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Alphafold 2.3.2 enhancement msa iptm #147

Merged
merged 33 commits into from
Oct 29, 2024
Merged

Alphafold 2.3.2 enhancement msa iptm #147

merged 33 commits into from
Oct 29, 2024

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neoformit
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  • Add PTM and IPTM scores to the default model confidence_scores.tsv output
  • Add optional MSA sequence coverage plot
  • Minor refactoring for readability
  • Add script for patching AF database pdb_mmcif

neoformit added 30 commits June 16, 2024 07:03
@neoformit
AF 2.3.2 Dockerfile
0495ed7
@neoformit
Add output timings.json
0f159b1
@neoformit
Alphafold test scripts
64b486d
@neoformit
Bump AF2 version
0617448
@neoformit
Test timings.json output collection
4eaad4f
@neoformit
Add matplotlib dep to dockerfile
357af8f
@neoformit
Fix dockerfile
9c140ac
@neoformit
Fix AF CLI test scripts
4ee9d5e
@neoformit
Fix AF outputs.py for unknown output count
dee8b09
@neoformit
Add new params to alphafold.xml
3c3b452
@neoformit
Update alphafold.xml help section
fb851ff
@neoformit
Output collection dynamic on model output count
d130b9c
@neoformit
Fix alphafold.xml lint errors
be1f8ef
@neoformit
Template alphafold.html to remove redundant buttons
182b274
@neoformit
Fix --output_models flag
338ba9d
@neoformit
Alphafold update test_outputs.sh script
661a7db
@neoformit
Fix AF2 HTML output
a154f48
@neoformit
Improve help text
fd8a7e6
@neoformit
Fix output filters
997e801
@neoformit
Set docker image tag
0aed9e0
@neoformit
AF2 final edits
c3a90eb
@neoformit
AF2 shed.yml
d5be032
@neoformit
AF outputs - add MSA plot
2d4577b
@neoformit
AF outputs - collect ptm/iptm scores
2832c42
@neoformit
Merge branch 'master' of https://github.com/usegalaxy-au/tools-au int…
c85fd21 
…o alphafold_2.3.2
@neoformit
Refactor --multimer arg
bba8125
@neoformit
Add AlphaFold patch_mmcif.py script
aa77f58
@neoformit
Update alphafold .gitignore
eea1e3b
@neoformit
Update patch_mmcif README
43986c2
@neoformit
Fix patch_mmcif.py to extract ids from both columns of pdb70_clu.tsv
b522f42
@neoformit neoformit merged commit 9d699d4 into master Oct 29, 2024
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@neoformit