molconvert misaligns functional groups exported to png

Exporting structures to graphical file formats such as png using molconvert does not produce properly aligned functional group labels. For example, groups such as "CO2Me" are often rendered with the connecting bond aligned to the center of the functional group (somewhere around the "2") rather that always at the terminal "C". This defect renders molconvert useless for generating graphics for structures which contain any multi-character functional group labels. I need to process sd files containing many hundreds of structures, so manually exporting individual images from Marvin Sketch (which does work properly) is not an option.

Hi, 

The problem is in that sdf does not support the possibility to store the information where to connect the bonds of the abbreviated groups.  I tried it and it looks like the same if you open an sdf in Marvin or you create a png from sdf.  If you draw an abbrevgroup in Marvin, it has all the information and after saving in mrv format the png created by molconvert looks fine.

Is it possible to use mrv format?

Best regards,

Peter

 

Exporting to a multi-structure .mrv file from Instant JChem and then converting to individual .png graphics using molconvert -m does produce accurate graphics. The only remaining difficulty is renaming the resulting large group of graphics files to have a usable name associated with each structure rendering. Separately exporting the appropriate name field from the Instant JChem database as a CSV file makes this possible via a file renaming utility or script. If done very carefully.

Thanks for the mrv tip!