Sping multicity round tripping in molfiles, SAChem added support for reading from V2000, makes sense to also support V3000 and output in both since there is currently information loss.

johnmay · johnmay · commit 42da2c17d6ae · 2021-01-17T22:29:22.000Z
diff --git a/base/core/src/main/java/org/openscience/cdk/CDKConstants.java b/base/core/src/main/java/org/openscience/cdk/CDKConstants.java
@@ -424,6 +424,10 @@ public class CDKConstants {
      */
     public static final String      CTAB_SGROUPS                 = "cdk:CtabSgroups";
 
+    /**
+     * Enumeration of all valid radical values.
+     */
+    public static final String      SPIN_MULTIPLICITY            = "cdk:SpinMultiplicity";
 
     /**
      * Property for reaction objects where the conditions of reactions can be placed.
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java
@@ -1073,6 +1073,8 @@ void readPropertiesFast(final BufferedReader input, final IAtomContainer contain
                         index = readMolfileInt(line, st) - 1;
                         int value = readMolfileInt(line, st + 4);
                         SPIN_MULTIPLICITY multiplicity = SPIN_MULTIPLICITY.ofValue(value);
+                        
+                        container.getAtom(offset + index).setProperty(CDKConstants.SPIN_MULTIPLICITY, multiplicity);
 
                         for (int e = 0; e < multiplicity.getSingleElectrons(); e++)
                             container.addSingleElectron(offset + index);
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java
@@ -694,16 +694,22 @@ else if (e.equals(new Expr(Expr.Type.ALIPHATIC_ORDER, 2).or(new Expr(Expr.Type.I
         if (container.getSingleElectronCount() > 0) {
             Map<Integer, SPIN_MULTIPLICITY> atomIndexSpinMap = new LinkedHashMap<Integer, SPIN_MULTIPLICITY>();
             for (int i = 0; i < container.getAtomCount(); i++) {
-                int eCount = container.getConnectedSingleElectronsCount(container.getAtom(i));
+                IAtom atom = container.getAtom(i);
+                int eCount = container.getConnectedSingleElectronsCount(atom);
                 switch (eCount) {
                     case 0:
                         continue;
                     case 1:
                         atomIndexSpinMap.put(i, SPIN_MULTIPLICITY.Monovalent);
                         break;
                     case 2:
-                        // information loss, divalent but singlet or triplet?
-                        atomIndexSpinMap.put(i, SPIN_MULTIPLICITY.DivalentSinglet);
+                        SPIN_MULTIPLICITY multiplicity = atom.getProperty(CDKConstants.SPIN_MULTIPLICITY);
+                        if (multiplicity != null)
+                            atomIndexSpinMap.put(i, multiplicity);
+                        else {
+                            // information loss, divalent but singlet or triplet?
+                            atomIndexSpinMap.put(i, SPIN_MULTIPLICITY.DivalentSinglet);
+                        }
                         break;
                     default:
                         logger.debug("Invalid number of radicals found: " + eCount);
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java
@@ -343,8 +343,9 @@ public void readAtomBlock(IAtomContainer readData) throws CDKException {
                                     }
                                     break;
                                 case "RAD":
-                                    int numElectons = MDLV2000Writer.SPIN_MULTIPLICITY.ofValue(Integer.parseInt(value))
-                                                                                      .getSingleElectrons();
+                                    MDLV2000Writer.SPIN_MULTIPLICITY spinMultiplicity = MDLV2000Writer.SPIN_MULTIPLICITY.ofValue(Integer.parseInt(value));
+                                    int numElectons = spinMultiplicity.getSingleElectrons();
+                                    atom.setProperty(CDKConstants.SPIN_MULTIPLICITY, spinMultiplicity);
                                     while (numElectons-- > 0) {
                                         readData.addSingleElectron(readData.getBuilder().newInstance(ISingleElectron.class, atom));
                                     }
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java
@@ -261,8 +261,12 @@ private void writeAtomBlock(IAtomContainer mol, IAtom[] atoms, Map<IChemObject,
                 case 1: // 2
                     rad = MDLV2000Writer.SPIN_MULTIPLICITY.Monovalent.getValue();
                     break;
-                case 2: // 1 or 3? Information loss as to which
-                    rad = MDLV2000Writer.SPIN_MULTIPLICITY.DivalentSinglet.getValue();
+                case 2:
+                    MDLV2000Writer.SPIN_MULTIPLICITY spinMultiplicity = atom.getProperty(CDKConstants.SPIN_MULTIPLICITY);
+                    if (spinMultiplicity != null)
+                        rad = spinMultiplicity.getValue();
+                    else // 1 or 3? Information loss as to which
+                        rad = MDLV2000Writer.SPIN_MULTIPLICITY.DivalentSinglet.getValue();
                     break;
             }
 

Original file line number	Diff line number	Diff line change
`@@ -343,8 +343,9 @@ public void readAtomBlock(IAtomContainer readData) throws CDKException {`
`343`	`343`	`}`
`344`	`344`	`break;`
`345`	`345`	`case "RAD":`
`346`		`- int numElectons = MDLV2000Writer.SPIN_MULTIPLICITY.ofValue(Integer.parseInt(value))`
`347`		`- .getSingleElectrons();`
	`346`	`+ MDLV2000Writer.SPIN_MULTIPLICITY spinMultiplicity = MDLV2000Writer.SPIN_MULTIPLICITY.ofValue(Integer.parseInt(value));`
	`347`	`+ int numElectons = spinMultiplicity.getSingleElectrons();`
	`348`	`+ atom.setProperty(CDKConstants.SPIN_MULTIPLICITY, spinMultiplicity);`
`348`	`349`	`while (numElectons-- > 0) {`
`349`	`350`	`readData.addSingleElectron(readData.getBuilder().newInstance(ISingleElectron.class, atom));`
`350`	`351`	`}`