Merge branch 'master' into fixInverse

ncats · Nov 9, 2023 · 75884dd · 75884dd
2 parents 4f3d448 + e96ad33
commit 75884dd
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Showing 5 changed files with 24 additions and 5 deletions.
diff --git a/...tances-core/src/main/java/gsrs/module/substance/controllers/LegacyGinasAppController.java b/...tances-core/src/main/java/gsrs/module/substance/controllers/LegacyGinasAppController.java
@@ -325,7 +325,23 @@ private static Chemical parseAndComputeCoordsIfNeeded(String input) throws IOExc
             			 }
             		 });
             	}
-                c.generateCoordinates();
+
+            	// It turns out that generating coordinates for a
+            	// structure with 2 charged species in CDK, for some reason
+            	// fails. Looks like it has something to do with trying to put charges near each other
+            	// to imply ionic interaction? Either way, adding 1 new free-floating moiety fixes this,
+            	// and layout can be generated then
+
+
+            	try {
+            		c.generateCoordinates();	
+            	}catch(Exception e) {
+            		Atom aa=c.addAtom("C");
+            		c.generateCoordinates();
+            		c.removeAtom(aa);
+            	}
+
+
 
             } catch (MolwitchException e) {
                 throw new IOException("error generating coordinates",e);

diff --git a/gsrs-module-substances-core/src/main/java/ix/core/chem/InchiStructureHasher.java b/gsrs-module-substances-core/src/main/java/ix/core/chem/InchiStructureHasher.java
@@ -30,7 +30,10 @@ public void hash(Chemical chem, String mol, BiConsumer<String, String> keyValueC
             stringBuilder.setCharAt(layerOffset, '_');
             stringBuilder.setCharAt(stringBuilder.length()-2, '_');
             String underscoredInsteadOfDash = stringBuilder.toString();
-            keyValueConsumer.accept(Structure.H_InChI_Key, underscoredInsteadOfDash);
+
+            // This used to use the underscore version for the "real" inchikey,
+            // but switching to use the dash form now.
+            keyValueConsumer.accept(Structure.H_InChI_Key, key);
             keyValueConsumer.accept(Structure.H_EXACT_HASH, underscoredInsteadOfDash);
             keyValueConsumer.accept(Structure.H_STEREO_INSENSITIVE_HASH, connectionOnly);
         }catch(IOException e){

diff --git a/gsrs-module-substances-core/src/main/java/ix/core/models/Structure.java b/gsrs-module-substances-core/src/main/java/ix/core/models/Structure.java
@@ -450,7 +450,7 @@ public String getInChIKey() {
             for (Value val : this.properties) {
                 if(val==null) continue;
                 if (Structure.H_InChI_Key.equals(val.label)) {
-                    return Objects.toString(val.getValue());
+                    return Objects.toString(val.getValue()).replaceAll("_", "-");                    
                 }
             }
             return getInChIKeyAndThrow();

diff --git a/gsrs-module-substances-core/src/main/resources/substances-core.conf b/gsrs-module-substances-core/src/main/resources/substances-core.conf
@@ -800,7 +800,7 @@ gsrs.renderers.list=[
             }
 },
 {
-    "name" : "CLEAN1",
+    "name" : "MONSTRUOUS",
     "renderer" :{
         "preset": "CLEAN",     //Note this part
         "options" : {

diff --git a/gsrs-ncats-substance-extension/pom.xml b/gsrs-ncats-substance-extension/pom.xml
@@ -80,7 +80,7 @@
         <dependency>
             <groupId>gov.nih.ncats</groupId>
             <artifactId>molwitch</artifactId>
-            <version>0.6.3-SNAPSHOT</version>
+            <version>0.6.5-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>org.projectlombok</groupId>