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[Cdk-commits] SF.net SVN: cdk:[13134] cdk/branches/cdk-1.2.x/src/test/org/openscience/cdk /atomtype/SybylAtomTypeMatcherTest.java
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From: <eg...@us...> - 2008-11-16 17:08:02
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Revision: 13134
http://cdk.svn.sourceforge.net/cdk/?rev=13134&view=rev
Author: egonw
Date: 2008-11-16 17:07:53 +0000 (Sun, 16 Nov 2008)
Log Message:
-----------
Added explicit tests
Modified Paths:
--------------
cdk/branches/cdk-1.2.x/src/test/org/openscience/cdk/atomtype/SybylAtomTypeMatcherTest.java
Modified: cdk/branches/cdk-1.2.x/src/test/org/openscience/cdk/atomtype/SybylAtomTypeMatcherTest.java
===================================================================
--- cdk/branches/cdk-1.2.x/src/test/org/openscience/cdk/atomtype/SybylAtomTypeMatcherTest.java 2008-11-16 17:07:30 UTC (rev 13133)
+++ cdk/branches/cdk-1.2.x/src/test/org/openscience/cdk/atomtype/SybylAtomTypeMatcherTest.java 2008-11-16 17:07:53 UTC (rev 13134)
@@ -133,7 +133,7 @@
for (IAtom atom : benzene.atoms()) {
atom.setAtomTypeName(null);
IAtomType matched = matcher.findMatchingAtomType(benzene, atom);
- Assert.assertEquals("C.2", matched.getAtomTypeName());
+ Assert.assertEquals("C.ar", matched.getAtomTypeName());
}
}
@@ -286,6 +286,195 @@
assertAtomTypeNames(testedAtomTypes, expectedTypes, mol);
}
+ @Test public void testMnF4() throws Exception {
+ IMolecule mol = new Molecule();
+ IAtom atom = new Atom("F");
+ IAtom atom2 = new Atom("Mn");
+ IAtom atom3 = new Atom("F");
+ IAtom atom4 = new Atom("F");
+ IAtom atom5 = new Atom("F");
+ mol.addAtom(atom); atom.setFormalCharge(-1);
+ mol.addAtom(atom2); atom2.setFormalCharge(+2);
+ mol.addAtom(atom3); atom3.setFormalCharge(-1);
+ mol.addAtom(atom4); atom4.setFormalCharge(-1);
+ mol.addAtom(atom5); atom5.setFormalCharge(-1);
+
+ String[] expectedTypes = {"F", "Mn", "F", "F", "F"};
+ assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+ }
+
+ @Test public void testAmide() throws Exception {
+ IMolecule mol = new Molecule();
+ IAtom atom = new Atom("O");
+ IAtom atom2 = new Atom("C");
+ IAtom atom3 = new Atom("N");
+ mol.addAtom(atom);
+ mol.addAtom(atom2);
+ mol.addAtom(atom3);
+ mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
+ mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
+
+ String[] expectedTypes = {"O.2", "C.2", "N.am"};
+ assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+ }
+
+ @Test public void testMethylAmine() throws Exception {
+ IMolecule mol = new Molecule();
+ IAtom atom = new Atom("N");
+ IAtom atom2 = new Atom("C");
+ mol.addAtom(atom);
+ mol.addAtom(atom2);
+ mol.addBond(0,1,CDKConstants.BONDORDER_SINGLE);
+
+ String[] expectedTypes = {"N.3", "C.3"};
+ assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+ }
+
+ @Test public void testAmmonia() throws Exception {
+ IMolecule mol = new Molecule();
+ IAtom atom = new Atom("H");
+ IAtom atom2 = new Atom("N");
+ IAtom atom3 = new Atom("H");
