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Stereochemistry integration tests.
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Signed-off-by: Stephan Beisken <sbeisken@gmail.com>
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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@johnmay @egonw
johnmay authored and egonw committed Dec 18, 2013
1 parent cce5d38 commit fefeb68
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Showing 3 changed files with 190 additions and 9 deletions.
9 changes: 5 additions & 4 deletions src/main/org/openscience/cdk/isomorphism/Ullmann.java
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Expand Up @@ -117,10 +117,11 @@ private Ullmann(IAtomContainer query,
@Override public Iterable<int[]> matchAll(IAtomContainer target) {
EdgeToBondMap bonds2 = EdgeToBondMap.withSpaceFor(target);
int[][] g2 = GraphUtil.toAdjList(target, bonds2);
return new UllmannIterable(query, target,
g1, g2,
bonds1, bonds2,
atomMatcher, bondMatcher);
return Iterables.filter(new UllmannIterable(query, target,
g1, g2,
bonds1, bonds2,
atomMatcher, bondMatcher),
new StereoMatchPredicate(query, target));
}

/**
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11 changes: 6 additions & 5 deletions src/main/org/openscience/cdk/isomorphism/VentoFoggia.java
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Expand Up @@ -125,11 +125,12 @@ private VentoFoggia(IAtomContainer query,
@Override public Iterable<int[]> matchAll(final IAtomContainer target) {
EdgeToBondMap bonds2 = EdgeToBondMap.withSpaceFor(target);
int[][] g2 = GraphUtil.toAdjList(target, bonds2);
return new VFIterable(query, target,
g1, g2,
bonds1, bonds2,
atomMatcher, bondMatcher,
subgraph);
return Iterables.filter(new VFIterable(query, target,
g1, g2,
bonds1, bonds2,
atomMatcher, bondMatcher,
subgraph),
new StereoMatchPredicate(query, target));
}

/**
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179 changes: 179 additions & 0 deletions src/test/org/openscience/cdk/isomorphism/SubstructureTest.java
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Expand Up @@ -80,6 +80,185 @@ public abstract class SubstructureTest {
assertMatch(smi("C1CC1.C1CC1"), smi("C1CC1.C1CC1"), 72);
}

@Test public void tetrahedral_match() throws Exception {
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@](C)(N)(O)CC"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@](C)(O)(CC)N"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@](C)(CC)(N)(O)"));

assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@@](C)(O)(N)CC"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@@](C)(CC)(O)N"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@@](C)(N)(CC)(O)"));

assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@](N)(O)(C)CC"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@](N)(CC)(O)C"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@](N)(C)(CC)O"));

assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@@](N)(C)(O)CC"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@@](N)(O)(CC)C"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@@](N)(CC)(C)O"));

assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@](O)(CC)(C)N"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@](O)(N)(CC)C"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@](O)(C)(N)(CC)"));

assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@@](O)(C)(CC)N"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@@](O)(CC)(N)C"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@@](O)(N)(C)(CC)"));

assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@](CC)(C)(O)N"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@](CC)(N)(C)O"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@](CC)(O)(N)C"));

assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@@](CC)(O)(C)N"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@@](CC)(C)(N)O"));
assertMatch(smi("[C@](C)(N)(O)CC"), smi("[C@@](CC)(N)(O)C"));
}

@Test public void tetrahedral_mismatch() throws Exception {
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@](C)(N)(O)CC"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@](C)(O)(CC)N"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@](C)(CC)(N)(O)"));

assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@@](C)(O)(N)CC"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@@](C)(CC)(O)N"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@@](C)(N)(CC)(O)"));

assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@](N)(O)(C)CC"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@](N)(CC)(O)C"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@](N)(C)(CC)O"));

assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@@](N)(C)(O)CC"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@@](N)(O)(CC)C"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@@](N)(CC)(C)O"));

assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@](O)(CC)(C)N"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@](O)(N)(CC)C"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@](O)(C)(N)(CC)"));

assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@@](O)(C)(CC)N"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@@](O)(CC)(N)C"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@@](O)(N)(C)(CC)"));

assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@](CC)(C)(O)N"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@](CC)(N)(C)O"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@](CC)(O)(N)C"));

assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@@](CC)(O)(C)N"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@@](CC)(C)(N)O"));
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("[C@@](CC)(N)(O)C"));
}

