Noel O'Boyle wrote:
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.
Could this be another problem with line endings? The file noel.txt has 0D 0D 0A at the end of every line. Attached is a version with just 0A instead. Maybe that behaves differently? Otherwise, I don't know and with only Windows would find it difficult to debug Linux piping.
The change in r3708 was to do with multiple files and I would not expect it to be exercised with a single file. But libxml2 is a bit opaque to me, so it may be.
Chris
<?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>
------------------------------------------------------------------------------
_______________________________________________ OpenBabel-Devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-devel
