Update

.ipynb_checkpoints/app-checkpoint.py

@@ -242,7 +242,7 @@ with gr.Blocks() as demo:
     molecule_output2 = Molecule3D(label="Protein Structure", reps=reps)
 
     with gr.Row():
-        pdb_input = gr.Textbox(value="2IWI", label="PDB ID", placeholder="Enter PDB ID here...")
+        #pdb_input = gr.Textbox(value="2IWI", label="PDB ID", placeholder="Enter PDB ID here...")
         segment_input = gr.Textbox(value="A", label="Chain ID", placeholder="Enter Chain ID here...")
         prediction_btn = gr.Button("Predict Random Binding Site Scores")
 

.ipynb_checkpoints/test2-checkpoint.ipynb

@@ -727,7 +727,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 6,
    "id": "30f35243-852f-4771-9a4b-5cdd198552b5",
    "metadata": {},
    "outputs": [
@@ -735,7 +735,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "* Running on local URL:  http://127.0.0.1:7863\n",
+      "* Running on local URL:  http://127.0.0.1:7865\n",
       "\n",
       "To create a public link, set `share=True` in `launch()`.\n"
      ]
@@ -743,7 +743,7 @@
     {
      "data": {
       "text/html": [
-       "<div><iframe src=\"http://127.0.0.1:7863/\" width=\"100%\" height=\"500\" allow=\"autoplay; camera; microphone; clipboard-read; clipboard-write;\" frameborder=\"0\" allowfullscreen></iframe></div>"
+       "<div><iframe src=\"http://127.0.0.1:7865/\" width=\"100%\" height=\"500\" allow=\"autoplay; camera; microphone; clipboard-read; clipboard-write;\" frameborder=\"0\" allowfullscreen></iframe></div>"
       ],
       "text/plain": [
        "<IPython.core.display.HTML object>"
@@ -756,7 +756,7 @@
      "data": {
       "text/plain": []
      },
-     "execution_count": 4,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -961,7 +961,7 @@
     "    molecule_output2 = Molecule3D(label=\"Protein Structure\", reps=reps)\n",
     "\n",
     "    with gr.Row():\n",
-    "        pdb_input = gr.Textbox(value=\"2IWI\", label=\"PDB ID\", placeholder=\"Enter PDB ID here...\")\n",
+    "        #pdb_input = gr.Textbox(value=\"2IWI\", label=\"PDB ID\", placeholder=\"Enter PDB ID here...\")\n",
     "        segment_input = gr.Textbox(value=\"A\", label=\"Chain ID\", placeholder=\"Enter Chain ID here...\")\n",
     "        prediction_btn = gr.Button(\"Predict Random Binding Site Scores\")\n",
     "\n",
@@ -976,8 +976,8 @@
     "    gr.Markdown(\"## Examples\")\n",
     "    gr.Examples(\n",
     "        examples=[\n",
-    "            [\"2IWI\", \"A\"],\n",
-    "            [\"7RPZ\", \"B\"],\n",
+    "            [\"7RPZ\", \"A\"],\n",
+    "            [\"2IWI\", \"B\"],\n",
     "            [\"3TJN\", \"C\"]\n",
     "        ],\n",
     "        inputs=[pdb_input, segment_input],\n",
@@ -1262,7 +1262,7 @@
     "    molecule_output2 = Molecule3D(label=\"Protein Structure\", reps=reps)\n",
     "\n",
     "    with gr.Row():\n",
-    "        pdb_input = gr.Textbox(value=\"2IWI\", label=\"PDB ID\", placeholder=\"Enter PDB ID here...\")\n",
+    "        #pdb_input = gr.Textbox(value=\"2IWI\", label=\"PDB ID\", placeholder=\"Enter PDB ID here...\")\n",
     "        segment_input = gr.Textbox(value=\"A\", label=\"Chain ID\", placeholder=\"Enter Chain ID here...\")\n",
     "        prediction_btn = gr.Button(\"Predict Random Binding Site Scores\")\n",
     "\n",

