Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Displaying a long peptide chain on a canvas. Snake-like layout #3280

Closed
olganaz opened this issue Sep 8, 2023 · 3 comments · Fixed by #3376
Closed

Displaying a long peptide chain on a canvas. Snake-like layout #3280

olganaz opened this issue Sep 8, 2023 · 3 comments · Fixed by #3376
Assignees
@OlgaMazurina @Andrey-Antonov
Labels
feature request Macromolecules [PE] Build chains from monomers
Milestone
Macromolecules Mi...

Comments

@olganaz
Copy link
Collaborator

olganaz commented Sep 8, 2023 •
edited
Loading

Displaying a long peptide chain on a canvas. Snake-like layout

  1. The user should be able to upload a long polypeptide chain onto the canvas.
  2. Bonds between monomers are formed by default between R2 of the first monomer and R1 of the next monomer.
  3. When the layout button is pressed, the monomers from the chain should be arranged on the screen in a snake-like pattern. And while this button is active - the "snake-like" mode is ON.
  4. Depending on the length of the chain, the algorithm should calculate the length of one row and the size of the monomers so that the entire chain fits on the canvas.
  5. Monomers in each row are ordered from left to right.
  6. The bond between the last monomer in a row and the next one should be shown as a broken line with smoothed corners.
  7. After creating layout new monomers can be added and existing monomers can be moved while the bonds remain rectangular and appropriately rebuilt.
  8. If there are multiple chains of monomers on the canvas, each chain is arranged independently of the others, but they altogether should fit on the canvas.
    a. Each interconnected set of monomers (chain) is arranged into the left-to-right (snake) view separately. "Snakes" are arranged from top to bottom, every snake starts from a new row.
    b. Once the layout button is pressed, the top (first) chain is defined by the top left monomer on canvas, i.e. the chain it is part of will be the first one.
    c. Similarly, second chain is the one that includes new top left monomer that is not part of the first chain, etc
@olganaz olganaz added the draft label Sep 8, 2023
@olganaz olganaz self-assigned this Sep 8, 2023
@olganaz olganaz added Macromolecules feature request epic: peptide MVP Collect tasks for the MVP of peptide editor [PE] Build chains from monomers and removed draft epic: peptide MVP Collect tasks for the MVP of peptide editor labels Sep 11, 2023
@OlgaMazurina OlgaMazurina assigned OlgaMazurina and unassigned olganaz Sep 12, 2023
@olganaz olganaz changed the title Peptide chain layout Layout button for peptide chain Sep 13, 2023
@olganaz olganaz changed the title Layout button for peptide chain Displaying a long peptide chain on a canvas. Snake-like layout Sep 18, 2023
@Andrey-Antonov
Copy link
Collaborator

image

OlgaMazurina pushed a commit that referenced this issue Sep 18, 2023
#3280 - add curves
782de13
OlgaMazurina pushed a commit that referenced this issue Sep 18, 2023
#3280 - replace import
e60a9fd
OlgaMazurina pushed a commit that referenced this issue Sep 18, 2023
#3280 - small fix
27663ef
OlgaMazurina pushed a commit that referenced this issue Sep 18, 2023
#3280 - revert broken test later
6c5483d
OlgaMazurina pushed a commit that referenced this issue Sep 18, 2023
#3280 - remove it
e940bce
@Andrey-Antonov
Copy link
Collaborator

image
image

OlgaMazurina pushed a commit that referenced this issue Sep 25, 2023
#3280 - add chain rearrange by clicking
61e3e42
OlgaMazurina pushed a commit that referenced this issue Sep 25, 2023
#3280 - small fix
66212cd
OlgaMazurina pushed a commit that referenced this issue Sep 26, 2023
#3280 - add state
c05a93b
OlgaMazurina pushed a commit that referenced this issue Sep 28, 2023
#3280 - fix broken functionality
6a8f3a3
OlgaMazurina pushed a commit that referenced this issue Sep 28, 2023
#3280 - fix selection
5604fe3
OlgaMazurina pushed a commit that referenced this issue Sep 28, 2023
#3280 - small fix
c7ed029
OlgaMazurina pushed a commit that referenced this issue Oct 10, 2023
#3280 - small fix
6bb68b5
OlgaMazurina pushed a commit that referenced this issue Oct 10, 2023
#3280 - update snapshot
d83552d
OlgaMazurina pushed a commit that referenced this issue Oct 10, 2023
#3280 - fix method and update sreenshots
e2873ba
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - add curves
86be235
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - replace import
ca45817
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - small fix
9ade77f
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - revert broken test later
994bf83
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - remove it
0af7763
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - add chain rearrange by clicking
d8de288
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - small fix
3f1be81
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - add state
4b795cd
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - fix broken functionality
2768619
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - fix selection
14173dc
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - small fix
50385ee
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - fixed distance
24101fb
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - add tests
3ab61dd
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - delete line
28ee098
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - update screenshots
5da2898
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - fix comments
2352b85
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - small fix
95bcce3
rrodionov91 pushed a commit that referenced this issue Oct 16, 2023
@rrodionov91
#3280 - fix method and update sreenshots
e408060
rrodionov91 added a commit that referenced this issue Oct 16, 2023
@OlgaMazurina @rrodionov91
Macro: #3280 - Displaying a long peptide chain on a canvas. Snake-lik…
54330ad 
…e layout (#3376)

* #3280 - add curves
* #3280 - add chain rearrange by clicking
* #3280 - made straight bond for R3+ attachment points
* #3280 - restricted snake bonds for R3+ connections and for RNA

---------

Co-authored-by: Olga Mazurina <olga_mazurina@epam.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>
OlgaMazurina added a commit that referenced this issue Oct 18, 2023
@OlgaMazurina @rrodionov91
Macro: #3280 - Displaying a long peptide chain on a canvas. Snake-lik…
bc496a5 
…e layout (#3376)

* #3280 - add curves
* #3280 - add chain rearrange by clicking
* #3280 - made straight bond for R3+ attachment points
* #3280 - restricted snake bonds for R3+ connections and for RNA

---------

Co-authored-by: Olga Mazurina <olga_mazurina@epam.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>
@MartaWilliams
Copy link
Collaborator

Tested
2023-10-24_10h12_15
2023-10-24_10h06_43
2023-10-24_10h19_58
2023-10-24_10h26_26

@y-holik y-holik mentioned this issue Oct 26, 2023
Closed
This was referenced Nov 17, 2023
Open
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@OlgaMazurina OlgaMazurina

@Andrey-Antonov Andrey-Antonov

Labels
feature request Macromolecules [PE] Build chains from monomers
Projects
None yet
Milestone
Macromolecules Milestone 1
Development

Successfully merging a pull request may close this issue.

Macro: #3280 - Displaying a long peptide chain on a canvas. Snake-like layout epam/ketcher
5 participants
@OlgaMazurina @MartaWilliams @OlZhur @Andrey-Antonov @olganaz