Support for dative bonds

[epam]

Support for dative bonds

[skearnes]

Note: it seems that dative bonds are encoded as type 9 in v3000 molfiles: https://sourceforge.net/p/rdkit/mailman/message/34538029/

See also http://help.accelrysonline.com/ulm/onelab/1.0/content/ulm_pdfs/direct/reference/ctfileformats2016.pdf

[AlexanderSavelyev]

Technical description: add new dative bond type

1. User can draw a dative bond by choosing new item from the bonds menu
   
2. User can draw a dative bond the same way as with other types of bonds (the only difference is that bond has a direction from first point to the second point) e.g. C->N
   
3. The type of the bond in molfile is 9.
4. No other verification are performed for the bond type

[AlexanderSavelyev]

added similar task for hydrogen bonds #72 (type 10) because usually it comes together

[AndreiMazol]

Dependencies: #21

[skearnes]

Hi there, now that #21 is resolved are there any additional blockers for this enhancement?

[AndreiMazol]

Hi @skearnes ,

to support server functions (clean up, layout & etc.) after adding new bond types it is necessary to implement #258, but this moment it is blocked by Indigo side.
We plan to start work on it in the nearest future.

[Svetlana-Asinovskaia]

The current representation of dative bonds is incorrect.

Expected result:

Actual result:

[Svetlana-Asinovskaia]

The length of dative bonds should be equal to the length of simple single bonds.
Expected result:

Actual result:

[Svetlana-Asinovskaia]

Comment about the length of dative bonds is invalid.

[Svetlana-Asinovskaia]

A bond is removed when trying to replace it with the dative bond and the console error after the Undo action appears.

Steps to reproduce:

1. Create a structure on the canvas (e.g. draw benzene with the 'Templates' tool)
2. With 'Dative bond' tool replace one of the bonds in benzene.
3. Click the 'Undo' button.
   Expected result: The bond is replaced with the dative bond.
   Actual result: The bond is deleted. the console error after the Undo action appears.
   

[Svetlana-Asinovskaia]

Stereo flag doesn't disappear after replacing the sterebond with the dative bond. It's possible to open the "Enhanced Stereochemistry" window and set the stereo mark.

[Svetlana-Asinovskaia]

Release/2.3 The issue is verified and closed.
The problem with stereocenters remaining after replacing the stereobonds with the dative bonds is associated with the "Enhanced stereochemistry" epic and will be solved within #554