In process

molsysmt/_private/digestion/argument/output_indices.py

@@ -0,0 +1,13 @@
+from ...exceptions import ArgumentError
+from ...variables import is_all
+
+def digest_output_indices(output_indices, caller=None):
+
+    if caller=='molsysmt.structure.get_contacts.get_contacts':
+
+        if isinstance(output_indices, str):
+            if output_indices.lower() in ['selection', 'atom', 'group']:
+                return output_indices.lower()
+
+    raise ArgumentError('output_indices', value=output_indices, caller=caller, message=None)
+

molsysmt/_private/digestion/argument/output_type.py

@@ -36,7 +36,7 @@ def digest_output_type(output_type, caller=None):
     elif caller=='molsysmt.structure.get_contacts.get_contacts':
 
         if isinstance(output_type, str):
-            if output_type.lower() in ['numpy.ndarray', 'dictionary']:
+            if output_type.lower() in ['pairs', 'sorted pairs', 'matrix']:
                 return output_type.lower()
 
     elif caller=='molsysmt.topology.get_covalent_blocks.get_covalent_blocks':

molsysmt/basic/selector/molsysmt.py

@@ -42,14 +42,33 @@ def select_standard(item, selection):
     from molsysmt.basic import convert, get_form
     from molsysmt.config import selection_shortcuts
 
+
+    tmp_selection = selection
+
+    shortcuts = selection_shortcuts['MolSysMT']
+
+    for key in shortcuts:
+        if key in selection:
+            tmp_selection = tmp_selection.replace(key, shortcuts[key])
+
+
+
     form_in = get_form(item)
 
     if form_in == 'molsysmt.Topology':
         tmp_item = item
     else:
-        tmp_item = convert(item, to_form='molsysmt.Topology', skip_digestion=True)
 
-    tmp_selection = selection
+        from molsysmt.attribute.bonds_are_required_to_get_attribute import bond_dependent_attributes
+
+        bonds_required_by_selection = False
+        for attribute in bond_dependent_attributes:
+            if attribute in tmp_selection:
+                bonds_required_by_selection = True
+                break
+
+        tmp_item = convert(item, to_form='molsysmt.Topology', get_missing_bonds=bonds_required_by_selection,
+                           skip_digestion=True)
 
 
     if '@' in selection:
@@ -100,12 +119,6 @@ def select_standard(item, selection):
                 var_value = list(var_value)
             locals()['auxiliar_variable_'+var_name]=var_value
 
-    shortcuts = selection_shortcuts['MolSysMT']
-
-    for key in shortcuts:
-        if key in selection:
-            tmp_selection = tmp_selection.replace(key, shortcuts[key])
-
     if is_all(tmp_selection):
 
         output = np.array(np.arange(tmp_item.atoms.shape[0]))

molsysmt/build/get_missing_bonds.py

@@ -30,17 +30,18 @@ def get_missing_bonds(molecular_system, threshold='2 angstroms', selection='all'
             bonds_templates = []
             bonds_distances = []
 
+            print('llega_0')
             n_atoms = get(molecular_system, n_atoms=True)
             atoms_water = select(molecular_system, selection='group_type=="water"')
             atoms_not_water = complementary_atom_indices(molecular_system, atoms_water)
             heavy_atoms_not_water = select(molecular_system, selection='atom_type!="H"', mask=atoms_not_water)
             h_atoms_no_water = [ii for ii in atoms_not_water if ii not in heavy_atoms_not_water] 
 
             if with_distances:
-
+                print('llega_1')
                 contacts_heavy_atoms = get_contacts(molecular_system, selection=heavy_atoms_not_water,
                                                     threshold=threshold, output_type='pairs',
-                                                    output_indices='atom_index', pbc=True)
+                                                    output_indices='atom', pbc=True, skip_digestion=False)
 
                 return contacts_heavy_atoms
 

molsysmt/form/nglview_NGLWidget/get_structural_attributes.py

@@ -23,10 +23,10 @@ def get_coordinates_from_atom(item, indices='all', structure_indices='all', skip
 
     coordinates = []
     for ii in structure_indices:
-        if is_all(atom_indices):
+        if is_all(indices):
             coordinates.append(item[0].get_coordinates(ii))
         else:
-            coordinates.append(item[0].get_coordinates(ii)[atom_indices,:])
+            coordinates.append(item[0].get_coordinates(ii)[indices,:])
     coordinates = np.array(coordinates)
     coordinates = puw.quantity(coordinates, unit='angstroms')
     coordinates = puw.standardize(coordinates)

molsysmt/structure/get_contacts.py

@@ -7,7 +7,7 @@
 @digest()
 def get_contacts(molecular_system, selection=None, center_of_atoms=False, weights=None, structure_indices="all",
                  selection_2=None, center_of_atoms_2=False, weights_2=None, structure_indices_2=None,
-                 threshold='12 angstroms', pbc=True, syntax='MolSysMT', output_type='map', output_indices=None,
+                 threshold='12 angstroms', pbc=True, syntax='MolSysMT', output_type='matrix', output_indices='selection',
                  skip_digestion=False):
 
     """
@@ -48,7 +48,7 @@ def get_contacts(molecular_system, selection=None, center_of_atoms=False, weight
 
     output = None
 
-    if output_type=='map':
+    if output_type=='matrix':
 
         output = contact_map
 
@@ -62,7 +62,7 @@ def get_contacts(molecular_system, selection=None, center_of_atoms=False, weight
             aux_pairs = np.column_stack(aux_pairs).tolist()
             pairs.append(aux_pairs)
 
-        if output_indices=='atom_index':
+        if output_indices=='atom':
 
             atom_indices = np.array(atom_indices)