diff --git a/build/lib/pycofbuilder/__init__.py b/build/lib/pycofbuilder/__init__.py
index 41a33dea..b9c040ca 100644
--- a/build/lib/pycofbuilder/__init__.py
+++ b/build/lib/pycofbuilder/__init__.py
@@ -43,6 +43,6 @@
 
 __author__ = "Felipe Lopes de Oliveira"
 __license__ = "MIT"
-__version__ = '0.0.6'
+__version__ = '0.0.8'
 __email__ = "felipe.lopes@nano.ufrj.br"
 __status__ = "Development"
diff --git a/build/lib/pycofbuilder/data/__pycache__/__init__.cpython-311.pyc b/build/lib/pycofbuilder/data/__pycache__/__init__.cpython-311.pyc
new file mode 100644
index 00000000..a9b73b2c
Binary files /dev/null and b/build/lib/pycofbuilder/data/__pycache__/__init__.cpython-311.pyc differ
diff --git a/build/lib/pycofbuilder/data/__pycache__/topology.cpython-311.pyc b/build/lib/pycofbuilder/data/__pycache__/topology.cpython-311.pyc
index 3a666390..95c8d283 100644
Binary files a/build/lib/pycofbuilder/data/__pycache__/topology.cpython-311.pyc and b/build/lib/pycofbuilder/data/__pycache__/topology.cpython-311.pyc differ
diff --git a/build/lib/pycofbuilder/data/__pycache__/topology.cpython-39.pyc b/build/lib/pycofbuilder/data/__pycache__/topology.cpython-39.pyc
new file mode 100644
index 00000000..29265257
Binary files /dev/null and b/build/lib/pycofbuilder/data/__pycache__/topology.cpython-39.pyc differ
diff --git a/build/lib/pycofbuilder/framework.py b/build/lib/pycofbuilder/framework.py
index 20376e51..958802de 100644
--- a/build/lib/pycofbuilder/framework.py
+++ b/build/lib/pycofbuilder/framework.py
@@ -33,11 +33,11 @@
                                 rotation_matrix_from_vectors,
                                 unit_vector,
                                 angle,
-                                get_framework_symm_text)
+                                get_framework_symm_text,
+                                get_bonds)
 
 # Import pycofbuilder io_tools
-from pycofbuilder.io_tools import (save_json,
-                                   save_chemjson,
+from pycofbuilder.io_tools import (save_chemjson,
                                    save_cif,
                                    save_xyz,
                                    save_turbomole,
@@ -120,6 +120,7 @@ def __init__(self, name: str = None, **kwargs):
         self.symm_tol = kwargs.get('symm_tol', 0.1)
         self.angle_tol = kwargs.get('angle_tol', 0.5)
         self.dist_threshold = kwargs.get('dist_threshold', 0.8)
+        self.bond_threshold = kwargs.get('bond_threshold', 1.3)
 
         self.bb1_name = None
         self.bb2_name = None
@@ -132,6 +133,7 @@ def __init__(self, name: str = None, **kwargs):
         self.atom_labels = []
         self.cellMatrix = np.eye(3)
         self.cellParameters = np.array([1, 1, 1, 90, 90, 90]).astype(float)
+        self.bonds = []
 
         self.lattice_sgs = None
         self.space_group = None
@@ -368,9 +370,24 @@ def from_building_blocks(self,
 
         result = net_build_dict[net](bb1, bb2, stacking, **kwargs)
 
+        structure = Structure(
+            self.cellMatrix,
+            self.atom_types,
+            self.atom_pos,
+            coords_are_cartesian=True,
+            site_properties={'source': self.atom_labels}
+        )
+
+        self.bonds = get_bonds(structure, self.bond_threshold)
+
         return result
 
-    def save(self, fmt: str = 'cif', supercell: list = [1, 1, 1], save_dir=None, primitive=False) -> None:
+    def save(self, 
+             fmt: str = 'cif',
+             supercell: list = [1, 1, 1],
+             save_dir=None,
+             primitive=False,
+             save_bonds=True) -> None:
         '''
         Save the structure in a specif file format.
 
