bugBKChem - Bugs: bug #26614, Feature Request: Multiple molecule...

 
 

bug #26614: Feature Request: Multiple molecule and whole scene handling in oasa.cdml

Submitted by:  None
Submitted on:  Tue 19 May 2009 01:46:07 PM UTC  
 
Category: NoneSeverity: 3 - Normal
Item Group: NoneStatus: In Progress
Privacy: PublicAssigned to: Beda Kosata <beda>
Open/Closed: Open

Add a New Comment (Rich MarkupRich Markup):
   

You are not logged in

Please log in, so followups can be emailed to you.

 

Tue 19 May 2009 03:13:27 PM UTC, comment #3:

Never mind.. found an answer in the source. It's working now. Thanks!

Reinis

Anonymous
Tue 19 May 2009 02:33:19 PM UTC, comment #2:

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

Anonymous
Tue 19 May 2009 01:58:15 PM UTC, comment #1:

It is possible to do a batch conversion from CDML to cairo using a batch script for BKChem. It is described here:

http://bkchem.zirael.org/wiki/bkchem_to_odf_conversion

you just need to rename the plugin to your desired output.
OASA will never be able to support the same output, because it handles only molecules - no graphics, text, etc. This is added on top of it in BKChem. You are right that the import of multiple molecules should be handled though - I am adding it to my long to-do list :)

Cheers
Beda

Beda Kosata <beda>
Project AdministratorIn charge of this item.
Tue 19 May 2009 01:46:07 PM UTC, original submission:

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'

Anonymous

 

(Note: upload size limit is set to 16384 kB, after insertion of the required escape characters.)

Attach File(s):
   
   
Comment:
   

No files currently attached

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by beda (Posted a comment)
  •  

    Do you think this task is very important?
    If so, you can click here to add your encouragement to it.
    This task has 0 encouragements so far.

    Only logged-in users can vote.

     

    Please enter the title of George Orwell's famous dystopian book (it's a date):

     

     

    Follow 2 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 19 May 2009 01:58:15 PM UTCbedaStatusNone=>In Progress
      Assigned toNone=>beda

    Back to the top


    Powered by Savane 3.1-cleanup