feat(runs): add analysis preset harness #245
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| description = "All grid-search evaluations, including optional external-tool checks." | ||
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| [defaults] | ||
| GRID_SEARCH_RESULTS_DIR = "/data/results/grid_search_results" | ||
| GRID_SEARCH_INPUTS_DIR = "/data/inputs" | ||
| PROTEIN_CONFIGS_CSV = "${GRID_SEARCH_INPUTS_DIR}/protein_analysis_config.csv" | ||
| TARGET_FILENAME = "refined-patched.cif" | ||
| N_JOBS = "16" | ||
| PATCH_CIF_PATTERN = "refined.cif" | ||
| GRID_SEARCH_DEPTH = "4" | ||
| PATCH_DEPTH = "${GRID_SEARCH_DEPTH}" | ||
| PATCH_INPUT_PDB_PATTERN = "processed/{pdb_id}/{pdb_id}_single_001_density_input.cif" | ||
| PATCH_RCSB_PATTERN = "${GRID_SEARCH_RESULTS_DIR}/([A-Za-z0-9]{4})" | ||
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| [shared_args] | ||
| grid-search-results-path = "${GRID_SEARCH_RESULTS_DIR}" | ||
| grid-search-inputs-path = "${GRID_SEARCH_INPUTS_DIR}" | ||
| protein-configs-csv = "${PROTEIN_CONFIGS_CSV}" | ||
| target-filename = "${TARGET_FILENAME}" | ||
| occupancies = [0.0, 0.25, 0.5, 0.75, 1.0] | ||
| n-jobs = "${N_JOBS}" | ||
| depth = "${GRID_SEARCH_DEPTH}" | ||
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| [[pre_jobs]] | ||
| name = "patch_outputs" | ||
| env = "analysis" | ||
| gpus = "none" | ||
| script = "scripts/patch_output_cif_files.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/patch_outputs" | ||
| args = { input-dir = "${GRID_SEARCH_RESULTS_DIR}", cif-pattern = "${PATCH_CIF_PATTERN}", rcsb-pattern = "${PATCH_RCSB_PATTERN}", depth = "${PATCH_DEPTH}", grid-search-input-dir = "${GRID_SEARCH_INPUTS_DIR}", input-pdb-pattern = "${PATCH_INPUT_PDB_PATTERN}" } | ||
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| [[jobs]] | ||
| name = "rscc" | ||
| env = "analysis" | ||
| gpu_count = 1 | ||
| script = "scripts/eval/rscc_grid_search_script.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/rscc" | ||
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| [[jobs]] | ||
| name = "lddt" | ||
| env = "analysis" | ||
| gpus = "none" | ||
| script = "scripts/eval/lddt_evaluation_script.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/lddt" | ||
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| [[jobs]] | ||
| name = "bond_geometry" | ||
| env = "analysis" | ||
| gpus = "none" | ||
| script = "scripts/eval/bond_geometry_eval.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/bond_geometry" | ||
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| [[jobs]] | ||
| name = "tortoize" | ||
| env = "analysis" | ||
| gpus = "none" | ||
| script = "scripts/eval/run_and_process_tortoize.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/tortoize" | ||
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| [[jobs]] | ||
| name = "phenix_clashscore" | ||
| env = "analysis" | ||
| gpus = "none" | ||
| script = "scripts/eval/run_and_process_phenix_clashscore.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/phenix_clashscore" |
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| description = "Classify altloc selections into side-chain, loop, and domain-shift categories." | ||
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| [defaults] | ||
| ALTLOC_ANALYSIS_DIR = "/data/results/altloc_analysis" | ||
| ALTLOC_INPUTS_DIR = "/data/inputs" | ||
| ALTLOC_SELECTIONS_CSV = "${ALTLOC_ANALYSIS_DIR}/altloc_selections.csv" | ||
| ALTLOC_CLASSIFICATIONS_CSV = "${ALTLOC_ANALYSIS_DIR}/altloc_region_classifications.csv" | ||
| CIF_ROOT = "${ALTLOC_INPUTS_DIR}" | ||
| DOMAIN_SHIFT_MIN_SPAN = "50" | ||
| LOOP_LDDT_THRESHOLD = "0.75" | ||
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| [shared_args] | ||
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Collaborator
There was a problem hiding this comment. I find this name, "shared_args" a little confusing. These are just the arguments to the script, right?
