Examples with CMLScalar org.xmlcml.cml.element.CMLScalar used on opensource projects

Example 1 with CMLScalar

use of org.xmlcml.cml.element.CMLScalar in project cdk by cdk.

the class Convertor method cdkAtomContainerToCMLMolecule.

private CMLMolecule cdkAtomContainerToCMLMolecule(IAtomContainer structure, boolean setIDs, boolean isRef) {
    CMLMolecule cmlMolecule = new CMLMolecule();
    if (useCMLIDs && setIDs) {
        IDCreator.createIDs(structure);
    }
    this.checkPrefix(cmlMolecule);
    if (structure.getID() != null && !structure.getID().equals(""))
        if (!isRef)
            cmlMolecule.setId(structure.getID());
        else
            cmlMolecule.setRef(structure.getID());
    if (structure.getTitle() != null) {
        cmlMolecule.setTitle(structure.getTitle());
    }
    if (structure.getProperty(CDKConstants.INCHI) != null) {
        CMLIdentifier ident = new CMLIdentifier();
        ident.setConvention("iupac:inchi");
        ident.setCMLValue(structure.getProperty(CDKConstants.INCHI).toString());
        cmlMolecule.appendChild(ident);
    }
    if (!isRef) {
        for (int i = 0; i < structure.getAtomCount(); i++) {
            IAtom cdkAtom = structure.getAtom(i);
            CMLAtom cmlAtom = cdkAtomToCMLAtom(structure, cdkAtom);
            if (structure.getConnectedSingleElectronsCount(cdkAtom) > 0) {
                cmlAtom.setSpinMultiplicity(structure.getConnectedSingleElectronsCount(cdkAtom) + 1);
            }
            cmlMolecule.addAtom(cmlAtom);
        }
        for (int i = 0; i < structure.getBondCount(); i++) {
            CMLBond cmlBond = cdkBondToCMLBond(structure.getBond(i));
            cmlMolecule.addBond(cmlBond);
        }
    }
    // ok, output molecular properties, but not TITLE, INCHI, or DictRef's
    Map<Object, Object> props = structure.getProperties();
    for (Object key : props.keySet()) {
        // but only if a String
        if (key instanceof String && !isRef && props.get(key) instanceof String) {
            Object value = props.get(key);
            if (!key.toString().equals(CDKConstants.TITLE) && !key.toString().equals(CDKConstants.INCHI)) {
                // ok, should output this
                CMLScalar scalar = new CMLScalar();
                this.checkPrefix(scalar);
                scalar.setDictRef("cdk:molecularProperty");
                scalar.setTitle(key.toString());
                scalar.setValue(value.toString());
                cmlMolecule.addScalar(scalar);
            }
        }
        // but it should be that IMolecularFormula is a extension of IAtomContainer
        if (key instanceof String && !isRef && key.toString().equals(CDKConstants.FORMULA)) {
            if (props.get(key) instanceof IMolecularFormula) {
                IMolecularFormula cdkFormula = (IMolecularFormula) props.get(key);
                CMLFormula cmlFormula = new CMLFormula();
                List<IIsotope> isotopesList = MolecularFormulaManipulator.putInOrder(MolecularFormulaManipulator.generateOrderEle(), cdkFormula);
                for (IIsotope iIsotope : isotopesList) {
                    cmlFormula.add(iIsotope.getSymbol(), cdkFormula.getIsotopeCount(iIsotope));
                }
                cmlMolecule.appendChild(cmlFormula);
            } else if (props.get(key) instanceof IMolecularFormulaSet) {
                IMolecularFormulaSet cdkFormulaSet = (IMolecularFormulaSet) props.get(key);
                for (IMolecularFormula cdkFormula : cdkFormulaSet.molecularFormulas()) {
                    List<IIsotope> isotopesList = MolecularFormulaManipulator.putInOrder(MolecularFormulaManipulator.generateOrderEle(), cdkFormula);
                    CMLFormula cmlFormula = new CMLFormula();
                    cmlFormula.setDictRef("cdk:possibleMachts");
                    for (IIsotope iIsotope : isotopesList) {
                        cmlFormula.add(iIsotope.getSymbol(), cdkFormula.getIsotopeCount(iIsotope));
                    }
                    cmlMolecule.appendChild(cmlFormula);
                }
            }
        }
    }
    for (String s : customizers.keySet()) {
        ICMLCustomizer customizer = customizers.get(s);
        try {
            customizer.customize(structure, cmlMolecule);
        } catch (Exception exception) {
            logger.error("Error while customizing CML output with customizer: ", customizer.getClass().getName());
            logger.debug(exception);
        }
    }
    return cmlMolecule;
}

