alogp.java

化学图形处理软件

		}

		if (hybrid.equals("sp3") && OxNum == 1) {
			frags[86]++;
			alogpfrag[i] = 86;
		} else if (hybrid.equals("sp3") && OxNum == 2) {
			frags[87]++;
			alogpfrag[i] = 87;
		} else if (hybrid.equals("sp3") && OxNum == 3) {
			frags[88]++;
			alogpfrag[i] = 88;
		} else if (hybrid.equals("sp2") && OxNum == 1) {
			frags[89]++;
			alogpfrag[i] = 89;
		} else if ((hybrid.equals("sp2") && OxNum > 1)
				|| (hybrid.equals("sp") && OxNum >= 1)
				|| (hybrid.equals("sp3") && OxNum == 4)
				|| !ca0.getSymbol().equals("C")) {
			frags[90]++;
			alogpfrag[i] = 90;
		}

	}

	private void calcGroup091_to_095(int i) {

		if (!fragment[i].equals("SsBr"))
			return;

		java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
		IAtom ca0 = (IAtom)ca.get(0);
		
		java.util.List bonds = atomContainer.getConnectedBondsList(ca0);

		int doublebondcount = 0;
		int triplebondcount = 0;

		String hybrid = "";

		for (int j = 0; j <= bonds.size() - 1; j++) {
			IBond bj = (IBond)bonds.get(j);
			if (bj.getOrder() == 2) {
				doublebondcount++;
			}

			if (bj.getOrder() == 3) {
				triplebondcount++;
			}

		}

		if (doublebondcount == 0 && triplebondcount == 0) {
			hybrid = "sp3";
		} else if (doublebondcount == 1) {
			hybrid = "sp2";
		} else if (doublebondcount == 2 || triplebondcount == 1) {
			hybrid = "sp";
		}

		java.util.List ca2 = atomContainer.getConnectedAtomsList(ca0);

		int OxNum = 0;

		for (int j = 0; j <= ca2.size() - 1; j++) {
			IAtom ca2j = (IAtom)ca2.get(j);
			String s = ca2j.getSymbol();

			// // F,O,Cl,Br,N

			// if (s.equals("F") || s.equals("O") || s.equals("Cl")
			// || s.equals("Br") || s.equals("N") || s.equals("S"))

			if (ap.getNormalizedElectronegativity(ca2j.getSymbol()) > 1) {
				OxNum += atomContainer.getBond(ca0, ca2j).getOrder();
			}

		}

		if (hybrid.equals("sp3") && OxNum == 1) {
			frags[91]++;
			alogpfrag[i] = 91;
		} else if (hybrid.equals("sp3") && OxNum == 2) {
			frags[92]++;
			alogpfrag[i] = 92;
		} else if (hybrid.equals("sp3") && OxNum == 3) {
			frags[93]++;
			alogpfrag[i] = 93;
		} else if (hybrid.equals("sp2") && OxNum == 1) {
			frags[94]++;
			alogpfrag[i] = 94;
		} else if ((hybrid.equals("sp2") && OxNum > 1)
				|| (hybrid.equals("sp") && OxNum >= 1)
				|| (hybrid.equals("sp3") && OxNum == 4)
				|| !ca0.getSymbol().equals("C")) {
			frags[95]++;
			alogpfrag[i] = 95;
		}

	}

	private void calcGroup096_to_100(int i) {

		if (!fragment[i].equals("SsI"))
			return;

		java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
		IAtom ca0 = (IAtom)ca.get(0);
		
		java.util.List bonds = atomContainer.getConnectedBondsList(ca0);

		int doublebondcount = 0;
		int triplebondcount = 0;

		String hybrid = "";

		for (int j = 0; j <= bonds.size() - 1; j++) {
			IBond bj = (IBond)bonds.get(j);
			if (bj.getOrder() == 2) {
				doublebondcount++;
			}

			else if (bj.getOrder() == 3) {
				triplebondcount++;
			}

		}

		if (doublebondcount == 0 && triplebondcount == 0) {
			hybrid = "sp3";
		} else if (doublebondcount == 1) {
			hybrid = "sp2";
		} else if (doublebondcount == 2 || triplebondcount == 1) {
			hybrid = "sp";
		}

		java.util.List ca2 = atomContainer.getConnectedAtomsList(ca0);

		int OxNum = 0;

		for (int j = 0; j <= ca2.size() - 1; j++) {
			IAtom ca2j = (IAtom)ca2.get(j);
			String s = ca2j.getSymbol();

			// // F,O,Cl,Br,N

			// if (s.equals("F") || s.equals("O") || s.equals("Cl")
			// || s.equals("Br") || s.equals("N") || s.equals("S"))

			if (ap.getNormalizedElectronegativity(ca2j.getSymbol()) > 1) {
				OxNum += atomContainer.getBond(ca0, ca2j).getOrder();
			}

