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Fix - avoid placing a wedge on the right-angled bond when a centre is… #998

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Merged
merged 4 commits into from
Aug 24, 2023
Merged

Fix - avoid placing a wedge on the right-angled bond when a centre is… #998

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49ce3d0
Fix - avoid placing a wedge on the right-angled bond when a centre is…
johnmay Aug 23, 2023
250bcf1
Update this template to avoid ambiguous stereo assignment.
johnmay Aug 23, 2023
41fff70
Better template orrientation.
johnmay Aug 23, 2023
44d3df0
Unused import
johnmay Aug 23, 2023
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2 changes: 1 addition & 1 deletion base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -699,7 +699,7 @@ else if (delta < -threshold) {
Vector2d v1 = toUnitVector(focus, bonds.get(0).getOther(focus));
Vector2d v2 = toUnitVector(focus, bonds.get(1).getOther(focus));
Vector2d v3 = toUnitVector(focus, bonds.get(2).getOther(focus));
String ambiuousStereoMesg = "Ambiguous stereochemistry - 3 neighbours and two";
String ambiuousStereoMesg = "Ambiguous stereochemistry - 3 neighbours and two bonds are co-linear";
if (Math.abs(signedAngle(v1,v2) - Math.PI) < threshold) {
if (elevationOf(focus, bonds.get(0)) == 0 &&
elevationOf(focus, bonds.get(1)) == 0 &&
Expand Down
38 changes: 28 additions & 10 deletions tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
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Expand Up @@ -637,6 +637,15 @@ private <T> void swap(List<T> l, int i, int j) {
l.set(j, tmp);
}

private IBond.Stereo invert(IBond.Stereo disp) {
switch (disp) {
case UP: return DOWN;
case DOWN: return UP;
default: return disp;
}
}


private IBond.Stereo flip(IBond.Stereo disp) {
switch (disp) {
case UP: return UP_INVERTED;
Expand Down Expand Up @@ -894,7 +903,10 @@ private void label(final ITetrahedralChirality element) {
// hydrogen is opposite all three neighbors. The central label needs to
// be inverted, atoms could be laid out like this automatically, consider
// CC1C[C@H]2CC[C@@H]1C2
// Like wise if the other two bonds are co-linear we should not place a
// wedge on the one off to the side (avoid is set).
int invert = -1;
int avoid = -1;
if (n == 3) {
// find a triangle of non-sequential neighbors (sorted clockwise)
// which has anti-clockwise winding
Expand All @@ -903,22 +915,26 @@ private void label(final ITetrahedralChirality element) {
Point2d b = focus.getPoint2d();
Point2d c = atoms[rank[(i + 2) % n]].getPoint2d();
double det = (a.x - c.x) * (b.y - c.y) - (a.y - c.y) * (b.x - c.x);
if (det > 0) {
invert = rank[(i + 1) % n];
break;
}
if (Math.abs(det) <= 0.05)
avoid = rank[(i + 1) % n]; // i,i+2 are co-linear, i+1=no wedge
else if (det > 0.05 && invert == -1)
invert = rank[(i + 1) % n]; // acute angle, invert wedge
}
}

// assign all up/down labels to an auxiliary array
IBond.Stereo[] labels = new IBond.Stereo[n];
IBond.Stereo refWedge = p > 0 ? UP : DOWN;
for (int i = 0; i < n; i++) {
int v = rank[i];

// 4 neighbors (invert every other one)
if (n == 4) p *= -1;

labels[v] = invert == v ? p > 0 ? DOWN : UP : p > 0 ? UP : DOWN;
// no wedge here (would be ambiguous)
if (avoid == v)
labels[v] = NONE;
// invert (if D3 acute, or odd index of D4)
else if (invert == v || (n == 4 && i % 2 == 0))
labels[v] = invert(refWedge);
else
labels[v] = refWedge;
}

// set the label for the highest priority and available bond
Expand All @@ -928,6 +944,8 @@ private void label(final ITetrahedralChirality element) {
IBond bond = bonds[v];
if (bond.getStereo() != NONE || bond.getOrder() != SINGLE)
continue;
if (labels[v] == NONE)
continue;
// first label
if (firstlabel == null) {
bond.setAtoms(new IAtom[]{focus, atoms[v]}); // avoids UP_INVERTED/DOWN_INVERTED
Expand Down
2 changes: 1 addition & 1 deletion tool/sdg/src/main/resources/org/openscience/cdk/layout/chebi-ring-templates.smi
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Expand Up @@ -440,7 +440,7 @@ N1NCCN1 |(.0,1.28,;1.21,.39,;.75,-1.03,;-.75,-1.03,;-1.21,.39,)|
OC1CC(O)CC(C)C1 |(-.0,3.0,;-.0,1.5,;-1.3,.75,;-1.3,-.75,;-2.6,-1.5,;.0,-1.5,;1.3,-.75,;2.6,-1.5,;1.3,.75,)|
OC1NC(N)NC(C)C1 |(-2.6,-1.5,;-1.3,-.75,;.0,-1.5,;1.3,-.75,;2.6,-1.5,;1.3,.75,;.0,1.5,;.0,3.0,;-1.3,.75,)|
NC1CC(N)C(C)C(N)C1 |(.0,-3.3,;.0,-1.8,;1.3,-1.05,;1.3,.45,;2.6,1.2,;.0,1.2,;.0,2.7,;-1.3,.45,;-2.6,1.2,;-1.3,-1.05,)|
O1CC2OC1CCC2 |(1.26,1.93,;-1.29,1.95,;-1.29,.1,;.01,.85,;1.3,.1,;1.3,-1.4,;.01,-2.15,;-1.29,-1.4,)|
O1CC2OC1CCC2 |(-0.75,1.64,;0.75,1.64,;1.69,0.47,;,-0.5,;-1.69,0.47,;-1.35,-0.99,;,-1.64,;1.35,-0.99,)|
OC1CC2N(C)C(CC2)C1 |(3.06,.0,;1.6,.0,;.86,-1.27,;-.6,-1.6,;-1.33,.0,;.17,.0,;-.6,1.6,;-2.01,.89,;-2.01,-.89,;.86,1.27,)|
N1CC2CN3CCCCC3C(C1)C2 |(-2.92,.73,;-2.92,-.77,;-1.85,-1.83,;-.35,-1.83,;.71,-.77,;2.01,-1.51,;3.31,-.77,;3.31,.73,;2.01,1.49,;.71,.73,;-.35,1.79,;-1.85,1.79,;-1.79,.18,)|
SC1CCCCC1 |(2.23,1.29,;.93,.54,;.93,-.96,;-.37,-1.71,;-1.67,-.96,;-1.67,.54,;-.37,1.29,)|
Expand Down
35 changes: 26 additions & 9 deletions tool/sdg/src/test/java/org/openscience/cdk/layout/NonPlanarBondsTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,17 +34,24 @@
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IStereoElement;
import org.openscience.cdk.interfaces.ITetrahedralChirality;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.io.MDLV2000Writer;
import org.openscience.cdk.silent.Atom;
import org.openscience.cdk.silent.AtomContainer;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.stereo.Atropisomeric;
import org.openscience.cdk.stereo.DoubleBondStereochemistry;
import org.openscience.cdk.stereo.ExtendedTetrahedral;
import org.openscience.cdk.stereo.StereoElementFactory;
import org.openscience.cdk.stereo.TetrahedralChirality;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;