@Test public void tetrahedral_match_implicit_h() throws Exception {
assertMatch(smi("[C@H](C)(N)(O)"), smi("[C@H](C)(N)(O)"));
assertMatch(smi("[C@H](C)(N)(O)"), smi("[C@]([H])(C)(N)(O)"));
assertMatch(smi("[C@H](C)(N)(O)"), smi("[C@@](C)([H])(N)(O)"));
}

@Test public void tetrahedral_mismatch_implicit_h() throws Exception {
assertMismatch(smi("[C@H](C)(N)(O)"), smi("[C@@H](C)(N)(O)"));
assertMismatch(smi("[C@H](C)(N)(O)"), smi("[C@@]([H])(C)(N)(O)"));
assertMismatch(smi("[C@H](C)(N)(O)"), smi("[C@](C)([H])(N)(O)"));
}

@Test public void tetrahedral_match_sulfoxide() throws Exception {
assertMatch(smi("[S@](=O)(C)CC"), smi("[S@](=O)(C)CC"));
assertMatch(smi("[S@](=O)(C)CC"), smi("[S@](C)(CC)(=O)"));
assertMatch(smi("[S@](=O)(C)CC"), smi("[S@](CC)(=O)C"));
assertMatch(smi("[S@](=O)(C)CC"), smi("[S@@](C)(=O)CC"));
assertMatch(smi("[S@](=O)(C)CC"), smi("[S@@](=O)(CC)C"));
assertMatch(smi("[S@](=O)(C)CC"), smi("[S@@](CC)(C)=O"));
}

@Test public void tetrahedral_mismatch_sulfoxide() throws Exception {
assertMismatch(smi("[S@@](=O)(C)CC"), smi("[S@](=O)(C)CC"));
assertMismatch(smi("[S@@](=O)(C)CC"), smi("[S@](C)(CC)(=O)"));
assertMismatch(smi("[S@@](=O)(C)CC"), smi("[S@](CC)(=O)C"));
assertMismatch(smi("[S@@](=O)(C)CC"), smi("[S@@](C)(=O)CC"));
assertMismatch(smi("[S@@](=O)(C)CC"), smi("[S@@](=O)(CC)C"));
assertMismatch(smi("[S@@](=O)(C)CC"), smi("[S@@](CC)(C)=O"));
}

@Test public void tetrahedral_missing_in_query() throws Exception {
assertMatch(smi("C(C)(N)(O)CC"), smi("[C@@](C)(N)(O)CC"));
}

@Test public void tetrahedral_missing_in_target() throws Exception {
assertMismatch(smi("[C@@](C)(N)(O)CC"), smi("C(C)(N)(O)CC"));
}

@Test public void tetrahedral_count() throws Exception {
// we can map any witch way 4 neighbours but 2 configuration so (4!/2) = 12
assertMatch(smi("[C@](C)(C)(C)C"), smi("[C@](C)(CC)(CCC)CCCC"), 12);
assertMatch(smi("[C@@](C)(C)(C)C"), smi("[C@](C)(CC)(CCC)CCCC"), 12);
assertMatch(smi("[C@](C)(C)(C)C"), smi("[C@@](C)(CC)(CCC)CCCC"), 12);
assertMatch(smi("[C@@](C)(C)(C)C"), smi("[C@@](C)(CC)(CCC)CCCC"), 12);
}

