helpGChemPaint - Support: sr #105937, Heteroatom drawing - takes too...


You are not allowed to post comments on this tracker with your current authentication level.

sr #105937: Heteroatom drawing - takes too much time

Submitted by:  Takashi Suyama <tak1150>
Submitted on:  Tue 10 Jul 2007 03:19:07 AM UTC  
Category:  None Priority:  5 - Normal
Severity:  3 - Normal Status:  Done
Privacy:  Public Assigned to:  Jean Bréfort <jean_brefort>
Open/Closed:  Closed Operating System:  GNU/Linux

( Jump to the original submission)

Thu 12 Jul 2007 03:16:50 PM UTC, comment #8:

Wow that's really great about the mapping of elements to the alphabets. Thank you!

Takashi Suyama <tak1150>
Thu 12 Jul 2007 09:30:25 AM UTC, comment #7:

Fixed in HEAD: typing a lowercase character selects an element and change the underlying atom if any. 26 elements can be selected this way, the list being:
a: Al; b: B; c: C; d: Na; e: Se; f: F; g: Ge; h: H; i: I; j: Ti; k: K; l: Li; m: Mg; n: N; o: O; p: P; q: Si; r: Br; s: S; t: Pt; u: Cu; v: V; w: W; x: Cl; y:Y; z: Zr.
While this list might not be ideal, it should be very useful (and it is possible to make it customizable in the future).
If you type an uppercase character, you get a contextual menu with the elements whose symbols start with the typed character.

As the default element is changed at the same time, you'll have to type 'c' again to come back to carbon as default.

I'll backport that to the 0.8 branch, so that it should be operational in 0.8.2

Concerning the bond issue, The AltGr key will also change the default orientation. This is much more difficult to backport and needs much more testing, so not before 0.10 (unless you use 0.9.x).

I also add shortcuts to change the bond length for the chain tool (0=auto, 1=10,...)

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Tue 10 Jul 2007 05:14:16 PM UTC, comment #6:

First, please, use one thread per item.

- element issue: we might have all three methods: the widget (slow), the contextual menu, and a one key method, perhaps using a modifier key?

- bond angle issue: it is not possible to use Ctrl, Shift or Alt keys, since they are already used by other features. Using the AltGr key is not perfect, since a user might want to use them at the same time as other modifiers, and it is almost impossible without a third hand. I fully agree that the lock trick is far from perfect, but I could not imagine a better way. I'll probably have to find a better solution anyway.

- I already thought about the settings issue. There are a few things that are not straightforward, otherwise, I would have published ACS and CS themes along with 0.8. One issue is that GChemPaint uses pixels while ACS standards use points. You might help a lot with that, I don't publish anything since I'm away from research since many years now, so I never really tried to conform with ACS or other standards. If you can build a theme with one of the standards inside, I'll add it to next version, and if it is not possible, or very difficult, I'll consider it as a bug and change GChemPaint internals so that it becomes possible.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Tue 10 Jul 2007 03:50:30 PM UTC, comment #5:

I agree about my proposal being not intuitive.

Perhaps you could have this feature along side the system you already have in 0.8.x (ie the periodic table to choose from).

That's the case in ChemDraw as well. They have a text mode ( too much mouse use, but intuitive) and the feature to just type in the atoms ( not intuitive but fast).

Bond issue:
I didn't know about the Caps lock thing. Could you have the reverse as the default?
Or can you do the reversing of the angle sign by holding down Shift or Ctrl? so that you don't have remember which sign you have? (as it is, you have to remember how many times you've pressed Caps Lock; odd numbers for reverse and even numbers for positive).

In fact, it'd be nice if the default drawing values are the same as, let's say, ACS standard (american chemical society) or CS (Royal Chemical society; the British one).
If that can be done, I can see in the future that the organizations like ACS would choose GChempaint as one of the standard file formats. Right now, they have ChemDraw as the standard submission format for publication (we are the editors for one of the ACS journals currently; JNP). Note: i have noticed that with Version 0.8.x, the compatibility with ChemDraw is pretty good, but it's always better if you can submit the native file format.

If you like, I'll post in another thread the ACS standard values for drawing structures (bond length, angles, width, atom font size, etc).

