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egonwegonw
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Added double bond stereo
Change-Id: I7a3ece179bc3b9136976634108d18cd69a20645e
1 parent 76577b4 commit 5b644f9

2 files changed

Lines changed: 88 additions & 2 deletions

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‎src/main/org/openscience/cdk/inchi/InChIGenerator.java‎

Lines changed: 49 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -54,6 +54,7 @@
5454
import org.openscience.cdk.interfaces.IAtomContainer;
5555
import org.openscience.cdk.interfaces.IAtomParity;
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import org.openscience.cdk.interfaces.IBond;
57+
import org.openscience.cdk.interfaces.IDoubleBondStereochemistry;
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import org.openscience.cdk.interfaces.IStereoElement;
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import org.openscience.cdk.interfaces.ITetrahedralChirality;
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import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
@@ -283,6 +284,7 @@ private void generateInchiFromCDKAtomContainer(IAtomContainer atomContainer) thr
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284285

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// Process bonds
287+
Map<IBond, JniInchiBond> bondMap = new HashMap<IBond, JniInchiBond>();
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Iterator<IBond> bonds = atomContainer.bonds().iterator();
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while (bonds.hasNext()) {
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IBond bond = bonds.next();
@@ -308,6 +310,7 @@ private void generateInchiFromCDKAtomContainer(IAtomContainer atomContainer) thr
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309311
// Create InChI bond
310312
JniInchiBond ibond = new JniInchiBond(at0, at1, order);
313+
bondMap.put(bond, ibond);
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input.addBond(ibond);
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313316
// Check for bond stereo definitions
@@ -393,6 +396,52 @@ else if (stereo == CDKConstants.UNSET) {
393396
JniInchiStereo0D jniStereo = new JniInchiStereo0D(atC, at0, at1, at2, at3,
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INCHI_STEREOTYPE.TETRAHEDRAL, p);
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input.addStereo0D(jniStereo);
399+
} else if (stereoElem instanceof IDoubleBondStereochemistry) {
400+
IDoubleBondStereochemistry dbStereo = (IDoubleBondStereochemistry)stereoElem;
401+
IBond[] surroundingBonds = dbStereo.getBonds();
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if (surroundingBonds[0] == null || surroundingBonds[1] == null)
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throw new CDKException("Cannot generate an InChI with incomplete double bond info");
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org.openscience.cdk.interfaces.IDoubleBondStereochemistry.
405+
Conformation stereoType = dbStereo.getStereo();
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IBond stereoBond = dbStereo.getStereoBond();
408+
JniInchiAtom at0 = null;
409+
JniInchiAtom at1 = null;
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JniInchiAtom at2 = null;
411+
JniInchiAtom at3 = null;
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// TODO: I should check for two atom bonds... or maybe that should happen when you
413+
// create a double bond stereochemistry
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if (stereoBond.contains(surroundingBonds[0].getAtom(0))) {
415+
// first atom is A
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at1 = (JniInchiAtom) atomMap.get(surroundingBonds[0].getAtom(0));
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at0 = (JniInchiAtom) atomMap.get(surroundingBonds[0].getAtom(1));
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} else {
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// first atom is X
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at0 = (JniInchiAtom) atomMap.get(surroundingBonds[0].getAtom(0));
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at1 = (JniInchiAtom) atomMap.get(surroundingBonds[0].getAtom(1));
422+
}
423+
if (stereoBond.contains(surroundingBonds[1].getAtom(0))) {
424+
// first atom is B
425+
at2 = (JniInchiAtom) atomMap.get(surroundingBonds[1].getAtom(0));
426+
at3 = (JniInchiAtom) atomMap.get(surroundingBonds[1].getAtom(1));
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} else {
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// first atom is Y
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at2 = (JniInchiAtom) atomMap.get(surroundingBonds[1].getAtom(1));
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at3 = (JniInchiAtom) atomMap.get(surroundingBonds[1].getAtom(0));
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}
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INCHI_PARITY p = INCHI_PARITY.UNKNOWN;
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if (stereoType == org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation.TOGETHER) {
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p = INCHI_PARITY.ODD;
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} else if (stereoType == org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation.OPPOSITE) {
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p = INCHI_PARITY.EVEN;
437+
} else {
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throw new CDKException("Unknown double bond stereochemistry");
439+
}
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JniInchiStereo0D jniStereo = new JniInchiStereo0D(
442+
null, at0, at1, at2, at3, INCHI_STEREOTYPE.DOUBLEBOND, p
443+
);
444+
input.addStereo0D(jniStereo);
396445
}
397446
}
398447

