Use the grammar's definition of nonWordCharacters

lib/highlighted-area-view.coffee

@@ -141,7 +141,8 @@ class HighlightedAreaView
 
     if atom.config.get('highlight-selected.onlyHighlightWholeWords')
       return unless @isWordSelected(lastSelection)
-      nonWordCharacters = atom.config.get('editor.nonWordCharacters')
+      selectionStart = lastSelection.getBufferRange().start
+      nonWordCharacters = @getNonWordCharacters(editor, selectionStart)
       allowedCharactersToSelect = atom.config.get('highlight-selected.allowedCharactersToSelect')
       nonWordCharactersToStrip = nonWordCharacters.replace(
         new RegExp("[#{allowedCharactersToSelect}]", 'g'), '')
@@ -253,19 +254,24 @@ class HighlightedAreaView
     else
       false
 
-  isNonWordCharacter: (character) ->
-    nonWordCharacters = atom.config.get('editor.nonWordCharacters')
-    new RegExp("[ \t#{escapeRegExp(nonWordCharacters)}]").test(character)
+  getNonWordCharacters: (editor, point) ->
+    scopeDescriptor = editor.scopeDescriptorForBufferPosition(point)
+    nonWordCharacters = atom.config.get('editor.nonWordCharacters', scope: scopeDescriptor)
+
+  isNonWord: (editor, range) ->
+    nonWordCharacters = @getNonWordCharacters(editor, range.start)
+    text = editor.getTextInBufferRange(range)
+    new RegExp("[ \t#{escapeRegExp(nonWordCharacters)}]").test(text)
 
   isNonWordCharacterToTheLeft: (selection) ->
     selectionStart = selection.getBufferRange().start
     range = Range.fromPointWithDelta(selectionStart, 0, -1)
-    @isNonWordCharacter(@getActiveEditor().getTextInBufferRange(range))
+    @isNonWord(@getActiveEditor(), range)
 
   isNonWordCharacterToTheRight: (selection) ->
     selectionEnd = selection.getBufferRange().end
     range = Range.fromPointWithDelta(selectionEnd, 0, 1)
-    @isNonWordCharacter(@getActiveEditor().getTextInBufferRange(range))
+    @isNonWord(@getActiveEditor(), range)
 
   setupStatusBar: =>
     return if @statusBarElement?

spec/fixtures/sample.php

@@ -1,5 +1,6 @@
 <?php
   $test = "$test";
   // Some $test @test file
+  // #test
   // Don't highlight thistest, or testthis
 ?>

spec/highlight-selected-spec.coffee

@@ -254,13 +254,24 @@ describe "HighlightSelected", ->
         expect(editorElement.querySelectorAll(
           '.highlight-selected .region')).toHaveLength(3)
 
-    describe "being able to highlight variables when not selecting '$'", ->
+    describe "not being able to highlight variables when not selecting '$'", ->
       beforeEach ->
         atom.config.set('highlight-selected.onlyHighlightWholeWords', true)
         range = new Range(new Point(1, 3), new Point(1, 7))
         editor.setSelectedBufferRange(range)
         advanceClock(20000)
 
-      it "finds 4 regions", ->
+      it "finds 0 regions", ->
         expect(editorElement.querySelectorAll(
-          '.highlight-selected .region')).toHaveLength(4)
+          '.highlight-selected .region')).toHaveLength(0)
+
+    describe "being able to highlight other strings when not selecting '@'", ->
+      beforeEach ->
+        atom.config.set('highlight-selected.onlyHighlightWholeWords', true)
+        range = new Range(new Point(3, 6), new Point(3, 10))
+        editor.setSelectedBufferRange(range)
+        advanceClock(20000)
+
+      it "finds 0 regions", ->
+        expect(editorElement.querySelectorAll(
+          '.highlight-selected .region')).toHaveLength(2)