xlogpdescriptor.java

化学图形处理软件

                                }
                            }
                        }else if (bondCount == 3) {
                            // N sp3
                            if (hsCount == 0) {
                                //if (rs.contains(atomi)&&ringSize>3) {
                                if (atomi.getFlag(CDKConstants.ISAROMATIC)|| (rs.contains(atomi)&& ((Integer)atomi.getProperty(CDKConstants.PART_OF_RING_OF_SIZE)).intValue()>3 && getPiSystemsCount(ac,atomi)>=1)){
                                    if (getAtomTypeXCount(ac, atomi) == 0) {
                                        xlogP += 0.881;
                                        //logger.debug("XLOGP: 51		 0.881");
                                    } else {
                                        xlogP -= 0.01;
                                        //logger.debug("XLOGP: 53		-0.01");
                                    }
                                } else {
                                    if (getAtomTypeXCount(ac, atomi) == 0) {
                                        if (getPiSystemsCount(ac, atomi) == 0) {
                                            xlogP += 0.159;
                                            //logger.debug("XLOGP: 49		 0.159");
                                        }
                                        if (getPiSystemsCount(ac, atomi) > 0) {
                                            xlogP += 0.761;
                                            //logger.debug("XLOGP: 50		 0.761");
                                        }
                                    } else {
                                        xlogP -= 0.239;
                                        //logger.debug("XLOGP: 52		-0.239");
                                    }
                                }
                            }else if (hsCount == 1) {
                                if (getAtomTypeXCount(ac, atomi) == 0) {
//									like pyrrole
                                    if (atomi.getFlag(CDKConstants.ISAROMATIC)|| (rs.contains(atomi)&& ((Integer)atomi.getProperty(CDKConstants.PART_OF_RING_OF_SIZE)).intValue()>3 && getPiSystemsCount(ac,atomi)>=2)) {
                                        xlogP += 0.545;
                                        hBondDonors.add(new Integer(i));
                                        //logger.debug("XLOGP: 46		 0.545");
                                    } else {
                                        if (getPiSystemsCount(ac, atomi) == 0) {
                                            xlogP -= 0.112;
                                            hBondDonors.add(new Integer(i));
                                            //logger.debug("XLOGP: 44		-0.112");
                                        }
                                        if (getPiSystemsCount(ac, atomi) > 0) {
                                            xlogP += 0.166;
                                            hBondDonors.add(new Integer(i));
                                            //logger.debug("XLOGP: 45		 0.166");
                                        }
                                    }
                                } else {
                                    if (rs.contains(atomi)) {
                                        xlogP += 0.153;
                                        hBondDonors.add(new Integer(i));
                                        //logger.debug("XLOGP: 48		 0.153");
                                    } else {
                                        xlogP += 0.324;
                                        hBondDonors.add(new Integer(i));
                                        //logger.debug("XLOGP: 47		 0.324");
                                    }
                                }
                            }else if (hsCount == 2) {
                                if (getAtomTypeXCount(ac, atomi) == 0) {
                                    if (getPiSystemsCount(ac, atomi) == 0) {
                                        xlogP -= 0.534;
                                        hBondDonors.add(new Integer(i));
                                        //logger.debug("XLOGP: 41		-0.534");
                                    }
                                    if (getPiSystemsCount(ac, atomi) == 1) {
                                        xlogP -= 0.329;
                                        hBondDonors.add(new Integer(i));
                                        //logger.debug("XLOGP: 42		-0.329");
                                    }