import javax.vecmath.Point2d;

import java.io.StringReader;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.List;

Expand Down Expand Up @@ -322,8 +329,8 @@ void clockwiseSortShouldHandleExactlyOppositeAtoms() throws Exception {
NonplanarBonds.assign(m);
assertThat(m.getBond(2).getStereo(), is(IBond.Stereo.UP));
}


// ethene is left alone and not marked as crossed
@Test
void dontCrossEtheneDoubleBond() {
Expand Down Expand Up @@ -411,8 +418,8 @@ void useCrossedBondIfNeeded() {
}

/**
* @cdk.inchi InChI=1S/C6H14S/c1-5-7(4)6(2)3/h5H2,1-4H3/t7-/m0/s1
*/
* @cdk.inchi InChI=1S/C6H14S/c1-5-7(4)6(2)3/h5H2,1-4H3/t7-/m0/s1
*/
@Test
void dontMarkTetrahedralCentresWithDoubleBondsAsUnspecified() {
IAtomContainer m = new AtomContainer();
Expand All @@ -436,7 +443,7 @@ void dontMarkTetrahedralCentresWithDoubleBondsAsUnspecified() {
assertThat(m.getBond(2).getStereo(), is(not(IBond.Stereo.UP_OR_DOWN)));
assertThat(m.getBond(3).getStereo(), is(not(IBond.Stereo.UP_OR_DOWN)));
}

@Test
void dontMarkRingBondsInBezeneAsUnspecified() {
IAtomContainer m = new AtomContainer();
Expand All @@ -454,7 +461,7 @@ void dontMarkRingBondsInBezeneAsUnspecified() {
m.addBond(0, 5, IBond.Order.SINGLE);
NonplanarBonds.assign(m);
for (IBond bond : m.bonds()) {
assertThat(bond.getStereo(), is(IBond.Stereo.NONE));
assertThat(bond.getStereo(), is(IBond.Stereo.NONE));
}
}

Expand Down Expand Up @@ -644,8 +651,8 @@ void atropisomerWedgeBonds() throws CDKException {
SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer mol = smipar.parseSmiles("OC1=CC=C2C=CC=CC2=C1C1=C(O)C=CC2=C1C=CC=C2");

IBond focus = mol.getBond(mol.getAtom(10),
mol.getAtom(11));
IBond focus = mol.getBond(mol.getAtom(10),
mol.getAtom(11));
List<IAtom> carriers = new ArrayList<>();
carriers.addAll(mol.getConnectedAtomsList(focus.getBegin()));
carriers.addAll(mol.getConnectedAtomsList(focus.getEnd()));
Expand All @@ -664,7 +671,7 @@ void atropisomerWedgeBonds() throws CDKException {
assertThat(bond2.getOrder(), is(IBond.Order.SINGLE));

Assertions.assertTrue(bond1.getStereo() == IBond.Stereo.DOWN ||
bond2.getStereo() == IBond.Stereo.DOWN, "One of the single bonds should have been wedged");
bond2.getStereo() == IBond.Stereo.DOWN, "One of the single bonds should have been wedged");

}

Expand Down Expand Up @@ -775,4 +782,14 @@ static IAtom atom(String symbol, int hCount, double x, double y) {
return a;
}

@Test
void testColinearD3bonds() throws CDKException {
SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer mol = smipar.parseSmiles("[C@@H]12[C@@H]([C@H]([C@@H]([C@@H](CO1)O2)O)O)O |(1.3,0.1,;1.3,-1.4,;0.01,-2.15,;-1.29,-1.4,;-1.29,0.1,;-1.29,1.95,;1.26,1.93,;0.01,0.85,;-2.59,-2.15,;0.01,-3.65,;2.6,-2.15,)|");
NonplanarBonds.assign(mol);
// there are 4
Assertions.assertEquals(5,
StereoElementFactory.using2DCoordinates(mol).withStrictMode().createAll().size());
}

}