Merge pull request #275 from hjkgrp/no_tab_flag

flag to use spaces instead of tabs in molSimplify construction

molSimplify/Scripts/inparse.py

@@ -582,6 +582,8 @@ def parseinputfile(args, inputfile_str=None):
                     args.jobdir = l[1]
                 else:
                     args.jobdirblank = True
+            if (l[0] == '-no_tabs'):
+                args.no_tabs = True
             ### parse structure generation arguments ###
             if (l[0] == '-bind' and len(l[1:]) > 0):
                 l = [_f for _f in re.split(' |,|\t', line) if _f]  # noqa: E741
@@ -1194,6 +1196,8 @@ def parseinputs_advanced(*p):
         "-reportonly", help='add this flag if you just want the report, without actual structure generation. Currently does not support pentadentates.')
     parser.add_argument(
         "-jobmanager", help='use jobmanager naming convention.', default=False)
+    parser.add_argument(
+        "-no_tabs", help="add this flag to use spaces instead of tabs in written xyz files", default=False)
     if len(p) == 1:  # only one input, printing help only
         args = parser.parse_args()
         return args

molSimplify/Scripts/structgen.py

@@ -3015,7 +3015,7 @@ def structgen(args: Namespace, rootdir: str, ligands: List[str], ligoc: List[int
 
     # write xyz file
     if (not args.reportonly) and (write_files):
-        core3D.writexyz(fname)
+        core3D.writexyz(fname, no_tabs=args.no_tabs)
     strfiles.append(fname)
     if write_files:
         # write report file

tests/test_inparse.py

@@ -40,7 +40,7 @@ def test_parseinputs_advanced(monkeypatch):
     defaults = dict(MLbonds=False, antigeoisomer=None, calccharge=True,
                     charge=None, decoration=False, decoration_index=False,
                     distort='0', genall=False, isomers=None, langles=False,
-                    ligalign=False, nconfs='1', oldANN=None, pangles=False,
+                    ligalign=False, nconfs='1', no_tabs=False, oldANN=None, pangles=False,
                     reportonly=None, scoreconfs=False, stereos=None,
                     jobmanager=False)
     assert args.__dict__ == defaults