@@ -392,7 +409,6 @@ def save(self, fmt: str = 'cif', supercell: list = [1, 1, 1], save_dir=None, pri
         '''
 
         save_dict = {
-            'json': save_json,
             'cjson': save_chemjson,
             'cif': save_cif,
             'xyz': save_xyz,
@@ -422,6 +438,11 @@ def save(self, fmt: str = 'cif', supercell: list = [1, 1, 1], save_dir=None, pri
 
         final_structure = structure.make_supercell(supercell, in_place=False)
 
+        if save_bonds:
+            bonds = get_bonds(final_structure, self.bond_threshold)
+        else:
+            bonds = []
+
         structure_dict = final_structure.as_dict()
 
         cell = structure_dict['lattice']['matrix']
@@ -440,7 +461,8 @@ def save(self, fmt: str = 'cif', supercell: list = [1, 1, 1], save_dir=None, pri
                        cell=cell,
                        atom_types=atom_types,
                        atom_labels=atom_labels,
-                       atom_pos=atom_pos)
+                       atom_pos=atom_pos,
+                       bonds=bonds)
 
 # --------------- Net creation methods -------------------------- #
 
diff --git a/build/lib/pycofbuilder/io_tools.py b/build/lib/pycofbuilder/io_tools.py
index e0d79d2c..3cf4c8f0 100644
--- a/build/lib/pycofbuilder/io_tools.py
+++ b/build/lib/pycofbuilder/io_tools.py
@@ -237,28 +237,39 @@ def read_cif(path, file_name):
         return None
 
 
-def save_xsf(path: str = None,
-             file_name: str = None,
-             cell: np.ndarray = np.eye(3),
-             atom_types: list = None,
-             atom_pos: list = None,
-             atom_labels: list = None,
-             frac_coords: bool = False):
+def save_xsf(path: str,
+             file_name: str,
+             cell: list,
+             atom_types: list,
+             atom_labels: list,
+             atom_pos: list,
+             atom_charges: list = None,
+             bonds: list = None,
+             bond_orders: list = None,
+             frac_coords=False):
     """
     Save a file in format `.xsf` on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.xsf` extention.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom label.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     file_name = file_name.split('.')[0]
@@ -290,31 +301,39 @@ def save_xsf(path: str = None,
     xsf_file.close()
 
 
-def save_pqr(path: str = None,
-             file_name: str = None,
-             cell: np.ndarray = np.eye(3),
-             atom_types: list = None,
-             atom_pos: list = None,
-             atom_labels: list = None,
-             partial_charges: list = None,
-             frac_coords: bool = False):
+def save_pqr(path: str,
+             file_name: str,
+             cell: list,
+             atom_types: list,
+             atom_labels: list,
+             atom_pos: list,
+             atom_charges: list = None,
+             bonds: list = None,
+             bond_orders: list = None,
+             frac_coords=False):
     """
     Save a file in format `.pqr` on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.pqr` extention.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom partial charges.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
-    partial_charges: list
+    atom_charges : list
         List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     file_name = file_name.split('.')[0]
@@ -337,7 +356,7 @@ def save_pqr(path: str = None,
                                                                                         cell[4],
                                                                                         cell[5]))
 
-    if partial_charges is None:
+    if atom_charges is None:
         atom_line = 'ATOM   {:>4} {:>2}   MOL A   0    {:>8.3f}{:>8.3f}{:>8.3f}   {:>15}\n'
         for i in range(len(atom_pos)):
             pqr_file.write(atom_line.format(i + 1,
@@ -354,34 +373,53 @@ def save_pqr(path: str = None,
                                             atom_pos[i][0],
                                             atom_pos[i][1],
                                             atom_pos[i][2],
-                                            partial_charges[i],
+                                            atom_charges[i],
                                             atom_types[i]))
 
+    if bonds and not bond_orders:
+        bond_orders = [1 for i in range(len(bonds))]
+
+    if bonds:
+        for i in range(len(bonds)):
+            for j in range(bond_orders[i]):
+                pqr_file.write(f'CONECT {bonds[i][0] + 1:4} {bonds[i][1] + 1:4}\n')
+
     pqr_file.close()
 
 
-def save_pdb(path: str = None,
-             file_name: str = None,
-             cell: np.ndarray = np.eye(3),
-             atom_types: list = None,
-             atom_pos: list = None,
-             atom_labels: list = None,
-             frac_coords: bool = False):
+def save_pdb(path: str,
+             file_name: str,
+             cell: list,
+             atom_types: list,
+             atom_labels: list,
+             atom_pos: list,
+             atom_charges: list = None,
+             bonds: list = None,
+             bond_orders: list = None,
+             frac_coords=False):
     """
     Save a file in format `.pdb` on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.pdb` extention.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom partial charges.
+        List of strings containing containg the N atom labels
     atom_pos : list
-        Nx3 array contaning the atoms coordinates in cartesian form.
+        Nx3 array contaning the atoms coordinates.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     file_name = file_name.split('.')[0]
@@ -414,37 +452,54 @@ def save_pdb(path: str = None,
                                         atom_pos[i][2],
                                         atom_types[i]))
 
