Ignore data sgroups from CXSMILES

cdk · Apr 23, 2017 · bea78e7 · bea78e7
1 parent e7c69d9
commit bea78e7
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Showing 3 changed files with 82 additions and 0 deletions.
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java
@@ -865,6 +865,9 @@ else if (val == CxSmilesState.Radical.Trivalent)
                     case CtabMultipleGroup:
                         // display shortcuts are not output
                         break;
+                    case CtabData:
+                        // can be generated but currently ignored
+                        break;
                     default:
                         throw new UnsupportedOperationException("Unsupported Sgroup Polymer");
 

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesGeneratorTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesGeneratorTest.java
@@ -24,6 +24,7 @@
 package org.openscience.cdk.smiles;
 
 import org.junit.Test;
+import org.openscience.cdk.AtomContainer;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.io.MDLV2000Reader;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
@@ -102,4 +103,12 @@ public void chebi53695() throws Exception {
         }
     }
 
+
+    @Test public void chembl367774() throws Exception {
+        try (MDLV2000Reader mdlr = new MDLV2000Reader(getClass().getResourceAsStream("CHEMBL367774.mol"))) {
+            IAtomContainer container = mdlr.read(new AtomContainer());
+            SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.CxSmiles);
+            assertThat(smigen.create(container), is("OC(=O)C1=CC(F)=CC=2NC(=NC12)C3=CC=C(C=C3F)C4=CC=CC=C4"));
+        }
+    }
 }
diff --git a/storage/smiles/src/test/resources/org/openscience/cdk/smiles/CHEMBL367774.mol b/storage/smiles/src/test/resources/org/openscience/cdk/smiles/CHEMBL367774.mol
@@ -0,0 +1,70 @@
+
+  SciTegic05171617282D
+
+ 26 29  0  0  0  0            999 V2000
+    0.0446    3.6095    0.0000 O   0  0
+   -0.9971    3.0138    0.0000 C   0  0
+   -2.0337    3.6184    0.0000 O   0  0
+   -1.0028    1.5132    0.0000 C   0  0
+   -2.3155    0.7475    0.0000 C   0  0
+   -2.3155   -0.7475    0.0000 C   0  0
+   -3.3560   -1.3452    0.0000 F   0  0
+   -1.0028   -1.5132    0.0000 C   0  0
+    0.2917   -0.7475    0.0000 C   0  0
+    1.7138   -1.2033    0.0000 N   0  0
+    2.5889    0.0182    0.0000 C   0  0
+    1.7138    1.2033    0.0000 N   0  0
+    0.2917    0.7475    0.0000 C   0  0
+    4.0896    0.0290    0.0000 C   0  0
+    4.7453   -1.3220    0.0000 C   0  0
+    6.2418   -1.4248    0.0000 C   0  0
+    7.0791   -0.1803    0.0000 C   0  0
+    6.4199    1.1671    0.0000 C   0  0
+    4.9234    1.2700    0.0000 C   0  0
+    4.3957    2.3477    0.0000 F   0  0
+    8.5763   -0.2831    0.0000 C   0  0
+    9.2377   -1.6295    0.0000 C   0  0
+   10.7344   -1.7299    0.0000 C   0  0
+   11.5697   -0.4840    0.0000 C   0  0
+   10.9083    0.8623    0.0000 C   0  0
+    9.4117    0.9628    0.0000 C   0  0
+  1  2  1  0
+  2  3  2  0
+  2  4  1  0
+  4  5  2  0
+  5  6  1  0
+  6  7  1  0
+  6  8  2  0
+  8  9  1  0
+  9 10  1  0
+ 10 11  1  0
+ 11 12  2  0
+ 12 13  1  0
+  4 13  1  0
+  9 13  2  0
+ 11 14  1  0
+ 14 15  2  0
+ 15 16  1  0
+ 16 17  2  0
+ 17 18  1  0
+ 18 19  2  0
+ 14 19  1  0
+ 19 20  1  0
+ 17 21  1  0
+ 21 22  2  0
+ 22 23  1  0
+ 23 24  2  0
+ 24 25  1  0
+ 25 26  2  0
+ 21 26  1  0
+M  STY  2   1 DAT   2 DAT
+M  SLB  2   1   1   2   2
+M  SAL   1  1  10
+M  SDT   1 MRV_IMPLICIT_H
+M  SDD   1     0.5304   -0.4125    DR    ALL  0       0
+M  SED   1 IMPL_H1
+M  SAL   2  1  12
+M  SDT   2 MRV_IMPLICIT_H
+M  SDD   2     0.5304   -0.4125    DR    ALL  0       0
+M  SED   2 IMPL_H1
+M  END