cleanup and improved warnings

atomhandling.py

@@ -386,7 +386,7 @@ def get_atoms_resinumber(self, atom):
                 resinum = '0'
             if len(resinum) > 4:
                 print('*** Invalid residue number in {}'.format(atom))
-                sys.exit(-1)
+                sys.exit()
             return str(resinum)
         else:
             return '0'
@@ -428,7 +428,7 @@ def get_atomcoordinates(self, atoms):
             i = i.upper()
             if i not in list(atom_dict):
                 print('\n*** Atom "{}" not found in res file! ***'.format(i))
-                sys.exit(0)
+                sys.exit()
         return atom_dict
 
     def get_atom_line_numbers(self, atoms):
@@ -539,13 +539,13 @@ def check_source_target(db_source_atoms, res_target_atoms, dbatoms):
     if nsrc != ntrg:
         print('*** Number of source and target atoms/peaks is different!! '
               '({} and {} atoms/peaks) ***'.format(nsrc, ntrg))
-        sys.exit(False)
+        sys.exit()
     # do the source atoms exist at all?:
     for i in db_source_atoms:
         i = i.upper()
         if i not in temp:
             print('\n*** Atom {} not found in database entry! ***'.format(i))
-            sys.exit(False)
+            sys.exit()
     return True
 
 
@@ -653,7 +653,7 @@ def set_sfac_table(self):
                 sfac.append(i)        # get appended to sfac
             if i not in self.elements:
                 print('*** Error, atom {} not valid ***'.format(i))
-                sys.exit(False)
+                sys.exit()
         for i in range(1, len(sfac+explicit_scat)+1):
             i = str(i).upper()
             unit.append(i)
@@ -837,7 +837,7 @@ def get_fragment_number_scheme(self, extranames=[]):
         print('passed all {} tests!'.format(attempted))
     else:
         print('{} of {} tests failed'.format(failed, attempted))
-    sys.exit()
+
 
 
 

dbfile.py

@@ -190,10 +190,10 @@ def find_db_tags(self):
             diff = c1 - c2
             duplicates = list(diff.elements())
             for i in duplicates:
-                print('\n*** Duplicate database entry "{}" found! Please remove/rename ' \
-                      'second entry\nand/or check all end tags in the database dsr_usr_db.txt or dsr_db.txt. ***'.format(
-                    duplicates.pop()))
-            sys.exit(False)
+                print('\n*** Duplicate database entry "{}" found! Please remove/rename '
+                      'second entry\nand/or check all end tags in the database dsr_usr_db.txt '
+                      'or dsr_db.txt. ***'.format(duplicates.pop()))
+            sys.exit()
         # # sort lower-case:
         dbnames.sort(key=lambda x: x[0].lower())
         return dbnames
@@ -358,9 +358,9 @@ def get_residue_from_head(head, fragment=''):
                         del resiline[n]
                 try:
                     return resiline[1].upper()
-                except(IndexError):
+                except IndexError:
                     print('*** Invalid residue definition in database entry {}. ***'.format(fragment))
-                    sys.exit(False)
+                    sys.exit()
         return False
 
     def get_fragment_atoms(self, fragment, db_name, line):
@@ -398,11 +398,11 @@ def get_fragment_atoms(self, fragment, db_name, line):
             print('*** Database entry of "{}" in line {} of "{}.txt" is corrupt. '
                   'No atoms found! ***'.format(fragment, line, db_name))
             print('*** Have you really followed the syntax? ***')
-            sys.exit(False)
+            sys.exit()
         if not end:
             print('*** Could not find end of dbentry for fragment "{}" in line {} of "{}.txt". '
                   'Check your database. ***'.format(fragment, line, db_name))
-            sys.exit(False)
+            sys.exit()
         if self.invert:
             atoms = invert_dbatoms_coordinates(atoms)
         return atoms
@@ -444,7 +444,7 @@ def get_head_lines(self, fragment, db, line):
             print('*** Error. No cell parameters found in the database entry ' \
                   'of "{}" ***'.format(fragment))
             print('*** Please add these parameters! ***')
-            sys.exit(False)
+            sys.exit()
         # nhead is list of strings
         head = unwrap_head_lines(head)
         return head, fragline, comment
@@ -520,7 +520,7 @@ def check_consistency(self, fragment):
         if len(dbentry['fragline']) != 8:
             print('*** The line starting with "FRAG" in the database entry of {} is not correct. ***\n '
                   '*** Are the cell parameters really correct? "FRAG 17 a b c alpha beta gamma" ***\n'.format(fragment))
-            sys.exit(False)
+            sys.exit()
         return True
 
