From bccc30a06f281f1021d2046b9b7053de8bbf9576 Mon Sep 17 00:00:00 2001
From: Diego Prada-Gracia <prada.gracia@gmail.com>
Date: Mon, 29 Apr 2024 23:46:32 -0600
Subject: [PATCH] In process

---
 .../digestion/argument/bond_indices.py        |  41 ++++
 molsysmt/build/__init__.py                    |   1 +
 molsysmt/build/remove_bonds.py                |  22 +++
 molsysmt/element/entity/get_entity_index.py   |  15 +-
 molsysmt/form/molsysmt_MolSys/__init__.py     |   4 +-
 molsysmt/form/molsysmt_MolSys/remove_bonds.py |   8 +
 .../to_molsysmt_Topology.py                   |  80 +++++---
 molsysmt/form/molsysmt_Topology/__init__.py   |   3 +
 molsysmt/form/molsysmt_Topology/add_bonds.py  |  10 +
 .../form/molsysmt_Topology/remove_bonds.py    |   8 +
 molsysmt/form/openmm_Modeller/__init__.py     |   6 +-
 molsysmt/native/topology.py                   |  42 +++++
 .../test_compare_with_molsysmt_MolSys.py      |   8 +-
 .../test_remove_bonds_molsysmt_MolSys.py      |  22 +++
 sandbox/Tests.ipynb                           | 176 +++++++++++++-----
 15 files changed, 359 insertions(+), 87 deletions(-)
 create mode 100644 molsysmt/_private/digestion/argument/bond_indices.py
 create mode 100644 molsysmt/build/remove_bonds.py
 create mode 100644 molsysmt/form/molsysmt_MolSys/remove_bonds.py
 create mode 100644 molsysmt/form/molsysmt_Topology/add_bonds.py
 create mode 100644 molsysmt/form/molsysmt_Topology/remove_bonds.py
 create mode 100644 molsysmt/tests/build/remove_bonds/test_remove_bonds_molsysmt_MolSys.py

diff --git a/molsysmt/_private/digestion/argument/bond_indices.py b/molsysmt/_private/digestion/argument/bond_indices.py
new file mode 100644
index 000000000..4e06423e5
--- /dev/null
+++ b/molsysmt/_private/digestion/argument/bond_indices.py
@@ -0,0 +1,41 @@
+from ...exceptions import ArgumentError
+from ...variables import is_all
+import numpy as np
+
+def digest_bond_indices(bond_indices, caller=None):
+    """ Checks if bond_indices has the expected type and value.
+
+    Parameters
+    ----------
+    indices : str or int or list or tuple or range.
+        The indices
+
+    caller: str, optional
+        Name of the function or method that is being digested.
+        For debugging purposes.
+
+    Returns
+    -------
+    str or ndarray or None
+        Either None, 'all' or an numpy array of integers with the indices.
+
+    Raises
+    -------
+    ArgumentError
+        If the given indices are not of the correct type.
+    """
+
+    if bond_indices is None:
+        return None
+    elif is_all(bond_indices):
+        return 'all'
+    elif isinstance(bond_indices, (int, np.int64, np.int32)):
+        return np.array([bond_indices], dtype='int64')
+    elif isinstance(bond_indices, (np.ndarray, list, tuple, range)):
+        if all(isinstance(ii, (int, np.int64, np.int32)) for ii in bond_indices):
+            return np.array(bond_indices, dtype='int64')
+        else:
+            return [digest_bond_indices(ii) for ii in bond_indices]
+
+    raise ArgumentError('bond_indices', caller=caller, message=None)
+
diff --git a/molsysmt/build/__init__.py b/molsysmt/build/__init__.py
index 109cfc8d7..6149db3d1 100644
--- a/molsysmt/build/__init__.py
+++ b/molsysmt/build/__init__.py
@@ -19,4 +19,5 @@
 from .define_new_chain import define_new_chain
 from .make_water_box import make_water_box
 from .remove_overlapping_molecules import remove_overlapping_molecules
+from .remove_bonds import remove_bonds
 
diff --git a/molsysmt/build/remove_bonds.py b/molsysmt/build/remove_bonds.py
new file mode 100644
index 000000000..c98191561
--- /dev/null
+++ b/molsysmt/build/remove_bonds.py
@@ -0,0 +1,22 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+from molsysmt._private.variables import is_all
+
+@digest()
+def remove_bonds(molecular_system, bond_indices='all', in_place=True, skip_digestion=False):
+
+    from molsysmt.basic import where_is_attribute
+    from molsysmt.form import _dict_modules
+
+    if in_place:
+
+        item, form = where_is_attribute(molecular_system, 'bond_index', check_if_None=False,
+                                        skip_digestion=True)
+
+        add_bonds_function = getattr(_dict_modules[form], f'remove_bonds')
+        add_bonds_function(item, bond_indices, skip_digestion=True)
+
+    else:
+
+        raise NotImplementedMethodError
+
diff --git a/molsysmt/element/entity/get_entity_index.py b/molsysmt/element/entity/get_entity_index.py
index c2dc668e6..767c924ce 100644
--- a/molsysmt/element/entity/get_entity_index.py
+++ b/molsysmt/element/entity/get_entity_index.py
@@ -3,7 +3,8 @@
 
 @digest()
 def get_entity_index(molecular_system, element='atom', selection='all',
-        redefine_molecules=False, redefine_indices=False, syntax='MolSysMT'):
+                     redefine_molecules=False, redefine_indices=False, syntax='MolSysMT',
+                     skip_digestion=False):
 
     if redefine_molecules or redefine_indices:
 