+ IAtom atom4 = new Atom("H");
+ IAtom atom5 = new Atom("H");
+ mol.addAtom(atom);
+ mol.addAtom(atom2);
+ atom2.setFormalCharge(+1);
+ mol.addAtom(atom3);
+ mol.addAtom(atom4);
+ mol.addAtom(atom5);
+ mol.addBond(0,1,CDKConstants.BONDORDER_SINGLE);
+ mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
+ mol.addBond(1,3,CDKConstants.BONDORDER_SINGLE);
+ mol.addBond(1,4,CDKConstants.BONDORDER_SINGLE);
+
+ String[] expectedTypes = {"H", "N.4", "H", "H", "H"};
+ assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+ }
+
+ @Test public void testMethanol() throws Exception {
+ IMolecule mol = new Molecule();
+ IAtom atom = new Atom("O");
+ IAtom atom2 = new Atom("C");
+ mol.addAtom(atom);
+ mol.addAtom(atom2);
+ mol.addBond(0,1,CDKConstants.BONDORDER_SINGLE);
+
+ String[] expectedTypes = {"O.3", "C.3"};
+ assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+ }
+
+ @Test public void testDMSO() throws Exception {
+ IMolecule mol = new Molecule();
+ IAtom atom = new Atom("O");
+ IAtom atom2 = new Atom("S");
+ IAtom atom3 = new Atom("C");
+ IAtom atom4 = new Atom("C");
+ mol.addAtom(atom);
+ mol.addAtom(atom2);
+ mol.addAtom(atom3);
+ mol.addAtom(atom4);
+ mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
+ mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
+ mol.addBond(1,3,CDKConstants.BONDORDER_SINGLE);
+
+ String[] expectedTypes = {"O.2", "S.O", "C.3", "C.3"};
+ assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+ }
+
+ @Test public void testDMSOO() throws Exception {
+ IMolecule mol = new Molecule();
+ IAtom atom = new Atom("O");
+ IAtom atom1 = new Atom("O");
+ IAtom atom2 = new Atom("S");
+ IAtom atom3 = new Atom("C");
+ IAtom atom4 = new Atom("C");
+ mol.addAtom(atom);
+ mol.addAtom(atom1);
+ mol.addAtom(atom2);
+ mol.addAtom(atom3);
+ mol.addAtom(atom4);
+ mol.addBond(0,2,CDKConstants.BONDORDER_DOUBLE);
+ mol.addBond(1,2,CDKConstants.BONDORDER_DOUBLE);
+ mol.addBond(2,3,CDKConstants.BONDORDER_SINGLE);
+ mol.addBond(2,4,CDKConstants.BONDORDER_SINGLE);
+
+ String[] expectedTypes = {"O.2", "O.2", "S.O2", "C.3", "C.3"};
+ assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+ }
+
+ @Test public void testCarbokation() throws Exception {
+ IMolecule mol = new Molecule();
+ IAtom atom = new Atom("H");
+ IAtom atom2 = new Atom("C"); atom2.setFormalCharge(+1);
+ IAtom atom3 = new Atom("H");
+ IAtom atom4 = new Atom("H");
+ mol.addAtom(atom);
+ mol.addAtom(atom2);
+ mol.addAtom(atom3);
+ mol.addAtom(atom4);
+ mol.addBond(0,1,CDKConstants.BONDORDER_SINGLE);
+ mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
+ mol.addBond(1,3,CDKConstants.BONDORDER_SINGLE);
+
+ String[] expectedTypes = {"H", "C.cat", "H", "H"};
+ assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+ }
+ @Test public void testSilicon() throws Exception {
+ IMolecule mol = new Molecule();
+ IAtom a1 = mol.getBuilder().newAtom("Si"); mol.addAtom(a1);
+ IAtom a2 = mol.getBuilder().newAtom("O"); mol.addAtom(a2);
+ IAtom a3 = mol.getBuilder().newAtom("O"); mol.addAtom(a3);
