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luost26 commited on
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  1. configs/test/abopt_singlecdr.yml +27 -0
  2. configs/test/codesign_multicdrs.yml +24 -0
  3. configs/test/codesign_single.yml +24 -0
  4. configs/test/fixbb.yml +24 -0
  5. data/examples/3QHF_Fv.pdb +0 -0
  6. data/examples/7DK2_AB_C.pdb +0 -0
  7. data/examples/Omicron_RBD.pdb +0 -0
configs/test/abopt_singlecdr.yml ADDED
@@ -0,0 +1,27 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ mode: abopt
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+ model:
3
+ checkpoint: ../trained_models/codesign_single.pt
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+
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+ sampling:
6
+ seed: 2022
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+ sample_structure: true
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+ sample_sequence: true
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+ cdrs:
10
+ - H_CDR3
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+ num_samples: 100
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+ optimize_steps:
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+ - 1
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+ - 2
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+ - 4
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+ - 8
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+ - 16
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+ - 32
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+ - 64
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+
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+ dataset:
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+ test:
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+ type: sabdab
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+ summary_path: ./data/sabdab_summary_all.tsv
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+ chothia_dir: ./data/all_structures/chothia
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+ processed_dir: ./data/processed
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+ split: test
configs/test/codesign_multicdrs.yml ADDED
@@ -0,0 +1,24 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ mode: multiple_cdrs
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+ model:
3
+ checkpoint: ../trained_models/codesign_multicdrs.pt
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+
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+ sampling:
6
+ seed: 2022
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+ sample_structure: true
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+ sample_sequence: true
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+ cdrs:
10
+ - H_CDR1
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+ - H_CDR2
12
+ - H_CDR3
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+ - L_CDR1
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+ - L_CDR2
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+ - L_CDR3
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+ num_samples: 100
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+
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+ dataset:
19
+ test:
20
+ type: sabdab
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+ summary_path: ./data/sabdab_summary_all.tsv
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+ chothia_dir: ./data/all_structures/chothia
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+ processed_dir: ./data/processed
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+ split: test
configs/test/codesign_single.yml ADDED
@@ -0,0 +1,24 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ mode: single_cdr
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+ model:
3
+ checkpoint: ../trained_models/codesign_single.pt
4
+
5
+ sampling:
6
+ seed: 2022
7
+ sample_structure: true
8
+ sample_sequence: true
9
+ cdrs:
10
+ - H_CDR1
11
+ - H_CDR2
12
+ - H_CDR3
13
+ - L_CDR1
14
+ - L_CDR2
15
+ - L_CDR3
16
+ num_samples: 100
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+
18
+ dataset:
19
+ test:
20
+ type: sabdab
21
+ summary_path: ./data/sabdab_summary_all.tsv
22
+ chothia_dir: ./data/all_structures/chothia
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+ processed_dir: ./data/processed
24
+ split: test
configs/test/fixbb.yml ADDED
@@ -0,0 +1,24 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ mode: single_cdr
2
+ model:
3
+ checkpoint: ../trained_models/fixbb.pt
4
+
5
+ sampling:
6
+ seed: 2022
7
+ sample_structure: false
8
+ sample_sequence: true
9
+ cdrs:
10
+ - H_CDR1
11
+ - H_CDR2
12
+ - H_CDR3
13
+ - L_CDR1
14
+ - L_CDR2
15
+ - L_CDR3
16
+ num_samples: 100
17
+
18
+ dataset:
19
+ test:
20
+ type: sabdab
21
+ summary_path: ./data/sabdab_summary_all.tsv
22
+ chothia_dir: ./data/all_structures/chothia
23
+ processed_dir: ./data/processed
24
+ split: test
data/examples/3QHF_Fv.pdb ADDED
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data/examples/7DK2_AB_C.pdb ADDED
The diff for this file is too large to render. See raw diff
 
data/examples/Omicron_RBD.pdb ADDED
The diff for this file is too large to render. See raw diff