@@ -12,18 +13,20 @@ def get_entity_index(molecular_system, element='atom', selection='all',
         if redefine_molecules:
 
             molecule_name_from_molecules = get_molecule_name(molecular_system, element='molecule',
-                    selection=selection, redefine_molecules=True, syntax=syntax)
+                    selection=selection, redefine_molecules=True, syntax=syntax, skip_digestion=True)
 
             molecule_type_from_molecules = get_molecule_type(molecular_system, element='molecule',
-                    selection=selection, redefine_molecules=True, syntax=syntax)
+                    selection=selection, redefine_molecules=True, syntax=syntax, skip_digestion=True)
 
         else:
 
             molecule_name_from_molecules = get_molecule_name(molecular_system, element='molecule',
-                    selection=selection, redefine_molecules=False, redefine_names=False, syntax=syntax)
+                    selection=selection, redefine_molecules=False, redefine_names=False, syntax=syntax,
+                                                            skip_digestion=True)
 
             molecule_type_from_molecules = get_molecule_type(molecular_system, element='molecule',
-                    selection=selection, redefine_molecules=False, redefine_types=False, syntax=syntax)
+                    selection=selection, redefine_molecules=False, redefine_types=False, syntax=syntax,
+                                                            skip_digestion=True)
 
         count = 0
         output = []
@@ -87,7 +90,7 @@ def get_entity_index(molecular_system, element='atom', selection='all',
 
         from molsysmt import get
         output = get(molecular_system, element=element, selection=selection, syntax=syntax,
-                     entity_index=True)
+                     entity_index=True, skip_digestion=True)
 
     return output
 
diff --git a/molsysmt/form/molsysmt_MolSys/__init__.py b/molsysmt/form/molsysmt_MolSys/__init__.py
index ea4143cc1..d6f95d6ee 100644
--- a/molsysmt/form/molsysmt_MolSys/__init__.py
+++ b/molsysmt/form/molsysmt_MolSys/__init__.py
@@ -15,7 +15,6 @@
 from .copy import copy
 from .add import add
 from .merge import merge
-from .add_bonds import add_bonds
 from .append_structures import append_structures
 from .get_topological_attributes import *
 from .get_structural_attributes import *
@@ -23,6 +22,9 @@
 from .set import *
 from .iterators import StructuresIterator, TopologyIterator
 
+from .add_bonds import add_bonds
+from .remove_bonds import remove_bonds
+
 from .to_mdtraj_Topology import to_mdtraj_Topology
 from .to_mdtraj_Trajectory import to_mdtraj_Trajectory
 from .to_molsysmt_Topology import to_molsysmt_Topology
diff --git a/molsysmt/form/molsysmt_MolSys/remove_bonds.py b/molsysmt/form/molsysmt_MolSys/remove_bonds.py
new file mode 100644
index 000000000..2518e2eff
--- /dev/null
+++ b/molsysmt/form/molsysmt_MolSys/remove_bonds.py
@@ -0,0 +1,8 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+from molsysmt._private.variables import is_all
+
+@digest(form='molsysmt.MolSys')
+def remove_bonds(item, bond_indices='all', skip_digestion=False):
+
+    return item.topology.remove_bonds(bond_indices=bond_indices, skip_digestion=True)
diff --git a/molsysmt/form/molsysmt_PDBFileHandler/to_molsysmt_Topology.py b/molsysmt/form/molsysmt_PDBFileHandler/to_molsysmt_Topology.py
index de2698c53..30c22f1a8 100644
--- a/molsysmt/form/molsysmt_PDBFileHandler/to_molsysmt_Topology.py
+++ b/molsysmt/form/molsysmt_PDBFileHandler/to_molsysmt_Topology.py
@@ -1,5 +1,6 @@
 from molsysmt._private.digestion import digest
 from molsysmt._private.variables import is_all
+from molsysmt import pyunitwizard as puw
 import pandas as pd
 import numpy as np
 
@@ -7,10 +8,9 @@
 def to_molsysmt_Topology(item, atom_indices='all', structure_indices=0, get_missing_bonds=True,
                          skip_digestion=False):
 
-    from molsysmt.native import Topology
-    from molsysmt.build import get_missing_bonds as _get_missing_bonds
+    from molsysmt.native import MolSys
 
-    tmp_item = Topology()
+    tmp_item = MolSys()
 
     atom_id_array = []
     atom_name_array = []
@@ -22,6 +22,7 @@ def to_molsysmt_Topology(item, atom_indices='all', structure_indices=0, get_miss
 
     occupancy_array = []
     alternate_location_array = []
+    coordinates_array = []
 
     group_index = -1
     former_group_id = None
@@ -30,8 +31,6 @@ def to_molsysmt_Topology(item, atom_indices='all', structure_indices=0, get_miss
     former_chain_name = None
     aux_dict_chain = {}
 
-
-
     for atom_record in item.entry.coordinate.model[0].record:
 
         atom_id_array.append(atom_record.serial)
@@ -58,6 +57,8 @@ def to_molsysmt_Topology(item, atom_indices='all', structure_indices=0, get_miss
 
         chain_index_array.append(chain_index)
 
+        coordinates_array.append([atom_record.x, atom_record.y, atom_record.z])
+
     atom_id_array = np.array(atom_id_array, dtype=int)
     atom_name_array = np.array(atom_name_array, dtype=str)
     group_index_array = np.array(group_index_array, dtype=int)
@@ -69,6 +70,8 @@ def to_molsysmt_Topology(item, atom_indices='all', structure_indices=0, get_miss
     occupancy_array = np.array(occupancy_array, dtype=float)
     alternate_location_array = np.array(alternate_location_array, dtype=str)
 
+    coordinates_array = np.array(coordinates_array, dtype=float)
+
     alt_atom_indices = np.where(alternate_location_array!=' ')[0]
     aux_dict = {}
 
