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Create Ambiguous restraints from residue selection #91

Merged
merged 47 commits into from
Apr 17, 2024
Merged

Create Ambiguous restraints from residue selection #91

merged 47 commits into from
Apr 17, 2024

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sverhoeven
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@sverhoeven sverhoeven commented Mar 26, 2024 •
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localhost_3000_scenarios_protein-protein (1)

hover

Refs #29

To test requires the haddock3-restraints webservice command running from haddocking/haddock3#841 which can be done with

docker compose -f deploy/arq/docker-compose.yml build --build-arg=HADDOCK3_GHORG=i-VRESSE --build-arg HADDOCK3_VERSION=web-service
docker compose -f deploy/arq/docker-compose.yml up

TODO

  • protein protein scenario
  • The download zip contains file called ambig.tbl.
  • after selecting chain then only show that chain in 3D
  • render sequence with
    • colored annotations like secondary structure or on surface
    • show numbers link in haddock3 2.4 website on in molstar
  • import from a space or comma separated list or act file or actpass file
  • show active residues in 3D
  • allow selection of active residues in 3D
  • show calculated passive residues in 3D
  • run haddock3 restraints webs service in deployments
  • document new web service
  • hover in either 3D ngl or 2D residue selector to see residue highlighted in other
  • antibody-antigen scenario

@sverhoeven sverhoeven mentioned this pull request Mar 27, 2024
Closed
sverhoeven and others added 26 commits March 28, 2024 17:13
@sverhoeven
Add colors to sequence + started on chain selection in 3D
ccb43aa
@sverhoeven
Import residues
1744678
@sverhoeven
Run haddock3 restraints web service in deployment
cbbda00
@sverhoeven
Format
3164828
@sverhoeven
Model ngl viewer components after react-ngl and disable strictmode
1421602
@sverhoeven
Show active/passive residues in 3D + remove non-surface residues + re…
0173584 
…generate restraints schema

Also sort display residue ids
@sverhoeven
Preprocessing pdb + toggle to show surface residues
fd59d16 
NGL does not like loading structure twice after a chain is selected.
@sverhoeven
Describe how haddock3 restraints web service is used on scenario pages.
d2366a4
@sverhoeven
For files standardize on gzip+base64 string value in request JSON object
7cb87bd
@sverhoeven
Use fflate to gzip and base64 encode the pdb files
3af983e
@sverhoeven
Losts of stuff
f6e18fc 
* After file upload and chain selection process it and show results
* Added restrain bodies as unambig restraints
* Center all button for ngl stage
* hover in ngl and residue selector
* click in ngl to select residue
* show error when calc_acces fails
* give ngl own error boundary
* fix hydration error with ClientOnly component
* reuse gzipped pdb file
@sverhoeven
Format
2c474b2
@sverhoeven
Add h3r ws to diagram
e376b3a
@sverhoeven
Hover in 3D will higlight in 2D
d870b2b
@sverhoeven
Add link
2a0aed0
@sverhoeven
Merge remote-tracking branch 'origin/main' into scenario-chains-residues
a6d96e8
@sverhoeven
Refresh catalogs + force offline=true and plot_matrix=true
e7c6249
@sverhoeven
Added playwright
fb08b9c 
Refs #8
@sverhoeven
Fix tests
c279917
@sverhoeven
Merge remote-tracking branch 'origin/scenario-chains-residues' into p…
a80da8c 
…laywright
@sverhoeven
Compile fast-rmsdmatrix
ce26552 
See haddocking/haddock3#809
@sverhoeven
Compile fast-rmsdmatrix
974c1fb 
See haddocking/haddock3#809
@sverhoeven
Fix webkit login failure
c978926 
The deployments are running http instead of https so secure cookie can not be used.
Seems like Chrome ignores secure on localhost

Fixes #93
@sverhoeven
Use GH annotations, nothing to upload
9e75bd1
@sverhoeven
Can only use scenario pages when logged in and allowed to submit job
5ff218f
@sverhoeven
Allow uploading run tarball to bypass queue in arq deployment
7e3bbf2
sverhoeven added 18 commits April 15, 2024 15:13
@sverhoeven
More tests
62758da
@sverhoeven
Merge pull request #92 from i-VRESSE/playwright
d94de05 
Playwright
@sverhoeven
Add fake cns to ci
1b4c0d8
@sverhoeven
Download processed file by name + regen restraints client
d245416
@sverhoeven
gdock repo has main as default branch now
96ef844
@sverhoeven
For antibody-antigen scenario replace restraints upload by generating…
29d194e 
… restraints from active/passive/surface residues
@sverhoeven
Upgrade vitest
f7af9e1 
As old version was no longer compatible with vs code extension
@sverhoeven
Re-enable strictmode
05a2c8a 
At https://github.com/i-VRESSE/haddock3-webapp/blame/scenario-chains-residues/app/scenarios/Antigen.client.tsx#L142-L146
found cause of ngl errors. Now the error is worked around by adding component to stage directly from file instead of from a sometimes invalid structure object.
@sverhoeven
Upgrade to prettier 3
6c27a01
@sverhoeven
test plot_matrix=true is set in config
bc3c1fb
@sverhoeven
In ngl dark mode swap colors and opacity for better visibility
61e2877
@sverhoeven
Prune headers sent to restraints web service
e0973cd
@sverhoeven
Add formatting commit to ignore list
3b204b4
@sverhoeven
Use same chain for active and passive residues
941ccfb
@sverhoeven
Move calls to restraints web service into app/scenarios/restraints.ts
90a6a73
@sverhoeven
Simplify reference field
b9acf4a
@sverhoeven
Show number above sequence in blocks of 10 amino acids
7b5335c
@sverhoeven
Sync docs
3a31d99
@sverhoeven sverhoeven marked this pull request as ready for review April 17, 2024 11:27
@sverhoeven sverhoeven merged commit d2ce585 into main Apr 17, 2024
2 checks passed
@sverhoeven sverhoeven deleted the scenario-chains-residues branch April 17, 2024 11:27
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