Pre-work we will store this info as an Sgroup.

johnmay · johnmay · commit a2c803960a2e · 2020-07-20T12:34:04.000+01:00
diff --git a/base/core/src/main/java/org/openscience/cdk/sgroup/SgroupType.java b/base/core/src/main/java/org/openscience/cdk/sgroup/SgroupType.java
@@ -76,7 +76,9 @@ public enum SgroupType {
     CtabGeneric("GEN"),
 
     // extension for handling positional variation and distributed coordination bonds
-    ExtMulticenter("N/A");
+    ExtMulticenter("_MAP", false),
+    // extension for handling bond attachment, LO: in CXSMILES
+    ExtAttachOrdering("_APO", false);
 
 
     static final Map<String, SgroupType> map = new HashMap<>();
@@ -86,12 +88,29 @@ public enum SgroupType {
             map.put(t.ctabKey, t);
     }
 
-    private final String ctabKey;
+    private final String  ctabKey;
+    private final boolean ctabStandard;
 
     SgroupType(String ctabKey) {
-        this.ctabKey = ctabKey;
+        this(ctabKey, true);
     }
 
+    SgroupType(String ctabKey, boolean ctabStandard) {
+        this.ctabKey      = ctabKey;
+        this.ctabStandard = ctabStandard;
+    }
+
+
+    /**
+     * Indicates if this SGroup type is support by standard CTAB
+     * (Molfile/SDfile) sgroups.
+     * @return true/false
+     */
+    public boolean isCtabStandard() {
+        return ctabStandard;
+    }
+
+
     public String getKey() {
         return ctabKey;
     }
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
@@ -912,11 +912,7 @@ private void writeSgroups(IAtomContainer container, BufferedWriter writer, Map<I
         sgroups = new ArrayList<>(sgroups);
 
         // remove non-ctab Sgroups
-        Iterator<Sgroup> iter = sgroups.iterator();
-        while (iter.hasNext()) {
-            if (iter.next().getType() == SgroupType.ExtMulticenter)
-                iter.remove();
-        }
+        sgroups.removeIf(sgroup -> !sgroup.getType().isCtabStandard());
 
         for (List<Sgroup> wrapSgroups : wrap(sgroups, 8)) {
             // Declare the SGroup type
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
@@ -541,11 +541,7 @@ private void writeSgroupBlock(List<Sgroup> sgroups, Map<IChemObject, Integer> id
         sgroups = new ArrayList<>(sgroups);
 
         // remove non-ctab Sgroups
-        Iterator<Sgroup> iter = sgroups.iterator();
-        while (iter.hasNext()) {
-            if (iter.next().getType() == SgroupType.ExtMulticenter)
-                iter.remove();
-        }
+        sgroups.removeIf(sgroup -> !sgroup.getType().isCtabStandard());
 
         if (sgroups.isEmpty())
             return;
@@ -670,8 +666,8 @@ private void writeMol(IAtomContainer mol) throws IOException, CDKException {
         List<Sgroup> sgroups = getSgroups(mol);
 
         int numSgroups = 0;
-        for (int i = 0; i < sgroups.size(); i++)
-            if (sgroups.get(i).getType() != SgroupType.ExtMulticenter)
+        for (Sgroup sgroup : sgroups)
+            if (sgroup.getType().isCtabStandard())
                 numSgroups++;
 
         writer.write("BEGIN CTAB\n");