@@ -96,51 +99,72 @@ def to_molsysmt_Topology(item, atom_indices='all', structure_indices=0, get_miss
             chosen = np.argmax(alt_occupancy)
         chosen = same_atoms.pop(chosen)
         atoms_to_be_removed_with_alt_loc += same_atoms
-    
+
     atom_id_array = np.delete(atom_id_array, atoms_to_be_removed_with_alt_loc)
     atom_name_array = np.delete(atom_name_array, atoms_to_be_removed_with_alt_loc)
     group_index_array = np.delete(group_index_array, atoms_to_be_removed_with_alt_loc)
     chain_index_array = np.delete(chain_index_array, atoms_to_be_removed_with_alt_loc)
 
+    if len(atoms_to_be_removed_with_alt_loc):
+        coordinates_array = np.delete(coordinates_array, atoms_to_be_removed_with_alt_loc)
+
     n_atoms = atom_id_array.shape[0]
     n_groups = group_name_array.shape[0]
     n_chains = chain_name_array.shape[0]
 
-    tmp_item.reset_atoms(n_atoms=n_atoms)
-    tmp_item.reset_groups(n_groups=n_groups)
-    tmp_item.reset_chains(n_chains=n_chains)
+    tmp_item.topology.reset_atoms(n_atoms=n_atoms)
+    tmp_item.topology.reset_groups(n_groups=n_groups)
+    tmp_item.topology.reset_chains(n_chains=n_chains)
 
-    tmp_item.atoms.atom_id = atom_id_array
-    tmp_item.atoms.atom_name = atom_name_array
-    tmp_item.atoms.group_index = group_index_array
-    tmp_item.atoms.chain_index = chain_index_array
+    tmp_item.topology.atoms.atom_id = atom_id_array
+    tmp_item.topology.atoms.atom_name = atom_name_array
+    tmp_item.topology.atoms.group_index = group_index_array
+    tmp_item.topology.atoms.chain_index = chain_index_array
 
-    tmp_item.rebuild_atoms(redefine_ids=False, redefine_types=True)
+    tmp_item.topology.rebuild_atoms(redefine_ids=False, redefine_types=True)
 
-    tmp_item.groups.group_id = group_id_array
-    tmp_item.groups.group_name = group_name_array
+    tmp_item.topology.groups.group_id = group_id_array
+    tmp_item.topology.groups.group_name = group_name_array
 
-    tmp_item.rebuild_groups(redefine_ids=False, redefine_types=True)
+    tmp_item.topology.rebuild_groups(redefine_ids=False, redefine_types=True)
 
-    tmp_item.chains.chain_name = chain_name_array
+    tmp_item.topology.chains.chain_name = chain_name_array
 
-    tmp_item.rebuild_chains(redefine_ids=True, redefine_types=False )
+    tmp_item.topology.rebuild_chains(redefine_ids=True, redefine_types=False )
+
+    del(atom_id_array, atom_name_array,
+        group_index_array, group_id_array, group_name_array,
+        chain_index_array, chain_name_array,
+        occupancy_array, alternate_location_array, alt_atom_indices, aux_dict)
 
     if get_missing_bonds:
 
+        from molsysmt.build import get_missing_bonds as _get_missing_bonds
+        from molsysmt.pbc import get_box_from_lengths_and_angles
+
+        cryst1 = item.entry.crystallographic_and_coordinate_transformation.cryst1
+        box_lengths = puw.quantity([[cryst1.a, cryst1.b, cryst1.c]], 'angstroms')
+        box_angles = puw.quantity([[cryst1.alpha, cryst1.beta, cryst1.gamma]], 'degrees')
+        box = get_box_from_lengths_and_angles(box_lengths, box_angles, skip_digestion=True)
+
+        coordinates = puw.quantity(coordinates_array, 'angstroms')
+        tmp_item.structures.append(coordinates=coordinates, box=box)
+
+        del(coordinates_array, box, box_lengths, box_angles)
+
         bonds = _get_missing_bonds(tmp_item, skip_digestion=True)
         bonds = np.array(bonds)
-        tmp_item.reset_bonds(n_bonds=bonds.shape[0])
-        tmp_item.bonds.drop(['order', 'type'], axis=1, inplace=True)
-        tmp_item.bonds.atom1_index=bonds[:,0]
-        tmp_item.bonds.atom2_index=bonds[:,1]
+        tmp_item.topology,reset_bonds(n_bonds=bonds.shape[0])
+        tmp_item.topology.bonds.drop(['order', 'type'], axis=1, inplace=True)
+        tmp_item.topology.bonds.atom1_index=bonds[:,0]
+        tmp_item.topology.bonds.atom2_index=bonds[:,1]
 
-        tmp_item.rebuild_components()
-        tmp_item.rebuild_molecules()
-        tmp_item.rebuild_chains(redefine_ids=False, redefine_types=True)
-        tmp_item.rebuild_entities()
+        tmp_item.topology.rebuild_components()
+        tmp_item.topology.rebuild_molecules()
+        tmp_item.topology.rebuild_chains(redefine_ids=False, redefine_types=True)
+        tmp_item.topology.rebuild_entities()
 
-    tmp_item = tmp_item.extract(atom_indices=atom_indices, copy_if_all=False, skip_digestion=True)
+    tmp_item = tmp_item.topology.extract(atom_indices=atom_indices, copy_if_all=False, skip_digestion=True)
 
     return tmp_item
 
diff --git a/molsysmt/form/molsysmt_Topology/__init__.py b/molsysmt/form/molsysmt_Topology/__init__.py
index 62a949001..e51a38fcb 100644
--- a/molsysmt/form/molsysmt_Topology/__init__.py
+++ b/molsysmt/form/molsysmt_Topology/__init__.py
@@ -20,6 +20,9 @@
 from .set import *
 from .iterators import TopologyIterator
 
