adjusted calculation of def hash based on stereochemistry: include

optical activity when stereochemistry is 'UNKNOWN' based on request from colleague
ncats · Oct 29, 2024 · 808d623 · 808d623
1 parent 251f201
commit 808d623
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Showing 2 changed files with 38 additions and 2 deletions.
diff --git a/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java b/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java
@@ -62,9 +62,43 @@ public void testOpticalInDefinitionalHashCalcNeg() throws Exception {
         List<DefinitionalElement> definitionalElements = new ArrayList<>();
         defHashCalculator.computeDefinitionalElements(chem, definitionalElements::add);
         definitionalElements.forEach(de-> System.out.printf("key: %s = %s\n", de.getKey(), de.getValue()));
+        Assertions.assertTrue(definitionalElements.stream().noneMatch(de->de.getKey().equals(opticalActivityKey)));
+    }
+
+    @Test
+    public void testOpticalInDefinitionalHashCalcNeg2() throws Exception {
+        String opticalActivityKey="structure.properties.opticalActivity";
+        String structureJson = "{\n" +
+                "    \"opticalActivity\": \"UNSPECIFIED\",\n" +
+                "    \"molfile\": \"\\n  ACCLDraw07282209012D\\n\\n  5  4  0  0  0  0  0  0  0  0999 V2000\\n   10.5000   -8.5938    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   11.5229   -8.0032    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0\\n   11.5229   -6.8217    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0\\n   12.5460   -8.5939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   13.5692   -8.0032    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0  0  0  0\\n  2  3  1  0  0  0  0\\n  2  4  1  0  0  0  0\\n  4  5  1  0  0  0  0\\nM  END\",\n" +
+                "    \"stereoCenters\": 1,\n" +
+                "    \"definedStereo\": 0,\n" +
+                "    \"ezCenters\": 0,\n" +
+                "    \"charge\": 0,\n" +
+                "    \"mwt\": 92.56726,\n" +
+                "    \"count\": 1,\n" +
+                "    \"stereochemistry\": \"UNKNOWN\"\n" +
+                "}\n" +
+                "";
+        ObjectMapper om = new ObjectMapper();
+        Structure rawStructure = om.readValue(structureJson, Structure.class);
+        Structure instrumentedStructure =structureProcessor.instrument(rawStructure.toChemical(), true);
+        GinasChemicalStructure ginasChemicalStructure = new GinasChemicalStructure(instrumentedStructure);
+        ginasChemicalStructure.setStereoChemistry(Structure.Stereo.UNKNOWN);
+
+        ChemicalSubstanceBuilder builder = new ChemicalSubstanceBuilder();
+        ChemicalSubstance chem =builder
+                .setStructure(ginasChemicalStructure)
+                .addName("2-chlorobutane")
+                .build();
+        ChemicalSubstanceDefinitionalElementImpl defHashCalculator = new ChemicalSubstanceDefinitionalElementImpl();
+        List<DefinitionalElement> definitionalElements = new ArrayList<>();
+        defHashCalculator.computeDefinitionalElements(chem, definitionalElements::add);
+        definitionalElements.forEach(de-> System.out.printf("key: %s = %s\n", de.getKey(), de.getValue()));
         Assertions.assertTrue(definitionalElements.stream().anyMatch(de->de.getKey().equals(opticalActivityKey)));
     }
 
+
     @Test
     public void testOpticalInDefinitionalHashCalcPos() throws Exception {
         String opticalActivityKey="structure.properties.opticalActivity";
@@ -96,7 +130,7 @@ public void testOpticalInDefinitionalHashCalcPos() throws Exception {
         List<DefinitionalElement> definitionalElements = new ArrayList<>();
         defHashCalculator.computeDefinitionalElements(chem, definitionalElements::add);
         definitionalElements.forEach(de-> System.out.printf("key: %s = %s\n", de.getKey(), de.getValue()));
-        Assertions.assertTrue(definitionalElements.stream().anyMatch(de->de.getKey().equals(opticalActivityKey)));
+        Assertions.assertTrue(definitionalElements.stream().noneMatch(de->de.getKey().equals(opticalActivityKey)));
     }
 
     @Test

diff --git a/...ain/java/gsrs/module/substance/definitional/ChemicalSubstanceDefinitionalElementImpl.java b/...ain/java/gsrs/module/substance/definitional/ChemicalSubstanceDefinitionalElementImpl.java
@@ -10,6 +10,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 import java.util.function.Consumer;
 @Slf4j
@@ -18,7 +19,8 @@ public class ChemicalSubstanceDefinitionalElementImpl implements DefinitionalEle
     @Autowired
     private StructureProcessor structureProcessor;
 
-    private List<String> stereoUsingOpticalActivities = Arrays.asList( "UNKNOWN", "MIXED", "EPIMERIC", "RACEMIC");
+    private List<String> stereoUsingOpticalActivities = Collections.singletonList("UNKNOWN");
+    //changed to UNKNOWN based on Slack conversation on 29 Oct 2024 Arrays.asList( "UNKNOWN", "MIXED", "EPIMERIC", "RACEMIC");
 
     @Override
     public boolean supports(Object s) {