Commits

Joe Townsend  committed 1bcec29

correcting numeric bond orders that had appeared in the tests for the molecular convention

  • Participants
  • Parent commits d2485ec

Comments (0)

Files changed (15)

File src/test/resources/org/xmlcml/www/convention/molecular/invalid/atomRefs2-must-contain-two-different-ids-2.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a1 a2" order="1">
+            <cml:bond id="b1" atomRefs2="a1 a2" order="S">
                 <cml:bondStereo atomRefs2="a1 a1">H</cml:bondStereo>
             </cml:bond>
-            <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+            <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
     </cml:molecule>
 </cml:cml>

File src/test/resources/org/xmlcml/www/convention/molecular/invalid/bondStereo-atomRefs2-must-match-parent-bonds-1.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a1 a2" order="1">
+            <cml:bond id="b1" atomRefs2="a1 a2" order="S">
                 <cml:bondStereo atomRefs2="a1 a3">H</cml:bondStereo>
             </cml:bond>
-            <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+            <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
     </cml:molecule>
 </cml:cml>

File src/test/resources/org/xmlcml/www/convention/molecular/invalid/bondStereo-atomRefs2-must-match-parent-bonds-2.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a1 a2" order="1">
+            <cml:bond id="b1" atomRefs2="a1 a2" order="S">
                 <cml:bondStereo atomRefs2="a2 a3">H</cml:bondStereo>
             </cml:bond>
-            <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+            <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
     </cml:molecule>
 </cml:cml>

File src/test/resources/org/xmlcml/www/convention/molecular/invalid/bondStereo-atomRefs2-must-match-parent-bonds-3.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a1 a2" order="1">
+            <cml:bond id="b1" atomRefs2="a1 a2" order="S">
                 <cml:bondStereo atomRefs2="a3 a1">H</cml:bondStereo>
             </cml:bond>
-            <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+            <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
     </cml:molecule>
 </cml:cml>

File src/test/resources/org/xmlcml/www/convention/molecular/invalid/bondStereo-atomRefs2-must-match-parent-bonds-4.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a1 a2" order="1">
+            <cml:bond id="b1" atomRefs2="a1 a2" order="S">
                 <cml:bondStereo atomRefs2="a3 a2">H</cml:bondStereo>
             </cml:bond>
-            <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+            <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
     </cml:molecule>
 </cml:cml>

File src/test/resources/org/xmlcml/www/convention/molecular/invalid/bondStereo-invalid-parent-1.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a1 a2" order="1" />
-            <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+            <cml:bond id="b1" atomRefs2="a1 a2" order="S" />
+            <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
         <cml:bondStereo atomRefs2="a1 a2">H</cml:bondStereo>
     </cml:molecule>

File src/test/resources/org/xmlcml/www/convention/molecular/invalid/bondStereo-invalid-parent-2.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a1 a2" order="1">
+            <cml:bond id="b1" atomRefs2="a1 a2" order="S">
                 <foreign-element>
                     <cml:bondStereo>H</cml:bondStereo>
                 </foreign-element>
             </cml:bond>
-                      <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+                      <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
     </cml:molecule>
 </cml:cml>

File src/test/resources/org/xmlcml/www/convention/molecular/invalid/cis-bondStereo-must-have-atomRefs4.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a1 a2" order="1">
+            <cml:bond id="b1" atomRefs2="a1 a2" order="S">
                 <cml:bondStereo>C</cml:bondStereo>
             </cml:bond>
-            <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+            <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
     </cml:molecule>
 </cml:cml>

File src/test/resources/org/xmlcml/www/convention/molecular/invalid/hatch-bondStereo-must-not-have-atomRefs4.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a1 a2" order="1">
+            <cml:bond id="b1" atomRefs2="a1 a2" order="S">
                 <cml:bondStereo atomRefs4="a1 a2 a3 a4">H</cml:bondStereo>
             </cml:bond>
-            <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+            <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
     </cml:molecule>
 </cml:cml>

File src/test/resources/org/xmlcml/www/convention/molecular/invalid/trans-bondStereo-must-have-atomRefs4.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a1 a2" order="1">
+            <cml:bond id="b1" atomRefs2="a1 a2" order="S">
                 <cml:bondStereo>T</cml:bondStereo>
             </cml:bond>
-            <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+            <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
     </cml:molecule>
 </cml:cml>

File src/test/resources/org/xmlcml/www/convention/molecular/invalid/wedge-bondStereo-must-not-have-atomRefs4.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a1 a2" order="1">
+            <cml:bond id="b1" atomRefs2="a1 a2" order="S">
                 <cml:bondStereo atomRefs4="a1 a2 a3 a4">W</cml:bondStereo>
             </cml:bond>
-            <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+            <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
     </cml:molecule>
 </cml:cml>

File src/test/resources/org/xmlcml/www/convention/molecular/valid/bondStereo-atomRefs2-must-match-parent-bonds-1.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a1 a2" order="1">
+            <cml:bond id="b1" atomRefs2="a1 a2" order="S">
                 <cml:bondStereo>H</cml:bondStereo>
             </cml:bond>
-            <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+            <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
     </cml:molecule>
 </cml:cml>

File src/test/resources/org/xmlcml/www/convention/molecular/valid/bondStereo-atomRefs2-must-match-parent-bonds-2.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a2 a1" order="1">
+            <cml:bond id="b1" atomRefs2="a2 a1" order="S">
                 <cml:bondStereo>H</cml:bondStereo>
             </cml:bond>
-            <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+            <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
     </cml:molecule>
 </cml:cml>

File src/test/resources/org/xmlcml/www/convention/molecular/valid/bondStereo-other-should-have-dictRef.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a1 a2" order="1">
+            <cml:bond id="b1" atomRefs2="a1 a2" order="S">
                 <cml:bondStereo dictRef="cmlDictionary:dummy">other</cml:bondStereo>
             </cml:bond>
-            <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+            <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
     </cml:molecule>
 </cml:cml>

File src/test/resources/org/xmlcml/www/convention/molecular/warning/bondStereo-other-should-have-dictRef.cml

             <cml:atom elementType="Br" id="a5" />
         </cml:atomArray>
         <cml:bondArray>
-            <cml:bond id="b1" atomRefs2="a1 a2" order="1">
+            <cml:bond id="b1" atomRefs2="a1 a2" order="S">
                 <cml:bondStereo>other</cml:bondStereo>
             </cml:bond>
-            <cml:bond id="b2" atomRefs2="a1 a3" order="1" />
-            <cml:bond id="b3" atomRefs2="a1 a4" order="1" />
-            <cml:bond id="b4" atomRefs2="a1 a5" order="1" />
+            <cml:bond id="b2" atomRefs2="a1 a3" order="S" />
+            <cml:bond id="b3" atomRefs2="a1 a4" order="S" />
+            <cml:bond id="b4" atomRefs2="a1 a5" order="S" />
         </cml:bondArray>
     </cml:molecule>
 </cml:cml>