bugBKChem - Bugs: bug #19259, Length of bonds, placement of...


bug #19259: Length of bonds, placement of heteroatoms

Submitted by:  None
Submitted on:  Fri 09 Mar 2007 03:38:37 PM UTC  
Votes:  1  
Category:  None Severity:  3 - Normal
Item Group:  general Status:  Fixed
Privacy:  Public Assigned to:  Beda Kosata <beda>
Open/Closed:  Closed

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Tue 30 Oct 2007 01:48:13 PM UTC, comment #6:

0.12.0_pre6 binary release for windows is packaged in the way suggested below. tuning.py is editable and allows for tuning of some aspects of BKChem exports and drawing.

Beda Kosata <beda>
Project AdministratorIn charge of this item.
Wed 06 Jun 2007 11:53:37 AM UTC, comment #5:

Finally, I could make it. Yes, it works as you suggested, but it is quite complicated. In order to get more wikipedians to use BKchem, it would be nice, if you could package the next version in that way. Concerning the parameters, we are currently figuring out the most appropriate values.

Regards, Leyo

Wed 16 May 2007 03:58:57 AM UTC, comment #4:

In the exe version all the compiled source code is packed as part of the exe file and therefore it is not possible to change it. However there is a trick to using tuning.py. At first you have to get the zip distribution and copy the file tuning.py to the same directory where the bkchem.exe resides. Then you have to open the bkchem.exe file with some zip-compatible program, I have tried it with a evaluation version of WinRAR, find the file tuning.pyc inside the archive and remove it. After resaving the archive (if needed) you should have a slightly smaller bkchem.exe and a tuning.py file sitting besides it. In this configuration it should be possible to change the tuning.py file to change the behaviour of BKChem.
If I don't forget to do it, I will package the next release in this way.

Beda Kosata <beda>
Project AdministratorIn charge of this item.
Mon 07 May 2007 11:43:58 AM UTC, comment #3:

Hi Beda. I have tried the exe-version of 0.12.0_pre2, but it does not contain the file "tuning.py". Also if I add this file to the correct folder, it does not work. As I have heard from another Wikipedia user, who has Python installed, the zip-version works. Thanks for your feedback.

Regards, Leyo

Fri 13 Apr 2007 09:46:35 AM UTC, comment #2:

In the recent relase 0.12.0_pre2 I have added the possibility to tweak possitioning of atoms in the SVG export.
It works only if you have the BKChem sources.
You can edit file bkchem/tuning.py and experimentally adjust the values in:

## SVG export
class SVG:
text_x_shift = 1.3
text_y_shift = 0

to some other value that would seem best to you.
The problem here is not 100% accurate measurement of text size by the underlying library and also the fact that the system might use slightly different font whan rendering SVG than what was used by BKChem (there is only name reference to the font, the font is not part of SVG).
(I am sorry that I did not respond before, but the savannah site went down just when I was working on it and I did not check back if the response was recorded properly.)
Please let me know if it works for you.

Beda Kosata <beda>
Project AdministratorIn charge of this item.
Thu 12 Apr 2007 05:37:14 PM UTC, comment #1:

It seems that BKchem displays the drawn chemical structure correct in its edit windows but slightly moves atoms in the output-svg.

Tom <rhododendron>
Fri 09 Mar 2007 03:38:37 PM UTC, original submission:

I draw chemical structures for Wikipedia. As I prefer SVG, I use BKchem to do that. Unfortunately, the length of the bonds is not steady, when adding heteroatoms (Br in the attached file). The oxygen atom is not placed exactly in the middle of an ether bond (e.g. http://commons.wikimedia.org/wiki/Image:Structure_Oxazolidine.svg or see attachment). Or if the ketogroup is aslant, the oxygen is also misplaced in my opinion. I know that these are little bugs, but I hope BKchem can be improved further.




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file #12163:  bug.svg added by None (15KiB - image/svg+xml - Please contact me on http://commons.wikimedia.org/wiki/User_talk:Leyo)


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    Follow 6 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2007-10-30 beda StatusReady For Test => Fixed
        Open/ClosedOpen => Closed
    2007-04-13 beda StatusNone => Ready For Test
        Assigned toNone => beda
    2007-04-12 rhododendron Carbon-Copy- => Added rhododendron
    2007-03-09 None Attached File- => Added bug.svg, #12163

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