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[Bkchem-user] Re: bkchem 0.9.0-pre1 some bugs

From: Beda Kosata
Subject: [Bkchem-user] Re: bkchem 0.9.0-pre1 some bugs
Date: Wed, 24 Nov 2004 08:31:13 +0000
User-agent: Mozilla Thunderbird 0.9 (X11/20041103)

I am reposting this letter to the mailing list because I thing that maybe the answers will be interesting to other people and because it rebounces off Piotrs mailserver with :

address@hidden on Wed, 24 Nov 2004 08:22:13 +0100
    The e-mail account does not exist at the organization this message
was sent to.  Check the e-mail address, or contact the recipient
directly to find out the correct address.
    < ns.vscht.cz #5.1.1 SMTP; 550 Brak rekordu SPF/MX nadawcy lub brak
poprawnej autoryzacji SMTP!>

Hi Piotr,
thanks for your letter. The first bug is simple to fix, I just forget to
take care of this case.

Piotr Wawrzyniak wrote:
Hi Beda.
I've just downloaded your bkchem, and tested it a little. I have found some bugs, that I thing could be corrected in the next pre release. Here what I've found:
1) Templates
When you don't have any templates yet, next change to templates mode (last icon on right), and then press mouse button on the desk, below error appears: #v+
Error: 4
IndexError Exception in Tk callback
Function: <bound method chem_paper._release1 of <paper.chem_paper object at 0xb6f2f3ec>> (type: <type 'instancemethod'>)
  Args: (<Tkinter.Event instance at 0xb6d9a50c>,)
  Event type: ButtonRelease (type num: 5)
Traceback (innermost last):
File "/usr/share/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__
    return apply(self.func, args)
File "/usr/share/python2.3/site-packages/bkchem/paper.py", line 225, in _release1
File "/usr/share/python2.3/site-packages/bkchem/modes.py", line 372, in mouse_up
File "/usr/share/python2.3/site-packages/bkchem/modes.py", line 972, in mouse_click
File "/usr/share/python2.3/site-packages/bkchem/modes.py", line 1043, in _get_transformed_template
File "/usr/share/python2.3/site-packages/bkchem/temp_manager.py", line 81, in get_transformed_template
IndexError: list index out of range

  Event contents:
    char: ??
    delta: 0
    height: ??
    keycode: ??
    keysym: ??
    keysym_num: ??
    num: 1
    send_event: False
    serial: 18702
    state: 256
    time: 624449
    type: 5
    widget: .-1224406964.-1224363924.-1225591572.-1225591828
    width: ??
    x: 324.0
    x_root: 475
    y: 147.0
    y_root: 348

2) New pdf, ps export:
When you export using these two new plugins, and when anything is selected, this in pdf/ps file one see also selections, it means these selection points. Maybe it is necessary to do self.paper.unselect_all() at first, or something other, that new library neads.

I know about it and you are right about the solution :)  However I
thought I will maybe leave it there to make it possible to do something
like "PDF screenshot". However it is probably not the way people want to
have it :) so I will fix it and probably add some switch for those who
would like to have the "screenshot mode".

3) The templates
The templates works quite fine. But I have some suggestions. The first maybe you should change a shortcut for selecting template atom. At present both hands are necessary to do it. I know, I overreact a little bit, but this shortcut is imho uncomfortable. Maybe two letters close one another i.e. ctrl+t+r. It could be also good to have this option after pressing the right mouse button. And another thing about templates. At present one have to select a template atom. It works fine but, imply many templates for the same molecule (if it has many bonding places). A solution could be to make something like drawing mode. At this mode, if two molecules will be close enough, it should be possible to connect them or to some atom, or bond, for example one could paint a naphthalene using two separate benzens ring, just by moving one to ring to the another. I release that sometimes such a feature could be bad idea, and thats why I suggest to make a special switch i menu for that. I hope I explained what I am thinking about quite clearly. I haven't look into source code, so I don't know how difficult will it be to implement.

Well, you are right that I could replace the shortcut, I thing something
like C-t would be enough :)  It was there mainly for historical reasons
(this function was in bkchem from version 0.1.0, however not usefull
because no user template mode was supported). On the other hand, you
don't need to push all the keys at one go you can do "C-t" then release
everything and then do "C-1" and it will work, its two independent
One thing about your template suggestion - it works :) If you put one benzene ring over a bond in another (the tolerance is a few pixels) bkchem will automatically concatenate it. In fact the template code and the code for concatenation share most of lines.

4. It could be useful to make one more option during instalation. Something similar to DESTDIR, for Makefiles. At present one can use option --root, but it also changes paths in executables (site_config.py, bkchem.py). Such thing could simplify making packages for distribution (rpm, deb, etc). At present I must 'sed' files (I know there are only two) and replaces paths.

I will try to do something about it :)

Wow I have made quite long letter, I hope not so boring. You do really good job, at present I am writing publication using your software, so keep doing your job. I will help you as much as I can, to make bkchem the better software.
Best regards

Thanks again for the bugreports and suggestions (and also the icon - its
nice, clean and certainly better than anything I would come with as I
don't have time for it :)


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