PEP-8 formatting NO_JIRA

Author: Alex-AMC

README.md

@@ -5,7 +5,7 @@
 
 A repository containing scripts that have been created to leverage the toolkit found within
 the [CCDC portfolio](https://www.ccdc.cam.ac.uk/solutions/) that are accessible via
-the [CSD Python API ](https://www.ccdc.cam.ac.uk/solutions/csd-core/components/csd-python-api/).
+the [CSD Python API](https://www.ccdc.cam.ac.uk/solutions/csd-core/components/csd-python-api/).
 
 The purpose of this platform is to distribute knowledge and allow for scientific collaborations. Scripts are provided on an as-is basis and while their use is not supported we do welcome feedback on potential improvements. All scripts are tested against the latest version of the CSD Python API as installed with the CSD Portfolio.
 

scripts/concat_mol2/concat_mol2.py

@@ -42,4 +42,4 @@ def main(delete_separate_files):
                         help='Remove contributing individual mol2 files after concatenation')
 
     args = parser.parse_args()
-    main(args.delete_contributors)
+    main(args.delete_contributors)

scripts/create_castep_input/create_castep_input.py

@@ -78,13 +78,12 @@ def make_castep_input(crystal, kp_spacing=0.06, cut_off=750.000, task='SinglePoi
         param_file.write('write_cell_structure : true\n')
         param_file.write('#continuation : default\n')
 
-
     return True
-    
+
+
 if __name__ == '__main__':
     helper = ApplicationInterface()
     entry = helper.current_entry
     crystal = entry.crystal
     os.chdir(helper.output_directory_path)
     make_castep_input(crystal)
-

scripts/create_gaussian_input/create_gaussian_input.py

@@ -19,7 +19,6 @@
 import sys
 import os
 import ccdc.io
-import glob
 
 
 def fatal(*args):
@@ -82,4 +81,4 @@ def file_writer(molecule, name):
             mol = reader.molecule(entry_id)
             file_writer(mol, identifier)
         except RuntimeError:
-            fatal(entry_id, '- structure not found')
+            fatal(entry_id, '- structure not found')

scripts/hydrogen_bond_propensity/hydrogen_bond_propensity_report.py

@@ -14,7 +14,14 @@
 hydrogen_bond_propensity_report.py
 - Writes a .docx report of a hydrogen bond propensity calculation
 """
+
+import argparse
+import os
+import sys
+import subprocess
+import csv
 import matplotlib
+
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 
@@ -23,14 +30,9 @@
 from ccdc.search import SubstructureSearch, ConnserSubstructure
 from ccdc.descriptors import CrystalDescriptors
 
-import argparse
-import os
-import sys
-import subprocess
-import csv
-
 try:
     import warnings
+
     with warnings.catch_warnings():
         warnings.simplefilter("ignore", category=DeprecationWarning)
         import docxtpl
@@ -81,7 +83,7 @@ def fg_diagram(mol, directory, con):
 def add_picture_subdoc(picture_location, docx_template, cm=7):
     # This function adds a picture to the .docx file
     return docxtpl.InlineImage(
-            docx_template, image_descriptor=picture_location, width=Cm(cm))
+        docx_template, image_descriptor=picture_location, width=Cm(cm))
 
 
 def launch_word_processor(output_file):
@@ -137,7 +139,7 @@ def propensity_calc(crystal, directory):
     observed_group = hbp.target_hbond_grouping()
 
     return hbp.functional_groups, hbp.fitting_data, hbp.donors, hbp.acceptors, model, \
-        propensities, intra_flag, groups, observed_group
+           propensities, intra_flag, groups, observed_group
 
 
 def coordination_scores_calc(crystal, directory):
@@ -214,8 +216,8 @@ def main(structure, directory, csdrefcode, noopen=False):
     work_directory = os.path.join(directory, str(structure).split('.')[0])
 
     # Get all the necessary data from a HBP calculation
-    functional_groups, fitting_data, donors, acceptors, model, propensities, intra_flag,\
-        groups, observed_groups = propensity_calc(crystal, work_directory)
+    functional_groups, fitting_data, donors, acceptors, model, propensities, intra_flag, \
+    groups, observed_groups = propensity_calc(crystal, work_directory)
 
