temporarily disable display dti
Browse files
app.py
CHANGED
@@ -148,40 +148,6 @@ def retrieval():
|
|
148 |
selected_encoder = st.selectbox(
|
149 |
'Select encoder for protein target',('None', 'SeqVec', 'UniRep', 'ESM-1b', 'ProtT5')
|
150 |
)
|
151 |
-
if selected_encoder == 'SeqVec':
|
152 |
-
from bio_embeddings.embed import SeqVecEmbedder
|
153 |
-
encoder = SeqVecEmbedder()
|
154 |
-
embeddings = encoder.embed_batch([sequence])
|
155 |
-
for emb in embeddings:
|
156 |
-
embedding = encoder.reduce_per_protein(emb)
|
157 |
-
break
|
158 |
-
elif selected_encoder == 'UniRep':
|
159 |
-
from jax_unirep.utils import load_params
|
160 |
-
params = load_params()
|
161 |
-
from jax_unirep.featurize import get_reps
|
162 |
-
embedding, h_final, c_final = get_reps([sequence])
|
163 |
-
embedding = embedding.mean(axis=0)
|
164 |
-
elif selected_encoder == 'ESM-1b':
|
165 |
-
from bio_embeddings.embed import ESM1bEmbedder
|
166 |
-
encoder = ESM1bEmbedder()
|
167 |
-
embeddings = encoder.embed_batch([sequence])
|
168 |
-
for emb in embeddings:
|
169 |
-
embedding = encoder.reduce_per_protein(emb)
|
170 |
-
break
|
171 |
-
elif selected_encoder == 'ProtT5':
|
172 |
-
from bio_embeddings.embed import ProtTransT5XLU50Embedder
|
173 |
-
encoder = ProtTransT5XLU50Embedder()
|
174 |
-
embeddings = encoder.embed_batch([sequence])
|
175 |
-
for emb in embeddings:
|
176 |
-
embedding = encoder.reduce_per_protein(emb)
|
177 |
-
break
|
178 |
-
else:
|
179 |
-
st.write('No pre-trained version of HyperPCM is available for the chosen encoder.')
|
180 |
-
embedding = None
|
181 |
-
if embedding is not None:
|
182 |
-
st.write(f'{selected_encoder} embedding')
|
183 |
-
st.write(embedding)
|
184 |
-
|
185 |
|
186 |
st.markdown('### Retrieval of top-5 drug coupound from ChEMBL:')
|
187 |
col1, col2, col3, col4, col5 = st.columns(5)
|
@@ -282,7 +248,7 @@ def display_protein():
|
|
282 |
|
283 |
page_names_to_func = {
|
284 |
'About': about_page,
|
285 |
-
'Display DTI': display_dti,
|
286 |
'Retrieve Top-k': retrieval
|
287 |
}
|
288 |
|
|
|
148 |
selected_encoder = st.selectbox(
|
149 |
'Select encoder for protein target',('None', 'SeqVec', 'UniRep', 'ESM-1b', 'ProtT5')
|
150 |
)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
151 |
|
152 |
st.markdown('### Retrieval of top-5 drug coupound from ChEMBL:')
|
153 |
col1, col2, col3, col4, col5 = st.columns(5)
|
|
|
248 |
|
249 |
page_names_to_func = {
|
250 |
'About': about_page,
|
251 |
+
#'Display DTI': display_dti,
|
252 |
'Retrieve Top-k': retrieval
|
253 |
}
|
254 |
|