Fix #431

KosinskiLab · Oct 23, 2024 · 8a9cf3b · 8a9cf3b
1 parent 1a6c704
commit 8a9cf3b
Show file tree

Hide file tree

Showing 33 changed files with 969 additions and 7 deletions.
diff --git a/alphapulldown/folding_backend/alphafold_backend.py b/alphapulldown/folding_backend/alphafold_backend.py
@@ -602,7 +602,8 @@ def postprocess(
             plot_pae_from_matrix(
                 seqs=prediction_result['seqs'],
                 pae_matrix=prediction_result['predicted_aligned_error'],
-                figure_name=figure_name,ranking=idx
+                figure_name=figure_name,
+                ranking=idx
             )
 
         # Save ranking_debug.json.

diff --git a/alphapulldown/objects.py b/alphapulldown/objects.py
@@ -264,6 +264,7 @@ def __init__(self, description, sequence, feature_dict, regions) -> None:
         self.regions = regions
         self.new_sequence = ""
         self.new_feature_dict = dict()
+        self.monomeric_description = description
         self.description = description
         self.prepare_new_self_description()
 

diff --git a/alphapulldown/scripts/run_structure_prediction.py b/alphapulldown/scripts/run_structure_prediction.py
@@ -233,7 +233,7 @@ def pre_modelling_setup(
         for feature_dir in flags.features_directory:
             # meta.json is named the same way as the pickle file
             if isinstance(interactor, ChoppedObject):
-                description = interactor.description.split('_')[0]
+                description = interactor.monomeric_description
             elif isinstance(interactor, MonomericObject):
                 description = interactor.description
             meta_json = glob.glob(

diff --git a/test/check_predict_structure.py b/test/check_predict_structure.py
@@ -203,7 +203,7 @@ def setUp(self) -> None:
             raise FileNotFoundError(f"Directory not found: {self.test_modelling_dir}")
         self.args = [
             sys.executable,
-            self.script_path,
+            self.script_path1,
             "--mode=custom",
             "--num_cycle=1",
             "--num_predictions_per_model=1",
@@ -279,7 +279,7 @@ def testRunWithTemplate(self):
         self.assertTrue(os.path.exists(os.path.join(self.test_features_dir, "3L4Q_C.pkl")))
         self.args = [
             sys.executable,
-            self.script_path,
+            self.script_path1,
             "--mode=custom",
             "--num_cycle=48",
             "--num_predictions_per_model=5",
@@ -316,7 +316,7 @@ def testRun_7(self):
         with tempfile.TemporaryDirectory() as tmpdir:
             self.args = [
                 sys.executable,
-                self.script_path,
+                self.script_path1,
                 "--mode=custom",
                 "--num_cycle=3",
                 "--num_predictions_per_model=1",
@@ -371,7 +371,7 @@ def testRun_8(self):
             # Firstly test running with padding AND multimeric template modelling
             self.args = [
                 sys.executable,
-                self.script_path,
+                self.script_path1,
                 "--mode=custom",
                 "--num_cycle=3",
                 "--num_predictions_per_model=1",
@@ -399,7 +399,7 @@ def testRun_9(self):
             # Then test running with padding WITHOUT multimeric template modelling
             self.args = [
                 sys.executable,
-                self.script_path,
+                self.script_path1,
                 "--mode=custom",
                 "--num_cycle=3",
                 "--num_predictions_per_model=1",

