xlogpdescriptor.java

化学图形处理软件

            //AtomContainer aminoacid = sp.parseSmiles("NCC(=O)O");
            if (UniversalIsomorphismTester.isSubgraph((org.openscience.cdk.AtomContainer)ac, aminoAcid)) {
                List list = UniversalIsomorphismTester.getSubgraphAtomsMap((org.openscience.cdk.AtomContainer)ac, aminoAcid);
                RMap map = null;
                IAtom atom1=null;
                for (int j = 0; j < list.size(); j++){
                    map = (RMap) list.get(j);
                    atom1 = ac.getAtom(map.getId1());
                    if (atom1.getSymbol().equals("O")&& ac.getMaximumBondOrder(atom1)==1){
                        if (ac.getConnectedBondsCount(atom1)==2 && getHydrogenCount(ac, atom1)==0){
                        }else{
                            xlogP -= 2.166;
                            //logger.debug("XLOGP: alpha amino acid	-2.166");
                            break;
                        }
                    }
                }
            }
        }

        IAtomContainer paba = createPaba(ac.getBuilder());
        // p-amino sulphonic acid
        if (UniversalIsomorphismTester.isSubgraph((org.openscience.cdk.AtomContainer)ac, paba)) {
            xlogP -= 0.501;
            //logger.debug("XLOGP: p-amino sulphonic acid	-0.501");
        }


        // salicylic acid
        if (salicylFlag){
            IAtomContainer salicilic = createSalicylicAcid(ac.getBuilder());
            if (UniversalIsomorphismTester.isSubgraph((org.openscience.cdk.AtomContainer)ac, salicilic)) {
                xlogP += 0.554;
                //logger.debug("XLOGP: salicylic acid	 0.554");
            }
        }


//		 ortho oxygen pair
        //AtomContainer orthopair = sp.parseSmiles("OCCO");
        QueryAtomContainer orthopair=new QueryAtomContainer();
        AromaticAtom atom1=new AromaticAtom();
        atom1.setSymbol("C");
        AromaticAtom atom2=new AromaticAtom();
        atom2.setSymbol("C");
        SymbolQueryAtom atom3=new SymbolQueryAtom();
        atom3.setSymbol("O");
        SymbolQueryAtom atom4=new SymbolQueryAtom();
        atom4.setSymbol("O");
        orthopair.addBond(new AromaticQueryBond(atom1,atom2,1.5));
        orthopair.addBond(new OrderQueryBond(atom1,atom3,1));
        orthopair.addBond(new OrderQueryBond(atom2,atom4,1));

        if (UniversalIsomorphismTester.isSubgraph((org.openscience.cdk.AtomContainer)ac, orthopair)) {
            xlogP -= 0.268;
            //logger.debug("XLOGP: Ortho oxygen pair	-0.268");
        }

        return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
                new DoubleResult(xlogP), new String[] {"XLogP"});
    }

    /**
     * Returns the specific type of the DescriptorResult object.
     * <p/>
     * The return value from this method really indicates what type of result will
     * be obtained from the {@link org.openscience.cdk.qsar.DescriptorValue} object. Note that the same result
     * can be achieved by interrogating the {@link org.openscience.cdk.qsar.DescriptorValue} object; this method
     * allows you to do the same thing, without actually calculating the descriptor.
     *
     * @return an object that implements the {@link org.openscience.cdk.qsar.result.IDescriptorResult} interface indicating
     *         the actual type of values returned by the descriptor in the {@link org.openscience.cdk.qsar.DescriptorValue} object
     */
    public IDescriptorResult getDescriptorResultType() {
        return new DoubleResult(0.0);
    }

    /**
     * Method initialise the HydrogenpairCheck with a value
     *
     * @param pairCheck value
     * @return void
     */
    public int[][] initializeHydrogenPairCheck(int [][] pairCheck) {
        for (int i = 0; i < pairCheck.length; i++) {
            for (int j = 0; j < pairCheck[0].length; j++) {
                    pairCheck[i][j] = 0;
            }
        }
        return pairCheck;
    }


    /**
     *  Check if atom or neighbour atom is part of a ring
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The hydrogenCount value
     */
    private boolean checkRingLink(IRingSet ringSet, org.openscience.cdk.interfaces.IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List neighbours = ac.getConnectedAtomsList(atom);
        if (ringSet.contains(atom)){
            return true;
        }
        for (int i = 0; i < neighbours.size(); i++) {
            IAtom neighbour = (IAtom)neighbours.get(i);
            if (ringSet.contains(neighbour)) {
                return true;
            }
        }
        return false;
    }



