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Add and consider bond stereo #7

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Merged
michaelwenk merged 2 commits into from
Apr 11, 2023
Merged

Add and consider bond stereo #7

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b680e23
fix: consider bond stereo configuration in StructureCompact class and…
michaelwenk Apr 11, 2023
aabccde
fix: close #6
michaelwenk Apr 11, 2023
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24 changes: 22 additions & 2 deletions src/casekit/nmr/analysis/HOSECodeShiftStatistics.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
import org.bson.Document;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.nmrshiftdb.util.AtomUtils;
import org.openscience.nmrshiftdb.util.ExtendedHOSECodeGenerator;
Expand All @@ -28,6 +29,8 @@ public class HOSECodeShiftStatistics {

private final static Gson GSON = new GsonBuilder().setLenient()
.create();
private final static StructureDiagramGenerator structureDiagramGenerator = new StructureDiagramGenerator();
private final static ExtendedHOSECodeGenerator extendedHOSECodeGenerator = new ExtendedHOSECodeGenerator();

public static Map<String, Map<String, List<Double>>> collectHOSECodeShifts(final List<DataSet> dataSetList,
final Integer maxSphere,
Expand Down Expand Up @@ -60,8 +63,6 @@ public static Map<String, Map<String, List<Double>>> collectHOSECodeShifts(final
public static boolean insert(final DataSet dataSet, final Integer maxSphere, final boolean use3D,
final boolean withExplicitH,
final Map<String, Map<String, List<Double>>> hoseCodeShifts) {
final StructureDiagramGenerator structureDiagramGenerator = new StructureDiagramGenerator();
final ExtendedHOSECodeGenerator extendedHOSECodeGenerator = new ExtendedHOSECodeGenerator();
final IAtomContainer structure;
Signal signal;
String hoseCode;
Expand Down Expand Up @@ -101,13 +102,32 @@ public static boolean insert(final DataSet dataSet, final Integer maxSphere, fin

if (use3D) {
try {
// store wedge bond information
final int[] ordinals = new int[structure.getBondCount()];
int k = 0;
for (final IBond bond : structure.bonds()) {
ordinals[k] = bond.getStereo()
.ordinal();
k++;
}
// set 2D coordinates
structureDiagramGenerator.setMolecule(structure);
structureDiagramGenerator.generateCoordinates(structure);
/* !!! No explicit H in mol !!! */
Utils.convertExplicitToImplicitHydrogens(structure);
/* add explicit H atoms */
AtomUtils.addAndPlaceHydrogens(structure);
// restore wedge bond information
k = 0;
for (final IBond bond : structure.bonds()) {
bond.setStereo(IBond.Stereo.values()[ordinals[k]]);

k++;
if (k
>= ordinals.length) {
break;
}
}
} catch (final CDKException | IOException | ClassNotFoundException e) {
e.printStackTrace();
}
Expand Down
6 changes: 4 additions & 2 deletions src/casekit/nmr/model/StructureCompact.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@
@Setter
public class StructureCompact {

private int[][][] bondProperties; // connected atom index, bond order, bond is in ring, bond is aromatic
private int[][][] bondProperties; // connected atom index, bond order, bond is in ring, bond is aromatic, bond stereo configuration
private Integer[][] atomProperties; // element symbol, hybridization, implicitHydrogenCount, valency, formalCharge, isInRingAtom, isAromaticAtom

public StructureCompact(final IAtomContainer ac) {
Expand All @@ -61,7 +61,8 @@ public StructureCompact(final IAtomContainer ac) {
? 1
: 0, bond.isAromatic()
? 1
: 0});
: 0,
bond.getStereo().ordinal()});
}
}
temp = new int[connectedAtomsList.size()][];
Expand Down Expand Up @@ -147,6 +148,7 @@ public IAtomContainer toAtomContainer() {
== 1);
bond.setIsAromatic(this.bondProperties[i][k][3]
== 1);
bond.setStereo(IBond.Stereo.values()[this.bondProperties[i][k][4]]);
ac.addBond(bond);
}
}
Expand Down
2 changes: 1 addition & 1 deletion src/casekit/nmr/utils/Utils.java
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Expand Up @@ -579,7 +579,7 @@ public static Float getBondOrderSum(final IAtomContainer ac, final int atomIndex
* @throws CDKException
*/
public static DataSet atomContainerToDataSet(final IAtomContainer structure) throws CDKException {
return atomContainerToDataSet(structure, true);
return atomContainerToDataSet(structure, false);
}

/**
Expand Down