Takashi Suyama <tak1150>
Tue 10 Jul 2007 03:03:00 PM UTC, comment #4:

About changing the element, the contextual menu, would work as follows:
If you type, say, an 's' or 'S', you get a menu with S, Sb, Sc, Se, Sg, Si, Sm, Sn, and Sr with the second letter used as shortcut, so that if you type 'i', you get Si. The drawback is that for sulfur, there is only one letter, so only this one can be usedd as shortcut (I don't know of any symbol with twice the same letter), so you'll need to type a second 's' or an arrow and return. The menu will also include abbreviations (such as Ph, of course, if you type a 'p') when GChempaint supports them.
Your other proposal is quite interesting, but much less intuitive IMHO, since the shorcuts for some elements might be all but trivial (say Cl if C is used for carbon and L for lithium).

About the bond angle issue, using the caps lock reverse the angle sign, so to draw a chain, you just need to change the state of the lock for each new bond. I could not find a more simple solution to this problem.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Tue 10 Jul 2007 02:42:32 PM UTC, comment #3:

Thanks for such a quick response. Forgive me if I'm being too picky, but the good thing about ChemDraw /Xdrawchem is that you only have to use the mouse twice to draw, let's say, acetone.

You take your mouse and draw the skeleton like you do in Gchempaint / xdrawchem, etc; that's one mouse use. Then you move the cursor to the atom that should be oxygen and you type O. This is nice. For speedy production of documents, the less often you have to use the mouse the better. So if you don't have to use the mouse to choose from the pop-up window, that would still be great.

Alternatively, I was thinking that you could map the keys only to frequently used atoms; H, Li, B, C, O, N, F, Na, Mg, Al, Si, P, S, Cl, K, Ca, Br, I (mostly the first 2 rows, but extra halogens, etc; I hardly see any published structures with any other heteroatoms). Now both Si and S start with the letter s. So maybe <s> could be mapped to S and <Shift>+<s> could be mapped Si. This may seem like extra things that users have to learn, but as a user I can tell you that I'd be happy to! Because it makes the process so much faster.

This reminded me of one other point; when you draw a chain by just clicking on the end atom (carbon), the bond added does not follow with the direction of the chain but diverts to the side (i'm sorry it's so wordy :( ). While the chain drawing tool that you already have is extremely useful, often times I have to add a single bond to the chain that's already drawn. I have tried to fix this by changing the default bond angle, but the value is limited to 0 to 180. It needs to be 240 degrees to have the effect I'm looking for. I've hopefully attached the files to show this.

Thank you for taking a look at these things. You're really appreciated.

(file #13284)

Takashi Suyama <tak1150>
Tue 10 Jul 2007 09:34:34 AM UTC, comment #2:

The way it works in xdrawchem is not portable to GChemPaint. xdrawchem accepts any text you type, even non existing symbols. This would give unusable GChemPaint files. One possibility would be to have a pop-up menu showing all known symbols starting with the typed character where the appropriate one might be choosen (it would become the default element). Would this be convenient for you?

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Tue 10 Jul 2007 06:02:58 AM UTC, comment #1:

Thank you for reporting. I'll have a look at XDrawChem to see how things work.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Tue 10 Jul 2007 03:19:07 AM UTC, original submission:


First of all, thank you so much for developing this great software! As a synthetic organic chemist, I use this program very frequently.

One major concern that I have had about the software is the ease of drawing heteroatoms. For example, in ChemDraw and XDrawChem, you can place the mouse cursor on top of an atom (carbon atom) and press a key on the keyboard for the heteroatom. This feature enables me to draw structures very fast.

I just love Gchempaint, however, for me to recommend it to my Windows/Chemdraw using colleagues, this issue of heteroatom drawing needs to be resolved.
You guys may even have better ideas than ChemDraw/Xdrawchem. In any case, I would greatly appreciate your consideration of this humble input from a loyal user. Thank you!

Takashi Suyama <tak1150>


Attached Files
file #13284:  bond_angle.gchempaint added by tak1150 (3KiB - application/x-gchempaint)


Depends on the following items: None found

Items that depend on this one: None found


Carbon-Copy List
  • -email is unavailable- added by jean_brefort (Posted a comment)
  • -email is unavailable- added by tak1150 (Submitted the item)

    Do you think this task is very important?
    If so, you can 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 5 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2007-07-12 jean_brefort StatusIn Progress => Done
        Open/ClosedOpen => Closed
    2007-07-10 jean_brefort StatusNone => In Progress
        Assigned toNone => jean_brefort
    2007-07-10 tak1150 Attached File- => Added bond_angle.gchempaint, #13284

    Back to the top

    Powered by Savane 3.3