mainGChemPaint - Support: sr #106032, Shameless wish list for 0.8.4


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sr #106032: Shameless wish list for 0.8.4

Submitter:  Takashi Suyama <tak1150>
Submitted:  Thu 27 Sep 2007 07:40:52 PM UTC
Category:  None Priority:  5 - Normal
Severity:  1 - Wish Status:  None
Privacy:  Public Assigned to:  jean_brefort
Open/Closed:  Open Operating System:  GNU/Linux

Jump to the original submission

Tue 15 Jul 2008 01:19:57 PM UTC, comment #11: 

about comment #6:

- point 1 is mostly fixed (no more white rectangle hiding the bonds), just I need to allow to align the H atom, if any, vertically as well as horizontally when better.

- point 2 is fixed.

Both are only in the 0.10 branch, of course, no chance for 0.8 since these needs too much API changes.

Jean Bréfort <jean_brefort>
Group administrator
Sun 21 Oct 2007 11:57:21 AM UTC, comment #10: 

item #3 (default theme choice) fixed in cvs. Will be in 0.8.4.

Jean Bréfort <jean_brefort>
Group administrator
Wed 03 Oct 2007 09:48:09 AM UTC, comment #9: 

Most of the to-do list is in the sources, most recent version being in gchemutils-0.9. Other items are just in my head.

Debian packaging is done by the debichem team. Michael and Daniel do an excellent job. Seems they are blocked at the moment by openbabel-2.1 (sa far as I can tell, there is a license issue with libinchi, and you know that license issues are important in debian).

Thanks for advocating gchempaint in Ubuntu forum. Jordan Mantha  (LaserJock)told me about that.

You can help with your feedback, and may be the documentation, my english being not so fluent.

Jean Bréfort <jean_brefort>
Group administrator
Tue 02 Oct 2007 08:48:47 PM UTC, comment #8: 

Thanks for your comments.

Is there a place where your to-do list can be posted? As I am beginning to use GChempaint more often, I come up with even more ideas for the program. I don't want to post redundant things that are already on your to-do list (but I suppose that redundancy may be good b/c it may be an indication that other users, such as myself, would really like that feature).

Is there something that I can do to help the project even though I don't know how to program? I have, for instance, advocated Gchempaint in Ubuntu forum, etc. I am writing an article on how to install the latest GChempaint in Ubuntu and am planning on posting it on my website as well. I have heard from several people that they have not been able to install the latest GChempaint b/c of dependency issues. eg libgoffice-0.4, etc.

Also I have been trying to make a deb out of it, but have not been successful. Where should I get help on such a thing? Debian people or the developer like yourself? There also is an issue with chem-mime-data; it messes up other mime libraries in Ubuntu so you have to reinstall all the otehr mime stuff. If I can manage to make a deb package for the latest version, I'd be happy to host a repository. Thanks again for your work.

Takashi Suyama <tak1150>
Tue 02 Oct 2007 08:24:05 PM UTC, comment #7: 

Answering to the last two comments:

- selecting part of a molecule is not trivial, but planned for 0.10. I have not a clear idea about how to do that, but it must be done.
- the gap issue between the heteroatom and the bond is high on my to do list. Basically at the moment, a white rectangle is drawn and hides the bonds behind the atom symbol. This is bad for several reasons, and have to be changed, so it will be fixed very soon, I hope.
- the double bond issue also occurs with trans double bonds in cycles. It needs more work to find what side is in the cycle in such a case. And for non cyclic double bonds, which side is better. Anyway, you are right, it must be fixed, I don't like that either.

Ideas from users other than me is very helpful. It often clarifies my thoughts. Just what is missing is time to implement everything.

Jean Bréfort <jean_brefort>
Group administrator
Tue 02 Oct 2007 05:52:43 PM UTC, comment #6: 

Forgot one more thing:

well, another wishlist-ish item:

I have been thinking about why ChemDraw (CD) structures look a bit more polished and neater. And I think I know why now. IMO there are 2 reasons.

1. In CD, the gap between the heteroatom (a letter) and the bonds is smaller thang GCP. This is not only an appearance issue but also a practical one. Sometimes it is hard to see that there is a bond. For instance, if there is -NH-, depending on the angle, the second bond is almost 1/5 of the original length. In CD, the position of "H" of NH shifts so that it is not in the way of a bond and the gap is inherently small and the GCP problem is less obvious.

