Complete Activity513 Chai/OpenFold3 seed68 manifests

activity_challenge/README.md

@@ -1,13 +1,11 @@
-# Activity Challenge Cofolding Predictions
+# Activity Challenge cofolding data
 
-Single-copy cofolding predictions for 513 PXR activity-challenge ligands.
+Current Activity Challenge remote packages in this dataset repository:
 
-Included sets:
-- `boltz_no_template`: Boltz no-template, 513 ligands x 5 models = 2,565 structures.
-- `chai1_msa_seed11_25_50_67`: Chai-1 MSA, 513 ligands x 4 seeds x 5 samples = 10,260 structures.
-- `openfold3_msa_seed11_25_50_67`: OpenFold3 MSA, 513 ligands x 4 seeds x 5 samples = 10,260 structures.
+- `boltz_no_template`: Boltz 1-copy/no-template package, 513 ligands x 5 models = 2,565 structures.
+- `chai1_msa_seed11_25_50_67`: Chai-1 MSA package, 513 ligands x 5 seeds (11,25,50,67,68) x 5 samples = 12,825 structures.
+- `openfold3_msa_seed11_25_50_67`: OpenFold3 MSA package, 513 ligands x 5 seeds (11,25,50,67,68) x 5 samples = 12,825 structures.
 
-For each set:
-- prediction archive(s) under the set folder.
-- `activity_challenge/manifests/<set>/model_manifest.csv`: row-level prediction manifest.
-- `activity_challenge/manifests/<set>/archive_inventory.csv`: complete archive file inventory.
+Note: the Chai-1 and OpenFold3 folder names predate the seed68 completion upload; the manifests now include seed68 and are the authoritative inventory.
+
+Blind/test caveat: activity labels are not included and must not be used for training. These structure packages are raw/diagnostic artifacts until campaign QC/scoring and Validator/Data Czar gates pass.

activity_challenge/chai1_msa_seed11_25_50_67/README.md

@@ -1,16 +1,18 @@
-# Activity Challenge Chai-1 MSA Predictions
+# Activity Challenge Chai-1 MSA seed 11/25/50/67/68 archive package
 
-Chai-1 MSA cofolding predictions for 513 PXR activity-challenge ligands.
+This folder contains Activity513 blind/test-side Chai-1 cofolding prediction archives for seeds 11, 25, 50, 67, and 68.
 
-Coverage:
-- Ligands: 513
-- Ligand copy count: 1
-- Seeds: 11, 25, 50, 67
+Scope:
+- Ligands: 513 Activity Challenge blind/test ligands
+- Seeds: 11, 25, 50, 67, 68
 - Samples per ligand per seed: 5
-- Structures: 10,260
+- Structures: 12,825 CIFs = 513 x 5 x 5
+- Ligand copy count: 1
+
+Manifest:
+- `activity_challenge/manifests/chai1_msa_seed11_25_50_67/model_manifest.csv`
+- `activity_challenge/manifests/chai1_msa_seed11_25_50_67/archive_manifest.csv`
 
-Files:
-- one `pxr_activity_blind513_5seed_5sample_20260515_chai_seed_<seed>.tar.gz` archive per seed.
-- `activity_challenge/manifests/chai1_msa_seed11_25_50_67/model_manifest.csv`: row-level prediction manifest.
-- `activity_challenge/manifests/chai1_msa_seed11_25_50_67/archive_manifest.csv`: archive-level manifest.
-- `activity_challenge/manifests/chai1_msa_seed11_25_50_67/archive_inventory.csv`: complete archive file inventory.
+Caveats:
+- Blind/test labels are not included and must not be used for training.
+- These are raw/diagnostic structural artifacts until downstream QC/scoring and Validator/Data Czar gates pass.

activity_challenge/manifests/chai1_msa_seed11_25_50_67/archive_manifest.csv

@@ -1,5 +1,6 @@
-engine,method,seed,path_in_repo,bytes,sha256
-chai,Chai-1,11,activity_challenge/chai1_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_chai_seed_11.tar.gz,159922532,58da7c04ff51762c680f83f75bae7cbda46294477d494c294d48c2f502b483db
-chai,Chai-1,25,activity_challenge/chai1_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_chai_seed_25.tar.gz,160133739,ddcefb00525c563aa89dadf1d985bd10787a96feff0735caeeca758f1bc3128c
-chai,Chai-1,50,activity_challenge/chai1_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_chai_seed_50.tar.gz,160404873,e2b8e5b079dcf1c35ff78498c0bdddbf746793dc4a6098df9db3616e82a61aae
-chai,Chai-1,67,activity_challenge/chai1_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_chai_seed_67.tar.gz,160863428,747fe8f17080263c124bfe79568eb18f55205b07b67d6008eff43abfd82c4baf
+engine,method,seed,path_in_repo,bytes,sha256,local_path
+chai,Chai-1,11,activity_challenge/chai1_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_chai_seed_11.tar.gz,159922532,58da7c04ff51762c680f83f75bae7cbda46294477d494c294d48c2f502b483db,
+chai,Chai-1,25,activity_challenge/chai1_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_chai_seed_25.tar.gz,160133739,ddcefb00525c563aa89dadf1d985bd10787a96feff0735caeeca758f1bc3128c,
+chai,Chai-1,50,activity_challenge/chai1_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_chai_seed_50.tar.gz,160404873,e2b8e5b079dcf1c35ff78498c0bdddbf746793dc4a6098df9db3616e82a61aae,
+chai,Chai-1,67,activity_challenge/chai1_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_chai_seed_67.tar.gz,160863428,747fe8f17080263c124bfe79568eb18f55205b07b67d6008eff43abfd82c4baf,
+chai,Chai-1,68,activity_challenge/chai1_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_chai_seed_68.tar.gz,161153890,35021b417119a66278b529b5d1478ea922f4f2b43e69ed03f4ee37192a07a7a4,/home/dan/projects/ADMET-PXR-AGENT/campaigns/openadmet_pxr/runs/activity513_seed68_chai_openfold_download_20260519T005451Z/archives/pxr_activity_blind513_5seed_5sample_20260515_chai_seed_68.tar.gz