Contributor
There was a problem hiding this comment. Yes — in this schema |
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| input-csv = "${ALTLOC_SELECTIONS_CSV}" | ||
| cif-root = "${CIF_ROOT}" | ||
| output-file = "${ALTLOC_CLASSIFICATIONS_CSV}" | ||
| domain-shift-min-span = "${DOMAIN_SHIFT_MIN_SPAN}" | ||
| loop-lddt-threshold = "${LOOP_LDDT_THRESHOLD}" | ||
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| [[jobs]] | ||
| name = "classify_altloc_regions" | ||
| env = "analysis" | ||
| gpus = "none" | ||
| script = "scripts/eval/classify_altloc_regions.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/altloc_classify" | ||
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| Original file line number | Diff line number | Diff line change |
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| description = "Build an analysis protein-config CSV by finding altloc selections in input CIFs." | ||
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| [defaults] | ||
| ALTLOC_ANALYSIS_DIR = "/data/results/altloc_analysis" | ||
| ALTLOC_INPUTS_DIR = "/data/inputs" | ||
| PROTEINS_CSV = "${ALTLOC_INPUTS_DIR}/proteins.csv" | ||
| ALTLOC_SELECTIONS_CSV = "${ALTLOC_ANALYSIS_DIR}/altloc_selections.csv" | ||
| ALTLOC_MIN_SPAN = "5" | ||
| ALTLOC_LABEL = "label_alt_id" | ||
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| [shared_args] | ||
| input-csv = "${PROTEINS_CSV}" | ||
| output-file = "${ALTLOC_SELECTIONS_CSV}" | ||
| min-span = "${ALTLOC_MIN_SPAN}" | ||
| altloc-label = "${ALTLOC_LABEL}" | ||
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| [[jobs]] | ||
| name = "find_altloc_selections" | ||
| env = "analysis" | ||
| gpus = "none" | ||
| script = "scripts/eval/find_altloc_selections.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/altloc_find" |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,55 @@ | ||
| description = "Analyze grid-search outputs with RSCC, LDDT clustering, and bond geometry." | ||
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| [defaults] | ||
| GRID_SEARCH_RESULTS_DIR = "/data/results/grid_search_results" | ||
| GRID_SEARCH_INPUTS_DIR = "/data/inputs" | ||
| PROTEIN_CONFIGS_CSV = "${GRID_SEARCH_INPUTS_DIR}/protein_analysis_config.csv" | ||
| TARGET_FILENAME = "refined-patched.cif" | ||
| N_JOBS = "16" | ||
| PATCH_CIF_PATTERN = "refined.cif" | ||
| GRID_SEARCH_DEPTH = "4" | ||
| PATCH_DEPTH = "${GRID_SEARCH_DEPTH}" | ||
| PATCH_INPUT_PDB_PATTERN = "processed/{pdb_id}/{pdb_id}_single_001_density_input.cif" | ||
| PATCH_RCSB_PATTERN = "${GRID_SEARCH_RESULTS_DIR}/([A-Za-z0-9]{4})" | ||
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| [shared_args] | ||
| grid-search-results-path = "${GRID_SEARCH_RESULTS_DIR}" | ||
| grid-search-inputs-path = "${GRID_SEARCH_INPUTS_DIR}" | ||
| protein-configs-csv = "${PROTEIN_CONFIGS_CSV}" | ||
| target-filename = "${TARGET_FILENAME}" | ||
| occupancies = [0.0, 0.25, 0.5, 0.75, 1.0] | ||
| n-jobs = "${N_JOBS}" | ||
| depth = "${GRID_SEARCH_DEPTH}" | ||
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| [[pre_jobs]] | ||
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Collaborator
There was a problem hiding this comment. Ditto here, best if we can cache the results or optionally skip this step.