2IWI_predictions.txt

@@ -1,244 +1,244 @@
-Y 32 0.32
-R 33 0.91
-L 34 0.65
-G 35 0.50
-P 36 0.82
-L 37 0.90
-L 38 0.19
-G 39 0.33
-K 40 0.10
-G 41 0.23
-G 42 0.54
-F 43 0.58
-G 44 0.25
-T 45 0.06
-V 46 0.10
-F 47 0.20
-A 48 0.34
-G 49 0.10
-H 50 0.59
-R 51 0.12
-L 52 0.03
-T 53 0.86
-D 54 0.08
-R 55 0.57
-L 56 0.96
-Q 57 0.75
-V 58 0.91
-A 59 0.80
-I 60 0.49
-K 61 0.52
-V 62 0.29
-I 63 0.87
-P 64 0.60
-R 65 0.99
-N 66 0.50
-R 67 0.51
-V 68 0.79
-L 69 0.16
-V 78 0.06
-T 79 0.89
-C 80 0.33
-P 81 0.40
-L 82 0.84
-E 83 0.07
-V 84 0.47
-A 85 0.67
-L 86 0.89
-L 87 0.86
-W 88 0.04
-K 89 0.34
-V 90 0.53
-G 91 0.83
-A 92 0.80
-G 93 0.85
-G 94 0.42
-G 95 0.08
-H 96 0.24
-P 97 0.78
-G 98 0.38
-V 99 0.39
-I 100 0.21
-R 101 0.77
-L 102 0.61
-L 103 0.50
-D 104 0.13
-W 105 0.76
-F 106 0.45
-F 112 0.89
-M 113 0.39
-L 114 0.11
-V 115 0.56
-L 116 0.04
-E 117 0.62
-R 118 0.39
-P 119 0.72
-L 120 0.38
+Y 32 0.77
+R 33 0.71
+L 34 0.07
+G 35 0.04
+P 36 0.28
+L 37 0.39
+L 38 0.81
+G 39 0.67
+K 40 0.56
+G 41 0.16
+G 42 0.52
+F 43 0.59
+G 44 0.64
+T 45 0.62
+V 46 0.11
+F 47 0.07
+A 48 0.35
+G 49 0.94
+H 50 0.23
+R 51 0.78
+L 52 0.08
+T 53 0.65
+D 54 0.45
+R 55 0.12
+L 56 0.08
+Q 57 0.67
+V 58 0.44
+A 59 0.48
+I 60 0.31
+K 61 0.01
+V 62 0.57
+I 63 0.40
+P 64 0.43
+R 65 0.56
+N 66 0.36
+R 67 0.80
+V 68 0.68
+L 69 0.33
+V 78 0.63
+T 79 0.11
+C 80 0.56
+P 81 0.01
+L 82 0.93
+E 83 0.19
+V 84 0.26
+A 85 0.26
+L 86 0.68
+L 87 0.44
+W 88 0.91
+K 89 0.65
+V 90 0.38
+G 91 0.30
+A 92 0.18
+G 93 0.56
+G 94 0.90
+G 95 0.89
+H 96 0.36
+P 97 0.23
+G 98 0.04
+V 99 0.65
+I 100 0.83
+R 101 0.35
+L 102 0.47
+L 103 0.53
+D 104 0.26
+W 105 0.12
+F 106 0.14
+F 112 0.22
+M 113 0.04
+L 114 0.84
+V 115 0.64
+L 116 0.82
+E 117 0.42
+R 118 0.79
+P 119 0.18
+L 120 0.68
 P 121 0.35
-A 122 0.03
-Q 123 0.85
-D 124 0.49
-L 125 0.19
-F 126 0.78
-D 127 0.52
-Y 128 0.88
-I 129 0.85
-T 130 0.82
-E 131 0.27
-K 132 0.67
-G 133 0.41
-P 134 0.95
-L 135 0.36
-G 136 0.52
-E 137 0.14
-G 138 0.95
-P 139 0.57
+A 122 0.40
+Q 123 0.48
+D 124 0.02
+L 125 0.66
+F 126 0.51
+D 127 0.21
+Y 128 0.33
+I 129 0.37
+T 130 0.16
+E 131 0.35
+K 132 0.10
+G 133 0.39
+P 134 0.64
+L 135 0.56
+G 136 0.59
+E 137 0.85
+G 138 0.21
+P 139 0.27
 S 140 0.27
-R 141 0.92
-C 142 0.13
-F 143 0.18
-F 144 0.12
-G 145 0.32
-Q 146 0.35
-V 147 0.95
-V 148 0.89
-A 149 0.76
-A 150 0.43
-I 151 0.09
-Q 152 0.89
-H 153 0.54
-C 154 0.47
-H 155 0.05
-S 156 0.10
-R 157 0.64
-G 158 0.32
-V 159 0.41
-V 160 0.18
-H 161 0.63
-R 162 0.14
-D 163 0.03
-I 164 0.63
-K 165 0.97
-D 166 0.73
-E 167 0.96
-N 168 0.25
-I 169 0.37
+R 141 0.12
+C 142 0.43
+F 143 0.32
+F 144 0.80
+G 145 0.49
+Q 146 0.81
+V 147 0.06
+V 148 0.40
+A 149 0.45
+A 150 0.77
+I 151 0.53
+Q 152 0.34
+H 153 0.33
+C 154 0.89
+H 155 0.51
+S 156 0.48
+R 157 0.21
+G 158 0.64
+V 159 0.00
+V 160 0.85
+H 161 0.55
+R 162 0.74
+D 163 0.41
+I 164 0.57
+K 165 0.63
+D 166 0.77
+E 167 0.06
