Comments (12)
Note: it seems that dative bonds are encoded as type 9 in v3000 molfiles: https://sourceforge.net/p/rdkit/mailman/message/34538029/
from ketcher.
Technical description: add new dative bond type
- User can draw a dative bond by choosing new item from the bonds menu
- 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
- The type of the bond in molfile is 9.
- No other verification are performed for the bond type
from ketcher.
added similar task for hydrogen bonds #72 (type 10) because usually it comes together
from ketcher.
Dependencies: #21
from ketcher.
Hi there, now that #21 is resolved are there any additional blockers for this enhancement?
from ketcher.
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.
from ketcher.
The current representation of dative bonds is incorrect.
from ketcher.
The length of dative bonds should be equal to the length of simple single bonds.
Expected result:
from ketcher.
Comment about the length of dative bonds is invalid.
from ketcher.
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:
- Create a structure on the canvas (e.g. draw benzene with the 'Templates' tool)
- With 'Dative bond' tool replace one of the bonds in benzene.
- 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.
from ketcher.
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.
from ketcher.
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
from ketcher.
Related Issues (20)
- System opens Select Connection point dialog while connecting twp peptides even if R2-R1 connection is possible HOT 1
- Aromatization of 5-membered, nitrogen-containing aromatic rings results in invalid SMILES
- Pasted sequences are not visible in the Snake mode.
- Wrong layout in the Sequence mode while Paste sequences to the Flex mode
- Autotests: Check if possible to create bond from specific AP of one monomer to specific AP of another monomer (CHEM, CHEM - Peptides, RNA - Peptides, RNA - CHEM)
- Sequence mode validation is ignored and User can paste Peptides while RNA/DNA options is selected. HOT 1
- New Sequences are created while we add cyclic to middle of sequence.
- Nothing happens, and the user doesn't receive any notifications.
- submit to public CDN
- Clear canvas button doesn't make system quit from edit mode that causes troubles HOT 1
- CI renders monomer labels in different way than on user machine
- Mol file with XSS should be opened correctly as KET file.
- User cannot select and Copy/Paste Chem objects from Macro on the Micro canvas.
- RNA Structure is broken while we Copy from Macro and Paste to Micro canvas.
- Autotests: Center to center connections for CHEM-CHEM, CHEM-Peptide, RNA-Peptide, RNA-CHEM
- In the “Modify in RNA Builder“ mode, the red icon does not appear on hovering the button “Switch to Micro/Marco mode“
- After clicking the Update button in the “Modify in RNA Builder” mode, the modified nucleotide should be highlighted in green
- The icons next to the “multiple” option in the RNA Builder in the "Modify in RNA Builder" mode do not match the design layout
- Duplicate appears while copy/paste Chem object with switching Macro/Micro canvas.
- Autotests: Automation of Bond tests (203-211)
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from ketcher.