xlogpdescriptor.java

化学图形处理软件

            IAtom neighbour = (IAtom)neighbours.get(i);
            if (neighbour.getSymbol().equals("O")) {
                bond = ac.getBond(neighbour, atom);
                if (chargeFlag && neighbour.getFormalCharge()==-1 && bond.getOrder() ==1){
                    odbcounter += 1;
                }
                if (!neighbour.getFlag(CDKConstants.ISAROMATIC)) {
                    if (bond.getOrder() == 2.0) {
                        odbcounter += 1;
                    }
                }
            }
        }
        return odbcounter;
    }


    /**
     *  Gets the doubleBondedSulfurCount attribute of the XLogPDescriptor object.
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The doubleBondedSulfurCount value
     */
    private int getDoubleBondedSulfurCount(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List neighbours = ac.getConnectedAtomsList(atom);
        IBond bond = null;
        int sdbcounter = 0;
        for (int i = 0; i < neighbours.size(); i++) {
            IAtom neighbour = (IAtom)neighbours.get(i);
            if (neighbour.getSymbol().equals("S")) {
                if (atom.getFormalCharge()==1 && neighbour.getFormalCharge()==-1){
                    sdbcounter+=1;
                }
                bond = ac.getBond(neighbour, atom);
                if (!neighbour.getFlag(CDKConstants.ISAROMATIC)) {
                    if (bond.getOrder() == 2.0) {
                        sdbcounter += 1;
                    }
                }
            }
        }
        return sdbcounter;
    }


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


    /**
     *  Gets the aromaticNitrogensCount attribute of the XLogPDescriptor object.
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The aromaticNitrogensCount value
     */
    private int getAromaticNitrogensCount(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List neighbours = ac.getConnectedAtomsList(atom);
        int narocounter = 0;
        for (int i = 0; i < neighbours.size(); i++) {
            IAtom neighbour = (IAtom)neighbours.get(i);
            if (neighbour.getSymbol().equals("N") && ((Boolean)neighbour.getProperty("IS_IN_AROMATIC_RING")).booleanValue()) {
                        narocounter += 1;
            }
        }
        return narocounter;
    }



    // a piSystem is a double or triple or aromatic bond:
    /**
     *  Gets the piSystemsCount attribute of the XLogPDescriptor object.
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The piSystemsCount value
     */
    private int getPiSystemsCount(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List neighbours = ac.getConnectedAtomsList(atom);
        int picounter = 0;
        java.util.List bonds=null;
        for (int i = 0; i < neighbours.size(); i++) {
            IAtom neighbour = (IAtom)neighbours.get(i);
            bonds = ac.getConnectedBondsList(neighbour);
            for (int j = 0; j < bonds.size(); j++) {
                IBond bond = (IBond)bonds.get(j);
                if (bond.getOrder()>1.0 && bond.getConnectedAtom(neighbour)!=atom
                        && !neighbour.getSymbol().equals("P")
                        && !neighbour.getSymbol().equals("S")){
                    picounter += 1;
                }/*else if (bonds[j].getConnectedAtom(neighbours[i])!=atom
						&& !neighbours[i].getSymbol().equals("P")
						&& !neighbours[i].getSymbol().equals("S") && bonds[j].getConnectedAtom(neighbours[i]).getFlag(CDKConstants.ISAROMATIC)){
					picounter += 1;
				}*/
            }
        }
        return picounter;
    }

    /**
     *  Gets the presenceOf Hydroxy group attribute of the XLogPDescriptor object.
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The presenceOfCarbonil value
     */
    private boolean getPresenceOfHydroxy(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        IAtom neighbour0 = (IAtom)ac.getConnectedAtomsList(atom).get(0);
        java.util.List first = null;
        if (neighbour0.getSymbol().equals("C")) {
            first = ac.getConnectedAtomsList(neighbour0);
            for (int i = 0; i < first.size(); i++) {
                IAtom conAtom = (IAtom)first.get(i);
                if (conAtom.getSymbol().equals("O")) {
                    if(ac.getBond(neighbour0, conAtom).getOrder()==1){
                        if (ac.getConnectedBondsCount(conAtom)>1 && getHydrogenCount(ac,conAtom)==0){
                            return false;
                        }else{
                            return true;
                        }
                    }
                }
            }
        }
        return false;
    }


