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Add support for hydrogen bonds #72

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AlexanderSavelyev opened this issue Oct 26, 2020 · 6 comments · Fixed by #501, #535 or #545
Closed

Add support for hydrogen bonds #72

AlexanderSavelyev opened this issue Oct 26, 2020 · 6 comments · Fixed by #501, #535 or #545
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@MagomedGasanov @Svetlana-Asinovskaia
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enhancement epic: bond tool
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Ketcher
Milestone
Release 2.3.0

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@AlexanderSavelyev
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AlexanderSavelyev commented Oct 26, 2020 •
edited by Svetlana-Asinovskaia

Add new hydrogen bond type

  1. User can draw a hydrogen bond by choosing new item from the bonds menu
    image
  2. User can draw a hydrogen bond the same way as with other types of bonds
    image
  3. The type of the bond in molfile is 10
    http://help.accelrysonline.com/ulm/onelab/1.0/content/ulm_pdfs/direct/reference/ctfileformats2016.pdf
  4. No other verification are performed for the bond type
@AlexanderSavelyev AlexanderSavelyev mentioned this issue Oct 26, 2020
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@AndreiMazol
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Dependencies: #21

@AndreiMazol AndreiMazol added the blocked Issue cannot be started while all dependencies are not resolved label Dec 9, 2020
@AndreiMazol AndreiMazol removed the blocked Issue cannot be started while all dependencies are not resolved label Jan 27, 2021
@AndreiMazol AndreiMazol added this to the Release 2.3.0 milestone Apr 21, 2021
@MagomedGasanov MagomedGasanov added this to To do in Ketcher Apr 23, 2021
@MagomedGasanov MagomedGasanov moved this from To do to In progress in Ketcher Apr 23, 2021
@MagomedGasanov MagomedGasanov linked a pull request May 1, 2021 that will close this issue
#72 add support for hydrogen bonds #501
Merged
@MagomedGasanov MagomedGasanov moved this from In progress to Code review in Ketcher May 1, 2021
AndreiMazol pushed a commit that referenced this issue May 14, 2021
@MagomedGasanov
#72 add support for hydrogen bonds (#501)
c789611 
* Add hydrogen icon

* Add support hydrogen bond

* Change type number of hydrogen bond
@MagomedGasanov MagomedGasanov moved this from Code review to Ready for testing in Ketcher May 14, 2021
@Svetlana-Asinovskaia Svetlana-Asinovskaia moved this from Ready for testing to In testing in Ketcher May 15, 2021
@Svetlana-Asinovskaia
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Svetlana-Asinovskaia commented May 17, 2021 •
edited

The current representation of hydrogen bonds is incorrect.

Expected result:
image

Actual result:
image

@Svetlana-Asinovskaia Svetlana-Asinovskaia moved this from In testing to To do in Ketcher May 17, 2021
@Svetlana-Asinovskaia
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The length of hydrogen bonds should be equal to the length of simple single bonds.

Expected result:
image

Actual result:
image

@MagomedGasanov MagomedGasanov moved this from To do to In progress in Ketcher May 24, 2021
@Svetlana-Asinovskaia
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Comment about the length of hydrogen bonds is invalid.

@MagomedGasanov MagomedGasanov linked a pull request May 24, 2021 that will close this issue
#68-#72 Support for dative and hydrogen bonds #533
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@MagomedGasanov MagomedGasanov moved this from In progress to Code review in Ketcher May 24, 2021
@MagomedGasanov MagomedGasanov moved this from Code review to In progress in Ketcher May 24, 2021
@MagomedGasanov MagomedGasanov removed a link to a pull request May 24, 2021
#68-#72 Support for dative and hydrogen bonds #533
Closed
@MagomedGasanov MagomedGasanov linked a pull request May 24, 2021 that will close this issue
#72 add support for hydrogen bonds p2 #535
Merged
@MagomedGasanov MagomedGasanov moved this from In progress to Code review in Ketcher May 24, 2021
@MagomedGasanov MagomedGasanov moved this from Code review to Ready for testing in Ketcher May 25, 2021
@Svetlana-Asinovskaia Svetlana-Asinovskaia moved this from Ready for testing to In testing in Ketcher May 25, 2021
@Svetlana-Asinovskaia
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Console error after deleting the bond.

Steps to reproduce:

  1. Create a structure (e.g. select cyclohexane from the Templates).
  2. Sprout the Single Up bond from any atom.
  3. Replace the Single Up bond with the hydrogen bond.
  4. Delete the structure with the 'Erase' tool.
    Expected result: The structure is deleted without errors.
    Actual result: Console error appears.
    2021-05-25_11h14_32

@Svetlana-Asinovskaia Svetlana-Asinovskaia moved this from In testing to To do in Ketcher May 25, 2021
@MagomedGasanov MagomedGasanov moved this from To do to In progress in Ketcher May 26, 2021
@MagomedGasanov MagomedGasanov linked a pull request May 27, 2021 that will close this issue
#72 add support for hydrogen bonds p3 #545
Merged
@MagomedGasanov MagomedGasanov moved this from In progress to Code review in Ketcher May 27, 2021
AndreiMazol pushed a commit that referenced this issue May 27, 2021
@MagomedGasanov
#72 add support for hydrogen bonds p3 (#545)
e3d43d8 
* Fix problem with changing a stereo bond

* Add check for this.path
@MagomedGasanov MagomedGasanov moved this from Code review to Ready for testing in Ketcher May 27, 2021
@Svetlana-Asinovskaia Svetlana-Asinovskaia moved this from Ready for testing to In testing in Ketcher May 27, 2021
@Svetlana-Asinovskaia
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Release/ 2.3 The issue is verified and closed. Currently it's not possible to use the Calculated values option for the structures with the hydrogen bonds (It will be solved within #540)

@Svetlana-Asinovskaia Svetlana-Asinovskaia moved this from In testing to Done in Ketcher May 27, 2021
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@MagomedGasanov MagomedGasanov

@Svetlana-Asinovskaia Svetlana-Asinovskaia

Labels
enhancement epic: bond tool
Projects
Ketcher
  
Done
Milestone
Release 2.3.0
4 participants
@AlexanderSavelyev @MagomedGasanov @AndreiMazol @Svetlana-Asinovskaia