Example 2 with CMLScalar

use of org.xmlcml.cml.element.CMLScalar in project cdk by cdk.

the class Convertor method cdkAtomToCMLAtom.

public CMLAtom cdkAtomToCMLAtom(IAtomContainer container, IAtom cdkAtom) {
    CMLAtom cmlAtom = new CMLAtom();
    this.checkPrefix(cmlAtom);
    addAtomID(cdkAtom, cmlAtom);
    addDictRef(cdkAtom, cmlAtom);
    cmlAtom.setElementType(cdkAtom.getSymbol());
    if (cdkAtom instanceof IPseudoAtom) {
        String label = ((IPseudoAtom) cdkAtom).getLabel();
        if (label != null)
            cmlAtom.setTitle(label);
        cmlAtom.setElementType("Du");
    }
    map2DCoordsToCML(cmlAtom, cdkAtom);
    map3DCoordsToCML(cmlAtom, cdkAtom);
    mapFractionalCoordsToCML(cmlAtom, cdkAtom);
    Integer formalCharge = cdkAtom.getFormalCharge();
    if (formalCharge != null)
        cmlAtom.setFormalCharge(formalCharge);
    // CML's hydrogen count consists of the sum of implicit and explicit
    // hydrogens (see bug #1655045).
    Integer totalHydrogen = cdkAtom.getImplicitHydrogenCount();
    if (totalHydrogen != null) {
        if (container != null) {
            for (IBond iBond : container.getConnectedBondsList(cdkAtom)) {
                for (IAtom atom : iBond.atoms()) {
                    if (atom.getAtomicNumber() == IElement.H && !Objects.equals(atom, cdkAtom))
                        totalHydrogen++;
                }
            }
        }
        // else: it is the implicit hydrogen count
        cmlAtom.setHydrogenCount(totalHydrogen);
    }
    // else: don't report it, people can count the explicit Hs themselves
    Integer massNumber = cdkAtom.getMassNumber();
    if (!(cdkAtom instanceof IPseudoAtom)) {
        if (massNumber != null) {
            cmlAtom.setIsotopeNumber(massNumber);
        }
    }
    if (cdkAtom.getCharge() != CDKConstants.UNSET) {
        CMLScalar scalar = new CMLScalar();
        this.checkPrefix(scalar);
        // scalar.setDataType("xsd:float");
        scalar.setDictRef("cdk:partialCharge");
        scalar.setValue(cdkAtom.getCharge());
        cmlAtom.addScalar(scalar);
    }
    writeProperties(cdkAtom, cmlAtom);
    if (cdkAtom.getFlag(CDKConstants.ISAROMATIC)) {
        CMLScalar aromAtom = new CMLScalar();
        aromAtom.setDictRef("cdk:aromaticAtom");
        cmlAtom.appendChild(aromAtom);
    }
    for (String s : customizers.keySet()) {
        ICMLCustomizer customizer = customizers.get(s);
        try {
            customizer.customize(cdkAtom, cmlAtom);
        } catch (Exception exception) {
            logger.error("Error while customizing CML output with customizer: ", customizer.getClass().getName());
            logger.debug(exception);
        }
    }
    return cmlAtom;
}

Example 3 with CMLScalar

use of org.xmlcml.cml.element.CMLScalar in project cdk by cdk.

the class QSARCustomizer method createScalar.

private Element createScalar(IDescriptorResult value) {
    Element scalar;
    if (value instanceof DoubleResult) {
        scalar = new CMLScalar();
        scalar.addAttribute(new Attribute("dataType", "xsd:double"));
        scalar.appendChild("" + ((DoubleResult) value).doubleValue());
    } else if (value instanceof IntegerResult) {
        scalar = new CMLScalar();
        scalar.addAttribute(new Attribute("dataType", "xsd:int"));
        scalar.appendChild("" + ((IntegerResult) value).intValue());
    } else if (value instanceof BooleanResult) {
        scalar = new CMLScalar();
        scalar.addAttribute(new Attribute("dataType", "xsd:boolean"));
        scalar.appendChild("" + ((BooleanResult) value).booleanValue());
    } else if (value instanceof IntegerArrayResult) {
        IntegerArrayResult result = (IntegerArrayResult) value;
        scalar = new CMLArray();
        scalar.addAttribute(new Attribute("dataType", "xsd:int"));
        scalar.addAttribute(new Attribute("size", "" + result.length()));
        StringBuilder buffer = new StringBuilder();
        for (int i = 0; i < result.length(); i++) {
            buffer.append(result.get(i) + " ");
        }
        scalar.appendChild(buffer.toString());
    } else if (value instanceof DoubleArrayResult) {
        DoubleArrayResult result = (DoubleArrayResult) value;
        scalar = new CMLArray();
        scalar.addAttribute(new Attribute("dataType", "xsd:double"));
        scalar.addAttribute(new Attribute("size", "" + result.length()));
        StringBuilder buffer = new StringBuilder();
        for (int i = 0; i < result.length(); i++) {
            buffer.append(result.get(i) + " ");
        }
        scalar.appendChild(buffer.toString());
    } else {
        // logger.error("Could not convert this object to a scalar element: ", value);
        scalar = new CMLScalar();
        scalar.appendChild(value.toString());
    }
    return scalar;
}

