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Begin integrating NP3
1 parent 98d9614 commit c196691

5 files changed

+41
-11
lines changed

‎notebooks/astex_method_interaction_analysis_plotting.ipynb‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -81,12 +81,13 @@
8181
" \"vina_p2rank\",\n",
8282
" \"diffdock\",\n",
8383
" \"dynamicbind\",\n",
84-
" \"neuralplexer\",\n",
8584
" \"rfaa\",\n",
8685
" \"chai-lab_ss\",\n",
8786
" \"chai-lab\",\n",
8887
" \"alphafold3_ss\",\n",
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" \"alphafold3\",\n",
89+
" \"neuralplexer3_ss\",\n",
90+
" \"neuralplexer3\",\n",
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"]\n",
9192
"max_num_repeats_per_method = (\n",
9293
" 1 # NOTE: Here, to simplify the analysis, we only consider the first run of each method\n",
@@ -106,12 +107,13 @@
106107
" \"vina_p2rank\": \"P2Rank-Vina\",\n",
107108
" \"diffdock\": \"DiffDock-L\",\n",
108109
" \"dynamicbind\": \"DynamicBind\",\n",
109-
" \"neuralplexer\": \"NeuralPLexer\",\n",
110110
" \"rfaa\": \"RoseTTAFold-AA\",\n",
111111
" \"chai-lab_ss\": \"Chai-1-Single-Seq\",\n",
112112
" \"chai-lab\": \"Chai-1\",\n",
113113
" \"alphafold3_ss\": \"AF3-Single-Seq\",\n",
114114
" \"alphafold3\": \"AF3\",\n",
115+
" \"neuralplexer3_ss\": \"NP3-Single-Seq\",\n",
116+
" \"neuralplexer3\": \"NP3\",\n",
115117
"}\n",
116118
"\n",
117119
"MAX_ASTEX_DIVERSE_ANALYSIS_PROTEIN_SEQUENCE_LENGTH = (\n",

‎notebooks/astex_method_interaction_analysis_plotting.py‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -46,12 +46,13 @@
4646
"vina_p2rank",
4747
"diffdock",
4848
"dynamicbind",
49-
"neuralplexer",
5049
"rfaa",
5150
"chai-lab_ss",
5251
"chai-lab",
5352
"alphafold3_ss",
5453
"alphafold3",
54+
"neuralplexer3_ss",
55+
"neuralplexer3",
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]
5657
max_num_repeats_per_method = (
5758
1 # NOTE: Here, to simplify the analysis, we only consider the first run of each method
@@ -71,12 +72,13 @@
7172
"vina_p2rank": "P2Rank-Vina",
7273
"diffdock": "DiffDock-L",
7374
"dynamicbind": "DynamicBind",
74-
"neuralplexer": "NeuralPLexer",
7575
"rfaa": "RoseTTAFold-AA",
7676
"chai-lab_ss": "Chai-1-Single-Seq",
7777
"chai-lab": "Chai-1",
7878
"alphafold3_ss": "AF3-Single-Seq",
7979
"alphafold3": "AF3",
80+
"neuralplexer3_ss": "NP3-Single-Seq",
81+
"neuralplexer3": "NP3",
8082
}
8183

8284
MAX_ASTEX_DIVERSE_ANALYSIS_PROTEIN_SEQUENCE_LENGTH = (

‎notebooks/dockgen_method_interaction_analysis_plotting.ipynb‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -81,12 +81,13 @@
8181
" \"vina_p2rank\",\n",
8282
" \"diffdock\",\n",
8383
" \"dynamicbind\",\n",
84-
" \"neuralplexer\",\n",
8584
" \"rfaa\",\n",
8685
" \"chai-lab_ss\",\n",
8786
" \"chai-lab\",\n",
8887
" \"alphafold3_ss\",\n",
8988
" \"alphafold3\",\n",
89+
" \"neuralplexer3_ss\",\n",
90+
" \"neuralplexer3\",\n",
9091
"]\n",
9192
"max_num_repeats_per_method = (\n",
9293
" 1 # NOTE: Here, to simplify the analysis, we only consider the first run of each method\n",
@@ -106,12 +107,13 @@
106107
" \"vina_p2rank\": \"P2Rank-Vina\",\n",
107108
" \"diffdock\": \"DiffDock-L\",\n",
108109
" \"dynamicbind\": \"DynamicBind\",\n",
109-
" \"neuralplexer\": \"NeuralPLexer\",\n",
110110
" \"rfaa\": \"RoseTTAFold-AA\",\n",
111111
" \"chai-lab_ss\": \"Chai-1-Single-Seq\",\n",
112112
" \"chai-lab\": \"Chai-1\",\n",
113113
" \"alphafold3_ss\": \"AF3-Single-Seq\",\n",
114114
" \"alphafold3\": \"AF3\",\n",
115+
" \"neuralplexer3_ss\": \"NP3-Single-Seq\",\n",
116+
" \"neuralplexer3\": \"NP3\",\n",
115117
"}\n",
116118
"\n",
117119
"MAX_DOCKGEN_ANALYSIS_PROTEIN_SEQUENCE_LENGTH = (\n",