                                    if (checkAminoAcid!=0){ checkAminoAcid+=1;}
                                } else {
                                    xlogP -= 1.082;
                                    hBondDonors.add(new Integer(i));
                                    //logger.debug("XLOGP: 43		-1.082");
                                }
                            }
                        }
                    }
                }
            }
            if (symbol.equals("O")) {
                if (bondCount == 1 && maxBondOrder==2.0) {
                    xlogP -= 0.399;
                    if (!getPresenceOfHydroxy(ac,atomi)){
                        hBondAcceptors.add(new Integer(i));
                    }
                    //logger.debug("XLOGP: 75	A=O	-0.399");
                }else if(bondCount == 1 && hsCount==0 && (getPresenceOfNitro(ac,atomi) || getPresenceOfCarbonil(ac,atomi)==1) || getPresenceOfSulfat(ac,atomi)){
                    xlogP -= 0.399;
                    if (!getPresenceOfHydroxy(ac,atomi)){
                        hBondAcceptors.add(new Integer(i));
                    }
                    //logger.debug("XLOGP: 75	A=O	-0.399");
                }else if (bondCount >= 1) {
                    if (hsCount == 0 && bondCount==2) {
                        if (getAtomTypeXCount(ac, atomi) == 0) {
                            if (getPiSystemsCount(ac, atomi) == 0) {
                                xlogP += 0.084;
                                //logger.debug("XLOGP: 72	R-O-R	 0.084");
                            }
                            if (getPiSystemsCount(ac, atomi) > 0) {
                                xlogP += 0.435;
                                //logger.debug("XLOGP: 73	R-O-R.1	 0.435");
                            }
                        }else if (getAtomTypeXCount(ac, atomi) == 1) {
                            xlogP += 0.105;
                            //logger.debug("XLOGP: 74	R-O-X	 0.105");
                        }
                    }else{
                        if (getAtomTypeXCount(ac, atomi) == 0) {
                            if (getPiSystemsCount(ac, atomi) == 0) {
                                xlogP -= 0.467;
                                hBondDonors.add(new Integer(i));
                                hBondAcceptors.add(new Integer(i));
                                //logger.debug("XLOGP: 69	R-OH	-0.467");
                            }
                            if (getPiSystemsCount(ac, atomi) == 1) {
                                xlogP += 0.082;
                                hBondDonors.add(new Integer(i));
                                hBondAcceptors.add(new Integer(i));
                                //logger.debug("XLOGP: 70	R-OH.1	 0.082");
                            }
                        }else if (getAtomTypeXCount(ac, atomi) == 1) {
                            xlogP -= 0.522;
                            hBondDonors.add(new Integer(i));
                            hBondAcceptors.add(new Integer(i));
                            //logger.debug("XLOGP: 71	X-OH	-0.522");
                        }
                    }
                }
            }
            if (symbol.equals("S")) {
                if ((bondCount == 1 && maxBondOrder==2) || (bondCount == 1 && atomi.getFormalCharge()==-1)) {
                    xlogP -= 0.148;
                    //logger.debug("XLOGP: 78	A=S	-0.148");
                }else if (bondCount == 2) {
                    if (hsCount == 0) {
                        xlogP += 0.255;
                        //logger.debug("XLOGP: 77	A-S-A	 0.255");
                    } else {
                        xlogP += 0.419;
                        //logger.debug("XLOGP: 76	A-SH	 0.419");
                    }
                }else if (bondCount == 3) {
                    if (getOxygenCount(ac, atomi) >= 1) {
                        xlogP -= 1.375;
                        //logger.debug("XLOGP: 79	A-SO-A	-1.375");
                    }
                }else if (bondCount == 4) {
                    if (getDoubleBondedOxygenCount(ac, atomi) >= 2) {
                        xlogP -= 0.168;
                        //logger.debug("XLOGP: 80	A-SO2-A	-0.168");
                    }
                }
            }
            if (symbol.equals("P")) {
                if (getDoubleBondedSulfurCount(ac, atomi) >= 1 && bondCount>=4) {
                    xlogP += 1.253;
                    //logger.debug("XLOGP: 82	S=PA3	 1.253");
                }else if (getOxygenCount(ac,atomi)>=1 || getDoubleBondedOxygenCount(ac, atomi) == 1 && bondCount>=4) {
                    xlogP -= 0.447;
                    //logger.debug("XLOGP: 81	O=PA3	-0.447");
                }
            }
            if (symbol.equals("F")) {
                if (getPiSystemsCount(ac, atomi) == 0) {
                    xlogP += 0.375;
                    //logger.debug("XLOGP: 83	F.0	 0.512");
                }else if (getPiSystemsCount(ac, atomi) == 1) {
                    xlogP += 0.202;
                    //logger.debug("XLOGP: 84	F.1	 0.202");
                }
            }
            if (symbol.equals("Cl")) {
                if (getPiSystemsCount(ac, atomi) == 0) {
                    xlogP += 0.512;
                    //logger.debug("XLOGP: 85	Cl.0	 0.512");
                }else if (getPiSystemsCount(ac, atomi) >= 1) {
                    xlogP += 0.663;
                    //logger.debug("XLOGP: 86	Cl.1	 0.663");
                }
            }
            if (symbol.equals("Br")) {
                if (getPiSystemsCount(ac, atomi) == 0) {
                    xlogP += 0.85;
                    //logger.debug("XLOGP: 87	Br.0	 0.85");
                }else if (getPiSystemsCount(ac, atomi) == 1) {
                    xlogP += 0.839;
                    //logger.debug("XLOGP: 88	Br.1	 0.839");
                }
            }
            if (symbol.equals("I")) {
                if (getPiSystemsCount(ac, atomi) == 0) {
                    xlogP += 1.05;
                    //logger.debug("XLOGP: 89	I.0	 1.05");
                }else if (getPiSystemsCount(ac, atomi) == 1) {
                    xlogP += 1.109;
                    //logger.debug("XLOGP: 90	I.1	 1.109");
                }
            }

//			Halogen pair 1-3
            int halcount=getHalogenCount(ac, atomi);
            if ( halcount== 2) {
                xlogP += 0.137;
                //logger.debug("XLOGP: Halogen 1-3 pair	 0.137");
            }else if (halcount==3){
                xlogP += (3*0.137);
                //logger.debug("XLOGP: Halogen 1-3 pair	 0.411");
            }else if (halcount==4){
                xlogP += (6*0.137);
                //logger.debug("XLOGP: Halogen 1-3 pair	 1.902");
            }

