Some modifications to nglview functions

molsysmt/_private/digestion/argument/color.py

@@ -12,4 +12,7 @@ def digest_color(color, caller=None):
         if len(color)==3:
             return color
 
+    if isinstance(color, str):
+        return color
+
     raise ArgumentError('color', value=color, caller=caller, message=None)

molsysmt/structure/least_rmsd_align.py

@@ -6,8 +6,9 @@
 @digest()
 def least_rmsd_align(molecular_system, selection='atom_name=="CA"', structure_indices='all',
           reference_molecular_system=None, reference_selection=None, reference_structure_index=0,
-          syntax='MolSysMT',
-          engine_sequence_alignment = 'Biopython', engine_least_rmsd_fit = 'MolSysMT'):
+          syntax='MolSysMT', engine_sequence_alignment = 'Biopython', engine_least_rmsd_fit = 'MolSysMT',
+          in_place=False, skip_digestion=False):
+
     """
     To be written soon...
     """
@@ -49,21 +50,38 @@ def least_rmsd_align(molecular_system, selection='atom_name=="CA"', structure_in
 
         from molsysmt.structure import least_rmsd_fit
 
-        output = least_rmsd_fit(molecular_system=molecular_system, selection=atoms_in_components_selected,
-                selection_fit=selection_to_be_fitted,
-                structure_indices=structure_indices, reference_molecular_system=reference_molecular_system,
-                reference_selection_fit=reference_selection_to_be_fitted,
-                                reference_structure_index=reference_structure_index,
-                to_form=None, in_place=False, engine='MolSysMT', syntax=syntax)
+        if in_place:
+
+            least_rmsd_fit(molecular_system=molecular_system, selection=atoms_in_components_selected,
+                    selection_fit=selection_to_be_fitted,
+                    structure_indices=structure_indices, reference_molecular_system=reference_molecular_system,
+                    reference_selection_fit=reference_selection_to_be_fitted,
+                    reference_structure_index=reference_structure_index,
+                    to_form=None, in_place=in_place, engine='MolSysMT', syntax=syntax, skip_digestion=True)
+
+            del(atoms_in_components_selected, selection_to_be_fitted, reference_selection_to_be_fitted)
+            del(structure_indices, reference_structure_index)
+
+            gc.collect()
+
+        else:
 
-        del(atoms_in_components_selected, selection_to_be_fitted, reference_selection_to_be_fitted)
-        del(structure_indices, reference_structure_index)
+            output = least_rmsd_fit(molecular_system=molecular_system, selection=atoms_in_components_selected,
+                    selection_fit=selection_to_be_fitted,
+                    structure_indices=structure_indices, reference_molecular_system=reference_molecular_system,
+                    reference_selection_fit=reference_selection_to_be_fitted,
+                                    reference_structure_index=reference_structure_index,
+                    to_form=None, in_place=in_place, engine='MolSysMT', syntax=syntax, skip_digestion=True)
+
+            del(atoms_in_components_selected, selection_to_be_fitted, reference_selection_to_be_fitted)
+            del(structure_indices, reference_structure_index)
+
+            gc.collect()
+
+            return output
 
     else:
 
         raise NotImplementedMethodError
 
-    gc.collect()
-
-    return output
 

molsysmt/structure/least_rmsd_fit.py

@@ -9,7 +9,7 @@
 @digest()
 def least_rmsd_fit(molecular_system=None, selection='all', selection_fit='atom_type!="H"', structure_indices='all',
         reference_molecular_system=None, reference_selection_fit=None, reference_structure_index=0,
-        to_form=None, in_place=False, syntax='MolSysMT', engine='MolSysMT'):
+        to_form=None, in_place=False, syntax='MolSysMT', engine='MolSysMT', skip_digestion=False):
     """
     To be written soon...
     """

molsysmt/thirds/nglview/__init__.py

@@ -1,8 +1,10 @@
 from .patching_nglview import adding_molsysmt
 
 from .show_gui import show_gui
+from .clear import clear
 
-from .color_by_value import color_by_value
+from .set_color import set_color
+from .set_color_by_value import set_color_by_value
 
 from .load_html_in_jupyter_notebook import load_html_in_jupyter_notebook
 from .write_html import write_html
@@ -12,6 +14,7 @@
 from .show_as_surface import show_as_surface
 from .show_as_licorice import show_as_licorice
 from .show_as_balls_and_sticks import show_as_balls_and_sticks
+from .show_as_cartoon import show_as_cartoon
 
 from .add_cylinders import add_cylinders
 from .add_contacts import add_contacts

molsysmt/thirds/nglview/clear.py

@@ -0,0 +1,13 @@
+from molsysmt._private.digestion import digest
+from molsysmt._private.variables import is_all
+
+# https://github.com/arose/ngl/blob/master/doc/usage/selection-language.md
+
+
+@digest(form='nglview.NGLWidget')
+def clear(view, skip_digestion=False):
+
+    view.clear_representations()
+
+    pass
+

molsysmt/thirds/nglview/set_color.py

@@ -0,0 +1,14 @@
+from molsysmt._private.digestion import digest
+from molsysmt._private.variables import is_all
+
+# https://github.com/arose/ngl/blob/master/doc/usage/selection-language.md
+
+@digest()
+def set_color(view, color, selection='all', syntax='MolSysMT'):
+
+    from molsysmt.basic import select
+
+    atoms_selection = select(view, element='atom', selection=selection, syntax=syntax, to_syntax='NGLView')
+    view.update_representation(component=0, selection=atoms_selection, color=color)
+
+    pass

molsysmt/thirds/nglview/color_by_value.py → molsysmt/thirds/nglview/set_color_by_value.py

@@ -4,7 +4,7 @@
 # https://github.com/arose/ngl/blob/master/doc/usage/selection-language.md
 
 @digest()
-def color_by_value(view, values, element='group', selection='all', cmap='bwr_r',
+def set_color_by_value(view, values, element='group', selection='all', cmap='bwr_r',
         min_value=None, max_value=None, representation='cartoon', syntax='MolSysMT'):
     """Adding a new representation colored by a color scale.
 

molsysmt/thirds/nglview/show_as_cartoon.py

@@ -0,0 +1,27 @@
+from molsysmt._private.digestion import digest
+from molsysmt._private.variables import is_all
+
+# https://github.com/arose/ngl/blob/master/doc/usage/selection-language.md
+
+
+@digest(form='nglview.NGLWidget')
+def show_as_cartoon(view, selection='all', color='blue', skip_digestion=False):
+
+    from molsysmt import select
+
+    nglview_selection=None
+
+    if isinstance(selection, str):
+        if selection=='molecule_type=="water"' or selection=='group_type=="water"':
+            nglview_selection='water'
+        if selection=='molecule_type=="ion"' or selection=='group_type=="ion"':
+            nglview_selection='ion'
+
+    if nglview_selection is None:
+        nglview_selection = select(view, element='atom', selection=selection, to_syntax='NGLView',
+                                  skip_digestion=True)
+
+    view.add_cartoon(selection=nglview_selection, color=color)
+
+    pass
+