Writing support.

johnmay · johnmay · commit 75c1e1e323d9 · 2020-09-29T11:51:56.000+01:00
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
@@ -1119,6 +1119,60 @@ private void writeSgroups(IAtomContainer container, BufferedWriter writer, Map<I
                         writer.write(formatMDLInt(compNumber, 3));
                         writer.write('\n');
                         break;
+                    case Data:
+                        String data = sgroup.getValue(SgroupKey.Data);
+                        if (data == null)
+                            break;
+                        // replace CR/LF with space
+                        data = data.replaceAll("[\r\n]", " ");
+                        while (data.length() > 69) {
+                            writer.write("M  SCD ");
+                            writer.write(formatMDLInt(id, 3));
+                            writer.write(' ');
+                            writer.write(data.substring(0, 69));
+                            writer.write('\n');
+                            data = data.substring(69);
+                        }
+                        writer.write("M  SED ");
+                        writer.write(formatMDLInt(id, 3));
+                        writer.write(' ');
+                        writer.write(data);
+                        writer.write('\n');
+                        break;
+                    case DataFieldName:
+                        char[] pad = new char[30];
+                        Arrays.fill(pad, ' ');
+                        String name = sgroup.getValue(SgroupKey.DataFieldName);
+                        String fmt = sgroup.getValue(SgroupKey.DataFieldFormat);
+                        String units = sgroup.getValue(SgroupKey.DataFieldUnits);
+                        if (name == null)
+                            break;
+                        if (name.length() > 30)
+                            name = name.substring(0, 30);
+                        writer.write("M  SDT ");
+                        writer.write(formatMDLInt(id, 3));
+                        writer.write(' ');
+                        writer.write(name);
+                        writer.write(pad, 0, 30-name.length());
+                        if (fmt != null && fmt.length()>0 &&
+                            (fmt.charAt(0) == 'N' ||
+                             fmt.charAt(0) == 'F' ||
+                             fmt.charAt(0) == 'T')) {
+                            writer.write(fmt.charAt(0) + " ");
+                        } else {
+                            writer.write("  ");
+                        }
+                        if (units != null) {
+                            if (units.length() > 20)
+                                units = units.substring(0, 20);
+                            writer.write(units);
+                        }
+                        writer.write('\n');
+                        break;
+                    case DataFieldFormat:
+                    case DataFieldUnits:
+                        // written as part of the field name
+                        break;
                 }
             }
 
diff --git a/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000WriterTest.java b/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000WriterTest.java
@@ -23,6 +23,7 @@
  */
 package org.openscience.cdk.io;
 
+import org.hamcrest.CoreMatchers;
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -1026,4 +1027,25 @@ public void roundTripWithAtomList() throws Exception {
             assertThat(writtenMol, containsString("M  ALS   1  3 F F   N   O"));
         }
     }
+
+    @Test
+    public void dataSgroupRoundTrip() {
+      String path = "/data/mdl/hbr_acoh_mix.mol";
+      try (InputStream in = getClass().getResourceAsStream(path)) {
+        MDLV2000Reader     mdlr    = new MDLV2000Reader(in);
+        IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
+        IAtomContainer     mol     = mdlr.read(builder.newAtomContainer());
+        try (StringWriter sw = new StringWriter();
+             MDLV2000Writer writer = new MDLV2000Writer(sw)) {
+          writer.write(mol);
+          String output = sw.toString();
+          assertThat(output,
+                     CoreMatchers.containsString("M  SDT   3 WEIGHT_PERCENT                N %"));
+          assertThat(output,
+                     CoreMatchers.containsString("M  SED   3 33%"));
+        }
+      } catch (IOException | CDKException e) {
+        Assert.fail(e.getMessage());
+      }
+    }
 }