activity_challenge/manifests/openfold3_msa_seed11_25_50_67/archive_manifest.csv

@@ -1,5 +1,6 @@
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-openfold3,OpenFold3,67,activity_challenge/openfold3_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_openfold3_seed_67.tar.gz,5003906735,468110ba82da9005ca26f9eba638fc079c30cbd97e3700935e40d8f7e2425f88
+engine,method,seed,path_in_repo,bytes,sha256,local_path
+openfold3,OpenFold3,11,activity_challenge/openfold3_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_openfold3_seed_11.tar.gz,5003871423,91458076fcd21ef0b1baa6522190181b0ec501ebca5b7ce9f7576df90812ba02,
+openfold3,OpenFold3,25,activity_challenge/openfold3_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_openfold3_seed_25.tar.gz,5003842746,a049611d626d693d16de39f160c2083a6bd37fe7394ff711979272cab836b91f,
+openfold3,OpenFold3,50,activity_challenge/openfold3_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_openfold3_seed_50.tar.gz,5003893094,2a61faba8af0cb81ae63b30a6b26d3136221ab550117a7f272ead58ed9ede5ce,
+openfold3,OpenFold3,67,activity_challenge/openfold3_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_openfold3_seed_67.tar.gz,5003906735,468110ba82da9005ca26f9eba638fc079c30cbd97e3700935e40d8f7e2425f88,
+openfold3,OpenFold3,68,activity_challenge/openfold3_msa_seed11_25_50_67/pxr_activity_blind513_5seed_5sample_20260515_openfold3_seed_68.tar.gz,5003910547,d38469b6c5c9479e08298b38f52eec71b8405a0affac2ac542f8d0e080582b0c,/home/dan/projects/ADMET-PXR-AGENT/campaigns/openadmet_pxr/runs/activity513_seed68_chai_openfold_download_20260519T005451Z/archives/pxr_activity_blind513_5seed_5sample_20260515_openfold3_seed_68.tar.gz

activity_challenge/openfold3_msa_seed11_25_50_67/README.md

@@ -1,16 +1,19 @@
-# Activity Challenge OpenFold3 MSA Predictions
+# Activity Challenge OpenFold3 MSA seed 11/25/50/67/68 archive package
 
-OpenFold3 MSA cofolding predictions for 513 PXR activity-challenge ligands.
+This folder contains Activity513 blind/test-side OpenFold3 cofolding prediction archives for seeds 11, 25, 50, 67, and 68.
 
-Coverage:
-- Ligands: 513
-- Ligand copy count: 1
-- Seeds: 11, 25, 50, 67
+Scope:
+- Ligands: 513 Activity Challenge blind/test ligands
+- Seeds: 11, 25, 50, 67, 68
 - Samples per ligand per seed: 5
-- Structures: 10,260
+- Structures: 12,825 CIFs = 513 x 5 x 5
+- Ligand copy count: 1
+
+Manifest:
+- `activity_challenge/manifests/openfold3_msa_seed11_25_50_67/model_manifest.csv`
+- `activity_challenge/manifests/openfold3_msa_seed11_25_50_67/archive_manifest.csv`
 
-Files:
-- one `pxr_activity_blind513_5seed_5sample_20260515_openfold3_seed_<seed>.tar.gz` archive per seed.
-- `activity_challenge/manifests/openfold3_msa_seed11_25_50_67/model_manifest.csv`: row-level prediction manifest.
-- `activity_challenge/manifests/openfold3_msa_seed11_25_50_67/archive_manifest.csv`: archive-level manifest.
-- `activity_challenge/manifests/openfold3_msa_seed11_25_50_67/archive_inventory.csv`: complete archive file inventory.
+Caveats:
+- Blind/test labels are not included and must not be used for training.
+- These are raw/diagnostic structural artifacts until downstream QC/scoring and Validator/Data Czar gates pass.
+- OpenFold3 archive inner paths contain `seed_42` labels under the outer seed folder; seed identity is recorded by archive/folder name and manifest `seed`.

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dataset_manifest.csv

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