+from .add_bonds import add_bonds
+from .remove_bonds import remove_bonds
+
 from .to_string_amino_acids_3 import to_string_amino_acids_3
 from .to_string_amino_acids_1 import to_string_amino_acids_1
 from .to_string_pdb_text import to_string_pdb_text
diff --git a/molsysmt/form/molsysmt_Topology/add_bonds.py b/molsysmt/form/molsysmt_Topology/add_bonds.py
new file mode 100644
index 000000000..49938b25e
--- /dev/null
+++ b/molsysmt/form/molsysmt_Topology/add_bonds.py
@@ -0,0 +1,10 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+from molsysmt import pyunitwizard as puw
+import numpy as np
+
+@digest(form='molsysmt.Topology')
+def add_bonds(item, bonded_atom_pairs, skip_digestion=False):
+
+    item.add_bonds(bonded_atom_pairs, skip_digestion=True)
+
diff --git a/molsysmt/form/molsysmt_Topology/remove_bonds.py b/molsysmt/form/molsysmt_Topology/remove_bonds.py
new file mode 100644
index 000000000..2c32fd42c
--- /dev/null
+++ b/molsysmt/form/molsysmt_Topology/remove_bonds.py
@@ -0,0 +1,8 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+from molsysmt._private.variables import is_all
+
+@digest(form='molsysmt.Topology')
+def remove_bonds(item, bond_indices='all', skip_digestion=False):
+
+    return item.remove_bonds(bond_indices=bond_indices, skip_digestion=True)
diff --git a/molsysmt/form/openmm_Modeller/__init__.py b/molsysmt/form/openmm_Modeller/__init__.py
index 4c4f1bbe5..c6171de36 100644
--- a/molsysmt/form/openmm_Modeller/__init__.py
+++ b/molsysmt/form/openmm_Modeller/__init__.py
@@ -2,9 +2,9 @@
 form_type = 'class'
 form_info = ["", ""]
 
-piped_topological_attribute = None
-piped_structural_attribute = None
-piped_any_attribute = None
+piped_topological_attribute = 'molsysmt.Topology'
+piped_structural_attribute = 'molsysmt.Structures'
+piped_any_attribute = 'molsysmt.MolSys'
 
 from .is_form import is_form
 
diff --git a/molsysmt/native/topology.py b/molsysmt/native/topology.py
index df44d88f0..3b73ef109 100644
--- a/molsysmt/native/topology.py
+++ b/molsysmt/native/topology.py
@@ -334,8 +334,46 @@ def add_bonds(self, bonded_atom_pairs, skip_digestion=False):
         self.bonds._sort_bonds()
         self.bonds._remove_empty_columns()
 
+        self.rebuild_components()
+        self.rebuild_molecules()
+        self.rebuild_entities()
+
         del(df_concatenado, aux_bonds_dataframe)
 
+    def remove_bonds(self, bond_indices='all', skip_digestion=False):
+
+        if is_all(bond_indices):
+
+            self.bonds = Bonds_DataFrame(n_bonds=0)
+
+        else:
+
+            tmp_dataframe = self.bonds.drop(bond_indices)
+
+            n_bonds = bonded_atom_pairs.shape[0]
+
+            self.bonds = Bonds_DataFrame(n_bonds=n_bonds)
+            self.bonds.atom1_index=tmp_dataframe.atom1_index
+            self.bonds.atom2_index=tmp_dataframe.atom2_index
+
+            if 'order' in tmp_dataframe:
+                self.bonds['order'] = tmp_dataframe['order']
+            else:
+                del self.bonds['order']
+
+            if 'type' in tmp_dataframe:
+                self.bonds['type'] = tmp_dataframe['type']
+            else:
+                del self.bonds['type']
+
+            self.bonds._sort_bonds()
+
+            del(tmp_dataframe)
+
+        self.rebuild_components()
+        self.rebuild_molecules()
+        self.rebuild_entities()
+
 
     def add_missing_bonds(self, selection='all', syntax='MolSysMT', skip_digestion=False):
 
@@ -347,6 +385,10 @@ def add_missing_bonds(self, selection='all', syntax='MolSysMT', skip_digestion=F
 
         self.add_bonds(bonds, skip_digestion=True)
 
+        self.rebuild_components()
+        self.rebuild_molecules()
+        self.rebuild_entities()
+
     def rebuild_atoms(self, redefine_ids=True, redefine_types=True):
 
         if redefine_ids:
diff --git a/molsysmt/tests/basic/compare/test_compare_with_molsysmt_MolSys.py b/molsysmt/tests/basic/compare/test_compare_with_molsysmt_MolSys.py
index 34864c6f8..4c2ab222d 100644
--- a/molsysmt/tests/basic/compare/test_compare_with_molsysmt_MolSys.py
+++ b/molsysmt/tests/basic/compare/test_compare_with_molsysmt_MolSys.py
@@ -51,17 +51,17 @@ def test_compare_all_eq_3():
 
     if comparison['chain_index']!=True:
         output = False
-    if comparison['chain_name']!=False:
+    if comparison['chain_name']!=True:
         output = False
-    if comparison['chain_id']!=False:
+    if comparison['chain_id']!=True:
         output = False
-    if comparison['chain_type']!=False:
+    if comparison['chain_type']!=True:
         output = False
 
     if comparison['molecule_index']!=True:
         output = False
     if comparison['molecule_type']!=True:
-        output = False
+        output = True
 
