Remove empty space from structures with R and S groups
Are you sure that the R and S are in the mol file and not part of the xml envelope?

Stereochemical R and S descriptors would not make any sense for a molecule like anthracene!

Is it conceivable that the letters come from Risk and Safety statements? 

It would be helpful if you could upload the original mol file somewhere.


EDIT 1

The file that you kindly uploaded is supposed to be a V2000 mol file, but it is not standards-compliant.

(The full specifications can be obtained from Accelrys upon registration.)

The first flaw is already in the header! The header is supposed to have a length of three lines.

The following CTAB should start with the counts line (in line 4 - note that we're not using zero-based indexing here).

With this flawed format, OpenBabel, a standard tool for the conversion of chemical data formats, casts an error.


EDIT 2

The rest of the file, including the stereochemical descriptors, seemed to be fine.

Once I had inserted the missing blank line in the header, a PNG could be generated using

obabel -imol 498268e9.txt -opng -O stuff.png




OpenBabel comes with bindings for Python, Java, C++ and whatnot. You might want to talk to your IT about some refactoring ;)