Correctly support SUP Sgroup in V3000

johnmay · johnmay · commit 3f0474742efe · 2020-07-19T12:13:08.000+01:00
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
@@ -548,19 +548,28 @@ public void readSGroup(IAtomContainer readData) throws CDKException {
                     options = parseOptions(exhaustStringTokenizer(tokenizer));
                 }
 
+                Sgroup sgroup = new Sgroup();
                 // now interpret line
                 if (type.startsWith("SUP")) {
+                    sgroup.setType(SgroupType.CtabAbbreviation);
                     Iterator<String> keys = options.keySet().iterator();
-                    int atomID = -1;
                     String label = "";
                     while (keys.hasNext()) {
                         String key = keys.next();
                         String value = options.get(key);
                         try {
                             if (key.equals("ATOMS")) {
                                 StringTokenizer atomsTokenizer = new StringTokenizer(value);
-                                Integer.parseInt(atomsTokenizer.nextToken()); // should be 1, int atomCount =
-                                atomID = Integer.parseInt(atomsTokenizer.nextToken());
+                                int nExpected = Integer.parseInt(atomsTokenizer.nextToken());
+                                while (atomsTokenizer.hasMoreTokens()) {
+                                    sgroup.addAtom(readData.getAtom(Integer.parseInt(atomsTokenizer.nextToken())-1));
+                                }
+                            } else if (key.equals("XBONDS")) {
+                                StringTokenizer xbonds = new StringTokenizer(value);
+                                int nExpected = Integer.parseInt(xbonds.nextToken());
+                                while (xbonds.hasMoreTokens()) {
+                                    sgroup.addBond(readData.getBond(Integer.parseInt(xbonds.nextToken())-1));
+                                }
                             } else if (key.equals("LABEL")) {
                                 label = value;
                             } else {
@@ -573,18 +582,16 @@ public void readSGroup(IAtomContainer readData) throws CDKException {
                             logger.debug(exception);
                             throw new CDKException(error, exception);
                         }
-                        if (atomID != -1 && label.length() > 0) {
-                            IAtom original = readData.getAtom(atomID - 1);
-                            IAtom replacement = original;
-                            if (!(original instanceof IPseudoAtom)) {
-                                replacement = readData.getBuilder().newInstance(IPseudoAtom.class,
-                                                                                original);
-                            }
-                            ((IPseudoAtom) replacement).setLabel(label);
-                            if (!replacement.equals(original))
-                                AtomContainerManipulator.replaceAtomByAtom(readData, original, replacement);
+                        if (!sgroup.getAtoms().isEmpty() && label.length() > 0) {
+                            sgroup.setSubscript(label);
                         }
                     }
+                    List<Sgroup> sgroups = readData.getProperty(CDKConstants.CTAB_SGROUPS);
+                    if (sgroups == null)
+                        sgroups = new ArrayList<>();
+                    sgroups.add(sgroup);
+                    readData.setProperty(CDKConstants.CTAB_SGROUPS,
+                                         sgroups);
                 } else {
                     logger.warn("Skipping unrecognized SGROUP type: " + type);
                 }
diff --git a/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java b/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java
@@ -69,6 +69,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.StringReader;
+import java.io.StringWriter;
 import java.nio.charset.StandardCharsets;
 import java.util.Iterator;
 import java.util.List;
@@ -1864,4 +1865,16 @@ public void testBadAtomCoordinateFormat() throws Exception {
             assertThat(expr, is(expected));
         }
     }
+
+    @Test public void sgroupsAbbrRoundTrip() throws IOException, CDKException {
+        StringWriter sw = new StringWriter();
+        try (InputStream in = getClass().getResourceAsStream("sgroup-sup.mol3");
+             MDLV3000Reader mdlr = new MDLV3000Reader(in);
+             MDLV2000Writer mdlw = new MDLV2000Writer(sw)) {
+            IAtomContainer mol = SilentChemObjectBuilder.getInstance().newAtomContainer();
+            mol = mdlr.read(mol);
+            mdlw.write(mol);
+        }
+        assertThat(sw.toString(), containsString("M  SAL   1  2   2   3"));
+    }
 }
diff --git a/storage/ctab/src/test/resources/org/openscience/cdk/io/sgroup-sup.mol3 b/storage/ctab/src/test/resources/org/openscience/cdk/io/sgroup-sup.mol3
@@ -0,0 +1,20 @@
+Acetonitrile
+
+
+  0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 3 2 1 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 64.4346 -22.1251 0 0
+M  V30 2 C 65.9747 -22.1251 0 0
+M  V30 3 N 67.5145 -22.1251 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 3 2 3
+M  V30 END BOND
+M  V30 BEGIN SGROUP
+M  V30 1 SUP 0 ATOMS=(2 2 3) SAP=(3 2 1 1) XBONDS=(1 1) LABEL=CN
+M  V30 END SGROUP
+M  V30 END CTAB
+M  END