Contributor
There was a problem hiding this comment. Agreed, same fix here: |
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| name = "patch_outputs" | ||
| env = "analysis" | ||
| gpus = "none" | ||
| script = "scripts/patch_output_cif_files.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/patch_outputs" | ||
| args = { input-dir = "${GRID_SEARCH_RESULTS_DIR}", cif-pattern = "${PATCH_CIF_PATTERN}", rcsb-pattern = "${PATCH_RCSB_PATTERN}", depth = "${PATCH_DEPTH}", grid-search-input-dir = "${GRID_SEARCH_INPUTS_DIR}", input-pdb-pattern = "${PATCH_INPUT_PDB_PATTERN}" } | ||
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| [[jobs]] | ||
| name = "rscc" | ||
| env = "analysis" | ||
| gpu_count = 1 | ||
| script = "scripts/eval/rscc_grid_search_script.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/rscc" | ||
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| [[jobs]] | ||
| name = "lddt" | ||
| env = "analysis" | ||
| gpus = "none" | ||
| script = "scripts/eval/lddt_evaluation_script.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/lddt" | ||
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| [[jobs]] | ||
| name = "bond_geometry" | ||
| env = "analysis" | ||
| gpus = "none" | ||
| script = "scripts/eval/bond_geometry_eval.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/bond_geometry" | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| description = "Evaluation jobs that require external executables: tortoize and phenix.clashscore." | ||
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| [defaults] | ||
| GRID_SEARCH_RESULTS_DIR = "/data/results/grid_search_results" | ||
| GRID_SEARCH_INPUTS_DIR = "/data/inputs" | ||
| PROTEIN_CONFIGS_CSV = "${GRID_SEARCH_INPUTS_DIR}/protein_analysis_config.csv" | ||
| TARGET_FILENAME = "refined-patched.cif" | ||
| N_JOBS = "16" | ||
| PATCH_CIF_PATTERN = "refined.cif" | ||
| GRID_SEARCH_DEPTH = "4" | ||
| PATCH_DEPTH = "${GRID_SEARCH_DEPTH}" | ||
| PATCH_INPUT_PDB_PATTERN = "processed/{pdb_id}/{pdb_id}_single_001_density_input.cif" | ||
| PATCH_RCSB_PATTERN = "${GRID_SEARCH_RESULTS_DIR}/([A-Za-z0-9]{4})" | ||
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| [shared_args] | ||
| grid-search-results-path = "${GRID_SEARCH_RESULTS_DIR}" | ||
| grid-search-inputs-path = "${GRID_SEARCH_INPUTS_DIR}" | ||
| protein-configs-csv = "${PROTEIN_CONFIGS_CSV}" | ||
| target-filename = "${TARGET_FILENAME}" | ||
| occupancies = [0.0, 0.25, 0.5, 0.75, 1.0] | ||
| n-jobs = "${N_JOBS}" | ||
| depth = "${GRID_SEARCH_DEPTH}" | ||
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| [[pre_jobs]] | ||
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Collaborator
There was a problem hiding this comment. I mention this below in runner.py, but it may be better to run this script separately, or use cached results, since we might want to modify analysis scripts and rerun them, without needing to re-run patching, which is unfortunately a little slow (it can be trivially parallelized, but still takes some time)
Contributor
There was a problem hiding this comment. Agreed. |
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| name = "patch_outputs" | ||
| env = "analysis" | ||
| gpus = "none" | ||
| script = "scripts/patch_output_cif_files.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/patch_outputs" | ||
| args = { input-dir = "${GRID_SEARCH_RESULTS_DIR}", cif-pattern = "${PATCH_CIF_PATTERN}", rcsb-pattern = "${PATCH_RCSB_PATTERN}", depth = "${PATCH_DEPTH}", grid-search-input-dir = "${GRID_SEARCH_INPUTS_DIR}", input-pdb-pattern = "${PATCH_INPUT_PDB_PATTERN}" } | ||
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| [[jobs]] | ||
| name = "tortoize" | ||
| env = "analysis" | ||
| gpus = "none" | ||
| script = "scripts/eval/run_and_process_tortoize.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/tortoize" | ||
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| [[jobs]] | ||
| name = "phenix_clashscore" | ||
| env = "analysis" | ||
| gpus = "none" | ||
| script = "scripts/eval/run_and_process_phenix_clashscore.py" | ||
| output_arg = "" | ||
| output_subdir = "analysis/phenix_clashscore" | ||
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Do we need to rebuilt the current images for us to be able to update code on the fly in actl?
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For code-only changes, no rebuild should be needed: ACTL syncs the checkout to
/home/dev/workspace, and the runner resolves scripts from that live checkout first. Rebuilds are still needed for dependency/pixi-lock changes or wrapper/image changes baked into/usr/local/bin;RUNTIME_PIXI=1is the escape hatch when intentionally testing a dependency change inside an existing pod.