     # Calculate the coordination scores separately
     coordination_scores = coordination_scores_calc(crystal, work_directory)
@@ -322,8 +324,8 @@ def main(structure, directory, csdrefcode, noopen=False):
 if __name__ == '__main__':
     # Set up the necessary arguments to run the script
     parser = argparse.ArgumentParser(
-            formatter_class=argparse.RawDescriptionHelpFormatter,
-            description=__doc__)
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        description=__doc__)
     parser.add_argument('input_structure', type=str,
                         help='Refcode or mol2 file of the component to be screened')
     parser.add_argument('-d', '--directory', default=os.getcwd(),

scripts/multi_component_hydrogen_bond_propensity/multi_component_hydrogen_bond_propensity_report.py

@@ -14,23 +14,25 @@
  - Performs a multi-component HBP calculation for a given library of co-formers
 """
 
+import sys
+import os
+import glob
+import argparse
+import tempfile
+import subprocess
+
 import matplotlib
+
 matplotlib.use('TkAgg')
 import matplotlib.pyplot as plt
 
 from ccdc import io, molecule
 from ccdc.diagram import DiagramGenerator
 from ccdc.descriptors import CrystalDescriptors
 
-import sys
-import os
-import glob
-import argparse
-import tempfile
-import subprocess
-
 try:
     import warnings
+
     with warnings.catch_warnings():
         warnings.simplefilter("ignore", category=DeprecationWarning)
         import docxtpl
@@ -54,9 +56,9 @@
 def cm2inch(*tupl):
     inch = 2.54
     if isinstance(tupl[0], tuple):
-        return tuple(i/inch for i in tupl[0])
+        return tuple(i / inch for i in tupl[0])
     else:
-        return tuple(i/inch for i in tupl)
+        return tuple(i / inch for i in tupl)
 
 
 def launch_word_processor(output_file):
@@ -113,7 +115,7 @@ def make_mc_chart(dictionary, directory, mol):
 def add_picture_subdoc(picture_location, docx_template, wd=7):
     # This function adds a picture to the .docx file
     return docxtpl.InlineImage(
-            docx_template, image_descriptor=picture_location, width=Cm(wd))
+        docx_template, image_descriptor=picture_location, width=Cm(wd))
 
 
 def propensity_calc(crystal, directory):
@@ -147,7 +149,7 @@ def propensity_calc(crystal, directory):
     # Perform regression
     model = hbp.perform_regression()
     print(model.equation)
-    print('Area under ROC curve: {} -- {}'.format(round(model.area_under_roc_curve, 3),  model.advice_comment))
+    print('Area under ROC curve: {} -- {}'.format(round(model.area_under_roc_curve, 3), model.advice_comment))
     hbp.calculate_propensities()
     propensities = hbp.inter_propensities
 
@@ -293,7 +295,7 @@ def make_mc_report(identifier, results, directory, diagram_file, chart_file):
 
     # Generate content for the report
     diagram = add_picture_subdoc(diagram_file, docx_template)
-    chart = add_picture_subdoc(chart_file, docx_template,wd=18)
+    chart = add_picture_subdoc(chart_file, docx_template, wd=18)
 
     # The context is the information that is given to the template to allow it to be populated
     context = {
@@ -375,15 +377,15 @@ def main(structure, work_directory, library, csdrefcode):
             'ccdc_coformers'
         )
     parser = argparse.ArgumentParser(
-            formatter_class=argparse.RawDescriptionHelpFormatter,
-            description=__doc__)
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        description=__doc__)
     parser.add_argument('input_structure', type=str,
-            help='Refcode or mol2 file of the component to be screened')
+                        help='Refcode or mol2 file of the component to be screened')
     parser.add_argument('-d', '--directory', default=os.getcwd(),
-            help='the working directory for the calculation')
+                        help='the working directory for the calculation')
     parser.add_argument('-c', '--coformer_library', type=str,
-            help='the directory of the desired coformer library',
-            default=ccdc_coformers_dir)
+                        help='the directory of the desired coformer library',
+                        default=ccdc_coformers_dir)
 
     args = parser.parse_args()
 

scripts/packing_similarity_dendrogram/packing_similarity_dendogram.py

@@ -15,6 +15,7 @@
 
 import sys
 import argparse
+import os
 import matplotlib
 
 matplotlib.use('Agg')
@@ -23,7 +24,6 @@
 import numpy as np
 
 import matplotlib.pyplot as plt
-import os
 
 
 def strip_terminal(name, reader):