On 9 May 2010 21:53, Chris Morley <[email protected]> wrote: > 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
I get the same result with that file. However, with the original file, if I compress some of the tags onto the same line I can get it to at least process all of the molecules: <bond atomRefs2="a2 a5" order="1"/></bondArray></molecule><molecule> <atomArray> However, then it baulks at the closing </cml>: ***************************** C[C@@](F)(Cl)Br C[C@@](F)(Cl)Br :1: parser error : StartTag: invalid element name </cml> ^ ============================== *** Open Babel Error in XML Parser StartTag: invalid element name C[C@@](F)(Cl)Br 3 molecules converted 1 errors 1 info messages 121 audit log messages ***************************** Using "babel -icml myfile.cml -ocan" still works just fine. I realise you can't debug this, Chris, but I'll file a bug with a description in any case. - Noel ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-Devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-devel