     def get_sum_formula(self, fragment):
@@ -552,9 +552,10 @@ def check_db_atom_consistency(self, fragment):
         while dbatoms:
             at = dbatoms.pop()
             if at in dbatoms:
-                print('*** Duplicate atom {0} in database entry "{1}" ({2}) ' \
-                      'found! Check your database... ***'.format(at, fragment, self.get_name_from_fragment(fragment)))
-                sys.exit(-1)
+                print('*** Duplicate atom {0} in database entry "{1}" ({2}) '
+                      'found! Check your database... ***'
+                      .format(at, fragment, self.get_name_from_fragment(fragment)))
+                sys.exit()
 
     def check_db_header_consistency(self, fragment):
         """
@@ -579,7 +580,6 @@ def check_db_header_consistency(self, fragment):
                 status = False
                 print('*** Bad line in header of database entry "{}" found! ({}.txt) ***'.format(fragment, db))
                 print(line)
-                # sys.exit(status)
             if line[:4] in RESTRAINT_CARDS:
                 line = line[5:].split()
                 for i in line:
@@ -593,8 +593,8 @@ def check_db_header_consistency(self, fragment):
             atom = atom.upper()
             if atom not in atoms:
                 status = False
-                print('\n*** Unknown atom "{}" in restraints of "{}: {}". ***'.format(atom, fragment,
-                                                                                      self.get_name_from_fragment(fragment)))
+                print('\n*** Unknown atom "{}" in restraints of "{}: {}". ***'
+                      .format(atom, fragment, self.get_name_from_fragment(fragment)))
         if not status:
             print('*** Check database entry. ***\n')
             sys.exit(status)
@@ -683,13 +683,13 @@ def search_for_error_response(self, fragment):
         print_search_results(result)
 
     def get_atoms_from_fragment(self, fragment):
-        '''
+        """
         returns the atoms from the dbentry:
         [['O1', '1', '0.01453', '-1.6659', '-0.10966'],
         ['C1', '1', '0.00146', '-0.26814', '-0.06351'], ... ]
         :param fragment: fragment name
         :type fragment: string
-        '''
+        """
         fragment = fragment.lower()
         try:
             return self._db_all_dict[fragment]['atoms']
@@ -846,12 +846,12 @@ def get_gradefiles(self, grade_tar_file):
         if grade_base_filename[1] == '.tgz':
             try:
                 gradefile = tarfile.open(grade_tar_file)  # , encoding="ascii")
-            except(IOError):
+            except IOError:
                 print('No such file or directory: {}'.format(grade_tar_file))
-                sys.exit(0)
+                sys.exit()
         else:
             print('*** File {} is not a valid file to import from ***'.format(grade_base_filename[1]))
-            sys.exit(0)
+            sys.exit()
         pdbfile = False
         dfixfile = False
         for i in gradefile.getnames():
@@ -1028,8 +1028,8 @@ def bild_grade_db_entry(self):
             name = name.decode()
         resi_name = name
         if not self._db_tags:
-            print('Unable to import fragment. Database is empty.')
-            sys.exit(False)
+            print('*** Unable to import fragment. Database is empty. ***')
+            sys.exit()
         for i in self._db_tags:
             while resi_name == i[0]:
                 num = num + 1
@@ -1055,9 +1055,9 @@ def import_error(self, filename):
         '''
         warns for import errors
         '''
-        print('Unable to import GRADE file {}'.format(filename))
-        print('GRADE import relies on GRADE v1.100 and up.')
-        sys.exit(False)
+        print('*** Unable to import GRADE file {}'.format(filename))
+        print('GRADE import relies on GRADE v1.100 and up. ***')
+        sys.exit()
 
     def write_user_database(self):
         """
@@ -1088,9 +1088,9 @@ def write_user_database(self):
                     dbentry = '<{}> \n{} \nRESI {} \n{} \n{} \n{} \n</{}>\n''\
                         '.format(resi_name, comment, resi_name, head, cell, atoms, resi_name)
                     f.write(dbentry)
-        except(IOError) as e:
+        except IOError as e:
             print(e)
-            sys.exit(-1)
+            sys.exit()
         # try to write existing dbentries:
         try:
             with open(self.user_db_path, 'a+') as fu:
@@ -1109,9 +1109,9 @@ def write_user_database(self):
                         dbentry = '\n<{}> \nREM {} \nRESI {} \n{} \n{} \n{} \n</{}>\n' \
                                   ''.format(name, comment, resi_name, head, fragline, atoms, name)
                         fu.write(dbentry)
-        except(IOError) as e:
+        except IOError as e:
             print(e)
-            sys.exit(-1)
+            sys.exit()
         print('User database successfully updated.')
 