     if comparison['bonded_atoms']!=True:
         output = False
diff --git a/molsysmt/tests/build/remove_bonds/test_remove_bonds_molsysmt_MolSys.py b/molsysmt/tests/build/remove_bonds/test_remove_bonds_molsysmt_MolSys.py
new file mode 100644
index 000000000..928716064
--- /dev/null
+++ b/molsysmt/tests/build/remove_bonds/test_remove_bonds_molsysmt_MolSys.py
@@ -0,0 +1,22 @@
+"""
+Unit and regression test for the is solvate module of the molsysmt package on molsysmt MolSys molecular
+systems.
+"""
+
+# Import package, test suite, and other packages as needed
+import pytest
+import molsysmt as msm
+from molsysmt import systems
+import numpy as np
+
+
+def test_remove_bonds_molsysmt_MolSys_1():
+
+    molsys = msm.convert(systems['T4 lysozyme L99A']['t4_lysozyme_L99A.h5msm'])
+    n_bonds_before = msm.get(molsys, n_bonds=True)
+    msm.build.remove_bonds(molsys)
+    n_bonds_after = msm.get(molsys, n_bonds=True)
+
+    assert n_bonds_before==2645
+    assert n_bonds_after==0
+
diff --git a/sandbox/Tests.ipynb b/sandbox/Tests.ipynb
index f0f62f83b..a0d10c277 100644
--- a/sandbox/Tests.ipynb
+++ b/sandbox/Tests.ipynb
@@ -28,7 +28,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "99da1f04440343a7af688013598d9547",
+       "model_id": "49a21aadf38949e584dcb9e5c69ba80e",
        "version_major": 2,
        "version_minor": 0
       },
@@ -56,77 +56,163 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "020376b7-c10e-4ef8-8b2a-fd04c900e938",
+   "id": "effbea99-d147-4c87-96bd-894cd565a116",
    "metadata": {},
    "outputs": [],
    "source": [
-    "molsys = msm.convert(systems['TcTIM']['1tcd.h5msm'], to_form='molsysmt.MolSys')"
+    "molsys = systems['T4 lysozyme L99A']['t4_lysozyme_L99A.h5msm']"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 5,
-   "id": "1fc79724-d236-45f6-a2e7-838a87c522c1",
+   "id": "aa0a59f4-725f-4d2e-b6d8-4f0a32e32726",
    "metadata": {},
    "outputs": [],
    "source": [
-    "view = msm.convert(molsys, to_form='nglview.NGLWidget')"
+    "molsys_ref = msm.convert(molsys, to_form='molsysmt.MolSys')"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 6,
-   "id": "cd4610ac-0e3b-455f-b0d1-1c809edbaca6",
+   "id": "f83375bd-b82c-47c0-8afa-e424960b39d2",
    "metadata": {},
    "outputs": [
     {
-     "ename": "NotImplementedFormError",
-     "evalue": "None",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
-      "File \u001b[0;32m/conda/miniconda3/envs/MolSysMT@uibcdf_3.10/lib/python3.10/site-packages/pyunitwizard/main.py:27\u001b[0m, in \u001b[0;36mget_form\u001b[0;34m(quantity_or_unit)\u001b[0m\n\u001b[1;32m     26\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 27\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdict_is_form\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;28;43mtype\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mquantity_or_unit\u001b[49m\u001b[43m)\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m     28\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n",
-      "\u001b[0;31mKeyError\u001b[0m: <class 'NoneType'>",
-      "\nDuring handling of the above exception, another exception occurred:\n",
-      "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
-      "File \u001b[0;32m/conda/miniconda3/envs/MolSysMT@uibcdf_3.10/lib/python3.10/site-packages/pyunitwizard/main.py:30\u001b[0m, in \u001b[0;36mget_form\u001b[0;34m(quantity_or_unit)\u001b[0m\n\u001b[1;32m     29\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 30\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdict_is_form\u001b[49m\u001b[43m[\u001b[49m\u001b[43mquantity_or_unit\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m     31\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n",
-      "\u001b[0;31mKeyError\u001b[0m: None",
-      "\nDuring handling of the above exception, another exception occurred:\n",
-      "\u001b[0;31mNotImplementedFormError\u001b[0m                   Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[6], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mmsm\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[43mview\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43melement\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43msystem\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mn_components\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:122\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    120\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m func(all_args[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mself\u001b[39m\u001b[38;5;124m'\u001b[39m], \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mfinal_args)\n\u001b[1;32m    121\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 122\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mfinal_args\u001b[49m\u001b[43m)\u001b[49m\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/basic/get.py:282\u001b[0m, in \u001b[0;36mget\u001b[0;34m(molecular_system, element, selection, structure_indices, mask, syntax, get_missing_bonds, output_type, skip_digestion, **kwargs)\u001b[0m\n\u001b[1;32m    280\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    281\u001b[0m         aux_get \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mgetattr\u001b[39m(_dict_modules[aux_form], \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mget_\u001b[39m\u001b[38;5;132;01m{\u001b[39;00min_attribute\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m_from_\u001b[39m\u001b[38;5;132;01m{\u001b[39;00melement\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m)\n\u001b[0;32m--> 282\u001b[0m         result \u001b[38;5;241m=\u001b[39m \u001b[43maux_get\u001b[49m\u001b[43m(\u001b[49m\u001b[43maux_item\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mdict_indices\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    284\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    286\u001b[0m     result \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:122\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    120\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m func(all_args[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mself\u001b[39m\u001b[38;5;124m'\u001b[39m], \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mfinal_args)\n\u001b[1;32m    121\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 122\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mfinal_args\u001b[49m\u001b[43m)\u001b[49m\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/form/nglview_NGLWidget/get_topological_attributes.py:4183\u001b[0m, in \u001b[0;36mget_n_components_from_system\u001b[0;34m(item, skip_digestion)\u001b[0m\n\u001b[1;32m   4180\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmolsysmt_Topology\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m get_n_components_from_system \u001b[38;5;28;01mas\u001b[39;00m aux_get\n\u001b[1;32m   4182\u001b[0m bonds_required \u001b[38;5;241m=\u001b[39m bonds_are_required_to_get_attribute(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mn_components\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msystem\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[0;32m-> 4183\u001b[0m tmp_item \u001b[38;5;241m=\u001b[39m \u001b[43mto_molsysmt_Topology\u001b[49m\u001b[43m(\u001b[49m\u001b[43mitem\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mget_missing_bonds\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbonds_required\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mskip_digestion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m   4184\u001b[0m output \u001b[38;5;241m=\u001b[39m