-    pdb_file.close()
+    if bonds and not bond_orders:
+        bond_orders = [1 for i in range(len(bonds))]
+
+    if bonds:
+        for i in range(len(bonds)):
+            for j in range(bond_orders[i]):
+                pdb_file.write(f'CONECT {bonds[i][0] + 1:4} {bonds[i][1] + 1:4}\n')
 
+    pdb_file.close()
 
-def save_gjf(path: str = None,
-             file_name: str = None,
-             cell: list = None,
-             atom_types: list = None,
-             atom_pos: list = None,
-             atom_labels: list = None,
-             frac_coords: bool = False,
-             text: str = 'opt pm6'):
 
+def save_gjf(path: str,
+             file_name: str,
+             cell: list,
+             atom_types: list,
+             atom_labels: list,
+             atom_pos: list,
+             atom_charges: list = None,
+             bonds: list = None,
+             bond_orders: list = None,
+             frac_coords=False,
+             header: str = 'opt pm6'):
     """
-    Save a file in format `.gjf` on the `path`.
+    Save a file in format `.pqr` on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.gjf` extention.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom partial charges.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
-    text : str
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
+    header : str
         Parameters for Gaussian calculations.
     """
-
     if len(cell) == 6:
         cell = cellpar_to_cell(cell)
 
@@ -457,7 +512,7 @@ def save_gjf(path: str = None,
 
     temp_file = open(os.path.join(path, file_name + '.gjf'), 'w')
     temp_file.write(f'%chk={file_name}.chk \n')
-    temp_file.write(f'# {text}\n')
+    temp_file.write(f'# {header}\n')
     temp_file.write('\n')
     temp_file.write(f'{file_name}\n')
     temp_file.write('\n')
@@ -476,28 +531,39 @@ def save_gjf(path: str = None,
     temp_file.close()
 
 
-def save_xyz(path: str = None,
-             file_name: str = None,
-             cell: np.ndarray = np.eye(3),
-             atom_types: list = None,
-             atom_pos: list = None,
-             atom_labels: list = None,
-             frac_coords: bool = False):
+def save_xyz(path: str,
+             file_name: str,
+             cell: list,
+             atom_types: list,
+             atom_labels: list,
+             atom_pos: list,
+             atom_charges: list = None,
+             bonds: list = None,
+             bond_orders: list = None,
+             frac_coords=False):
     """
     Save a file in format `.xyz` on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.xyz` extention.
+        Name of the file. Does not neet to contain the extention.
+    cell : numpy array
+        Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
     atom_types : list
         List of strings containing containg the N atom types
+    atom_label : list
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
-    cell : numpy array
-        Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     if len(cell) == 3:
@@ -527,27 +593,39 @@ def save_xyz(path: str = None,
     temp_file.close()
 
 
-def save_turbomole(path: str = None,
-                   file_name: str = None,
-                   cell: np.ndarray = np.eye(3),
-                   atom_types: list = None,
-                   atom_pos: list = None,
-                   atom_labels: list = None,
-                   frac_coords: bool = False):
-    """Save the structure in Turbomole .coord format
+def save_turbomole(path: str,
+                   file_name: str,
+                   cell: list,
+                   atom_types: list,
+                   atom_labels: list,
+                   atom_pos: list,
+                   atom_charges: list = None,
+                   bonds: list = None,
+                   bond_orders: list = None,
+                   frac_coords=False):
+    """
+    Save the structure in Turbomole .coord format on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.coord` extention.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom partial charges.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     if cell.shape == (3, 3):
@@ -575,29 +653,39 @@ def save_turbomole(path: str = None,
         temp_file.write('$end\n')
 
 
-def save_vasp(path: str = None,
-              file_name: str = None,
-              cell: np.ndarray = np.eye(3),
-              atom_types: list = None,
-              atom_pos: list = None,
-              atom_labels: list = None,
-              frac_coords: bool = False):
-    """Save the structure in VASP .vasp format
+def save_vasp(path: str,
+              file_name: str,
+              cell: list,
+              atom_types: list,
+              atom_labels: list,
+              atom_pos: list,
+              atom_charges: list = None,
+              bonds: list = None,
+              bond_orders: list = None,
+              frac_coords=False):
+    """
+    Save the structure in VASP .vasp format on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.vasp` extention.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom partial charges.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
-    coords_are_cartesian : bool
-        If True, the coordinates are in cartesian coordinates.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     if cell.shape == 6:
@@ -634,15 +722,19 @@ def save_vasp(path: str = None,
                                                                             atom_types[i]))
 