Example 4 with CMLScalar

use of org.xmlcml.cml.element.CMLScalar in project cdk by cdk.

the class PDBAtomCustomizer method customize.

@Override
public void customize(IAtom atom, Object nodeToAdd) throws Exception {
    if (!(nodeToAdd instanceof Element))
        throw new CDKException("NodeToAdd must be of type nu.xom.Element!");
    Element element = (Element) nodeToAdd;
    if (atom instanceof IPDBAtom) {
        IPDBAtom pdbAtom = (IPDBAtom) atom;
        if (hasContent(pdbAtom.getAltLoc())) {
            CMLScalar scalar = new CMLScalar();
            scalar.addAttribute(new Attribute("dictRef", "pdb:altLoc"));
            scalar.appendChild(pdbAtom.getAltLoc());
            element.appendChild(scalar);
        }
        if (hasContent(pdbAtom.getChainID())) {
            Element scalar = new CMLScalar();
            scalar.addAttribute(new Attribute("dictRef", "pdb:chainID"));
            scalar.appendChild(pdbAtom.getChainID());
            element.appendChild(scalar);
        }
        {
            Element scalar = new CMLScalar();
            scalar.addAttribute(new Attribute("dictRef", "pdb:hetAtom"));
            scalar.appendChild("" + pdbAtom.getHetAtom());
            element.appendChild(scalar);
        }
        if (hasContent(pdbAtom.getICode())) {
            Element scalar = new CMLScalar();
            scalar.addAttribute(new Attribute("dictRef", "pdb:iCode"));
            scalar.appendChild(pdbAtom.getICode());
            element.appendChild(scalar);
        }
        if (hasContent(pdbAtom.getName())) {
            Element scalar = new Element("label");
            scalar.addAttribute(new Attribute("dictRef", "pdb:name"));
            scalar.appendChild(pdbAtom.getName());
            element.appendChild(scalar);
        }
        {
            Element scalar = new CMLScalar();
            scalar.addAttribute(new Attribute("dictRef", "pdb:oxt"));
            scalar.appendChild("" + pdbAtom.getOxt());
            element.appendChild(scalar);
        }
        if (hasContent(pdbAtom.getRecord())) {
            Element scalar = new CMLScalar();
            scalar.addAttribute(new Attribute("dictRef", "pdb:record"));
            scalar.appendChild(pdbAtom.getRecord());
            element.appendChild(scalar);
        }
        if (hasContent(pdbAtom.getResName())) {
            Element scalar = new CMLScalar();
            scalar.addAttribute(new Attribute("dictRef", "pdb:resName"));
            scalar.appendChild(pdbAtom.getResName());
            element.appendChild(scalar);
        }
        if (hasContent(pdbAtom.getResSeq())) {
            Element scalar = new CMLScalar();
            scalar.addAttribute(new Attribute("dictRef", "pdb:resSeq"));
            scalar.appendChild(pdbAtom.getResSeq());
            element.appendChild(scalar);
        }
        if (hasContent(pdbAtom.getSegID())) {
            Element scalar = new CMLScalar();
            scalar.addAttribute(new Attribute("dictRef", "pdb:segID"));
            scalar.appendChild(pdbAtom.getSegID());
            element.appendChild(scalar);
        }
        if (pdbAtom.getSerial() != 0) {
            Element scalar = new CMLScalar();
            scalar.addAttribute(new Attribute("dictRef", "pdb:serial"));
            scalar.appendChild("" + pdbAtom.getSerial());
            element.appendChild(scalar);
        }
        if (pdbAtom.getTempFactor() != -1.0) {
            Element scalar = new CMLScalar();
            scalar.addAttribute(new Attribute("dictRef", "pdb:tempFactor"));
            scalar.appendChild("" + pdbAtom.getTempFactor());
            element.appendChild(scalar);
        }
        element.addAttribute(new Attribute("occupancy", "" + pdbAtom.getOccupancy()));
        // remove isotope info
        Attribute isotopeInfo = element.getAttribute("isotopeNumber");
        if (isotopeInfo != null)
            element.removeAttribute(isotopeInfo);
    }
}

