acceleratedscience
diff --git a/‎docs/output/markdown/commands.md‎
Lines changed: 343 additions & 348 deletions b/‎docs/output/markdown/commands.md‎
Lines changed: 343 additions & 348 deletions
diff --git a/‎openad/app/main_lib.py‎
Lines changed: 9 additions & 9 deletions b/‎openad/app/main_lib.py‎
Lines changed: 9 additions & 9 deletions
diff --git a/‎openad/core/grammar.py‎
Lines changed: 10 additions & 4 deletions b/‎openad/core/grammar.py‎
Lines changed: 10 additions & 4 deletions
diff --git a/‎openad/flask_apps/molsgrid/index.html‎
Lines changed: 0 additions & 218 deletions b/‎openad/flask_apps/molsgrid/index.html‎
Lines changed: 0 additions & 218 deletions
diff --git a/‎openad/flask_apps/molsgrid/molsgrid.css‎
Lines changed: 0 additions & 14 deletions b/‎openad/flask_apps/molsgrid/molsgrid.css‎
Lines changed: 0 additions & 14 deletions
@@ -31,9 +31,9 @@
 )
 
 # molecules
-from openad.molecules.mol_functions import df_has_molecules
-from openad.molecules.mol_batch_files import load_batch_molecules, merge_molecule_property_data
-from openad.molecules.mol_commands import (
+from openad.smols.smol_functions import df_has_molecules
+from openad.smols.smol_batch_files import load_batch_molecules, merge_molecule_property_data
+from openad.smols.smol_commands import (
     display_molecule,
     display_property_sources,
     add_molecule,
@@ -52,11 +52,11 @@
     show_mol,
     show_molset,
     show_molset_df,
-    show_molsgrid_DEPRECATED,  # TRASH
     merge_molecules,
 )
+from openad.mmols.mmol_commands import show_mmol
 
-from openad.molecules.molecule_cache import attach_all_results, clear_results
+from openad.smols.smol_cache import attach_all_results, clear_results
 
 import openad.app.login_manager as login_manager
 
@@ -283,17 +283,17 @@ def lang_parse(cmd_pointer, parser):
         return merge_molecule_property_data(cmd_pointer, parser)
     elif parser.getName() == "export_molecules":
         return export_molecule_set(cmd_pointer, parser)
-    elif parser.getName() == "show_molsgrid":
-        return show_molsgrid_DEPRECATED(cmd_pointer, parser)
-    elif parser.getName() == "show_molsgrid_df":
-        return show_molsgrid_DEPRECATED(cmd_pointer, parser)
     elif parser.getName() == "show_mol":
         return show_mol(cmd_pointer, parser)
     elif parser.getName() == "show_molset":
         return show_molset(cmd_pointer, parser)
     elif parser.getName() == "show_molset_df":
         return show_molset_df(cmd_pointer, parser)
 
+    # Macromolecules
+    elif parser.getName() == "show_mmol":
+        return show_mmol(cmd_pointer, parser)
+
     # File system commands
     elif parser.getName() == "list_files":
         return list_files(cmd_pointer, parser)
 
@@ -37,7 +37,8 @@
 # Main
 from openad.core.help import help_dict_create
 import openad.toolkit.toolkit_main as toolkit_main  # Not using "from" to avoid circular import.
-from openad.molecules.mol_grammar import mol_grammar_add
+from openad.smols.smol_grammar import smol_grammar_add
+from openad.mmols.mmol_grammar import mmol_grammar_add
 
 
 # Helpers
@@ -157,6 +158,14 @@ def field_list_act(toks):
 grammar_help = []  # Help text
 
 
+# Add molecule grammar
+smol_grammar_add(statements=statements, grammar_help=grammar_help)
+
+# Add protein grammar
+mmol_grammar_add(statements=statements, grammar_help=grammar_help)
+
+# TODO: Organize all other grammar also by individual files
+
 ##########################################################################
 # region - General
 ##########################################################################
@@ -286,9 +295,6 @@ def field_list_act(toks):
     )
 )
 
-# Add molecule Grammar
-mol_grammar_add(statements=statements, grammar_help=grammar_help)
-
 # endregion
 
 ##########################################################################