 
-def save_qe(path: str = None,
-            file_name: str = None,
-            cell: np.ndarray = np.eye(3),
-            atom_types: list = None,
-            atom_pos: list = None,
-            atom_labels: list = None,
-            frac_coords: bool = False,
-            calc_type: str = 'scf'):
-    '''
+def save_qe(path: str,
+            file_name: str,
+            cell: list,
+            atom_types: list,
+            atom_labels: list,
+            atom_pos: list,
+            atom_charges: list = None,
+            bonds: list = None,
+            bond_orders: list = None,
+            frac_coords=False,
+            calc_type: str = 'scf',
+            kspacing: float = 0.3):
+    """
     Save the structure in Quantum Espresso .pwscf format.
 
     The `input_dict` can be used to specify the input parameters for the
@@ -657,20 +749,28 @@ def save_qe(path: str = None,
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.pwscf` extention.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom labels.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
     frac_coords : bool
         If True, the coordinates are in fractional coordinates.
     calc_type : str
-       Type of pw.x calculation. Can be 'scf', 'nscf', 'bands', and 'vc-relax'.
-    '''
+        Type of calculation. Can be 'scf', 'vc-relax', 'relax', 'md', 'vc-md', 'vc-tddft', 'tddft'.
+    kspacing : float
+        Kpoints spacing in 1/Angstrom.
+    """
 
     if len(cell) == 6:
         cell_matrix = cellpar_to_cell(cell)
@@ -721,7 +821,7 @@ def save_qe(path: str = None,
     # If the kpoints grid is not specified, calculate it automatically
     if 'k_points' not in input_dict.keys():
         if 'kspacing' not in input_dict.keys():
-            input_dict['kspacing'] = 0.3
+            input_dict['kspacing'] = kspacing
         input_dict['kpoints'] = get_kgrid(cell_matrix, input_dict['kspacing'])
 
     with open(os.path.join(path, file_name + '.pwscf'), 'w') as f:
@@ -809,68 +909,38 @@ def convert_cif_2_qe(out_path, file_name):
             k_dist=0.3)
 
 
-def save_json(path, file_name, cell, atom_types, atom_pos, atom_labels, frac_coords=False):
+def save_chemjson(path: str,
+                  file_name: str,
+                  cell: list,
+                  atom_types: list,
+                  atom_labels: list,
+                  atom_pos: list,
+                  atom_charges: list = None,
+                  bonds: list = None,
+                  frac_coords=False):
     """
     Save a file in format `.json` on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.cif` extention.
-    atom_label : list
-        List of strings containing containg the N atom partial charges.
-    atom_pos : list
-        Nx3 array contaning the atoms coordinates.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
-    """
-
-    file_name = file_name.split('.')[0]
-
-    cof_json = create_COF_json(file_name)
-
-    if len(cell) == 3:
-        cell_par = cell_to_cellpar(np.array(cell)).tolist()
-        cell_matrix = np.array(cell).astype(float).tolist()
-
-    if len(cell) == 6:
-        cell_par = np.array(cell).astype(float).tolist()
-        cell_matrix = cellpar_to_cell(cell_par).tolist()
-
-    cof_json['system']['geo_opt'] = False
-
-    cof_json['geometry']['cell_matrix'] = cell_matrix
-    cof_json['geometry']['cell_parameters'] = cell_par
-    cof_json['geometry']['atom_labels'] = list(atom_types)
-    cof_json['geometry']['atom_pos'] = list(atom_pos)
-
-    write_json(path, file_name, cof_json)
-
-
-def save_chemjson(path,
-                  file_name,
-                  cell,
-                  atom_types,
-                  atom_pos,
-                  atom_labels,
-                  frac_coords=False):
-    """
-    Save a file in format `.json` on the `path`.
-
-    Parameters
-    ----------
-    path : str
-        Path to the file.
-    file_name : str
-        Name of the file. Does not neet to contain the `.cif` extention.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom partial charges.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
-    cell : numpy array
-        Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     file_name = file_name.split('.')[0]
@@ -887,18 +957,20 @@ def save_chemjson(path,
                                       AtomTypes=atom_types,
                                       AtomPositions=atom_pos,
                                       AtomLabels=atom_labels,
-                                      CartesianPositions=not frac_coords)
+                                      CartesianPositions=not frac_coords,
+                                      BondIndexes=bonds)
 
     write_json(path, file_name, chemJSON)
 