aux_get(tmp_item, skip_digestion\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[1;32m   4186\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m output\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:52\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m     48\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m     49\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m     51\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m kwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mskip_digestion\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mFalse\u001b[39;00m):\n\u001b[0;32m---> 52\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     54\u001b[0m     \u001b[38;5;66;03m# Define caller\u001b[39;00m\n\u001b[1;32m     56\u001b[0m     caller \u001b[38;5;241m=\u001b[39m func\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__module__\u001b[39m\u001b[38;5;241m+\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m+\u001b[39mfunc\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__name__\u001b[39m\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/form/nglview_NGLWidget/to_molsysmt_Topology.py:10\u001b[0m, in \u001b[0;36mto_molsysmt_Topology\u001b[0;34m(item, atom_indices, get_missing_bonds, skip_digestion)\u001b[0m\n\u001b[1;32m      7\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mstring_pdb_text\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m to_molsysmt_Topology \u001b[38;5;28;01mas\u001b[39;00m string_pdb_text_to_molsysmt_Topology\n\u001b[1;32m      9\u001b[0m tmp_item \u001b[38;5;241m=\u001b[39m to_string_pdb_text(item, skip_digestion\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[0;32m---> 10\u001b[0m tmp_item \u001b[38;5;241m=\u001b[39m \u001b[43mstring_pdb_text_to_molsysmt_Topology\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtmp_item\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43matom_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     11\u001b[0m \u001b[43m                                                \u001b[49m\u001b[43mget_missing_bonds\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mget_missing_bonds\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mskip_digestion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m     13\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m tmp_item\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:52\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m     48\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m     49\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m     51\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m kwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mskip_digestion\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mFalse\u001b[39;00m):\n\u001b[0;32m---> 52\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     54\u001b[0m     \u001b[38;5;66;03m# Define caller\u001b[39;00m\n\u001b[1;32m     56\u001b[0m     caller \u001b[38;5;241m=\u001b[39m func\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__module__\u001b[39m\u001b[38;5;241m+\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m+\u001b[39mfunc\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__name__\u001b[39m\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/form/string_pdb_text/to_molsysmt_Topology.py:10\u001b[0m, in \u001b[0;36mto_molsysmt_Topology\u001b[0;34m(item, atom_indices, get_missing_bonds, skip_digestion)\u001b[0m\n\u001b[1;32m      7\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmolsysmt_PDBFileHandler\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m to_molsysmt_Topology \u001b[38;5;28;01mas\u001b[39;00m molsysmt_PDBFileHandler_to_molsysmt_Topology\n\u001b[1;32m      9\u001b[0m tmp_item \u001b[38;5;241m=\u001b[39m to_molsysmt_PDBFileHandler(item, skip_digestion\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[0;32m---> 10\u001b[0m tmp_item \u001b[38;5;241m=\u001b[39m \u001b[43mmolsysmt_PDBFileHandler_to_molsysmt_Topology\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtmp_item\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43matom_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     11\u001b[0m \u001b[43m                                                        \u001b[49m\u001b[43mget_missing_bonds\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mget_missing_bonds\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     12\u001b[0m \u001b[43m                                                        \u001b[49m\u001b[43mskip_digestion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m     14\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m tmp_item\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:52\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m     48\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m     49\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m     51\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m kwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mskip_digestion\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mFalse\u001b[39;00m):\n\u001b[0;32m---> 52\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     54\u001b[0m     \u001b[38;5;66;03m# Define caller\u001b[39;00m\n\u001b[1;32m     56\u001b[0m     caller \u001b[38;5;241m=\u001b[39m func\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__module__\u001b[39m\u001b[38;5;241m+\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m+\u001b[39mfunc\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__name__\u001b[39m\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/form/molsysmt_PDBFileHandler/to_molsysmt_Topology.py:131\u001b[0m, in \u001b[0;36mto_molsysmt_Topology\u001b[0;34m(item, atom_indices, structure_indices, get_missing_bonds, skip_digestion)\u001b[0m\n\u001b[1;32m    127\u001b[0m tmp_item\u001b[38;5;241m.\u001b[39mrebuild_chains(redefine_ids\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m, redefine_types\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m )\n\u001b[1;32m    129\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m get_missing_bonds:\n\u001b[0;32m--> 131\u001b[0m     bonds \u001b[38;5;241m=\u001b[39m \u001b[43m_get_missing_bonds\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtmp_item\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mskip_digestion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m    132\u001b[0m     bonds \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39marray(bonds)\n\u001b[1;32m    133\u001b[0m     tmp_item\u001b[38;5;241m.\u001b[39mreset_bonds(n_bonds\u001b[38;5;241m=\u001b[39mbonds\u001b[38;5;241m.