Example 5 with CMLScalar

use of org.xmlcml.cml.element.CMLScalar in project cdk by cdk.

the class MDMoleculeCustomizer method customize.

/**
 * Customize Molecule.
 */
@Override
public void customize(IAtomContainer molecule, Object nodeToAdd) throws Exception {
    if (!(nodeToAdd instanceof CMLMolecule))
        throw new CDKException("NodeToAdd must be of type nu.xom.Element!");
    // The nodeToAdd
    CMLMolecule molToCustomize = (CMLMolecule) nodeToAdd;
    if ((molecule instanceof MDMolecule)) {
        MDMolecule mdmol = (MDMolecule) molecule;
        molToCustomize.setConvention("md:mdMolecule");
        molToCustomize.addNamespaceDeclaration("md", "http://www.bioclipse.net/mdmolecule/");
        // Residues
        if (mdmol.getResidues().size() > 0) {
            for (Residue residue : mdmol.getResidues()) {
                int number = residue.getNumber();
                CMLMolecule resMol = new CMLMolecule();
                resMol.setDictRef("md:residue");
                resMol.setTitle(residue.getName());
                // Append resNo
                CMLScalar residueNumber = new CMLScalar(number);
                residueNumber.addAttribute(new Attribute("dictRef", "md:resNumber"));
                resMol.addScalar(residueNumber);
                // prefix for residue atom id
                String rprefix = "r" + number;
                // Append atoms
                CMLAtomArray ar = new CMLAtomArray();
                for (int i = 0; i < residue.getAtomCount(); i++) {
                    CMLAtom cmlAtom = new CMLAtom();
                    // System.out.println("atom ID: "+ residue.getAtom(i).getID());
                    // cmlAtom.addAttribute(new Attribute("ref", residue.getAtom(i).getID()));
                    // the next thing is better, but throws an exception
                    // 
                    // setRef to keep consistent usage
                    // setId to satisfy Jumbo 54. need for all atoms to have id
                    cmlAtom.setRef(residue.getAtom(i).getID());
                    cmlAtom.setId(rprefix + "_" + residue.getAtom(i).getID());
                    ar.addAtom(cmlAtom);
                }
                resMol.addAtomArray(ar);
                molToCustomize.appendChild(resMol);
            }
        }
        // Chargegroups
        if (mdmol.getChargeGroups().size() > 0) {
            for (ChargeGroup chargeGroup : mdmol.getChargeGroups()) {
                int number = chargeGroup.getNumber();
                // FIXME: persist the ChargeGroup
                CMLMolecule cgMol = new CMLMolecule();
                cgMol.setDictRef("md:chargeGroup");
                // etc: add name, refs to atoms etc
                // Append chgrpNo
                CMLScalar cgNo = new CMLScalar(number);
                cgNo.addAttribute(new Attribute("dictRef", "md:cgNumber"));
                cgMol.appendChild(cgNo);
                // prefix for residue atom id
                String cprefix = "cg" + number;
                // Append atoms from chargeGroup as it is an AC
                CMLAtomArray ar = new CMLAtomArray();
                for (int i = 0; i < chargeGroup.getAtomCount(); i++) {
                    CMLAtom cmlAtom = new CMLAtom();
                    // setRef to keep consistent usage
                    // setId to satisfy Jumbo 5.4 need for all atoms to have id
                    cmlAtom.setRef(chargeGroup.getAtom(i).getID());
                    cmlAtom.setId(cprefix + "_" + chargeGroup.getAtom(i).getID());
                    // Append switching atom?
                    if (chargeGroup.getAtom(i).equals(chargeGroup.getSwitchingAtom())) {
                        CMLScalar scalar = new CMLScalar();
                        scalar.setDictRef("md:switchingAtom");
                        cmlAtom.addScalar(scalar);
                    }
                    ar.addAtom(cmlAtom);
                }
                cgMol.addAtomArray(ar);
                molToCustomize.appendChild(cgMol);
            }
        }
    }
}