@Test public void geometric_trans_match() throws Exception {
assertMatch(smi("F/C=C/F"), smi("F/C=C/F"));
assertMatch(smi("F/C=C/F"), smi("F\\C=C\\F"));
// shouldn't mater which substituents are used
assertMatch(smi("F/C=C/F"), smi("F/C(/[H])=C/F"));
assertMatch(smi("F/C=C/F"), smi("FC(/[H])=C/F"));
assertMatch(smi("F/C=C/F"), smi("F/C=C([H])/F"));
assertMatch(smi("F/C=C/F"), smi("F/C=C(\\[H])F"));
assertMatch(smi("F/C=C/F"), smi("FC(/[H])=C(\\[H])F"));
// or the order is different
assertMatch(smi("F/C=C/F"), smi("C(\\F)=C/F"));
assertMatch(smi("F/C=C/F"), smi("C(/F)=C\\F"));
}

@Test public void geometric_cis_match() throws Exception {
assertMatch(smi("F/C=C\\F"), smi("F/C=C\\F"));
assertMatch(smi("F/C=C\\F"), smi("F\\C=C/F"));
assertMatch(smi("F\\C=C/F"), smi("F/C=C\\F"));
assertMatch(smi("F\\C=C/F"), smi("F\\C=C/F"));
// shouldn't mater which substituents are used
assertMatch(smi("F/C=C\\F"), smi("F/C(/[H])=C\\F"));
assertMatch(smi("F/C=C\\F"), smi("FC(/[H])=C\\F"));
assertMatch(smi("F/C=C\\F"), smi("F/C=C([H])\\F"));
assertMatch(smi("F/C=C\\F"), smi("F/C=C(/[H])F"));
assertMatch(smi("F/C=C\\F"), smi("FC(/[H])=C(/[H])F"));
// or the order is different
assertMatch(smi("F/C=C\\F"), smi("C(\\F)=C\\F"));
assertMatch(smi("F/C=C\\F"), smi("C(/F)=C/F"));
}

@Test public void geometric_trans_mismatch() throws Exception {
assertMismatch(smi("F/C=C/F"), smi("F/C=C\\F"));
assertMismatch(smi("F/C=C/F"), smi("F\\C=C/F"));
assertMismatch(smi("F\\C=C\\F"), smi("F/C=C\\F"));
assertMismatch(smi("F\\C=C\\F"), smi("F\\C=C/F"));
}

@Test public void geometric_cis_mismatch() throws Exception {
assertMismatch(smi("F/C=C\\F"), smi("F/C=C/F"));
assertMismatch(smi("F/C=C\\F"), smi("F\\C=C\\F"));
assertMismatch(smi("F\\C=C/F"), smi("F/C=C/F"));
assertMismatch(smi("F\\C=C/F"), smi("F\\C=C\\F"));
}

@Test public void geometric_missing_in_query() throws Exception {
assertMatch(smi("FC=CF"), smi("F/C=C/F"));
assertMatch(smi("FC=CF"), smi("F\\C=C\\F"));
assertMatch(smi("FC=CF"), smi("F\\C=C/F"));
assertMatch(smi("FC=CF"), smi("F/C=C\\F"));
}

@Test public void geometric_missing_in_target() throws Exception {
assertMismatch(smi("F/C=C/F"), smi("FC=CF"));
assertMismatch(smi("F/C=C\\F"), smi("FC=CF"));
assertMismatch(smi("F\\C=C/F"), smi("FC=CF"));
assertMismatch(smi("F\\C=C\\F"), smi("FC=CF"));
}

@Test public void geometric_count() throws Exception {
assertMatch(smi("C/C=C/C"), smi("CC(/CC)=C(/CC)C"), 4);
assertMatch(smi("C/C=C\\C"), smi("CC(/CC)=C(/CC)C"), 4);
assertMatch(smi("C\\C=C\\C"), smi("CC(/CC)=C(/CC)C"), 4);
assertMatch(smi("C\\C=C/C"), smi("CC(/CC)=C(/CC)C"), 4);
}

@Test public void cubane_automorphisms() throws Exception {
assertMatch(smi("C12C3C4C1C1C2C3C41"),
smi("C12C3C4C1C1C2C3C41"),
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