\u001b[39mshape[\u001b[38;5;241m0\u001b[39m])\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:52\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m     48\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m     49\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m     51\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m kwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mskip_digestion\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mFalse\u001b[39;00m):\n\u001b[0;32m---> 52\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     54\u001b[0m     \u001b[38;5;66;03m# Define caller\u001b[39;00m\n\u001b[1;32m     56\u001b[0m     caller \u001b[38;5;241m=\u001b[39m func\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__module__\u001b[39m\u001b[38;5;241m+\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m+\u001b[39mfunc\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__name__\u001b[39m\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/build/get_missing_bonds.py:68\u001b[0m, in \u001b[0;36mget_missing_bonds\u001b[0;34m(molecular_system, threshold, selection, structure_indices, syntax, engine, with_templates, with_distances, sorted, skip_digestion)\u001b[0m\n\u001b[1;32m     48\u001b[0m     \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m     50\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m with_distances:\n\u001b[1;32m     51\u001b[0m \n\u001b[1;32m     52\u001b[0m     \u001b[38;5;66;03m# Protein:\u001b[39;00m\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     65\u001b[0m     \u001b[38;5;66;03m# Enlace C-C: aproximadamente 1.54 Å\u001b[39;00m\n\u001b[1;32m     66\u001b[0m     \u001b[38;5;66;03m# Enlace P-O: aproximadamente 1.61 Å\u001b[39;00m\n\u001b[0;32m---> 68\u001b[0m     contacts_heavy_atoms \u001b[38;5;241m=\u001b[39m \u001b[43mget_contacts\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmolecular_system\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mselection\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mheavy_atoms_not_water\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     69\u001b[0m \u001b[43m                                        \u001b[49m\u001b[43mthreshold\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mthreshold\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43moutput_type\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mpairs\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m     70\u001b[0m \u001b[43m                                        \u001b[49m\u001b[43moutput_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43matom\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpbc\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mskip_digestion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m     72\u001b[0m     bonds_distances \u001b[38;5;241m+\u001b[39m\u001b[38;5;241m=\u001b[39m contacts_heavy_atoms[\u001b[38;5;241m0\u001b[39m]\n\u001b[1;32m     74\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(h_atoms_not_water):\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:52\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m     48\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m     49\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m     51\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m kwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mskip_digestion\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mFalse\u001b[39;00m):\n\u001b[0;32m---> 52\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     54\u001b[0m     \u001b[38;5;66;03m# Define caller\u001b[39;00m\n\u001b[1;32m     56\u001b[0m     caller \u001b[38;5;241m=\u001b[39m func\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__module__\u001b[39m\u001b[38;5;241m+\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m+\u001b[39mfunc\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__name__\u001b[39m\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/structure/get_contacts.py:31\u001b[0m, in \u001b[0;36mget_contacts\u001b[0;34m(molecular_system, selection, center_of_atoms, weights, structure_indices, selection_2, center_of_atoms_2, weights_2, structure_indices_2, threshold, pbc, syntax, output_type, output_indices, skip_digestion)\u001b[0m\n\u001b[1;32m     28\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m     29\u001b[0m     atom_indices_2 \u001b[38;5;241m=\u001b[39m select(molecular_system, selection\u001b[38;5;241m=\u001b[39mselection_2, syntax\u001b[38;5;241m=\u001b[39msyntax)\n\u001b[0;32m---> 31\u001b[0m all_dists \u001b[38;5;241m=\u001b[39m \u001b[43mget_distances\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmolecular_system\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmolecular_system\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mselection\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     32\u001b[0m \u001b[43m            \u001b[49m\u001b[43mcenter_of_atoms\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcenter_of_atoms\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mweights\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mweights\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstructure_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstructure_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     33\u001b[0m \u001b[43m            \u001b[49m\u001b[43mselection_2\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom_indices_2\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcenter_of_atoms_2\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcenter_of_atoms_2\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mweights_2\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mweights_2\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     34\u001b[0m \u001b[43m            \u001b[49m\u001b[43mstructure_indices_2\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstructure_indices_2\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpbc\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mpbc\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     36\u001b[0m length_units \u001b[38;5;241m=\u001b[39m puw\u001b[38;5;241m.\u001b[39mget_unit(all_dists)\n\u001b[1;32m     37\u001b[0m threshold \u001b[38;5;241m=\u001b[39m puw\u001b[38;5;241m.\u001b[39mget_value(threshold, to_unit\u001b[38;5;241m=\u001b[39mlength_units)\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:122\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    120\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m func(all_args[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mself\u001b[39m\u001b[38;5;124m'\u001b[39m], \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mfinal_args)\n\u001b[1;32m    121\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 122\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mfinal_args\u001b[49m\u001b[43m)\u001b[49m\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/structure/get_distances.py:84\u001b[0m, in \u001b[0;36mget_distances\u001b[0;34m(molecular_system, selection, structure_indices, center_of_atoms, weights, molecular_system_2, selection_2, structure_indices_2, center_of_atoms_2, weights_2, pairs, pbc, engine, syntax)\u001b[0m\n\u001b[1;32m     80\u001b[0m             in_memory \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[1;32m     82\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m in_memory:\n\u001b[0;32m---> 84\u001b[0m     output \u001b[38;5;241m=\u001b[39m \u001b[43m_get_distances_in_memory\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmolecular_system\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     85\u001b[0m \u001b[43m            \u001b[49m\u001b[43mselection\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom_indices\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstructure_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstructure_indices\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcenter_of_atoms\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcenter_of_atoms\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mweights\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mweights\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     86\u001b[0m \u001b[43m            \u001b[49m\u001b[43mmolecular_system_2\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmolecular_system_2\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mselection_2\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom_indices_2\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstructure_indices_2\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstructure_indices_2\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     