diff --git a/...edictions/TEST/TEST_PAE_plot_ranked_0.png → ...ta/predictions/TEST/pae_plot_ranked_0.png b/...edictions/TEST/TEST_PAE_plot_ranked_0.png → ...ta/predictions/TEST/pae_plot_ranked_0.png
diff --git a/...edictions/TEST/TEST_PAE_plot_ranked_1.png → ...ta/predictions/TEST/pae_plot_ranked_1.png b/...edictions/TEST/TEST_PAE_plot_ranked_1.png → ...ta/predictions/TEST/pae_plot_ranked_1.png
diff --git a/...edictions/TEST/TEST_PAE_plot_ranked_2.png → ...ta/predictions/TEST/pae_plot_ranked_2.png b/...edictions/TEST/TEST_PAE_plot_ranked_2.png → ...ta/predictions/TEST/pae_plot_ranked_2.png
diff --git a/...edictions/TEST/TEST_PAE_plot_ranked_3.png → ...ta/predictions/TEST/pae_plot_ranked_3.png b/...edictions/TEST/TEST_PAE_plot_ranked_3.png → ...ta/predictions/TEST/pae_plot_ranked_3.png
diff --git a/...edictions/TEST/TEST_PAE_plot_ranked_4.png → ...ta/predictions/TEST/pae_plot_ranked_4.png b/...edictions/TEST/TEST_PAE_plot_ranked_4.png → ...ta/predictions/TEST/pae_plot_ranked_4.png
diff --git a/...5B6L2_1-10_2-5_3-12_PAE_plot_ranked_0.png → ...5B6L2_1-10_2-5_3-12/pae_plot_ranked_0.png b/...5B6L2_1-10_2-5_3-12_PAE_plot_ranked_0.png → ...5B6L2_1-10_2-5_3-12/pae_plot_ranked_0.png
diff --git a/...5B6L2_1-10_2-5_3-12_PAE_plot_ranked_1.png → ...5B6L2_1-10_2-5_3-12/pae_plot_ranked_1.png b/...5B6L2_1-10_2-5_3-12_PAE_plot_ranked_1.png → ...5B6L2_1-10_2-5_3-12/pae_plot_ranked_1.png
diff --git a/...5B6L2_1-10_2-5_3-12_PAE_plot_ranked_2.png → ...5B6L2_1-10_2-5_3-12/pae_plot_ranked_2.png b/...5B6L2_1-10_2-5_3-12_PAE_plot_ranked_2.png → ...5B6L2_1-10_2-5_3-12/pae_plot_ranked_2.png
diff --git a/...5B6L2_1-10_2-5_3-12_PAE_plot_ranked_3.png → ...5B6L2_1-10_2-5_3-12/pae_plot_ranked_3.png b/...5B6L2_1-10_2-5_3-12_PAE_plot_ranked_3.png → ...5B6L2_1-10_2-5_3-12/pae_plot_ranked_3.png
diff --git a/...5B6L2_1-10_2-5_3-12_PAE_plot_ranked_4.png → ...5B6L2_1-10_2-5_3-12/pae_plot_ranked_4.png b/...5B6L2_1-10_2-5_3-12_PAE_plot_ranked_4.png → ...5B6L2_1-10_2-5_3-12/pae_plot_ranked_4.png
diff --git a/..._TEST/TEST_and_TEST_PAE_plot_ranked_0.png → ...tions/TEST_and_TEST/pae_plot_ranked_0.png b/..._TEST/TEST_and_TEST_PAE_plot_ranked_0.png → ...tions/TEST_and_TEST/pae_plot_ranked_0.png
diff --git a/..._TEST/TEST_and_TEST_PAE_plot_ranked_1.png → ...tions/TEST_and_TEST/pae_plot_ranked_1.png b/..._TEST/TEST_and_TEST_PAE_plot_ranked_1.png → ...tions/TEST_and_TEST/pae_plot_ranked_1.png
diff --git a/..._TEST/TEST_and_TEST_PAE_plot_ranked_2.png → ...tions/TEST_and_TEST/pae_plot_ranked_2.png b/..._TEST/TEST_and_TEST_PAE_plot_ranked_2.png → ...tions/TEST_and_TEST/pae_plot_ranked_2.png
diff --git a/..._TEST/TEST_and_TEST_PAE_plot_ranked_3.png → ...tions/TEST_and_TEST/pae_plot_ranked_3.png b/..._TEST/TEST_and_TEST_PAE_plot_ranked_3.png → ...tions/TEST_and_TEST/pae_plot_ranked_3.png
diff --git a/..._TEST/TEST_and_TEST_PAE_plot_ranked_4.png → ...tions/TEST_and_TEST/pae_plot_ranked_4.png b/..._TEST/TEST_and_TEST_PAE_plot_ranked_4.png → ...tions/TEST_and_TEST/pae_plot_ranked_4.png
diff --git a/...T_and_TEST_and_TEST_PAE_plot_ranked_0.png → ...T_and_TEST_and_TEST/pae_plot_ranked_0.png b/...T_and_TEST_and_TEST_PAE_plot_ranked_0.png → ...T_and_TEST_and_TEST/pae_plot_ranked_0.png
diff --git a/...T_and_TEST_and_TEST_PAE_plot_ranked_1.png → ...T_and_TEST_and_TEST/pae_plot_ranked_1.png b/...T_and_TEST_and_TEST_PAE_plot_ranked_1.png → ...T_and_TEST_and_TEST/pae_plot_ranked_1.png
diff --git a/...T_and_TEST_and_TEST_PAE_plot_ranked_2.png → ...T_and_TEST_and_TEST/pae_plot_ranked_2.png b/...T_and_TEST_and_TEST_PAE_plot_ranked_2.png → ...T_and_TEST_and_TEST/pae_plot_ranked_2.png
diff --git a/...T_and_TEST_and_TEST_PAE_plot_ranked_3.png → ...T_and_TEST_and_TEST/pae_plot_ranked_3.png b/...T_and_TEST_and_TEST_PAE_plot_ranked_3.png → ...T_and_TEST_and_TEST/pae_plot_ranked_3.png
diff --git a/...T_and_TEST_and_TEST_PAE_plot_ranked_4.png → ...T_and_TEST_and_TEST/pae_plot_ranked_4.png b/...T_and_TEST_and_TEST_PAE_plot_ranked_4.png → ...T_and_TEST_and_TEST/pae_plot_ranked_4.png
diff --git a/test/test_data/predictions/ccp4_v9.log b/test/test_data/predictions/ccp4_v9.log
