some reformatting

XChemExplorer.py

@@ -519,10 +519,9 @@ def select_ground_state_mtz(self):
         self.ground_state_mtz_button_label.setText(mtz)
 
     def add_ground_state_db(self):
-        db_dict = {}
-        db_dict['DimplePANDDApath'] = self.panddas_directory
-        db_dict['PDB_file'] = str(self.ground_state_pdb_button_label.text())
-        db_dict['MTZ_file'] = str(self.ground_state_mtz_button_label.text())
+        db_dict = {'DimplePANDDApath': self.panddas_directory,
+                   'PDB_file': str(self.ground_state_pdb_button_label.text()),
+                   'MTZ_file': str(self.ground_state_mtz_button_label.text())}
         self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile, 'ground_state', 'ground_state',
                                                                  db_dict)
 
@@ -2278,7 +2277,7 @@ def rerun_dimple_on_all_autoprocessing_files(self):
                                 job_list = self.get_job_list_for_dimple_rerun(xtal, job_list, db_dict, entry)
                         except KeyError:
                             continue
-        if job_list != []:
+        if job_list:
             self.update_log.insert('trying to run DIMPLE on ALL auto-processing files')
             self.check_before_running_dimple(job_list)
 
@@ -2352,7 +2351,7 @@ def run_dimple_on_selected_autoprocessing_file(self):
                         print('    ' + str(os.path.join(db_dict['DataProcessingPathToMTZfile']) + ' is missing'))
 
 
-        if job_list != []:
+        if job_list:
             self.update_log.insert('trying to run DIMPLE on SELECTED auto-processing files')
             self.check_before_running_dimple(job_list)
 
@@ -2362,7 +2361,7 @@ def remove_selected_dimple_files(self):
             if self.initial_model_dimple_dict[xtal][0].isChecked():
                 job_list.append(xtal)
 
-        if job_list != []:
+        if job_list:
             msgBox = QtGui.QMessageBox()
             msgBox.setText("Do you really want to delete {0!s} Dimple files?".format(len(job_list)))
             msgBox.addButton(QtGui.QPushButton('Go'), QtGui.QMessageBox.YesRole)
@@ -2480,7 +2479,7 @@ def get_job_list_for_dimple_rerun(self, xtal, job_list, db_dict, entry):
                     suitable_reference.append([reference[0], difference])
                 except ValueError:
                     continue
-        if suitable_reference != []:
+        if suitable_reference:
             reference_file = min(suitable_reference, key=lambda x: x[1])[0]
             visit = entry[1]
             run = entry[2]
@@ -2690,7 +2689,7 @@ def change_filename_root(self, text):
         self.settings['filename_root'] = self.filename_root
 
     def button_clicked(self):
-        if self.data_source_set == False:
+        if not self.data_source_set:
             print('sender text bit')
             if self.sender().text() == "Create New Data\nSource (SQLite)":
                 file_name = str(QtGui.QFileDialog.getSaveFileName(self.window, 'Save file', self.database_directory))
@@ -2899,7 +2898,7 @@ def check_status_create_png_of_soaked_compound(self):
             for cif_file in glob.glob(os.path.join(folder, '*.cif')):
                 if os.path.isfile(cif_file):
                     cif_file_generated += 1
-        if timestamp_list != []:
+        if timestamp_list:
             last_timestamp = max(timestamp_list)
         else:
             last_timestamp = 'n/a'
@@ -3167,7 +3166,7 @@ def create_cif_pdb_png_files(self, todo):
                     if self.initial_model_dimple_dict[str(item[0])][0].isChecked():
                         compound_list.append([str(item[0]), compoundID, str(item[2])])
 
-        if compound_list != []:
+        if compound_list:
             self.update_log.insert(
                 'trying to create cif and pdb files for ' + str(len(compound_list)) + ' compounds using ACEDRG...')
             if self.external_software['qsub']:
@@ -3554,8 +3553,7 @@ def preferences_restraints_generation_combobox_changed(self):
     def refinement_outcome_combobox_changed(self):
         for xtal in self.refinement_table_dict:
             if self.sender() == self.refinement_table_dict[xtal]:
-                db_dict = {}
-                db_dict['RefinementOutcome'] = str(self.sender().currentText())
+                db_dict = {'RefinementOutcome': str(self.sender().currentText())}
                 self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile, xtal, 'ligand_bound',
                                                                          db_dict)
 
@@ -3625,8 +3623,7 @@ def dataset_outcome_combobox_change_outcome(self, text):
 #                self.data_collection_dict[xtal].append(['user_changed_selection'])
 #            # finally need to update outcome field in data source accordingly
             self.update_log.insert('updating dataset outcome in datasource for {0!s}'.format(xtal))
-            update_dict = {}
-            update_dict['DataCollectionOutcome'] = outcome
+            update_dict = {'DataCollectionOutcome': outcome}
             self.db.update_insert_data_source(xtal, update_dict)
 
     def set_run_dimple_flag(self, state):
@@ -4104,7 +4101,7 @@ def user_update_selected_autoproc_datasets_summary_table(self):
                         for n, entry in enumerate(self.data_collection_dict[key]):
                             print('==>', n)
                             if entry[0] == 'logfile':
-                                if entry[8] == True:
+                                if entry[8]:
                                     print('===> found:', n)
                                     self.data_collection_column_three_dict[key][0].selectRow(n)
                         break

compile_test.py

@@ -1,7 +1,7 @@
 import os, sys
 
 # set XCE environment variables
-os.environ['XChemExplorer_DIR']=os.path.join(os.getcwd(), 'XChemExplorer/')
+os.environ['XChemExplorer_DIR'] = os.path.join(os.getcwd(), 'XChemExplorer/')
 
 print('XCE path = ' + os.environ['XChemExplorer_DIR'])
 
