[OpenBabel-Devel] XML changes

Sun, 09 May 2010 12:42:46 -0700 

Hi Chris,

I've just been following up a test failure (testsym.py) on Linux
related to CML roundtripping, presumably due to r3708.

It seems that a CML file with multiple molecules, when passed through
babel -icml myfile.cml -osmi, produces multiple SMIs on Windows or
Linux. However, if piped through babel it only works on Windows. In
other words...

(1) Windows: "type noel.txt | babel -icml -ocan" is fine
but
(2) Linux: "cat noel.txt | ../bin/babel -icml - -ocan" gives

***************************************************
:1: parser error : Extra content at the end of the document
a4" order="1"/>   <bond atomRefs2="a2 a5" order="1"/>  </bondArray> </molecule>
                                                                               ^
==============================
*** Open Babel Error  in XML Parser
  Extra content at the end of the document

C[C@@](F)(Cl)Br 
1 molecule converted
1 errors 1 info messages 42 audit log messages
***************************************************

Note that the error is actually at the end of </molecule>. noel.txt is attached.

- Noel

<?xml version="1.0"?>

<cml xmlns="http://www.xml-cml.org/schema";>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="C"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a4 a5">1</atomParity>

   </atom>

   <atom id="a3" elementType="Cl"/>

   <atom id="a4" elementType="Br"/>

   <atom id="a5" elementType="F"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="C"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a5 a4">1</atomParity>

   </atom>

   <atom id="a3" elementType="Cl"/>

   <atom id="a4" elementType="F"/>

   <atom id="a5" elementType="Br"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="C"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a5 a4">1</atomParity>

   </atom>

   <atom id="a3" elementType="Br"/>

   <atom id="a4" elementType="Cl"/>

   <atom id="a5" elementType="F"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="C"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a4 a5">1</atomParity>

   </atom>

   <atom id="a3" elementType="Br"/>

   <atom id="a4" elementType="F"/>

   <atom id="a5" elementType="Cl"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="C"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a4 a5">1</atomParity>

   </atom>

   <atom id="a3" elementType="F"/>

   <atom id="a4" elementType="Cl"/>

   <atom id="a5" elementType="Br"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="C"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a5 a4">1</atomParity>

   </atom>

   <atom id="a3" elementType="F"/>

   <atom id="a4" elementType="Br"/>

   <atom id="a5" elementType="Cl"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="Cl"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a5 a4">1</atomParity>

   </atom>

   <atom id="a3" elementType="C"/>

   <atom id="a4" elementType="Br"/>

   <atom id="a5" elementType="F"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="Cl"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a4 a5">1</atomParity>

   </atom>

   <atom id="a3" elementType="C"/>

   <atom id="a4" elementType="F"/>

   <atom id="a5" elementType="Br"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="Cl"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a4 a5">1</atomParity>

   </atom>

   <atom id="a3" elementType="Br"/>

   <atom id="a4" elementType="C"/>

   <atom id="a5" elementType="F"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="Cl"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a5 a4">1</atomParity>

   </atom>

   <atom id="a3" elementType="Br"/>

   <atom id="a4" elementType="F"/>

   <atom id="a5" elementType="C"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="Cl"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a5 a4">1</atomParity>

   </atom>

   <atom id="a3" elementType="F"/>

   <atom id="a4" elementType="C"/>

   <atom id="a5" elementType="Br"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="Cl"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a4 a5">1</atomParity>

   </atom>

   <atom id="a3" elementType="F"/>

   <atom id="a4" elementType="Br"/>

   <atom id="a5" elementType="C"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="Br"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a4 a5">1</atomParity>

   </atom>

   <atom id="a3" elementType="C"/>

   <atom id="a4" elementType="Cl"/>

   <atom id="a5" elementType="F"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="Br"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a5 a4">1</atomParity>

   </atom>

   <atom id="a3" elementType="C"/>

   <atom id="a4" elementType="F"/>

   <atom id="a5" elementType="Cl"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="Br"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a5 a4">1</atomParity>

   </atom>

   <atom id="a3" elementType="Cl"/>

   <atom id="a4" elementType="C"/>

   <atom id="a5" elementType="F"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="Br"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a4 a5">1</atomParity>

   </atom>

   <atom id="a3" elementType="Cl"/>

   <atom id="a4" elementType="F"/>

   <atom id="a5" elementType="C"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="Br"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a4 a5">1</atomParity>

   </atom>

   <atom id="a3" elementType="F"/>

   <atom id="a4" elementType="C"/>

   <atom id="a5" elementType="Cl"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="Br"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a5 a4">1</atomParity>

   </atom>

   <atom id="a3" elementType="F"/>

   <atom id="a4" elementType="Cl"/>

   <atom id="a5" elementType="C"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="F"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a5 a4">1</atomParity>

   </atom>

   <atom id="a3" elementType="C"/>

   <atom id="a4" elementType="Cl"/>

   <atom id="a5" elementType="Br"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="F"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a4 a5">1</atomParity>

   </atom>

   <atom id="a3" elementType="C"/>

   <atom id="a4" elementType="Br"/>

   <atom id="a5" elementType="Cl"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="F"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a4 a5">1</atomParity>

   </atom>

   <atom id="a3" elementType="Cl"/>

   <atom id="a4" elementType="C"/>

   <atom id="a5" elementType="Br"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="F"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a5 a4">1</atomParity>

   </atom>

   <atom id="a3" elementType="Cl"/>

   <atom id="a4" elementType="Br"/>

   <atom id="a5" elementType="C"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="F"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a5 a4">1</atomParity>

   </atom>

   <atom id="a3" elementType="Br"/>

   <atom id="a4" elementType="C"/>

   <atom id="a5" elementType="Cl"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

 <molecule>

  <atomArray>

   <atom id="a1" elementType="F"/>

   <atom id="a2" elementType="C">

    <atomParity atomRefs4="a1 a3 a4 a5">1</atomParity>

   </atom>

   <atom id="a3" elementType="Br"/>

   <atom id="a4" elementType="Cl"/>

   <atom id="a5" elementType="C"/>

  </atomArray>

  <bondArray>

   <bond atomRefs2="a1 a2" order="1"/>

   <bond atomRefs2="a2 a3" order="1"/>

   <bond atomRefs2="a2 a4" order="1"/>

   <bond atomRefs2="a2 a5" order="1"/>

  </bondArray>

 </molecule>

</cml>



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