		}

		if (hybrid.equals("sp3") && OxNum == 1) {
			frags[96]++;
			alogpfrag[i] = 96;
		} else if (hybrid.equals("sp3") && OxNum == 2) {
			frags[97]++;
			alogpfrag[i] = 97;
		} else if (hybrid.equals("sp3") && OxNum == 3) {
			frags[98]++;
			alogpfrag[i] = 98;
		} else if (hybrid.equals("sp2") && OxNum == 1) {
			frags[99]++;
			alogpfrag[i] = 99;
		} else if ((hybrid.equals("sp2") && OxNum > 1)
				|| (hybrid.equals("sp") && OxNum >= 1)
				|| (hybrid.equals("sp3") && OxNum == 4)
				|| !ca0.getSymbol().equals("C")) {
			frags[100]++;
			alogpfrag[i] = 100;
		}

	}

	private void calcGroup101_to_104(int i) {
		IAtom ai = atomContainer.getAtom(i);
		String s = ai.getSymbol();

		if (ai.getFormalCharge() == -1) {
			if (s.equals("F")) {
				frags[101]++;
				alogpfrag[i] = 101;
			} else if (s.equals("Cl")) {
				frags[102]++;
				alogpfrag[i] = 102;
			} else if (s.equals("Br")) {
				frags[103]++;
				alogpfrag[i] = 103;
			} else if (s.equals("I")) {
				frags[104]++;
				alogpfrag[i] = 104;
			}

		}

	}

	private void calcGroup106(int i) {

		// S in SH
		if (fragment[i].equals("SsSH")) {
			frags[106]++;
			alogpfrag[i] = 106;
		}
	}

	private void calcGroup107(int i) {

		// S in R2S, RS-SR
		// R = any group linked through C
		// if (!Fragment[i].equals("SssS")) return;

		// In ALOGP, for malathion PSC is consider to have group 107 (even
		// though has P instead of R)
		
		// for lack of fragment, use this fragment for SaaS
		
		if (fragment[i].equals("SssS") || fragment[i].equals("SaaS")) {
			frags[107]++;
			alogpfrag[i] = 107;
		}

		// IAtom [] ca=atomContainer.getConnectedAtoms(atomContainer.getAtomAt(i));
		//		
		// if ((ca[0].getSymbol().equals("C") && ca[1].getSymbol().equals("C"))
		// ||
		// (ca[0].getSymbol().equals("C") && ca[1].getSymbol().equals("S")) ||
		// (ca[0].getSymbol().equals("S") && ca[1].getSymbol().equals("C"))) {
		// frags[107]++;
		// alogpfrag[i]=107;
		// }

	}

	private void calcGroup108(int i) {

		// S in R=S

		// In ALOGP, for malathion P=S is consider to have group 108 (even
		// though has P instead of R)
		if (fragment[i].equals("SdS")) {
			frags[108]++;
			alogpfrag[i] = 108;
		}		

	}
	
	private void calcGroup109(int i) {
		
		// for now S in O-S(=O)-O is assigned to this group
		// (it doesn't check which atoms are singly bonded to S 
		if (!fragment[i].equals("SdssS")) return;
		
		
		java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
		IAtom ai = atomContainer.getAtom(i);
		int SdOCount=0;
		int SsCCount=0;
		
		for (int j = 0; j <= ca.size() - 1; j++) {
			if (atomContainer.getBond(ai, ((IAtom)ca.get(j))).getOrder() == 1) {
				if (((IAtom)ca.get(j)).getSymbol().equals("C")) {
					SsCCount++;		
				}
			} else if (atomContainer.getBond(ai, ((IAtom)ca.get(j))).getOrder() == 2) {
				if (((IAtom)ca.get(j)).getSymbol().equals("O")) {
					SdOCount++;
				}
			}
		}
		if (SdOCount==1) { // for now dont check if SsCCount==2
			frags[109]++;
			alogpfrag[i] = 109;
		}
	}
	
	private void calcGroup110(int i) {
		if (!fragment[i].equals("SddssS"))
			return;
		
		java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
		IAtom ai = atomContainer.getAtom(i);
		int SdOCount=0;
		int SsCCount=0;
		
		for (int j = 0; j <= ca.size() - 1; j++) {
			if (atomContainer.getBond(ai, ((IAtom)ca.get(j))).getOrder() == 1) {
				if (((IAtom)ca.get(j)).getSymbol().equals("C")) {
					SsCCount++;		
				}
			} else if (atomContainer.getBond(ai, ((IAtom)ca.get(j))).getOrder() == 2) {
				if (((IAtom)ca.get(j)).getSymbol().equals("O")) {
					SdOCount++;
				}
			}
		}
		if (SdOCount==2) { // for now dont check if SsCCount==2
			frags[110]++;
			alogpfrag[i] = 110;
		}
		