    /**
     *  Gets the presenceOfN=O attribute of the XLogPDescriptor object.
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The presenceOfNitor [boolean]
     */
    private boolean getPresenceOfNitro(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List neighbours = ac.getConnectedAtomsList(atom);
        java.util.List second = null;
        IBond bond = null;
        //int counter = 0;
        for (int i = 0; i < neighbours.size(); i++) {
            IAtom neighbour = (IAtom)neighbours.get(i);
            if (neighbour.getSymbol().equals("N")) {
                second = ac.getConnectedAtomsList(neighbour);
                for (int b = 0; b < second.size(); b++) {
                    IAtom conAtom = (IAtom)second.get(b);
                    if (conAtom.getSymbol().equals("O")) {
                        bond = ac.getBond(neighbour, conAtom);
                        if (bond.getOrder() == 2.0) {
                            return true;
                        }
                    }
                }
            }
        }
        return false;
    }

    /**
     *  Gets the presenceOfSulfat A-S(O2)-A attribute of the XLogPDescriptor object.
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The presenceOfSulfat [boolean]
     */
    private boolean getPresenceOfSulfat(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List neighbours = ac.getConnectedAtomsList(atom);
        //org.openscience.cdk.interfaces.IAtom[] second = null;
        //IBond bond = null;
        //int counter = 0;
        for (int i = 0; i < neighbours.size(); i++) {
            IAtom neighbour = (IAtom)neighbours.get(i);
            if (neighbour.getSymbol().equals("S") && getOxygenCount(ac,neighbour)>=2 && ac.getConnectedBondsCount(neighbour)==4){
                return true;
            }
        }
        return false;
    }

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


    /**
     *  Gets the ifCarbonIsHydrophobic attribute of the XLogPDescriptor object.
     *  C must be sp2 or sp3 and, for all distances C-1-2-3 only C atoms are permitted
     *
     *@param  ac    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The ifCarbonIsHydrophobic value
     */
    private boolean getIfCarbonIsHydrophobic(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List first = ac.getConnectedAtomsList(atom);
        java.util.List second = null;
        java.util.List third = null;
        //org.openscience.cdk.interfaces.IAtom[] fourth = null;
        if (first.size() > 0) {
            for (int i = 0; i < first.size(); i++) {
                IAtom firstAtom = (IAtom)first.get(i);
                if (firstAtom.getSymbol().equals("C") || firstAtom.getSymbol().equals("H")) {
                } else {
                    return false;
                }
                second = ac.getConnectedAtomsList(firstAtom);
                if (second.size() > 0) {
                    for (int b = 0; b < second.size(); b++) {
                        IAtom secondAtom = (IAtom)second.get(b);
                        if (secondAtom.getSymbol().equals("C") || secondAtom.getSymbol().equals("H")) {
                        } else {
                            return false;
                        }
                        third = ac.getConnectedAtomsList(secondAtom);
                        if (third.size() > 0) {
                            for (int c = 0; c < third.size(); c++) {
                                IAtom thirdAtom = (IAtom)third.get(c);
                                if (thirdAtom.getSymbol().equals("C") || thirdAtom.getSymbol().equals("H")) {
                                } else {
                                    return false;
                                }
                                //fourth = ac.getConnectedAtoms(third[c]);
                                //if (fourth.length > 0) {
                                //	for (int d = 0; d < fourth.length; d++) {
                                //		if (fourth[d].getSymbol().equals("C") || fourth[d].getSymbol().equals("H")) {
                                //		} else {
                                //			return false;
                                //		}
                                //	}
                                //} else {
                                //	return false;