    /**
     *  Gets the hydrogenCount attribute of the XLogPDescriptor object.
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The hydrogenCount value
     */
    private int getHydrogenCount(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List neighbours = ac.getConnectedAtomsList(atom);
        int hcounter = 0;
        for (int i = 0; i < neighbours.size(); i++) {
            IAtom neighbour = (IAtom)neighbours.get(i);
            if (neighbour.getSymbol().equals("H")) {
                hcounter += 1;
            }
        }
        return hcounter;
    }


    /**
     *  Gets the HalogenCount attribute of the XLogPDescriptor object.
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The alogenCount value
     */
    private int getHalogenCount(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List neighbours = ac.getConnectedAtomsList(atom);
        int acounter = 0;
        for (int i = 0; i < neighbours.size(); i++) {
            IAtom neighbour = (IAtom)neighbours.get(i);
            if (neighbour.getSymbol().equals("F") || neighbour.getSymbol().equals("I") || neighbour.getSymbol().equals("Cl") || neighbour.getSymbol().equals("Br")) {
                acounter += 1;
            }
        }
        return acounter;
    }

    /**
     *  Gets the atomType X Count attribute of the XLogPDescriptor object.
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The nitrogenOrOxygenCount value
     */
    private int getAtomTypeXCount(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List neighbours = ac.getConnectedAtomsList(atom);
        int nocounter = 0;
        IBond bond=null;
        for (int i = 0; i < neighbours.size(); i++) {
            IAtom neighbour = (IAtom)neighbours.get(i);
            if ((neighbour.getSymbol().equals("N") || neighbour.getSymbol().equals("O")) && !((Boolean)neighbour.getProperty("IS_IN_AROMATIC_RING")).booleanValue()) {
                //if (ac.getMaximumBondOrder(neighbours[i]) == 1.0) {
                bond = ac.getBond(neighbour, atom);
                if (bond.getOrder() != 2.0) {
                    nocounter += 1;
                }
            }
        }
        return nocounter;
    }


    /**
     *  Gets the aromaticCarbonsCount attribute of the XLogPDescriptor object.
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The aromaticCarbonsCount value
     */
    private int getAromaticCarbonsCount(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List neighbours = ac.getConnectedAtomsList(atom);
        int carocounter = 0;
        for (int i = 0; i < neighbours.size(); i++) {
            IAtom neighbour = (IAtom)neighbours.get(i);
            if (neighbour.getSymbol().equals("C") && neighbour.getFlag(CDKConstants.ISAROMATIC)) {
                carocounter += 1;
            }
        }
        return carocounter;
    }


    /**
     *  Gets the carbonsCount attribute of the XLogPDescriptor object.
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The carbonsCount value
     */
    private int getCarbonsCount(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List neighbours = ac.getConnectedAtomsList(atom);
        int ccounter = 0;
        for (int i = 0; i < neighbours.size(); i++) {
            IAtom neighbour = (IAtom)neighbours.get(i);
            if (neighbour.getSymbol().equals("C")) {
                if (!neighbour.getFlag(CDKConstants.ISAROMATIC)) {
                    ccounter += 1;
                }
            }
        }
        return ccounter;
    }

    /**
     *  Gets the oxygenCount attribute of the XLogPDescriptor object.
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The carbonsCount value
     */
    private int getOxygenCount(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List neighbours = ac.getConnectedAtomsList(atom);
        int ocounter = 0;
        for (int i = 0; i < neighbours.size(); i++) {
            IAtom neighbour = (IAtom)neighbours.get(i);
            if (neighbour.getSymbol().equals("O")) {
                if (!neighbour.getFlag(CDKConstants.ISAROMATIC)) {
                    ocounter += 1;
                }
            }
        }
        return ocounter;
    }


    /**
     *  Gets the doubleBondedCarbonsCount attribute of the XLogPDescriptor object.
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The doubleBondedCarbonsCount value
     */
    private int getDoubleBondedCarbonsCount(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List neighbours = ac.getConnectedAtomsList(atom);
        IBond bond = null;
        int cdbcounter = 0;
        for (int i = 0; i < neighbours.size(); i++) {
            IAtom neighbour = (IAtom)neighbours.get(i);
            if (neighbour.getSymbol().equals("C")) {
                bond = ac.getBond(neighbour, atom);
                if (bond.getOrder() == 2.0) {
                    cdbcounter += 1;
                }
            }
        }
        return cdbcounter;
    }


    /**
     *  Gets the doubleBondedOxygenCount attribute of the XLogPDescriptor object.
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The doubleBondedOxygenCount value
     */
    private int getDoubleBondedOxygenCount(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List neighbours = ac.getConnectedAtomsList(atom);
        IBond bond = null;
        int odbcounter = 0;
        boolean chargeFlag=false;
        if (atom.getFormalCharge()>=1){
            chargeFlag=true;
        }
        for (int i = 0; i < neighbours.size(); i++) {