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Better handling of Explicit hydrogens on inorganic stereochemistry
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@johnmay
johnmay committed Nov 15, 2024
1 parent e284749 commit 55ec152
Showing 1 changed file with 59 additions and 7 deletions.
66 changes: 59 additions & 7 deletions cdkdepict-lib/src/main/java/org/openscience/cdk/app/DepictController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,11 @@
import org.openscience.cdk.smarts.SmartsPattern;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.stereo.ExtendedTetrahedral;
import org.openscience.cdk.stereo.Octahedral;
import org.openscience.cdk.stereo.SquarePlanar;
import org.openscience.cdk.stereo.Stereocenters;
import org.openscience.cdk.stereo.TetrahedralChirality;
import org.openscience.cdk.stereo.TrigonalBipyramidal;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.ReactionManipulator;
import org.openscience.cdk.tools.manipulator.ReactionSetManipulator;
Expand All @@ -67,9 +70,11 @@
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.StringReader;
import java.util.ArrayDeque;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Deque;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
Expand Down Expand Up @@ -739,20 +744,47 @@ private void setHydrogenDisplay(IAtomContainer mol, HydrogenDisplayType hDisplay
IAtom focus = (IAtom) se.getFocus();
if (focus.getImplicitHydrogenCount() == 1 &&
shouldAddH(mol, focus, mol.getConnectedBondsList(focus))) {
focus.setImplicitHydrogenCount(0);
IAtom hydrogen = sproutHydrogen(mol, focus);
IStereoElement tmp = se.map(Collections.singletonMap(focus, hydrogen));
// need to keep focus same
TetrahedralChirality e = new TetrahedralChirality(focus,
(IAtom[]) tmp.getCarriers().toArray(new IAtom[4]),
tmp.getConfig());
getExplHCarriers(mol, se, focus),
se.getConfig());
e.setGroupInfo(se.getGroupInfo());
ses.add(e);
} else {
ses.add(se);
}
}
break;
case IStereoElement.SquarePlanar:
{
IAtom focus = (IAtom) se.getFocus();
if (focus.getImplicitHydrogenCount() > 0) {
ses.add(new SquarePlanar(focus, getExplHCarriers(mol, se, focus), se.getConfig()));
} else {
ses.add(se);
}
}
break;
case IStereoElement.TrigonalBipyramidal:
{
IAtom focus = (IAtom) se.getFocus();
if (focus.getImplicitHydrogenCount() > 0) {
ses.add(new TrigonalBipyramidal(focus, getExplHCarriers(mol, se, focus), se.getConfig()));
} else {
ses.add(se);
}
}
break;
case IStereoElement.Octahedral:
{
IAtom focus = (IAtom) se.getFocus();
if (focus.getImplicitHydrogenCount() > 0) {
ses.add(new Octahedral(focus, getExplHCarriers(mol, se, focus), se.getConfig()));
} else {
ses.add(se);
}
}
break;
case IStereoElement.CisTrans: {
IBond focus = (IBond) se.getFocus();
IAtom begin = focus.getBegin();
Expand Down Expand Up @@ -823,6 +855,20 @@ private void setHydrogenDisplay(IAtomContainer mol, HydrogenDisplayType hDisplay
}
}

// utility to sprout multiple hydrogens for stereo centres
private IAtom[] getExplHCarriers(IAtomContainer mol, IStereoElement se, IAtom focus) {
Deque<IAtom> hydrogens = new ArrayDeque<>();
for (int i = 0; i < focus.getImplicitHydrogenCount(); i++) {
hydrogens.add(sproutHydrogen(mol, focus));
}
focus.setImplicitHydrogenCount(0);
List<IAtom> carriers = new ArrayList<>();
for (IAtom carrier : (List<IAtom>) se.getCarriers()) {
carriers.add(carrier.equals(focus) && !hydrogens.isEmpty() ? hydrogens.poll() : carrier);
}
return carriers.toArray(new IAtom[0]);
}

private boolean shouldAddH(IAtomContainer mol, IAtom atom, Iterable<IBond> bonds) {
int count = 0;
for (IBond bond : bonds) {
Expand Down Expand Up @@ -1221,8 +1267,7 @@ public static ResponseEntity<Object> handleException(Exception ex, WebRequest re
new HttpHeaders(),
HttpStatus.BAD_REQUEST);
} else {
ex.printStackTrace();
LoggerFactory.getLogger(DepictController.class).error("Unexpected Error: " + ex);
LoggerFactory.getLogger(DepictController.class).error("Unexpected Error: ", ex);
return new ResponseEntity<>("<!DOCTYPE html><html><title>500 - Internal Server Error</title><body><div>" +
"<h1>" + ex.getClass().getSimpleName() + "</h1>" +
ex.getMessage() +
Expand All @@ -1231,4 +1276,11 @@ public static ResponseEntity<Object> handleException(Exception ex, WebRequest re
HttpStatus.INTERNAL_SERVER_ERROR);
}
}

public static void main(String[] args) throws IOException, CDKException {
new DepictController().depict("ClC1=NC=2N(C(=C1)N(CC3=CC=CC=C3)CC4=CC=CC=C4)N=CC2C(OCC)=O>C1(=CC(=CC(=N1)C)N)N2C[C@H](CCC2)O.O1CCOCC1.CC1(C2=C(C(=CC=C2)P(C3=CC=CC=C3)C4=CC=CC=C4)OC5=C(C=CC=C15)P(C6=CC=CC=C6)C7=CC=CC=C7)C.C=1C=CC(=CC1)\\C=C\\C(=O)\\C=C\\C2=CC=CC=C2.C=1C=CC(=CC1)\\C=C\\C(=O)\\C=C\\C2=CC=CC=C2.C=1C=CC(=CC1)\\C=C\\C(=O)\\C=C\\C2=CC=CC=C2.[Pd].[Pd].[Cs]OC(=O)O[Cs]>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N(CC4=CC=CC=C4)CC5=CC=CC=C5)N=CC3C(OCC)=O)N6C[C@H](CCC6)O>CO.C1CCOC1.O.O[Li]>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N(CC4=CC=CC=C4)CC5=CC=CC=C5)N=CC3C(O)=O)N6C[C@H](CCC6)O>CN(C)C(=[N+](C)C)ON1C2=C(C=CC=N2)N=N1.F[P-](F)(F)(F)(F)F.[NH4+].[Cl-].CN(C)C=O.CCN(C(C)C)C(C)C>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N(CC4=CC=CC=C4)CC5=CC=CC=C5)N=CC3C(N)=O)N6C[C@H](CCC6)O>>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N)N=CC3C(N)=O)N4C[C@H](CCC4)O |f:4.5.6.7.8,16.17,18.19| US20190241576A1",
"svg",
"bot",
new HashMap<>());
}
}

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