Add a comment so SAChem pick up why their logic was a bad idea and guard against future modification.

johnmay · johnmay · commit 120e17e2a20e · 2021-01-17T21:23:19.000Z
diff --git a/base/core/src/main/java/org/openscience/cdk/config/IsotopeFactory.java b/base/core/src/main/java/org/openscience/cdk/config/IsotopeFactory.java
@@ -214,8 +214,16 @@ public IIsotope getMajorIsotope(int elem) {
             }
             if (major != null)
                 this.majorIsotope[elem] = major;
-            else
+            else {
                 logger.error("Could not find major isotope for: ", elem);
+                // Note for SAChem:
+                // Major (most abundant) isotope means something specific and in general
+                // you shouldn't assign it to a structure unless you're working with mass
+                // spectra definitely setting the InChI values is not sensible "(98)Tc" is synthetic
+                // for example!!!
+                // see also:
+                // https://www.nextmovesoftware.com/talks/Mayfield_BuildingOnSand_InChI_201708.pdf
+            }
         }
         return clone(major);
     }

Original file line number	Diff line number	Diff line change
`@@ -214,8 +214,16 @@ public IIsotope getMajorIsotope(int elem) {`
`214`	`214`	`}`
`215`	`215`	`if (major != null)`
`216`	`216`	`this.majorIsotope[elem] = major;`
`217`		`- else`
	`217`	`+ else {`
`218`	`218`	`logger.error("Could not find major isotope for: ", elem);`
	`219`	`+ // Note for SAChem:`
	`220`	`+ // Major (most abundant) isotope means something specific and in general`
	`221`	`+ // you shouldn't assign it to a structure unless you're working with mass`
	`222`	`+ // spectra definitely setting the InChI values is not sensible "(98)Tc" is synthetic`
	`223`	`+ // for example!!!`
	`224`	`+ // see also:`
	`225`	`+ // https://www.nextmovesoftware.com/talks/Mayfield_BuildingOnSand_InChI_201708.pdf`
	`226`	`+ }`
`219`	`227`	`}`
`220`	`228`	`return clone(major);`
`221`	`229`	`}`