Make it an option to omit major isotopes depiction (default will be t…

…o include them)
cdk · Sep 11, 2017 · d8cd6d6 · d8cd6d6
1 parent afb7a68
commit d8cd6d6
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Showing 2 changed files with 19 additions and 3 deletions.
diff --git a/...src/main/java/org/openscience/cdk/renderer/generators/standard/StandardAtomGenerator.java b/...src/main/java/org/openscience/cdk/renderer/generators/standard/StandardAtomGenerator.java
@@ -30,6 +30,7 @@
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IIsotope;
 import org.openscience.cdk.interfaces.IPseudoAtom;
+import org.openscience.cdk.renderer.RendererModel;
 import org.openscience.cdk.renderer.generators.standard.AbbreviationLabel.FormattedText;
 
 import java.awt.Font;
@@ -111,9 +112,10 @@ private StandardAtomGenerator(Font font, double adjunctSpacing, double scriptSiz
      * @param container structure to which the atom belongs
      * @param atom      the atom to generate the symbol for
      * @param position  the hydrogen position
+     * @param model     additional rendering options
      * @return atom symbol
      */
-    AtomSymbol generateSymbol(IAtomContainer container, IAtom atom, HydrogenPosition position) {
+    AtomSymbol generateSymbol(IAtomContainer container, IAtom atom, HydrogenPosition position, RendererModel model) {
         if (atom instanceof IPseudoAtom) {
             IPseudoAtom pAtom = (IPseudoAtom) atom;
             if (pAtom.getAttachPointNum() <= 0)
@@ -127,7 +129,9 @@ AtomSymbol generateSymbol(IAtomContainer container, IAtom atom, HydrogenPosition
 
             // unset the mass if it's the major isotope (could be an option)
             Integer mass = atom.getMassNumber();
-            if (mass != null && isMajorIsotope(number, mass)) {
+            if (mass != null &&
+                model.get(StandardGenerator.OmitMajorIsotopes.class) &&
+                isMajorIsotope(number, mass)) {
                 mass = null;
             }
 

diff --git a/...sic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardGenerator.java b/...sic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardGenerator.java
@@ -371,7 +371,7 @@ private AtomSymbol[] generateAtomSymbols(IAtomContainer container,
                 if (remapped) {
                     symbols[i] = atomGenerator.generateAbbreviatedSymbol(symbolRemap.get(atom), hPosition);
                 } else {
-                    symbols[i] = atomGenerator.generateSymbol(container, atom, hPosition);
+                    symbols[i] = atomGenerator.generateSymbol(container, atom, hPosition, parameters);
                 }
 
                 if (symbols[i] != null) {
@@ -1072,4 +1072,16 @@ public Double getDefault() {
             return 0.6;
         }
     }
+
+    /**
+     * Whether Major Isotopes e.g. 12C, 16O should be omitted.
+     */
+    public static final class OmitMajorIsotopes extends AbstractGeneratorParameter<Boolean> {
+
+        /**{@inheritDoc} */
+        @Override
+        public Boolean getDefault() {
+            return false;
+        }
+    }
 }