[CLEAN] removed bo_utils.py.

devmogul · Jun 5, 2023 · cd06734 · cd06734
1 parent 10e975f
commit cd06734
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Showing 4 changed files with 13 additions and 34 deletions.
diff --git a/AntBO/bo/bo_utils.py b/AntBO/bo/bo_utils.py
diff --git a/AntBO/bo/localbo_utils.py b/AntBO/bo/localbo_utils.py
@@ -4,10 +4,15 @@
 import random
 from copy import deepcopy
 
-from bo.bo_utils import check_cdr_constraints, idx_to_AA, N_glycosylation_pattern
 from bo.kernels import *
 import re
 
+COUNT_AA = 5
+AA = 'ACDEFGHIKLMNPQRSTVWY'
+AA_to_idx = {aa: i for i, aa in enumerate(AA)}
+idx_to_AA = {value: key for key, value in AA_to_idx.items()}
+N_glycosylation_pattern = 'N[^P][ST][^P]'
+
 
 # from Bio.SeqUtils.ProtParam import ProteinAnalysis
 
@@ -44,6 +49,11 @@ def check_cdr_constraints_all(x, x_center_local=None, hamming=None, config=None)
     return int(not (c1)), int(not (c2)), int(not (c3))
 
 
+def check_cdr_constraints(x) -> bool:
+    constr = check_cdr_constraints_all(x)
+    return np.all(constr)
+
+
 def onehot2ordinal(x, categorical_dims):
     """Convert one-hot representation of strings back to ordinal representation."""
     from itertools import chain

diff --git a/AntBO/bo/main.py b/AntBO/bo/main.py
@@ -24,7 +24,7 @@
 def get_x_y_from_csv(csv_path):
     data = pd.read_csv(csv_path)
     x = data["x"].values
-    from bo.bo_utils import AA_to_idx
+    from bo.localbo_utils import AA_to_idx
     x = np.array([[AA_to_idx[cat] for cat in xx] for xx in x])
     y = torch.tensor(data["y"].values).reshape(-1, 1)
     return x, y

diff --git a/AntBO/bo/optimizer.py b/AntBO/bo/optimizer.py
@@ -5,7 +5,7 @@
 from bo.localbo_cat import CASMOPOLITANCat
 from bo.localbo_utils import from_unit_cube, latin_hypercube, to_unit_cube, ordinal2onehot, onehot2ordinal,\
     random_sample_within_discrete_tr_ordinal
-from bo.bo_utils import check_cdr_constraints
+from bo.localbo_utils import check_cdr_constraints
 import torch
 import logging
 from gpytorch.utils.errors import NotPSDError, NanError