Modular functions, support grouping chains, and partial support for Chai-1 models - #22

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y1zhou wants to merge 44 commits into

DunbrackLab:mainfrom

Commits on Nov 30, 2025

refactor: WIP initial attempt to clean up the script with LLMs
y1zhou
committed
5e8061a

Commits on Dec 1, 2025

ci: add pre-commit config
y1zhou
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c700025
refactor: clean up main function
y1zhou
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c74d2c1
feat: refactor the file IO section
y1zhou
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649faaa
refactor: WIP of cleaning up the calculate_scores beast
y1zhou
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3321ed9
fix(pdockq): fix bug where chain1 residue indices were not included in pDockQ calculations
y1zhou
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1d8142c
test: helper script to compare differences to the original script
y1zhou
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775a33e

Commits on Dec 2, 2025

perf: merge pDockQ and pDockQ2 functions to avoid recomputing masks
y1zhou
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6f1ab17
fix: WIP get per-residue scores calculated correctly
y1zhou
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392d1fb
feat: reach parity with the orignal script for all except row orders in the .pml output
y1zhou
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39fffbc
feat: add cli arg for forcing the input model type and skip guessing
y1zhou
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b3bdb67
test: add example files because the original ones were missing iptm inputs
y1zhou
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2f365de
refactor: move per-residue line formatting to a separate dataclass
y1zhou
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6f8412b
refactor: moving around code chunks for better readability
y1zhou
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efbbc5b
Initial plan
Copilot
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5b27a26
Refactor summary_lines to use SummaryResult dataclass

Copilot
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y1zhou
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256b52e
Update aggregate_byres_scores docstring with return type details

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y1zhou
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3b72ef1
Rename SummaryResult to ChainPairScoreResults and update field names

Copilot
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y1zhou
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1e11f5a
Merge pull request #1 from y1zhou/copilot/refactor-summary-lines-dataclass
y1zhou
authored
443b43c

Commits on Dec 4, 2025

Initial plan
Copilot
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5e4e1f1
Add --chain-groups CLI argument for calculating scores between specified chain groups

Copilot
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y1zhou
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c7949a2
Add tests for chain group functionality

Copilot
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y1zhou
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d09cb52
Address code review feedback - improve warning messages and documentation

Copilot
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y1zhou
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5b87ff3
Refactor chain group scoring to reuse existing functions

Copilot
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y1zhou
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1dd0697
Address review feedback: np.isin, g1/g2 naming, PyMOL script, ellipsis token, -g flag

Copilot
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y1zhou
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f9c457f

Commits on Dec 5, 2025

fix: adjust ordering of chain groups
y1zhou
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669ee85
fix: modify output whitespace to be as close to the original as possible
y1zhou
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0410ca9
refactor: remove unused functions and update variable names for clarity
y1zhou
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4cf9598
Fix value differences in output: correct ipTM_af max calc, max row naming, and byres ordering

Copilot
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y1zhou
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efdb80b
Group chain pair outputs together: asym A->B, B->A, then max, with blank line separator

Copilot
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y1zhou
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99f2168
style: add back the newlines separating chain pairs in the output
y1zhou
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5526d87
Add test_scoring.py with integration tests comparing output against sample files

Copilot
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y1zhou
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b39e431
Refactor: Extract normalize_whitespace function to module level

Copilot
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y1zhou
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0c51f6b
Refactor test_scoring.py to run ipsae once per input file set

Copilot
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y1zhou
committed
a1326ae

Commits on Dec 8, 2025

Merge pull request #2 from y1zhou/copilot/add-cli-argument-chain-groups
y1zhou
authored
969031b

Commits on Dec 9, 2025

Commits on Dec 18, 2025