	}
	
	private void calcGroup111(int i) {
		if (fragment[i].equals("SssssSi")) {
			frags[111]++;
			alogpfrag[i] = 111;			
		}
	}
	
	private void calcGroup116_117_120(int i) {

		// S in R=S

		java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
		IAtom ai = atomContainer.getAtom(i);
		
		int XCount=0;
		int RCount=0;
		boolean PdX=false;

		if (!fragment[i].equals("SdsssP")) return;
		
		for (int j = 0; j <= ca.size() - 1; j++) {
			if (atomContainer.getBond(ai, ((IAtom)ca.get(j))).getOrder() == 1) {
				if (((IAtom)ca.get(j)).getSymbol().equals("C")) {
					RCount++;
				} else {
					XCount++;
				}
			} else if (atomContainer.getBond(ai, ((IAtom)ca.get(j))).getOrder() == 2) {
				if (!((IAtom)ca.get(j)).getSymbol().equals("C")) {
					PdX=true;
				}
			}
		}
		
		if (PdX) {
			if (RCount == 3) {
				frags[116]++;
				alogpfrag[i] = 116;
			} else if (XCount == 3) {
				frags[117]++;
				alogpfrag[i] = 117;
			} else if (XCount == 2 && RCount == 1) {
				frags[120]++;
				alogpfrag[i] = 120;
			}
		}

	}
	private void calcGroup118_119(int i) {
		if (!fragment[i].equals("SsssP")) return;
	
		java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
		IAtom ai = atomContainer.getAtom(i);
		int XCount=0;
		int RCount=0;

		for (int j = 0; j <= ca.size() - 1; j++) {
			if (atomContainer.getBond(ai, ((IAtom)ca.get(j))).getOrder() == 1) {
				if (((IAtom)ca.get(j)).getSymbol().equals("C")) {
					RCount++;
				} else {
					XCount++;
				}
			}
		}
		
		if (XCount==3) {
			frags[118]++;
			alogpfrag[i] = 118;			
		} else if (RCount==3) {
			frags[119]++;
			alogpfrag[i] = 119;
		}

		
	}

	public boolean inSameAromaticRing(IAtomContainer atomContainer, IAtom atom1,
			IAtom atom2, IRingSet rs) {
		boolean SameRing = false;
		
		for (int i = 0; i <= rs.getAtomContainerCount() - 1; i++) {
			IRing r = (IRing)rs.getAtomContainer(i);
			
			if (!r.getFlag(CDKConstants.ISAROMATIC))
				continue;
			
			// ArrayList al=new ArrayList();
			
			boolean HaveOne = false;
			boolean HaveTwo = false;
			
			for (int j = 0; j <= r.getAtomCount() - 1; j++) {
				if (atomContainer.getAtomNumber(r.getAtom(j)) == atomContainer.getAtomNumber(atom1))
					HaveOne = true;
				if (atomContainer.getAtomNumber(r.getAtom(j)) == atomContainer.getAtomNumber(atom2))
					HaveTwo = true;
			}
			
			if (HaveOne && HaveTwo) {
				SameRing = true;
				return SameRing;
			}
			
		} // end ring for loop
		
		return SameRing;
	}


	public DescriptorValue calculate(IAtomContainer container) throws CDKException {
		rs = null;
		try {
			AllRingsFinder arf = new AllRingsFinder();
			rs = arf.findAllRings(container);
		} catch (Exception e) {
			throw new CDKException("Could not find all rings: " + e.getMessage(), e);
		}
		fragment = new String[container.getAtomCount()];
		IAtomTypeMatcher eStateMatcher = new EStateAtomTypeMatcher();
		for (int i=0; i<container.getAtomCount(); i++) {
			IAtomType atomType = eStateMatcher.findMatchingAtomType(container, container.getAtom(i));
			if (atomType == null) {
				fragment[i] = null;
			} else {
				fragment[i] = atomType.getAtomTypeName();
			}
		}
		calculate(container, fragment, rs);
		
		DoubleArrayResult results = new DoubleArrayResult();
		results.add(ALOGP);
		results.add(ALOGP2);
		results.add(AMR);

		return new DescriptorValue(getSpecification(), getParameterNames(),
			getParameters(), results, new String[] {"ALogP", "ALogP2", "AMR"} );
	}

    /**
     * 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 DoubleArrayResult();
    }


    public DescriptorSpecification getSpecification() {
        return new DescriptorSpecification(
                "http://www.epa.gov/toddmartin/#ALOGP",
                this.getClass().getName(),
                "$Id: AminoAcidCountDescriptor.java 6171 2006-05-04 19:29:58 +0000 (Thu, 04 May 2006) egonw $",
                "The Chemistry Development Kit");
    }


	public String[] getParameterNames() {
		return new String[0];
	}


	public Object getParameterType(String name) {
		return null;
	}


	public void setParameters(Object[] params) throws CDKException {
		return; // nothing to set
	}


	public Object[] getParameters() {
		return null;
	}	
	
}// end class