@@ -15,4 +15,5 @@
 
 # try to import all of XCE stuff
 from XChemExplorer import *
+
 print('Successfully imported XCE... compile was succesful')

helpers/phenix_find_TLS_groups.py

@@ -14,8 +14,7 @@ def FindTLSgroups(pdbFile):
         if found: 
             if line.startswith('}'):
                 break 
-            temp = [] 
-            temp.append(line.split()) 
+            temp = [line.split()]
             OutRefmac = OutRefmac + '\nTLS    {0!s}\nRANGE '.format((GroupNames)[i]) + str(temp[0][3])[:-1] + ' ' + \
                         str(temp[0][6]) +'.\'  ' + str(temp[0][3])[:-1] + ' ' + str(temp[0][8]) + '.\' ALL\n'
             i += 1

helpers/select_ground_state_dataset.py

@@ -58,7 +58,7 @@ def select_dataset_with_lowest_Rfree(panddaDir,datasetListwithoutEvent):
                 datasetList.append([dataset,float(Rfree)])
             except ValueError:
                 pass
-    if datasetList != []:
+    if datasetList:
         lowestRfree=min(datasetList,key=lambda x: x[1])[0]
     return lowestRfree
 

helpers/update_data_source_after_refinement.py

@@ -82,7 +82,7 @@ def parse_molprobity_output(inital_model_directory,xtal,db_dict):
                     db_dict['RefinementMolProbityScore'] = line.split()[3]
                     if float(line.split()[3]) < 2:
                         db_dict['RefinementMolProbityScoreTL'] = 'green'
-                    if float(line.split()[3]) >= 2 and float(line.split()[3]) < 3:
+                    if 2 <= float(line.split()[3]) < 3:
                         db_dict['RefinementMolProbityScoreTL'] = 'orange'
                     if float(line.split()[3]) >= 3:
                         db_dict['RefinementMolProbityScoreTL'] = 'red'
@@ -93,7 +93,7 @@ def parse_molprobity_output(inital_model_directory,xtal,db_dict):
 
                     if float(line.split()[3]) < 0.3:
                         db_dict['RefinementRamachandranOutliersTL'] = 'green'
-                    if float(line.split()[3]) >= 0.3 and float(line.split()[3]) < 1:
+                    if 0.3 <= float(line.split()[3]) < 1:
                         db_dict['RefinementRamachandranOutliersTL'] = 'orange'
                     if float(line.split()[3]) >= 1:
                         db_dict['RefinementRamachandranOutliersTL'] = 'red'
@@ -103,7 +103,7 @@ def parse_molprobity_output(inital_model_directory,xtal,db_dict):
                     db_dict['RefinementRamachandranFavored'] = line.split()[2]
                     if float(line.split()[2]) < 90:
                         db_dict['RefinementRamachandranFavoredTL'] = 'red'
-                    if float(line.split()[2]) >= 90 and float(line.split()[2]) < 98:
+                    if 90 <= float(line.split()[2]) < 98:
                         db_dict['RefinementRamachandranFavoredTL'] = 'orange'
                     if float(line.split()[2]) >= 98:
                         db_dict['RefinementRamachandranFavoredTL'] = 'green'

helpers/update_data_source_for_new_dimple_pdb.py

@@ -16,8 +16,7 @@
 
     db=XChemDB.data_source(db_file)
     if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple.pdb')):
-        db_dict={}
-        db_dict['DimplePathToPDB']=os.path.join(inital_model_directory,xtal,'dimple.pdb')
+        db_dict= {'DimplePathToPDB': os.path.join(inital_model_directory, xtal, 'dimple.pdb')}
         dimple_ran_successfully=False
         if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple.mtz')):
             db_dict['DimplePathToMTZ']=os.path.join(inital_model_directory,xtal,'dimple.mtz')

helpers/update_status_flag.py

@@ -8,14 +8,13 @@
 
 def update_data_source(db_file,xtal,db_column,status):
     db=XChemDB.data_source(db_file)
-    db_dict={}
-    db_dict[db_column] = status
+    db_dict= {db_column: status}
     db.update_data_source(xtal,db_dict)
 
-if __name__=='__main__':
-    db_file=sys.argv[1]
-    xtal=sys.argv[2]
-    db_column=sys.argv[3]
-    status=sys.argv[4]
+if __name__ == '__main__':
+    db_file = sys.argv[1]
+    xtal = sys.argv[2]
+    db_column = sys.argv[3]
+    status = sys.argv[4]
 
-    update_data_source(db_file,xtal,db_column,status)
+    update_data_source(db_file, xtal, db_column, status)