+N 168 0.67
+I 169 0.65
 L 170 0.79
-I 171 0.26
-D 172 0.80
-L 173 0.98
-R 174 0.06
-R 175 0.56
-G 176 0.29
-C 177 0.43
-A 178 0.17
-K 179 0.52
-L 180 0.51
-I 181 0.54
-D 182 0.04
-F 183 0.33
-G 184 0.05
-S 185 0.92
-G 186 0.92
-A 187 0.83
-L 188 0.49
-L 189 0.88
-H 190 0.60
-D 191 0.17
-E 192 0.17
-P 193 0.31
-Y 194 0.61
-T 195 0.02
-D 196 0.11
-F 197 0.33
-D 198 0.85
-G 199 0.82
-T 200 0.10
-R 201 0.69
-V 202 0.70
-Y 203 0.21
-S 204 0.80
-P 205 0.65
-P 206 0.75
-E 207 0.01
-W 208 0.81
-I 209 0.83
-S 210 0.72
-R 211 0.80
-H 212 0.64
-Q 213 0.36
-Y 214 0.54
-H 215 0.97
-A 216 0.75
-L 217 0.54
-P 218 0.25
-A 219 0.04
-T 220 0.28
-V 221 0.46
-W 222 0.67
-S 223 0.24
-L 224 0.05
-G 225 0.65
-I 226 0.42
-L 227 0.46
-L 228 0.12
-Y 229 0.68
-D 230 0.82
-M 231 0.51
-V 232 0.75
-C 233 0.41
-G 234 0.54
-D 235 0.43
-I 236 0.09
-P 237 0.12
-F 238 0.80
-E 239 0.57
-R 240 0.42
-D 241 0.34
-Q 242 0.08
-E 243 0.40
-I 244 0.68
-L 245 0.09
-E 246 0.75
-A 247 0.38
-E 248 0.68
-L 249 0.62
-H 250 0.56
-F 251 0.08
-P 252 0.60
-A 253 0.12
-H 254 0.77
-V 255 0.92
-S 256 0.67
-P 257 0.48
-D 258 0.27
-C 259 0.90
-C 260 0.16
-A 261 0.50
-L 262 0.78
-I 263 0.11
-R 264 0.67
-R 265 0.85
-C 266 0.80
-L 267 0.11
-A 268 0.95
-P 269 0.30
-K 270 0.34
-P 271 0.85
-S 272 0.94
-S 273 0.04
-R 274 0.83
-P 275 0.68
-S 276 0.16
-L 277 0.13
-E 278 0.74
-E 279 0.28
-I 280 0.45
-L 281 0.46
-L 282 0.23
-D 283 0.24
-P 284 0.58
-W 285 0.78
-M 286 0.59
-Q 287 0.30
-T 288 0.30
+I 171 0.42
+D 172 0.39
+L 173 0.49
+R 174 0.63
+R 175 0.39
+G 176 0.72
+C 177 0.88
+A 178 0.79
+K 179 0.76
+L 180 0.81
+I 181 0.30
+D 182 0.22
+F 183 0.31
+G 184 0.85
+S 185 0.67
+G 186 0.25
+A 187 0.50
+L 188 0.96
+L 189 0.26
+H 190 0.13
+D 191 0.29
+E 192 0.02
+P 193 0.65
+Y 194 0.32
+T 195 0.41
+D 196 0.82
+F 197 0.34
+D 198 0.15
+G 199 0.20
+T 200 0.46
+R 201 0.22
+V 202 0.26
+Y 203 0.29
+S 204 0.51
+P 205 0.70
+P 206 0.14
+E 207 0.89
+W 208 0.09
+I 209 0.54
+S 210 0.16
+R 211 0.69
+H 212 0.63
+Q 213 0.06
+Y 214 0.02
+H 215 0.17
+A 216 0.23
+L 217 0.65
+P 218 0.13
+A 219 0.91
+T 220 0.97
+V 221 0.77
+W 222 0.40
+S 223 0.91
+L 224 1.00
+G 225 0.97
+I 226 0.24
+L 227 0.44
+L 228 0.19
+Y 229 0.06
+D 230 0.32
+M 231 0.93
+V 232 0.35
+C 233 0.79
+G 234 0.50
+D 235 0.49
+I 236 0.10
+P 237 0.49
+F 238 0.12
+E 239 0.47
+R 240 0.40
+D 241 0.63
+Q 242 1.00
+E 243 0.55
+I 244 0.78
+L 245 0.92
+E 246 0.29
+A 247 0.37
+E 248 0.78
+L 249 0.54
+H 250 0.64
+F 251 0.30
+P 252 0.25
+A 253 0.01
+H 254 0.51
+V 255 0.81
+S 256 0.93
+P 257 0.79
+D 258 0.74
+C 259 0.31
+C 260 0.51
+A 261 0.91
+L 262 0.04
+I 263 0.21
+R 264 0.07
+R 265 0.34
+C 266 0.93
+L 267 0.80
+A 268 0.75
+P 269 0.59
+K 270 0.62
+P 271 0.18
+S 272 0.32
+S 273 0.54
+R 274 0.14
+P 275 0.38
+S 276 0.29
+L 277 0.97
+E 278 0.72
+E 279 0.05
+I 280 0.26
+L 281 0.24
+L 282 0.42
+D 283 0.84
+P 284 0.36
+W 285 0.79
+M 286 0.05
+Q 287 0.81
+T 288 0.39

app.py

@@ -242,7 +242,7 @@ with gr.Blocks() as demo:
     molecule_output2 = Molecule3D(label="Protein Structure", reps=reps)
 
     with gr.Row():
-        pdb_input = gr.Textbox(value="2IWI", label="PDB ID", placeholder="Enter PDB ID here...")
+        #pdb_input = gr.Textbox(value="2IWI", label="PDB ID", placeholder="Enter PDB ID here...")
         segment_input = gr.Textbox(value="A", label="Chain ID", placeholder="Enter Chain ID here...")
         prediction_btn = gr.Button("Predict Random Binding Site Scores")
 

test2.ipynb

@@ -727,7 +727,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 6,
    "id": "30f35243-852f-4771-9a4b-5cdd198552b5",
    "metadata": {},
    "outputs": [
@@ -735,7 +735,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "* Running on local URL:  http://127.0.0.1:7863\n",
+      "* Running on local URL:  http://127.0.0.1:7865\n",
       "\n",
       "To create a public link, set `share=True` in `launch()`.\n"
      ]
@@ -743,7 +743,7 @@
     {
      "data": {
       "text/html": [
-       "<div><iframe src=\"http://127.0.0.1:7863/\" width=\"100%\" height=\"500\" allow=\"autoplay; camera; microphone; clipboard-read; clipboard-write;\" frameborder=\"0\" allowfullscreen></iframe></div>"
+       "<div><iframe src=\"http://127.0.0.1:7865/\" width=\"100%\" height=\"500\" allow=\"autoplay; camera; microphone; clipboard-read; clipboard-write;\" frameborder=\"0\" allowfullscreen></iframe></div>"
       ],
       "text/plain": [
        "<IPython.core.display.HTML object>"
@@ -756,7 +756,7 @@
      "data": {
       "text/plain": []
      },
-     "execution_count": 4,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -961,7 +961,7 @@
     "    molecule_output2 = Molecule3D(label=\"Protein Structure\", reps=reps)\n",
     "\n",
     "    with gr.Row():\n",
-    "        pdb_input = gr.Textbox(value=\"2IWI\", label=\"PDB ID\", placeholder=\"Enter PDB ID here...\")\n",
+    "        #pdb_input = gr.Textbox(value=\"2IWI\", label=\"PDB ID\", placeholder=\"Enter PDB ID here...\")\n",
     "        segment_input = gr.Textbox(value=\"A\", label=\"Chain ID\", placeholder=\"Enter Chain ID here...\")\n",
     "        prediction_btn = gr.Button(\"Predict Random Binding Site Scores\")\n",
     "\n",
@@ -976,8 +976,8 @@
     "    gr.Markdown(\"## Examples\")\n",
     "    gr.Examples(\n",
     "        examples=[\n",
-    "            [\"2IWI\", \"A\"],\n",
-    "            [\"7RPZ\", \"B\"],\n",
+    "            [\"7RPZ\", \"A\"],\n",
+    "            [\"2IWI\", \"B\"],\n",
     "            [\"3TJN\", \"C\"]\n",
     "        ],\n",
     "        inputs=[pdb_input, segment_input],\n",
@@ -1262,7 +1262,7 @@
     "    molecule_output2 = Molecule3D(label=\"Protein Structure\", reps=reps)\n",
     "\n",
     "    with gr.Row():\n",
-    "        pdb_input = gr.Textbox(value=\"2IWI\", label=\"PDB ID\", placeholder=\"Enter PDB ID here...\")\n",
+    "        #pdb_input = gr.Textbox(value=\"2IWI\", label=\"PDB ID\", placeholder=\"Enter PDB ID here...\")\n",
     "        segment_input = gr.Textbox(value=\"A\", label=\"Chain ID\", placeholder=\"Enter Chain ID here...\")\n",
     "        prediction_btn = gr.Button(\"Predict Random Binding Site Scores\")\n",
     "\n",