87\u001b[0m \u001b[43m            \u001b[49m\u001b[43mcenter_of_atoms_2\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcenter_of_atoms_2\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mweights_2\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mweights_2\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpairs\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mpairs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpbc\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mpbc\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msyntax\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msyntax\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     89\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m     91\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m NotImplementedMethodError\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/structure/get_distances.py:171\u001b[0m, in \u001b[0;36m_get_distances_in_memory\u001b[0;34m(molecular_system, selection, structure_indices, center_of_atoms, weights, molecular_system_2, selection_2, structure_indices_2, center_of_atoms_2, weights_2, pairs, pbc, aux_dict, syntax)\u001b[0m\n\u001b[1;32m    167\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m pairs:\n\u001b[1;32m    169\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m coordinates_2 \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m--> 171\u001b[0m         coordinates, length_unit \u001b[38;5;241m=\u001b[39m \u001b[43mpuw\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_value_and_unit\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcoordinates\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    173\u001b[0m         \u001b[38;5;28;01mif\u001b[39;00m pbc:\n\u001b[1;32m    174\u001b[0m             box \u001b[38;5;241m=\u001b[39m get(molecular_system, element\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msystem\u001b[39m\u001b[38;5;124m'\u001b[39m, structure_indices\u001b[38;5;241m=\u001b[39mstructure_indices, box\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n",
-      "File \u001b[0;32m/conda/miniconda3/envs/MolSysMT@uibcdf_3.10/lib/python3.10/site-packages/pyunitwizard/main.py:180\u001b[0m, in \u001b[0;36mget_value_and_unit\u001b[0;34m(quantity, to_unit, to_form, parser, standardized)\u001b[0m\n\u001b[1;32m    177\u001b[0m     quantity \u001b[38;5;241m=\u001b[39m standardize(quantity)\n\u001b[1;32m    178\u001b[0m     to_unit \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[0;32m--> 180\u001b[0m value \u001b[38;5;241m=\u001b[39m \u001b[43mconvert\u001b[49m\u001b[43m(\u001b[49m\u001b[43mquantity\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mto_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mto_unit\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mparser\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mparser\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mto_type\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mvalue\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m    181\u001b[0m unit \u001b[38;5;241m=\u001b[39m convert(quantity, to_unit\u001b[38;5;241m=\u001b[39mto_unit, to_form\u001b[38;5;241m=\u001b[39mto_form, parser\u001b[38;5;241m=\u001b[39mparser, to_type\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124munit\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m    183\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m value, unit\n",
-      "File \u001b[0;32m/conda/miniconda3/envs/MolSysMT@uibcdf_3.10/lib/python3.10/site-packages/pyunitwizard/main.py:547\u001b[0m, in \u001b[0;36mconvert\u001b[0;34m(quantity_or_unit, to_unit, to_form, parser, to_type)\u001b[0m\n\u001b[1;32m    522\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\" Converts a quantity or unit to a different unit and/or to a different\u001b[39;00m\n\u001b[1;32m    523\u001b[0m \u001b[38;5;124;03m    form and/or type. \u001b[39;00m\n\u001b[1;32m    524\u001b[0m \n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    543\u001b[0m \u001b[38;5;124;03m        be a float or a numpy array.\u001b[39;00m\n\u001b[1;32m    544\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m    545\u001b[0m output \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[0;32m--> 547\u001b[0m form_in \u001b[38;5;241m=\u001b[39m \u001b[43mget_form\u001b[49m\u001b[43m(\u001b[49m\u001b[43mquantity_or_unit\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    548\u001b[0m to_form \u001b[38;5;241m=\u001b[39m digest_to_form(to_form, form_in)\n\u001b[1;32m    549\u001b[0m parser \u001b[38;5;241m=\u001b[39m digest_parser(parser)\n",
-      "File \u001b[0;32m/conda/miniconda3/envs/MolSysMT@uibcdf_3.10/lib/python3.10/site-packages/pyunitwizard/main.py:32\u001b[0m, in \u001b[0;36mget_form\u001b[0;34m(quantity_or_unit)\u001b[0m\n\u001b[1;32m     30\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m dict_is_form[quantity_or_unit]\n\u001b[1;32m     31\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[0;32m---> 32\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m NotImplementedFormError(\u001b[38;5;28mtype\u001b[39m(quantity_or_unit))\n",
-      "\u001b[0;31mNotImplementedFormError\u001b[0m: None"
-     ]
+     "data": {
+      "text/plain": [
+       "2645"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "msm.get(molsys_ref, n_bonds=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "9dc3125c-8c88-458a-839d-8e1fb5f08a94",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.build.remove_bonds(molsys_ref)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "0f2e011a-e04a-4eab-98f1-df632c2cc111",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
     }
    ],
    "source": [
-    "msm.get(view, element='system', n_components=True)"
+    "msm.get(molsys_ref, n_bonds=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2bfbe476-e055-4ba0-aaf4-7acefa3af748",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.build.get_missing_bonds(molsys_ref)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a03e5920-0979-4447-b51e-0bd06c02a49b",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "85eb504d-6b8c-49dd-b907-2badaffb61a9",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "947878fd-4868-4ead-8e87-6b416c1803be",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "60db1fdc-7ed5-4f3a-9da5-984952bb8a65",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "molsys = msm.convert(molsys, to_form='nglview.NGLWidget')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0a5d8789-a163-444d-a08c-7f04cc82e44e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "n_molecules_ref, n_structures_ref = msm.get(molsys_ref, element='system', n_molecules=True, n_structures=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cdc1cceb-f9d2-4826-a80d-677a799eb0be",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.convert(molsys, to_form='molsysmt.Topology', get_missing_bonds=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6db05926-2da0-408e-a18e-3a7c9a24cf6a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.get(molsys, element='system', n_molecules=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6edaa896-669c-4926-adaf-804cc59518da",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "n_molecules, n_structures = msm.get(molsys, element='system', n_molecules=True, n_structures=True)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "59e18040-4290-4bed-8bf3-1021d2a4234a",
+   "id": "0a294fc7-05e2-4a73-b6e7-b4cfd181a4bb",
    "metadata": {},
    "outputs": [],
    "source": []