iBabel
By drc at Wed, Oct 5 2005 2:15pm |
Hi,
A while back I wrote an Applescript Studio front-end to OpenBabel, iBabel gives access to chemical file conversion, sub-structure searching, overlays, sorting and manipulation of lists of compounds. I've now updated this application to include structure viewing capabilities, using JMOLand JChempaint. http://www.macinchem.fsnet.co.uk/applescripts.htm
There is a new version of OpenBabel due to be released in a month or two and I was wondering if there was anything I should consider adding to iBabel?
Thanks
Movie export?
Is it possible to use iBabel to export movies? The app looks really nice by the way.
Movie export
Not at the moment, I'll see what might be possible
iBabel 2.0
Hi,
OpenBabel 2.0 has now been released and I have rebuilt iBabel. A couple of beta testers have used the new version without problem so I hope to release it soon. If anyone else would be willing to test it prior to release please let me know.
TIA
iBabel2.0 February 2006
Hello
I just installed iBabel on Mac OS X 10.3.8 and it does not work..i get messages like segmentation faults in the viewer, or error mentioning that some variables are not defined like one with outfile...
suggestions are welcome, because i am really looking forward to run it..this is very much needed in research
b
iBabel 2.x
Did you download the latest version (http://sourceforge.net/project/showfiles.php?group_id=40728)?
Together with the latest version of OpenBabel from the same site?
iBabel
Yes i have the last version of iBabel (i did not take the source though) and i compiles OpenBabel 2 before, OPenBabel2 seems to work ok for format conversion, i just tried it..
so not sure what to do...
many thanks
iBabel 2.0
Hi,
I'll have to try and find a machine running 10.3.8. I only have >10.4
I'll get back to you
iBabel
on OS X 10.3.8, iBabel 2 does not run on my machine, when i try to convert a smiles string to sdf it crashes, when i try to view, also
on mac oS X 10.4.2, it does not crash, but i can not convert a smiles string, i get the message variable_output_type not defined..same thing if i want to convert a 3D mol2 (one molecule that works in the viewer) to sdf for instance
i can not view a smiles string in the viewer, it works when i have a 3D mol2 as input with jmol..
this is where i am with the testing so far..
bruno
iBabel 2.0
Hi,
Can you try choosing the output file type from the dropdown menu.
Regarding SMILES conversion, OpenBabel does not (currently) have the ability to create 2D structures file types from SMILES. If you want to view a SMILES string you need to also install Marvin. Similarly OpenBabel cannot create 3D structures from 2D. Perhaps I should include all the Openbabel documentation, since I wrote it I can easily do this but it makes for a very long readme!
The creation of 2D or 3D structures is on the OpenBabel wishlist, if anyone has time to spare all help is welcome.
Thanks for the feedback it is very useful and much appreciated.
C
iBabel
it might be the autodetect for the file extension for the output that does not work..or maybe i made a mistake..now, with SDF 3D as input, it runs ok..
i think no need to add OpenBabel doc, most people can easily get there...but i missed the point with smile, i thought it could create a 2D...so this is my mistake in reading the manual..
maybe in the manual to use iBabel, some examples would be good about running Search and Similarity...
yet, no way to run on 10.3, the Java stuff seems to be a problem
for the 2d to 3d this is a real pain, we are working on that but so far not too good...in about one year we may have something, yet still single conf..
b
1D to 2D to 3D
The conversion (and coordinate creation) of SMILES to a 2D file format is on the OpenBabel wish list, as is the creation of 3D structures. If you can help at all your contributions would be very welcome. In additon, I'm sure any comments to the OpenBabel group will help prioritise the various requests.
C