsTo(zfract, atts.getValue(i));
                } else {
                    logger.warn("Unparsed attribute: " + att);
                }
                if (!atomsCounted) {
                    atomCounter += count;
                    atomsCounted = true;
                }
            }
        } else if ("bond".equals(name)) {
            bondCounter++;
            for (int i = 0; i < atts.getLength(); i++) {
                String att = atts.getQName(i);
                logger.debug("B2 ", att, "=", atts.getValue(i));
                
                if (att.equals("id")) {
                    bondid.add(atts.getValue(i));
                    logger.debug("B3 ", bondid);
                } else if (att.equals("atomRefs") || // this is CML 1.x support
                           att.equals("atomRefs2")) { // this is CML 2.0 support
                    
                    // expect exactly two references
                    try {
                        StringTokenizer st = new StringTokenizer(
                            atts.getValue(i)
                        );
                        bondARef1.add((String)st.nextElement());
                        bondARef2.add((String)st.nextElement());
                    } catch (Exception e) {
                        logger.error("Error in CML file: ", e.getMessage());
                        logger.debug(e);
                    }
                } else if (att.equals("order")) { // this is CML 2.0 support
                    order.add(atts.getValue(i).trim());
                } else if (att.equals("dictRef")) {
                    bondDictRefs.add(atts.getValue(i).trim());
                }
            }
            
            stereoGiven = false;
            curRef = 0;
        } else if ("bondArray".equals(name)) {
            boolean bondsCounted = false;
            for (int i = 0; i < atts.getLength(); i++) {
                String att = atts.getQName(i);
                int count = 0;
                if (att.equals("bondID")) {
                    count = addArrayElementsTo(bondid, atts.getValue(i));
                } else if (att.equals("atomRefs1")) {
                    count = addArrayElementsTo(bondARef1, atts.getValue(i));
                } else if (att.equals("atomRefs2")) {
                    count = addArrayElementsTo(bondARef2, atts.getValue(i));
                } else if (att.equals("atomRef1")) {
                    count = addArrayElementsTo(bondARef1, atts.getValue(i));
                } else if (att.equals("atomRef2")) {
                    count = addArrayElementsTo(bondARef2, atts.getValue(i));
                } else if (att.equals("order")) {
                    count = addArrayElementsTo(order, atts.getValue(i));
                } else {
                    logger.warn("Unparsed attribute: " + att);
                }
                if (!bondsCounted) {
                    bondCounter += count;
                    bondsCounted = true;
                }
            }
            curRef = 0;
        } else if ("bondStereo".equals(name)) {
            for (int i = 0; i < atts.getLength(); i++) {
                if (atts.getQName(i).equals("dictRef")) {
                	if (atts.getValue(i).startsWith("cml:"))
                	bondStereo.add(atts.getValue(i).substring(4));
                    stereoGiven=true;
                }
            }
        } else if ("bondType".equals(name)) {
            for (int i = 0; i < atts.getLength(); i++) {
                if (atts.getQName(i).equals("dictRef")) {
                	if (atts.getValue(i).equals("cdk:aromaticBond"))
                		bondAromaticity.add(Boolean.TRUE);
                }
            }
        } else if ("molecule".equals(name)) {
            newMolecule();
            BUILTIN = "";
//            cdo.startObject("Molecule");
            if (currentChemModel == null) currentChemModel = currentChemFile.getBuilder().newChemModel();
            if (currentMoleculeSet == null) currentMoleculeSet = currentChemFile.getBuilder().newMoleculeSet();
            currentMolecule = currentChemFile.getBuilder().newMolecule();
            for (int i = 0; i < atts.getLength(); i++) {
                if (atts.getQName(i).equals("id")) {
//                    cdo.setObjectProperty("Molecule", "id", atts.getValue(i));
                	currentMolecule.setID(atts.getValue(i));
                } else if (atts.getQName(i).equals("dictRef")) {
//                	cdo.setObjectProperty("Molecule", "dictRef", atts.getValue(i));
                	currentMolecule.setProperty(new DictRef(DICTREF, atts.getValue(i)), atts.getValue(i));
                }
            }
        } else if ("crystal".equals(name)) {
            newCrystalData();
//            cdo.startObject("Crystal");
            currentMolecule = currentChemFile.getBuilder().newCrystal(currentMolecule);
            for (int i = 0; i < atts.getLength(); i++) {
                String att = atts.getQName(i);
                if (att.equals("z")) {
//                    cdo.setObjectProperty("Crystal", "z", atts.getValue(i));
                	((ICrystal)currentMolecule).setZ(Integer.parseInt(atts.getValue(i)));
                }
            }
        } else if ("symmetry".equals(name)) {
            for (int i = 0; i < atts.getLength(); i++) {
                String att = atts.getQName(i);
                if (att.equals("spaceGroup")) {
//                    cdo.setObjectProperty("Crystal", "spacegroup", atts.getValue(i));
                	((ICrystal)currentMolecule).setSpaceGroup(atts.getValue(i));
                }
            }
        } else if ("identifier".equals(name)) {
        	if (atts.getValue("convention") != null && 
        		atts.getValue("convention").equals("iupac:inchi") &&
        		atts.getValue("value") != null) {
//                cdo.setObjectProperty("Molecule", "inchi", atts.getValue("value"));
        		currentMolecule.setProperty(CDKConstants.INCHI, atts.getValue("value"));
            }
        } else if ("scalar".equals(name)) {
            if (xpath.endsWith("crystal", "scalar"))
                crystalScalar++;
        } else if ("label".equals(name)) {
            if (xpath.endsWith("atomType", "label")) {
//            	cdo.setObjectProperty("Atom", "atomTypeLabel", atts.getValue("value"));
            	currentAtom.setAtomTypeName(atts.getValue("value"));
            }
        } else if ("list".equals(name)) {
//            cdo.startObject("MoleculeSet");
        	if (DICTREF.equals("cdk:model")) {
        		currentChemModel = currentChemFile.getBuilder().newChemModel();
        	} else if (DICTREF.equals("cdk:moleculeSet")) {
        		currentMoleculeSet = currentChemFile.getBuilder().newMoleculeSet();
        		currentMolecule = currentChemFile.getBuilder().newMolecule();
        	} else {
        		// the old default
        		currentMoleculeSet = currentChemFile.getBuilder().newMoleculeSet();
        		currentMolecule = currentChemFile.getBuilder().newMolecule();
        	}
        }
    }

    public void endElement(CMLStack xpath, String uri, String name, String raw) {
        logger.debug("EndElement: ", name);

