package mic.rules;
import java.util.logging.Level;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;
import toxTree.exceptions.DecisionMethodException;
import toxTree.tree.rules.StructureAlertCDK;
import ambit2.core.data.MoleculeTools;
import ambit2.smarts.query.SMARTSException;
/**
* Aromatic N-acyl amine.
*
*
* [a;!$(a(a[A;!#1])(a[A;!#1]));!$(aa[CX3](=O)[OX2H1]);!$(aa[SX4](=[OX1])(=[OX1])([O]));!$(aaa[SX4](=[OX1])(=[OX1])([O]));!$(aaaa[SX4](=[OX1])(=[OX1])([O]));!$(aaaaa[SX4](=[OX1])(=[OX1])([O]));!$(aaaaaa[SX4](=[OX1])(=[OX1])([O]))]!@[$([NX3;v3]([#1,CH3])C(=O)([#1,CH3]))]
*
*
* @author Nina Jeliazkova
*
*/
public class SA28ter extends StructureAlertCDK {
/**
*
*/
private static final long serialVersionUID = 6392891031735444965L;
public static String SA28ter_title = "Aromatic N-acyl amine";
public static String[][] amines = { { SA28ter_title,
"[NX3;v3]([#1,CH3])C(=O)([#1,CH3])" } };
public SA28ter() {
super();
try {
setContainsAllSubstructures(true);
StringBuffer b = new StringBuffer();
b.append("[a");
for (int i = 0; i < SA28.exclusion_rules.length; i++) {
b.append(";!$(");
b.append(SA28.exclusion_rules[i][1]);
b.append(")");
}
b.append("]!@[");
for (int i = 0; i < amines.length; i++) {
if (i > 0)
b.append(',');
b.append("$(");
b.append(amines[i][1]);
b.append(")");
}
b.append("]");
addSubstructure(SA28ter_title, b.toString());
setID("SA28ter");
setTitle(SA28ter_title);
StringBuffer e = new StringBuffer();
e.append("");
e.append(SA28ter_title);
e.append("
");
e.append("However:");
e.append("");
e.append("- ");
e
.append("Aromatic amino groups with ortho-disubstitution or with a carboxylic acid substituent in ortho position should be excluded.");
e.append("
- ");
e
.append("If a sulfonic acid group (-SO3H) is present on the ring that contains also the amino group, the substance should be excluded from the alert.");
e.append("
- ");
e
.append("see also the two examples of exceptions for the nitro alert (alert 27)");
e.append("
");
e.append("");
setExplanation(e.toString());
examples[0] = "CCOC=1C=C(C)C(NC(C)=O)=C(C)C=1(N)";
examples[1] = "CCOC=1C=CC(=CC=1(N))NC(C)=O";
editable = false;
} catch (SMARTSException x) {
logger.log(Level.SEVERE,x.getMessage(),x);
}
}
protected boolean isAPossibleHit(IAtomContainer mol, IAtomContainer processedObject) throws DecisionMethodException {
IMolecularFormula formula = MolecularFormulaManipulator.getMolecularFormula(mol);
return
MolecularFormulaManipulator.containsElement(formula,MoleculeTools.newElement(formula.getBuilder(),"N"));
}
}