+ IAtom a4 = mol.getBuilder().newAtom("O"); mol.addAtom(a4);
+ IAtom a5 = mol.getBuilder().newAtom("C"); mol.addAtom(a5);
+ IAtom a6 = mol.getBuilder().newAtom("C"); mol.addAtom(a6);
+ IAtom a7 = mol.getBuilder().newAtom("C"); mol.addAtom(a7);
+ IAtom a8 = mol.getBuilder().newAtom("H"); mol.addAtom(a8);
+ IAtom a9 = mol.getBuilder().newAtom("H"); mol.addAtom(a9);
+ IAtom a10 = mol.getBuilder().newAtom("H"); mol.addAtom(a10);
+ IAtom a11 = mol.getBuilder().newAtom("H"); mol.addAtom(a11);
+ IAtom a12 = mol.getBuilder().newAtom("H"); mol.addAtom(a12);
+ IAtom a13 = mol.getBuilder().newAtom("H"); mol.addAtom(a13);
+ IAtom a14 = mol.getBuilder().newAtom("H"); mol.addAtom(a14);
+ IAtom a15 = mol.getBuilder().newAtom("H"); mol.addAtom(a15);
+ IAtom a16 = mol.getBuilder().newAtom("H"); mol.addAtom(a16);
+ IAtom a17 = mol.getBuilder().newAtom("H"); mol.addAtom(a17);
+ IBond b1 = mol.getBuilder().newBond(a1, a2, IBond.Order.SINGLE); mol.addBond(b1);
+ IBond b2 = mol.getBuilder().newBond(a1, a3, IBond.Order.SINGLE); mol.addBond(b2);
+ IBond b3 = mol.getBuilder().newBond(a1, a4, IBond.Order.SINGLE); mol.addBond(b3);
+ IBond b4 = mol.getBuilder().newBond(a2, a5, IBond.Order.SINGLE); mol.addBond(b4);
+ IBond b5 = mol.getBuilder().newBond(a3, a6, IBond.Order.SINGLE); mol.addBond(b5);
+ IBond b6 = mol.getBuilder().newBond(a4, a7, IBond.Order.SINGLE); mol.addBond(b6);
+ IBond b7 = mol.getBuilder().newBond(a5, a8, IBond.Order.SINGLE); mol.addBond(b7);
+ IBond b8 = mol.getBuilder().newBond(a5, a9, IBond.Order.SINGLE); mol.addBond(b8);
+ IBond b9 = mol.getBuilder().newBond(a5, a10, IBond.Order.SINGLE); mol.addBond(b9);
+ IBond b10 = mol.getBuilder().newBond(a6, a11, IBond.Order.SINGLE); mol.addBond(b10);
+ IBond b11 = mol.getBuilder().newBond(a6, a12, IBond.Order.SINGLE); mol.addBond(b11);
+ IBond b12 = mol.getBuilder().newBond(a6, a13, IBond.Order.SINGLE); mol.addBond(b12);
+ IBond b13 = mol.getBuilder().newBond(a7, a14, IBond.Order.SINGLE); mol.addBond(b13);
+ IBond b14 = mol.getBuilder().newBond(a7, a15, IBond.Order.SINGLE); mol.addBond(b14);
+ IBond b15 = mol.getBuilder().newBond(a7, a16, IBond.Order.SINGLE); mol.addBond(b15);
+ IBond b16 = mol.getBuilder().newBond(a1, a17, IBond.Order.SINGLE); mol.addBond(b16);
+
+ String[] expectedTypes = {"Si", "O.3", "O.3", "O.3", "C.3", "C.3", "C.3",
+ "H", "H", "H", "H", "H", "H", "H", "H", "H", "H"};
+ assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+ }
+
+ @Test public void testThioAmide() throws Exception {
+ IMolecule mol = new Molecule();
+ IAtom atom = new Atom("S");
+ IAtom atom2 = new Atom("C");
+ IAtom atom3 = new Atom("N");
+ mol.addAtom(atom);
+ mol.addAtom(atom2);
+ mol.addAtom(atom3);
+ mol.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
+ mol.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
+
+ String[] expectedTypes = {"S.2", "C.2", "N.am"};
+ assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+ }
@Test public void countTestedAtomTypes() {
super.countTestedAtomTypes(testedAtomTypes);
}
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