//			sp2 Oxygen 1-5 pair
            if (getPresenceOfCarbonil(ac, atomi) == 2) {// sp2 oxygen 1-5 pair
                if(!rs.contains(atomi)) {
                    xlogP += 0.580;
                    //logger.debug("XLOGP: sp2 Oxygen 1-5 pair	 0.580");
                }
            }
        }
        //logger.debug("XLOGP: Before Correction:"+xlogP);
        List path=null;
        SimpleGraph moleculeGraph=null;
        int [][] pairCheck=null;
//		//logger.debug("Acceptors:"+hBondAcceptors.size()+" Donors:"+hBondDonors.size());
        if (hBondAcceptors.size()>0 && hBondDonors.size()>0){
            moleculeGraph=MoleculeGraphs.getMoleculeGraph(ac);
            pairCheck=initializeHydrogenPairCheck(new int[atomCount][atomCount]);
        }
        for (int i=0; i<hBondAcceptors.size();i++){
            for (int j=0; j<hBondDonors.size();j++){
                if (checkRingLink(rs,ac,ac.getAtom(((Integer)hBondAcceptors.get(i)).intValue())) || checkRingLink(rs,ac,ac.getAtom(((Integer)hBondDonors.get(j)).intValue()))){
                    path=BFSShortestPath.findPathBetween(moleculeGraph,ac.getAtom(((Integer)hBondAcceptors.get(i)).intValue()), ac.getAtom(((Integer)hBondDonors.get(j)).intValue()));
//					//logger.debug(" Acc:"+checkRingLink(rs,ac,atoms[((Integer)hBondAcceptors.get(i)).intValue()])
//					+" S:"+atoms[((Integer)hBondAcceptors.get(i)).intValue()].getSymbol()
//					+" Nr:"+((Integer)hBondAcceptors.get(i)).intValue()
//					+" Don:"+checkRingLink(rs,ac,atoms[((Integer)hBondDonors.get(j)).intValue()])
//					+" S:"+atoms[((Integer)hBondDonors.get(j)).intValue()].getSymbol()
//					+" Nr:"+((Integer)hBondDonors.get(j)).intValue()
//					+" i:"+i+" j:"+j+" path:"+path.size());
                    if (checkRingLink(rs,ac,ac.getAtom(((Integer)hBondAcceptors.get(i)).intValue())) && checkRingLink(rs,ac,ac.getAtom(((Integer)hBondDonors.get(j)).intValue()))){
                        if (path.size()==3 && pairCheck[((Integer)hBondAcceptors.get(i)).intValue()][((Integer)hBondDonors.get(j)).intValue()]==0){
                            xlogP += 0.429;
                            pairCheck[((Integer)hBondAcceptors.get(i)).intValue()][((Integer)hBondDonors.get(j)).intValue()]=1;
                            pairCheck[((Integer)hBondDonors.get(j)).intValue()][((Integer)hBondAcceptors.get(i)).intValue()]=1;
                            //logger.debug("XLOGP: Internal HBonds 1-4	 0.429");
                        }
                    }else{
                        if (path.size()==4 && pairCheck[((Integer)hBondAcceptors.get(i)).intValue()][((Integer)hBondDonors.get(j)).intValue()]==0){
                            xlogP += 0.429;
                            pairCheck[((Integer)hBondAcceptors.get(i)).intValue()][((Integer)hBondDonors.get(j)).intValue()]=1;
                            pairCheck[((Integer)hBondDonors.get(j)).intValue()][((Integer)hBondAcceptors.get(i)).intValue()]=1;
                            //logger.debug("XLOGP: Internal HBonds 1-5	 0.429");
                        }
                    }
                }
            }
        }

        if (checkAminoAcid>1){
//			alpha amino acid
            QueryAtomContainer aminoAcid =
                QueryAtomContainerCreator.createBasicQueryContainer(
                        createAminoAcid(ac.getBuilder())
                );

            Iterator bonds = aminoAcid.bonds();
            IAtom bondAtom0=null;
            IAtom bondAtom1=null;
            while (bonds.hasNext()) {
                IBond bond = (IBond) bonds.next();
                bondAtom0=bond.getAtom(0);
                bondAtom1=bond.getAtom(1);
                if ((bondAtom0.getSymbol().equals("C") && bondAtom1.getSymbol().equals("N")) || (bondAtom0.getSymbol().equals("N") && bondAtom1.getSymbol().equals("C"))&& bond.getOrder()==1){
                    aminoAcid.removeBond(bondAtom0,bondAtom1);
                    aminoAcid.addBond(new AnyOrderQueryBond((IQueryAtom)bondAtom0,(IQueryAtom)bondAtom1,1));
                    break;
                }
            }