diff --git a/test/test_data/predictions/good.csv b/test/test_data/predictions/good.csv
@@ -0,0 +1,6 @@
+jobs,iptm_ptm,iptm,pDockQ/mpDockQ,average_interface_pae,average_interface_plddt,binding_energy,interface,Num_intf_residues,Polar,Hydrophobic,Charged,contact_pairs, sc, hb, sb, int_solv_en, int_area,pi_score
+TEST_and_TEST_and_TEST,0.09161740784114437,0.08377959013960515,1.0412359506547133,22.18181003584226,26.24696552424502,-2791.6307034091355,B_C,128,0.313,0.266,0.203,311,-0.1,54,1,-29.56,3137.7,0.84
+TEST_and_TEST_and_TEST,0.09161740784114437,0.08377959013960515,1.0412359506547133,22.04758064516131,26.38746819979306,-2791.6307034091355,B_D,121,0.306,0.248,0.215,292,-0.074,45,1,-25.7,2952.73,0.83
+TEST_and_TEST_and_TEST,0.09161740784114437,0.08377959013960515,1.0412359506547133,22.01209386281587,26.048184313630387,-4145.3558803465485,C_D,121,0.306,0.248,0.215,303,-0.114,51,3,-26.71,2962.97,0.84
+TEST_and_A0A075B6L2_1-10_2-5_3-12,0.103099058355066,0.0630861297249794,0.0,No interface residues detected,No interface residues detected,None,B_C,,,,,,,,,,,
+TEST_and_TEST,0.061528983957974445,0.05123987793922424,0.02954929206105133,23.81369346733668,32.230952380952374,-2127.2260633214273,B_C,84,0.25,0.274,0.286,132,0.127,22,0,-19.39,2047.56,0.39
diff --git a/test/test_data/predictions/pae_plot_ranked_0.png b/test/test_data/predictions/pae_plot_ranked_0.png
diff --git a/test/test_data/predictions/pae_plot_ranked_1.png b/test/test_data/predictions/pae_plot_ranked_1.png
diff --git a/test/test_data/predictions/pae_plot_ranked_2.png b/test/test_data/predictions/pae_plot_ranked_2.png
diff --git a/test/test_data/predictions/pae_plot_ranked_3.png b/test/test_data/predictions/pae_plot_ranked_3.png
diff --git a/test/test_data/predictions/pae_plot_ranked_4.png b/test/test_data/predictions/pae_plot_ranked_4.png
diff --git a/test/test_data/predictions/predictions_with_good_interpae.csv b/test/test_data/predictions/predictions_with_good_interpae.csv
@@ -0,0 +1,10 @@
+jobs,iptm_ptm,iptm,pDockQ/mpDockQ,average_interface_pae,average_interface_plddt,binding_energy,interface,Num_intf_residues,Polar,Hydrophobic,Charged,contact_pairs, sc, hb, sb, int_solv_en, int_area,pi_score
+TEST_and_TEST_and_TEST,0.09161740784114437,0.08377959013960515,1.0412359506547133,22.18181003584226,26.24696552424502,-2791.6307034091355,B_C,128,0.313,0.266,0.203,311,-0.1,54,1,-29.56,3137.7,
+TEST_and_TEST_and_TEST,0.09161740784114437,0.08377959013960515,1.0412359506547133,22.18181003584226,26.24696552424502,-2791.6307034091355,B_C,128,0.313,0.266,0.203,311,-0.1,54,1,-29.56,3137.7,
+TEST_and_TEST_and_TEST,0.09161740784114437,0.08377959013960515,1.0412359506547133,22.04758064516131,26.38746819979306,-2791.6307034091355,B_D,121,0.306,0.248,0.215,292,-0.074,45,1,-25.7,2952.73,
+TEST_and_TEST_and_TEST,0.09161740784114437,0.08377959013960515,1.0412359506547133,22.04758064516131,26.38746819979306,-2791.6307034091355,B_D,121,0.306,0.248,0.215,292,-0.074,45,1,-25.7,2952.73,
+TEST_and_TEST_and_TEST,0.09161740784114437,0.08377959013960515,1.0412359506547133,22.01209386281587,26.048184313630387,-4145.3558803465485,C_D,121,0.306,0.248,0.215,303,-0.114,51,3,-26.71,2962.97,
+TEST_and_TEST_and_TEST,0.09161740784114437,0.08377959013960515,1.0412359506547133,22.01209386281587,26.048184313630387,-4145.3558803465485,C_D,121,0.306,0.248,0.215,303,-0.114,51,3,-26.71,2962.97,
+TEST_and_A0A075B6L2_1-10_2-5_3-12,0.103099058355066,0.0630861297249794,0.0,No interface residues detected,No interface residues detected,None,B_C,,,,,,,,,,,
+TEST_and_TEST,0.061528983957974445,0.05123987793922424,0.02954929206105133,23.81369346733668,32.230952380952374,-2127.2260633214273,B_C,84,0.25,0.274,0.286,132,0.127,22,0,-19.39,2047.56,
+TEST_and_TEST,0.061528983957974445,0.05123987793922424,0.02954929206105133,23.81369346733668,32.230952380952374,-2127.2260633214273,B_C,84,0.25,0.274,0.286,132,0.127,22,0,-19.39,2047.56,
diff --git a/test/test_data/predictions/r4s.res b/test/test_data/predictions/r4s.res