In process

molsysmt/_private/digestion/argument/attribute_type.py

@@ -0,0 +1,17 @@
+from ...exceptions import ArgumentError
+from ...variables import is_all
+
+def digest_attribute_type(attribute_type, caller=None):
+
+    if caller=='molsysmt.basic.compare.compare':
+
+        if attribute_type is None:
+            return None
+        elif is_all(attribute_type):
+            return 'all'
+        elif isinstance(attribute_type, str):
+            if attribute_type.lower() in ['topological', 'structural', 'mechanical']:
+                return attribute_type.lower()
+
+    raise ArgumentError('attribute_type', value=attribute_type, caller=caller, message=None)
+

molsysmt/basic/compare.py

@@ -6,7 +6,7 @@
 @digest()
 def compare(molecular_system, molecular_system_2, selection='all', structure_indices='all',
         selection_2='all', structure_indices_2='all',  syntax='MolSysMT', rule='equal',
-        output_type='boolean', attributes_type=None, **kwargs):
+        output_type='boolean', attribute_type=None, **kwargs):
     """
     Comparing molecular systems.
 
@@ -67,7 +67,7 @@ def compare(molecular_system, molecular_system_2, selection='all', structure_ind
         * 'dictionary': a dictionary is returned with the input attribute names as keys, and the corresponding booleans (True
         or False) as values.
 
-    attribute_types : {'topological', 'structural', 'mecanichal', None}, default None
+    attribute_type : {'topological', 'structural', 'mecanichal', None}, default None
         If no specific attributes are introduced as additional keywords, a set of attributes can be
         chosen:
 
@@ -168,14 +168,14 @@ def compare(molecular_system, molecular_system_2, selection='all', structure_ind
 
     atts_false = []
 
-    if isinstance(attributes_type, str):
-        if attributes_type == 'topological':
+    if isinstance(attribute_type, str):
+        if attribute_type == 'topological':
             atts_to_be_compared += _topological_attributes
-        elif attributes_type == 'structural':
+        elif attribute_type == 'structural':
             atts_to_be_compared += _structural_attributes
-        elif attributes_type == 'mechanical':
+        elif attribute_type == 'mechanical':
             atts_to_be_compared += _mechanical_attributes
-        elif is_all(attributes_type):
+        elif is_all(attribute_type):
             atts_to_be_compared += list(attributes.keys())
 
     for key in kwargs.keys():

molsysmt/build/get_missing_bonds.py

@@ -16,8 +16,9 @@ def get_missing_bonds(molecular_system, threshold='2 angstroms', selection='all'
 
     if engine=="MolSysMT":
 
+        from molsysmt._private.atom_indices import complementary_atom_indices
         from molsysmt.basic import get, select, get_form
-        from molsysmt.structure import get_neighbors
+        from molsysmt.structure import get_contacts
         from molsysmt.element.group.amino_acid import get_bonded_atom_pairs as _bonds_in_amino_acid
         from molsysmt.element.group.terminal_capping import get_bonded_atom_pairs as _bonds_in_terminal_capping
         from molsysmt.element.group.terminal_capping import is_n_terminal_capping, is_c_terminal_capping
@@ -29,6 +30,20 @@ def get_missing_bonds(molecular_system, threshold='2 angstroms', selection='all'
             bonds_templates = []
             bonds_distances = []
 
+            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:
+
+                contacts_heavy_atoms = get_contacts(molecular_system, selection=heavy_atoms_not_water,
+                                                    threshold=threshold, output_type='pairs',
+                                                    output_indices='atom_index', pbc=True)
+
+                return contacts_heavy_atoms
+
             if with_templates:
 
                 aux_peptidic_bonds_C={}

molsysmt/tests/basic/get/test_get_nglview_NGLWidget.py

@@ -8,6 +8,7 @@
 import numpy as np
 
 
+
 def test_get_nglview_NGLWidget_1():
     molsys = msm.convert([systems['nglview']['md_1u19.gro'], systems['nglview']['md_1u19.xtc']],
                          to_form='molsysmt.MolSys')