Thanks for your reply! I see that it can be done using bkchem, still I would prefer to be able to use it like a library. I tried to adjust that example script to use PNG(Cairo), but it fails:
 $ bkchem -b ~/Desktop/svg2png.py pydna.svg
Traceback (most recent call last):
  File "/usr/lib64/python2.5/site-packages/bkchem/bkchem.py", line 138, in <module>
    myapp.process_batch( opts)
  File "//usr/lib64/python2.5/site-packages/bkchem/main.py", line 1487, in process_batch
    execfile( plugin, the_globals)
  File "/home/reinis/Desktop/svg2png.py", line 18, in <module>
    convert_file( arg)
  File "/home/reinis/Desktop/svg2png.py", line 7, in convert_file
    if App.plugin_export( plugin, filename=outname):
  File "//usr/lib64/python2.5/site-packages/bkchem/main.py", line 1094, in plugin_export
    plugin = self.plugins[ pl_id]
KeyError: 'cairo_png'

Are the syntax for available plugins listed somewhere?


Reinis

It would be really useful to be able to export whole BKChem scene with multiple molecules, text and other objects to graphics (cairo) from Python script so it looks the same as it would be exported from BKChem.

Right now it even doesn't handle gracefully multiple molecules in one file (crashes when trying to remap atom ids; OASA-0.13.0):
In [73]: mol = oasa.cdml.file_to_mol(g)
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)

/home/reinis/Hack/XML/PyDOM/<ipython console> in <module>()

/usr/lib64/python2.5/site-packages/oasa/cdml.pyc in file_to_mol(f)
    110
    111 def file_to_mol( f):
--> 112   return text_to_mol( f.read())
    113
    114 def text_to_mol( text):

/usr/lib64/python2.5/site-packages/oasa/cdml.pyc in text_to_mol(text)
    115   gen = read_cdml( text)
    116   try:
--> 117     mol = gen.next()
    118   except StopIteration:
    119     return None

/usr/lib64/python2.5/site-packages/oasa/cdml.pyc in read_cdml(text)
     78         continue
     79       v1 = atom_id_remap[ bond_el.getAttribute( 'start')]
---> 80       v2 = atom_id_remap[ bond_el.getAttribute( 'end')]
     81       e = bond( order=int( type[1]), type=type[0])
     82       mol.add_edge( v1, v2, e=e)

KeyError: u'atom16912'