 

dsr.py

@@ -33,7 +33,7 @@
 program_name = '\n'+((width//2)-9)*'-'+' D S R - v{} '.format(VERSION)+((width//2)-8)*'-'
 
 # TODO and ideas:
-'''
+"""
 - Add Rcomplete
 
 From SHELXL user guide:
@@ -49,7 +49,7 @@
   -> learn JANA
   -> What do I need to change?
 
-'''
+"""
 
 
 class DSR():
@@ -100,9 +100,7 @@ def __init__(self, options):
             self.gdb = global_DB(invert=self.invert)
         except Exception as e:  # @UnusedVariable
             print("*** Initializing the database failed ***")
-            #print(self.helpmsg)
             raise
-            #sys.exit()
         #  List of database Fragments:
         if self.list_db_csv:
             print('DSR version: {}'.format(VERSION))
@@ -153,7 +151,7 @@ def __init__(self, options):
         if self.import_grade:
             mog = ImportGRADE(self.import_grade, self.invert)
             mog.write_user_database()
-            sys.exit(1)
+            sys.exit()
         if not any(list(vars(self.options.all_options).values())+[self.res_file]):
             self.options.error()
         if self.res_file == False:

dsrparse.py

@@ -67,7 +67,7 @@ def find_dsr_command(self, line=False):
         indexnum = misc.find_multi_lines(self._reslist, self._dsr_regex)
         try:
             line_number = int(indexnum[0])
-        except(IndexError):
+        except IndexError:
             print('*** no proper DSR command found! \n'
                     'Have you really saved your .res file? ***\n')
             sys.exit()

export.py

@@ -17,6 +17,7 @@
 import atomhandling as at
 from atoms import Element
 from dbfile import global_DB
+from misc import wrap_headlines
 from restraints import Restraints
 
 __metaclass__ = type  # use new-style classes
@@ -226,8 +227,6 @@ def format_atoms_for_export(self, fragname, gui=False):
         'C5 6 2.98081 10.44432 9.51725', 'C6 6 3.92045 9.74974 10.25408',
         'C7 6 3.53891 8.69091 11.05301']
         
-        #>>> print(exp.format_atoms_for_export(fragname="", gui=True))
-        #sys.exit()
         """
         fragname = fragname.lower()
         el = Element()
@@ -314,7 +313,7 @@ def write_res_file(self, fragment):
         except IOError:
             print('*** Could not write file {} ***'.format(resfile))
             import sys
-            sys.exit(-1)
+            sys.exit()
         f.close()
 
 

misc.py

@@ -431,7 +431,7 @@ def remove_file(filename, exit_dsr=False, terminate=False):
                 pgrogname = terminate
                 pgrogname.terminate()
             if exit_dsr:
-                sys.exit(0)
+                sys.exit()
 
 
 def copy_file(source, target):

options.py

@@ -21,7 +21,7 @@
 try:
     from argparse import RawTextHelpFormatter
 except ImportError:
-    print('\nYour Python version is incompatible with DSR! \nPlease use Python 2.7 or above.\n')
+    print('\n*** Your Python version is incompatible with DSR! \nPlease use Python 2.7 or above. ***\n')
     sys.exit()
 from argparse import ArgumentParser, SUPPRESS
 

pyperclip.py

@@ -151,10 +151,8 @@ def xselGetClipboard():
                 getcb = qtGetClipboard
                 setcb = qtSetClipboard
             except:
-#                import sys
-                print('\nDSR requires Pyperclip to export fragments to the clipboard.')
-                print('Pyperclip requires the xclip command or the gtk or PyQt4 module installed.\n')
-#               sys.exit()
+                print('\n*** DSR requires Pyperclip to export fragments to the clipboard.')
+                print('Pyperclip requires the xclip command or the gtk or PyQt4 module installed. ***\n')
 try:
     copy = setcb
     paste = getcb