2. For double bonds that are in the middle of an alkyl chain, CD can make it so that one of the bonds in the double bond is integrated into the alkyl chain and the second bond in the double bond is separate. Please see the attached pic to see what I'm not-so-elegantly describing. It is labeled scheme 3.



Takashi Suyama <tak1150>
Tue 02 Oct 2007 05:40:58 PM UTC, comment #5: 

Thank you. I found the document. I didn't think to go through "Help" menu b/c the last time I tried it, the help viewer did not start. But it all worked with the newest release.

If I may add another item to the wish list.
I read in the documentation that you cannot select a part of the molecule. I have been meaning to ask you about this and the doc answered the question. But I really would like to be able to select parts of a molecule. Would this be a difficult task? Are these wishlist items helpful to you or more of annoyance? Thanks for your time!


Takashi Suyama <tak1150>
Mon 01 Oct 2007 08:11:38 PM UTC, comment #4: 

You should be able to access the documentation throught the Help menu (Help/Contents). Otherwise, it is a docbook xml document normally installed in /usr/share/gnome/help/gchempaint/C/ (replace /usr/share by whatever you use as datadir).

Jean Bréfort <jean_brefort>
Group administrator
Mon 01 Oct 2007 07:53:10 PM UTC, comment #3: 

sorry; a silly question. Where is the documentation? Is it in /usr/... somewhere? Thanks.

Takashi Suyama <tak1150>
Mon 01 Oct 2007 07:46:53 PM UTC, comment #2: 

2. Great idea!
3. yes. when creating a new file. there may be more themes to choose from as Gchempaint grows in the future.

Thank you for looking through the list.

Takashi Suyama <tak1150>
Fri 28 Sep 2007 06:18:15 AM UTC, comment #1: 

1. should already work, try Ctrl+_.

2. may be the default element should not change when the event occurs on an atom, and change only if it occurs elesewhere, or use a modifier key to switch between the two behaviors.

3. you mean decide which theme is used by default when creating a new file? Probably the default theme as it exists is a kludge. Seems reasonable.

4. already works, just drag the mouse while pressing the Shift key when creating a new arrow.

5. and 6. I was thinking about such a thing. It is possible to add variants to all cycle tools. For a 6-size cycle, default would still be a six-membered ring of atoms of the default element, but for others we might have benzene and all sorts of heterocycles. The non trivial item is the choice of the bounded atom(s). This is more a feature for 0.10, probably. At the moment, you can merge two molecules. The way it works is explained in the documentation. Draw the two molecules (might be templates), move one to the other so that at least one atom of each molecule is approximately at the same position (they must be atoms of the same element), select both molecule and click on the merge button.

Jean Bréfort <jean_brefort>
Group administrator
Thu 27 Sep 2007 07:40:52 PM UTC, original submission:  

Here is my selfish wish list for the future releases of Gchempaint:

1. To be able to write subscripts in the text mode (eg CH4)
2. Have the "keyboard to heteroatom" feature default back to C (carbon) without having to press c.
3. To be able to change the default theme via GUI
4. To be able to draw arrows in any length just with a mouse (ie when you drag with the mouse, the arrow gets lengthened or shortened).
5. Have a default benzene ring unit; just like cyclohexane, cyclopentane, etc, you can just select it from the tool bar directly. Reason: when you use the benzene ring from the template, you cannot add it to an existing structure very well. And I use benzene rings a lot.
6. Related to above: to be able to add template structures directly on to an existing structures especially at the end of a chain or onto a bond.

Thank you for your work and for considering these wishes :)

Takashi Suyama <tak1150>


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file #14064:  Screenshot.png added by tak1150 (21KiB - image/png)


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  • -email is unavailable- added by jean_brefort (Posted a comment)
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    Follow 4 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2007-12-24 jean_brefort Attached File#14695 Removed
    2007-12-23 None Attached File- Added xanax.htm, #14695
    2007-10-02 tak1150 Attached File- Added Screenshot.png, #14064
    2007-09-28 jean_brefort Assigned toNone jean_brefort

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