Updates to run as package in Python 3

rabdam/Subroutines/PDBCUR.py

@@ -576,7 +576,7 @@ def clean_atom_rec(atoms_list, disulfide_bonds, seqres, cryst1_line,
                          and atm.insCode == inscode1 and atm.resiType == 'CYS')
                         or
                         (atm.chainID == chain2 and atm.resiNum == resnum2
-                         and atm.insCode == inscode2 and atom.resiType == 'CYS'))
+                         and atm.insCode == inscode2 and atm.resiType == 'CYS'))
                 ):
                     pause = True
                     print('\n\nERROR: One or more disulfide bonds has been '

rabdam/Subroutines/output.py

@@ -322,7 +322,7 @@ def plot_Bnet_histogram(self, bnet_df, median, prot_or_na):
         plt.ylabel('Normalised Frequency')
         plt.title(self.pdb_code + ' Bnet kernel density plot')
 
-        # Extracts an array of 128 (x, y) coordinate pairs evenly spaced
+        # Extracts an array of 100 (x, y) coordinate pairs evenly spaced
         # along the x(BDamage)-axis from the kernel density plot. These
         # coordinate pairs are used to calculate, via the trapezium rule,
         # the area under the curve between the smallest value of x and the

rabdam/rabdam.py

@@ -46,10 +46,13 @@ def parse_command_line_arguments(command_line, test=False):
         else:
             from rabdam.Subroutines.checkDependencies import check_RABDAM_dependencies
     else:
-        if __name__ == '__main__' or 'CCP4' in list(os.environ.keys()):
+        if __name__ == '__main__':
             from Subroutines.checkDependencies import check_RABDAM_dependencies
         else:
-            from rabdam.Subroutines.checkDependencies import check_RABDAM_dependencies
+            if sys.version_info[0] < 3:
+                from Subroutines.checkDependencies import check_RABDAM_dependencies
+            else:
+                from rabdam.Subroutines.checkDependencies import check_RABDAM_dependencies
 
     # Reads in command line inputs. There are three recognised flags: -i, -f
     # and -o. Program inputs are specified by either the -i or the -f flag;
@@ -466,10 +469,13 @@ def main(test=False):
     import time
     import numpy as np
 
-    if __name__ == '__main__' or 'CCP4' in list(os.environ.keys()):
+    if __name__ == '__main__':
         from Subroutines.CalculateBDamage import rabdam
     else:
-        from rabdam.Subroutines.CalculateBDamage import rabdam
+        if sys.version_info[0] < 3:
+            from Subroutines.CalculateBDamage import rabdam
+        else:
+            from rabdam.Subroutines.CalculateBDamage import rabdam
 
     # Parses in command line arguments
     args = parse_command_line_arguments(sys.argv[1:])

setup.py

@@ -1,7 +1,7 @@
 
 from setuptools import setup, find_packages
 
-with open('README.md', 'r') as f:
+with open('README.md', 'r', encoding='utf-8') as f:
     long_description = f.read()
 
 setup(