        String cData = currentChars;
        if ("bond".equals(name)) {
        	if (!stereoGiven)
                bondStereo.add("");
            if (bondStereo.size() > bondDictRefs.size())
                bondDictRefs.add(null);
            if (bondAromaticity.size() > bondDictRefs.size())
            	bondAromaticity.add(null);
        } else if ("atom".equals(name)) {
            if (atomCounter > eltitles.size()) {
                eltitles.add(null);
            }
            if (atomCounter > hCounts.size()) {
                /* while strictly undefined, assume zero 
                implicit hydrogens when no number is given */
                hCounts.add("0");
            }
            if (atomCounter > atomDictRefs.size()) {
                atomDictRefs.add(null);
            }
            if (atomCounter > isotope.size()) {
                isotope.add(null);
            }
            if (atomCounter > spinMultiplicities.size()) {
                spinMultiplicities.add(null);
            }
            if (atomCounter > occupancies.size()) {
                occupancies.add(null);
            }
            if (atomCounter > formalCharges.size()) {
                /* while strictly undefined, assume zero 
                implicit hydrogens when no number is given */
                formalCharges.add("0");
            }
            /* It may happen that not all atoms have
            associated 2D or 3D coordinates. accept that */
            if (atomCounter > x2.size() && x2.size() != 0) {
                /* apparently, the previous atoms had atomic
                coordinates, add 'null' for this atom */
                x2.add(null);
                y2.add(null);
            }
            if (atomCounter > x3.size() && x3.size() != 0) {
                /* apparently, the previous atoms had atomic
                coordinates, add 'null' for this atom */
                x3.add(null);
                y3.add(null);
                z3.add(null);
            }
            
            if (atomCounter > xfract.size() && xfract.size() != 0) {
                /* apparently, the previous atoms had atomic
                coordinates, add 'null' for this atom */
                xfract.add(null);
                yfract.add(null);
                zfract.add(null);
            }
        } else if ("molecule".equals(name)) {
            storeData();
//            cdo.endObject("Molecule");
            if (currentMolecule instanceof IMolecule) {
                logger.debug("Adding molecule to set");
                currentMoleculeSet.addMolecule((IMolecule)currentMolecule);
                logger.debug("#mols in set: " + currentMoleculeSet.getMoleculeCount());
            } else if (currentMolecule instanceof ICrystal) {
                logger.debug("Adding crystal to chemModel");
                currentChemModel.setCrystal((ICrystal)currentMolecule);
                currentChemSequence.addChemModel(currentChemModel);
            }
        } else if ("crystal".equals(name)) {
            if (crystalScalar > 0) {
                // convert unit cell parameters to cartesians
                Vector3d[] axes = CrystalGeometryTools.notionalToCartesian(
                    unitcellparams[0], unitcellparams[1], unitcellparams[2],
                    unitcellparams[3], unitcellparams[4], unitcellparams[5]
                );
                cartesianAxesSet = true;
//                cdo.startObject("a-axis");
//                cdo.setObjectProperty("a-axis", "x", new Double(aAxis.x).toString());
//                cdo.setObjectProperty("a-axis", "y", new Double(aAxis.y).toString());
//                cdo.setObjectProperty("a-axis", "z", new Double(aAxis.z).toString());
//                cdo.endObject("a-axis");
//                cdo.startObject("b-axis");
//                cdo.setObjectProperty("b-axis", "x", new Double(bAxis.x).toString());
//                cdo.setObjectProperty("b-axis", "y", new Double(bAxis.y).toString());
//                cdo.setObjectProperty("b-axis", "z", new Double(bAxis.z).toString());
//                cdo.endObject("b-axis");
//                cdo.startObject("c-axis");
//                cdo.setObjectProperty("c-axis", "x", new Double(cAxis.x).toString());
//                cdo.setObjectProperty("c-axis", "y", new Double(cAxis.y).toString());
//                cdo.setObjectProperty("c-axis", "z", new Double(cAxis.z).toString());
//                cdo.endObject("c-axis");
                ((ICrystal)currentMolecule).setA(axes[0]);
                ((ICrystal)currentMolecule).setB(axes[1]);
                ((ICrystal)currentMolecule).setC(axes[2]);
            } else {
                logger.error("Could not find crystal unit cell parameters");
            }
//            cdo.endObject("Crystal");
        } else if ("list".equals(name)) {
//            cdo.endObject("MoleculeSet");
        	// FIXME: I really should check the DICTREF, but there is currently
        	// no mechanism for storing these for use with endTag() :(
        	// So, instead, for now, just see if it already has done the setting
        	// to work around duplication
        	if (currentChemModel.getMoleculeSet() != currentMoleculeSet) {
        		currentChemModel.setMoleculeSet(currentMoleculeSet);
        		currentChemSequence.addChemModel(currentChemModel);
        	}
        } else if ("coordinate3".equals(name)) {
            if (BUILTIN.equals("xyz3")) {