‎notebooks/dockgen_method_interaction_analysis_plotting.py‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -46,12 +46,13 @@
4646
"vina_p2rank",
4747
"diffdock",
4848
"dynamicbind",
49-
"neuralplexer",
5049
"rfaa",
5150
"chai-lab_ss",
5251
"chai-lab",
5352
"alphafold3_ss",
5453
"alphafold3",
54+
"neuralplexer3_ss",
55+
"neuralplexer3",
5556
]
5657
max_num_repeats_per_method = (
5758
1 # NOTE: Here, to simplify the analysis, we only consider the first run of each method
@@ -71,12 +72,13 @@
7172
"vina_p2rank": "P2Rank-Vina",
7273
"diffdock": "DiffDock-L",
7374
"dynamicbind": "DynamicBind",
74-
"neuralplexer": "NeuralPLexer",
7575
"rfaa": "RoseTTAFold-AA",
7676
"chai-lab_ss": "Chai-1-Single-Seq",
7777
"chai-lab": "Chai-1",
7878
"alphafold3_ss": "AF3-Single-Seq",
7979
"alphafold3": "AF3",
80+
"neuralplexer3_ss": "NP3-Single-Seq",
81+
"neuralplexer3": "NP3",
8082
}
8183

8284
MAX_DOCKGEN_ANALYSIS_PROTEIN_SEQUENCE_LENGTH = (

‎posebench/__init__.py‎

Lines changed: 25 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -17,6 +17,7 @@
1717
"rfaa": "RoseTTAFold-All-Atom",
1818
"chai-lab": "chai-lab",
1919
"alphafold3": "alphafold3",
20+
"neuralplexer3": "NeuralPLexer3",
2021
"vina": "Vina",
2122
"tulip": "TULIP",
2223
"p2rank": "P2Rank",
@@ -111,7 +112,7 @@ def resolve_method_protein_dir(
111112
"results",
112113
f"{dataset}{pocket_only_suffix}",
113114
)
114-
elif method in ["neuralplexer", "flowdock", "rfaa", "chai-lab", "alphafold3"]:
115+
elif method in ["neuralplexer", "flowdock", "rfaa", "chai-lab", "alphafold3", "neuralplexer3"]:
115116
return os.path.join(
116117
"forks",
117118
METHOD_TITLE_MAPPING.get(method, method),
@@ -160,11 +161,21 @@ def resolve_method_ligand_dir(
160161
"rfaa",
161162
"chai-lab",
162163
"alphafold3",
164+
"neuralplexer3",
163165
"tulip",
164166
]:
165167
output_suffix = (
166168
"s"
167-
if method in ["neuralplexer", "flowdock", "rfaa", "chai-lab", "alphafold3", "tulip"]
169+
if method
170+
in [
171+
"neuralplexer",
172+
"flowdock",
173+
"rfaa",
174+
"chai-lab",
175+
"alphafold3",
176+
"tulip",
177+
"neuralplexer3",
178+
]
168179
else ""
169180
)
170181
return os.path.join(
@@ -233,11 +244,21 @@ def resolve_method_output_dir(
233244
"rfaa",
234245
"chai-lab",
235246
"alphafold3",
247+
"neuralplexer3",
236248
"tulip",
237249
]:
238250
output_suffix = (
239251
"s"
240-
if method in ["neuralplexer", "flowdock", "rfaa", "chai-lab", "alphafold3", "tulip"]
252+
if method
253+
in [
254+
"neuralplexer",
255+
"flowdock",
256+
"rfaa",
257+
"chai-lab",
258+
"alphafold3",
259+
"tulip",
260+
"neuralplexer3",
261+
]
241262
else ""
242263
)
243264
return os.path.join(
@@ -295,6 +316,7 @@ def resolve_method_input_csv_path(
295316
"rfaa",
296317
"chai-lab",
297318
"alphafold3",
319+
"neuralplexer3",
298320
"vina",
299321
"tulip",
300322
]:

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