change in incipient bonds

User 870ab5b546

04-06-2007 19:59:54

Hi,





In Marvin 4.1.8, a dashed line no longer appears after I draw an electron-flow arrow pointing to an incipient bond between two atoms. The dashed line appears *while* I'm drawing the arrow, but it disappears when the drawing is finished. Unfortunately, after the dashed line is drawn, there is then no way for the user to determine which two atoms the incipient bond is connecting (without looking at the MRV code). It would be OK to omit the dashed line from the drawing if mousing over the electron-flow arrow restored it temporarily -- but it doesn't. Please fix!





-- Bob

User f359e526a1

05-06-2007 06:27:33

Sure, wil have a look ASAP.

User ef5e605ae6

08-06-2007 14:36:21

Hi Bob,
bobgr wrote:
In Marvin 4.1.8, a dashed line no longer appears after I draw an electron-flow arrow pointing to an incipient bond between two atoms. The dashed line appears *while* I'm drawing the arrow, but it disappears when the drawing is finished.
Yes, according to your earlier request:
Quote:
When an electron flow arrow point between two unconnected atoms, a dashed line represents a "forming" bond. This is a bit misleading for chemists, and students. They do not expect any lines between those atoms.
Your current problem is only in the 4.1 branch:
Quote:
Unfortunately, after the dashed line is drawn, there is then no way for the user to determine which two atoms the incipient bond is connecting (without looking at the MRV code).
In the 4.2 development version, the user can determine which two atoms the incipient bond is connecting because incipient bond highlighting shows both atoms. I used a java2d code for this that I did not want to put into the 4.1 branch. But it seems to be safe so I moved it now. It is not a dashed line but something else. I hope you will like it because I will not be available from Tuesday until the end of July.





Peter

User 870ab5b546

20-06-2007 00:41:49

I just had a look, and I like it very much. Thanks! I assume it will be available in Marvin 4.1.9?

ChemAxon 7c2d26e5cf

20-06-2007 09:54:49

Yes, it will be there.

User 870ab5b546

29-08-2007 12:33:46

Which version of Marvin was the last version to have the dashed line where the incipient bonds were being made?

ChemAxon 7c2d26e5cf

29-08-2007 17:41:34

Marvin 4.1.6 was the last version where incipient bonds are visualized (dashed line).


By the way, you can browse among the online versions of earlier Marvin releases via the following URL:


http://www.chemaxon.com/marvin-archive/

User 870ab5b546

26-09-2007 13:29:22

I very much like the way the electron-flow arrows sources and sinks are now highlighted.





One minor complaint: The blue boxes do not appear when I mouse over the very center of the arrow, where the black circle appears. Instead, I need to mouse over the arrow on either side of the blue circle, avoiding both the very middle and the ends. If I have a crowded structure, this can be difficult to do. Mousing over the middle of the arrow should bring up the black circle *and* the blue boxes.

ChemAxon 7c2d26e5cf

27-09-2007 09:44:57

OK, we will implement this feature. But I can not promise to do it till Marvin 5.0.

User ef5e605ae6

06-11-2007 14:31:22

The bug was caused by the presence of the middle point in the arrow, which acquired the focus instead of the arrow object. I removed the middle point, so the arrow can be highlighted now even when you move the pointer to its center.


Unfortunately I totally forgot why these middle points were created at all. Maybe it was required for normal MPolylines and it is just a superfluous side effect in the derived MEFlow class. Neverthless, if you need that middle point for the electron flow arrows because of some reason, then tell me as soon as possible and I try to find another fix before the 5.0 release.

User ef5e605ae6

06-11-2007 14:41:22

The middle point seems to be needed for normal lines to curve them. But an electron flow arrow is always curved, it does not matter where you drag it. So the fix is probably okay.

User 870ab5b546

07-11-2007 22:08:21

The middle circle allows you to change the size and direction of the arc. It's not absolutely necessary, but it's useful for making the pictures look nicer. I think it's better to leave it in.

User ef5e605ae6

08-11-2007 04:52:40

It remains in normal arcs and arrows. I only removed it from electron flow arrows, where it is does not have any function but causes the mentioned bug.

User 870ab5b546

08-11-2007 15:39:41

Even in electron-flow arrows, the middle circle can be used to change the size of the arc, which can be useful. See the figure.

User ef5e605ae6

08-11-2007 15:48:37

No, I tried it yesterday. The middle circle does not have any function, you change the size by dragging the arc.

User 870ab5b546

08-11-2007 17:55:14

Yes, you're right. I always used the circle, but it's not necessary.