‎src/test/org/openscience/cdk/inchi/InChIGeneratorTest.java‎

Lines changed: 39 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -25,9 +25,12 @@
2525
import org.openscience.cdk.*;
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import org.openscience.cdk.interfaces.IAtom;
2727
import org.openscience.cdk.interfaces.IAtomContainer;
28+
import org.openscience.cdk.interfaces.IBond;
29+
import org.openscience.cdk.interfaces.IDoubleBondStereochemistry;
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import org.openscience.cdk.interfaces.ITetrahedralChirality;
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import org.openscience.cdk.interfaces.IBond.Order;
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import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
33+
import org.openscience.cdk.stereo.DoubleBondStereochemistry;
3134
import org.openscience.cdk.stereo.TetrahedralChirality;
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3336
import javax.vecmath.Point2d;
@@ -277,8 +280,7 @@ protected InChIGeneratorFactory getFactory() throws Exception {
277280
Assert.assertEquals(genZ.getReturnStatus(), INCHI_RET.OKAY);
278281
Assert.assertEquals("InChI=1/C2H2Cl2/c3-1-2-4/h1-2H/b2-1-", genZ.getInchi());
279282
}
280-
281-
283+
282284
/**
283285
* Tests 3D coordinates are correctly passed to InChI.
284286
*
@@ -680,4 +682,39 @@ public void testTetrahedralStereo() throws Exception {
680682
genL.getInchi()
681683
);
682684
}
685+
686+
@Test public void testDoubleBondStereochemistry() throws Exception {
687+
// (E)-1,2-dichloroethene
688+
IAtomContainer acE = new AtomContainer();
689+
IAtom a1E = new Atom("C");
690+
IAtom a2E = new Atom("C");
691+
IAtom a3E = new Atom("Cl");
692+
IAtom a4E = new Atom("Cl");
693+
a1E.setImplicitHydrogenCount(1);
694+
a2E.setImplicitHydrogenCount(1);
695+
acE.addAtom(a1E);
696+
acE.addAtom(a2E);
697+
acE.addAtom(a3E);
698+
acE.addAtom(a4E);
699+
700+
acE.addBond(new Bond(a1E, a2E, CDKConstants.BONDORDER_DOUBLE));
701+
acE.addBond(new Bond(a1E, a3E, CDKConstants.BONDORDER_SINGLE));
702+
acE.addBond(new Bond(a2E, a4E, CDKConstants.BONDORDER_SINGLE));
703+
704+
IBond[] ligands = new IBond[2];
705+
ligands[0] = acE.getBond(1);
706+
ligands[1] = acE.getBond(2);
707+
IDoubleBondStereochemistry stereo = new DoubleBondStereochemistry(
708+
acE.getBond(0), ligands, org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation.OPPOSITE
709+
);
710+
acE.addStereoElement(stereo);
711+
712+
InChIGenerator genE = getFactory().getInChIGenerator(acE);
713+
Assert.assertEquals(INCHI_RET.OKAY, genE.getReturnStatus());
714+
System.out.println(genE.getMessage());
715+
Assert.assertEquals(
716+
"InChI=1S/C2H2Cl2/c3-1-2-4/h1-2H/b2-1+",
717+
genE.getInchi()
718+
);
719+
}
683720
}

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