make linux gui script runnable from other directories & update Protei…

…nGym URLs

gui/qt_window.py

@@ -186,51 +186,51 @@ def on_readyReadStandardOutput(self):
 
     @QtCore.Slot()
     def pypef_mklsts(self):
-        self.version_text.setText("Running MKLSTS...")
         wt_fasta_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select WT FASTA File")[0]
         csv_variant_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select variant CSV File")[0]
         if wt_fasta_file and csv_variant_file:
+            self.version_text.setText("Running MKLSTS...")
             self.exec_pypef(f'mklsts --wt {wt_fasta_file} --input {csv_variant_file}')
 
     @QtCore.Slot()
     def pypef_gremlin(self):
-        self.version_text.setText("Running GREMLIN (DCA) optimization on MSA...")
         wt_fasta_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select WT FASTA File")[0]
         msa_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select Multiple Sequence Alignment (MSA) file (in FASTA or A2M format)")[0]
         if wt_fasta_file and msa_file:
+            self.version_text.setText("Running GREMLIN (DCA) optimization on MSA...")
             self.exec_pypef(f'param_inference --wt {wt_fasta_file} --msa {msa_file}')  # --opt_iter 100
 
     @QtCore.Slot()
     def pypef_gremlin_dca_test(self):
-        self.version_text.setText("Testing GREMLIN (DCA) performance on provided test set...")
         test_set_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select Test Set File in \"FASL\" format")[0]
         params_pkl_file = QtWidgets.QFileDialog.getOpenFileName(self, "GREMLIN parameter Pickle file")[0]
         if test_set_file and params_pkl_file:
+            self.version_text.setText("Testing GREMLIN (DCA) performance on provided test set...")
             self.exec_pypef(f'hybrid --ts {test_set_file} -m {params_pkl_file} --params {params_pkl_file}')  # --opt_iter 100
 
     @QtCore.Slot()
     def pypef_gremlin_dca_predict(self):
-        self.version_text.setText("Predicting using the GREMLIN (DCA) model on provided prediction set...")
         prediction_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select Prediction Set File in FASTA format")[0]
         params_pkl_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select GREMLIN parameter Pickle file")[0]
         if prediction_file and params_pkl_file:
+            self.version_text.setText("Predicting using the GREMLIN (DCA) model on provided prediction set...")
             self.exec_pypef(f'hybrid --ps {prediction_file} -m {params_pkl_file} --params {params_pkl_file}')  # --opt_iter 100
 
     @QtCore.Slot()
     def pypef_gremlin_hybrid_train(self):
-        self.version_text.setText("Hybrid (DCA-supervised) model training...")
         training_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select Training Set File in \"FASL\" format")[0]
         params_pkl_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select GREMLIN parameter Pickle file")[0]
         if training_file and params_pkl_file:
+            self.version_text.setText("Hybrid (DCA-supervised) model training...")
             self.exec_pypef(f'hybrid --ls {training_file} --ts {training_file} -m {params_pkl_file} --params {params_pkl_file}')  # --opt_iter 100
 
     @QtCore.Slot()
     def pypef_gremlin_hybrid_train_test(self):
-        self.version_text.setText("...")
         training_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select Training Set File in \"FASL\" format")[0]
         test_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select Test Set File in \"FASL\" format")[0]
         params_pkl_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select GREMLIN parameter Pickle file")[0]
         if training_file and test_file and params_pkl_file:
+            self.version_text.setText("Hybrid (DCA-supervised) model training and testing...")
             self.exec_pypef(f'hybrid --ls {training_file} --ts {test_file} -m {params_pkl_file} --params {params_pkl_file}')  # --opt_iter 100
 
     def exec_pypef(self, cmd):

gui_setup.sh

@@ -1,6 +1,9 @@
 #!/bin/bash
 set -e 
 
+# Only required for WSL(?):
+# sudo apt-get install -y libxcb-cursor-dev
+
 python -m pip install -U pypef pyside6
 
 printf "
@@ -11,8 +14,9 @@ if __name__ == '__main__':
     run_main()
 " > run.py
 
-printf "#!/bin/bash
-python gui/qt_window.py
+printf "#!/bin/bash\n
+SCRIPT_DIR=\$( cd -- \"\$( dirname -- \"\${BASH_SOURCE[0]}\" )\" &> /dev/null && pwd )\n
+python "\${SCRIPT_DIR}/gui/qt_window.py"\n
 " > run_pypef_gui.sh
 
 echo "Finished installation..."

scripts/ProteinGym_runs/download_proteingym_and_extract_data.py

@@ -10,26 +10,26 @@
 
 
 
-def download_proteingym_data():
-    url = 'https://marks.hms.harvard.edu/proteingym/DMS_substitutions.csv'
+def download_proteingym_data(version: str = '1.1'):
+    url = f'https://marks.hms.harvard.edu/proteingym/ProteinGym_v{version}/DMS_substitutions.csv'
     print(f'Getting {url}...')
     urllib.request.urlretrieve(url, os.path.join(os.path.dirname(__file__), '_Description_DMS_substitutions_data.csv'))
 
-    url = 'https://marks.hms.harvard.edu/proteingym/DMS_ProteinGym_substitutions.zip'
+    url = f'https://marks.hms.harvard.edu/proteingym/ProteinGym_v{version}/DMS_ProteinGym_substitutions.zip'
     print(f'Getting {url}...')
     urllib.request.urlretrieve(url, os.path.join(os.path.dirname(__file__), 'DMS_ProteinGym_substitutions.zip'))
     with zipfile.ZipFile(os.path.join(os.path.dirname(__file__), 'DMS_ProteinGym_substitutions.zip'), "r") as zip_ref:
         zip_ref.extractall(os.path.join(os.path.dirname(__file__), 'DMS_ProteinGym_substitutions'))
     os.remove(os.path.join(os.path.dirname(__file__), 'DMS_ProteinGym_substitutions.zip'))
 
-    url = 'https://marks.hms.harvard.edu/proteingym/DMS_msa_files.zip'
+    url = f'https://marks.hms.harvard.edu/proteingym/ProteinGym_v{version}/DMS_msa_files.zip'
     print(f'Getting {url}...')
     urllib.request.urlretrieve(url, os.path.join(os.path.dirname(__file__), 'DMS_msa_files.zip'))
     with zipfile.ZipFile(os.path.join(os.path.dirname(__file__), 'DMS_msa_files.zip'), "r") as zip_ref:
         zip_ref.extractall(os.path.join(os.path.dirname(__file__), 'DMS_msa_files'))
     os.remove(os.path.join(os.path.dirname(__file__), 'DMS_msa_files.zip'))
 
-    url = 'https://marks.hms.harvard.edu/proteingym/ProteinGym_AF2_structures.zip'
+    url = f'https://marks.hms.harvard.edu/proteingym/ProteinGym_v{version}/ProteinGym_AF2_structures.zip'
     print(f'Getting {url}...')
     urllib.request.urlretrieve(url, os.path.join(os.path.dirname(__file__), 'ProteinGym_AF2_structures.zip'))
     with zipfile.ZipFile(os.path.join(os.path.dirname(__file__), 'ProteinGym_AF2_structures.zip'), "r") as zip_ref: