Parsing a document

I'm trying to take a string and read it into an MDocument using parseMRV() and finding no success. Here's my string - what's wrong with it?





<MDocument> <MChemicalStruct> <molecule molID="m1"> <atomArray atomID="a1 a2 a3 a4 a5 a6" elementType="C C C C C C" x2="-10.324999809265137 -11.658669150313395 -11.658669150313395 -10.324999809265137 -8.991330468216878 -8.991330468216878" y2="9.531700674941323 8.761683734382283 7.221649853264202 6.451632912705161 7.221649853264202 8.761683734382283"></atomArray> <bondArray> <bond atomRefs2="a1 a2" order="1"></bond> <bond atomRefs2="a1 a6" order="2"></bond> <bond atomRefs2="a2 a3" order="2"></bond> <bond atomRefs2="a3 a4" order="1"></bond> <bond atomRefs2="a4 a5" order="2"></bond> <bond atomRefs2="a5 a6" order="1"></bond> </bondArray> </molecule>


</MChemicalStruct> </MDocument>

Nevermind...





Apparently, there must be newlines in the content in order for it to parse properly...

Can you confirm that you use Marvin 4.1.x?

Looks like 4.1.6...





I did a quick and dirty addition of newlines after tags and that worked so I ended up using JDOM to read in the XML and write it back out with the newline option turned on and then MDocument.parseMRV() read it in without problems.

Meanwhile, I have found a bug in current Marvin (5.0.2_1):MDocument.parseMRV(String) throws NullPointerException.


I fixed it in this moment.


Marvin 5.0.x accepts also one line MRV sources (without '\n'-s).


In new Marvin, the CML root tag is obligate but it also accept old MRV-s for backward compatibility.

Code:

<?xml version="1.0" ?> <cml> <MDocument> ... </MDocument> ... </cml>