 
-def save_cif(path,
-             file_name,
-             cell,
-             atom_types,
-             atom_pos,
-             atom_labels=None,
-             partial_charges=False,
+def save_cif(path: str,
+             file_name: str,
+             cell: list,
+             atom_types: list,
+             atom_labels: list,
+             atom_pos: list,
+             atom_charges: list = None,
+             bonds: list = None,
              frac_coords=False):
     """
     Save a file in format `.cif` on the `path`.
@@ -906,15 +978,23 @@ def save_cif(path,
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.cif` extention.
+        Name of the file. Does not neet to contain the extention.
+    cell : numpy array
+        Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom partial charges.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
-    cell : numpy array
-        Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     file_name = file_name.split('.')[0]
@@ -932,7 +1012,7 @@ def save_cif(path,
 
 _audit_creation_date     {date.today().strftime("%Y-%d-%m")}
 _audit_creation_method   pyCOFBuilder
-_audit_author_name       'Felipe Lopes de Oliveira'
+_audit_author_name       '{os.getlogin()}'
 
 _chemical_name_common                  '{file_name}'
 _cell_length_a                          {a:>10.6f}
@@ -956,7 +1036,7 @@ def save_cif(path,
    _atom_site_fract_z
 """
 
-    if partial_charges is not False:
+    if atom_charges:
         cif_text += '   _atom_site_charge\n'
 
     if frac_coords is False:
@@ -966,22 +1046,33 @@ def save_cif(path,
 
     for i in range(len(atom_pos)):
         u, v, w = atom_pos[i][0], atom_pos[i][1], atom_pos[i][2]
-        if partial_charges is not False:
-            cif_text += '{:<7}    {} {:>15.9f} {:>15.9f} {:>15.9f} {:>10.5f}\n'.format(
+        if atom_charges:
+            atom_labels[i] = f"{atom_types[i]}{str(i + 1)}_{atom_labels[i]}"
+            cif_text += '{:<15}    {} {:>15.9f} {:>15.9f} {:>15.9f} {:>10.5f}\n'.format(
                 f"{atom_types[i]}{str(i + 1)}_{atom_labels[i]}",
                 atom_types[i],
                 u,
                 v,
                 w,
-                partial_charges[i])
+                atom_charges[i])
         else:
-            cif_text += '{:<7}    {} {:>15.9f} {:>15.9f} {:>15.9f}\n'.format(
+            atom_labels[i] = f"{atom_types[i]}{str(i + 1)}_{atom_labels[i]}"
+            cif_text += '{:<15}    {} {:>15.9f} {:>15.9f} {:>15.9f}\n'.format(
                 f"{atom_types[i]}{str(i + 1)}_{atom_labels[i]}",
                 atom_types[i],
                 u,
                 v,
                 w)
 
+    if bonds:
+        cif_text += '\nloop_\n'
+        cif_text += '_geom_bond_atom_site_label_1\n'
+        cif_text += '_geom_bond_atom_site_label_2\n'
+        cif_text += '_geom_bond_distance\n'
+
+        for bond in bonds:
+            cif_text += f'{atom_labels[bond[0]]:10} {atom_labels[bond[1]]:10} {bond[2]:.5f}\n'
+
     # Write cif_text to file
     cif_file = open(os.path.join(path, file_name + '.cif'), 'w')
     cif_file.write(cif_text)
@@ -1189,10 +1280,10 @@ def create_structure_CJSON(StructureName: str,
                            CellParameters: list = None,
                            CellMatrix: list = None,
                            AtomTypes: list = None,
+                           AtomLabels: list = [],
                            AtomPositions: list = None,
                            CartesianPositions: bool = False,
-                           AtomLabels: list = [],
-                           Bonds: list = [],
+                           BondIndexes: list = [],
                            BondOrders: list = [],
                            PartialCharges: dict = {},
                            ) -> dict:
@@ -1208,11 +1299,20 @@ def create_structure_CJSON(StructureName: str,
         List with the cell parameters.
     CellMatrix : list
         List with the cell matrix. Optional
+    AtomTypes : list
+        List with the atom types.
     AtomLabels : list
         List with the atom labels.
     AtomPositions : list
         List with the atom positions.
-
+    CartesianPositions : bool
+        If True, the coordinates are in cartesian coordinates.
+    BondIndexes : list
+        List with the bonds indexes and bond length.
+    BondOrders : list
+        List with the bond orders.
+    PartialCharges : dict
+        Dictionary with the partial charges.
     """
 
     chemJSON = create_empty_CJSON()
@@ -1252,10 +1352,16 @@ def create_structure_CJSON(StructureName: str,
         CartPosition = np.array([np.dot(V_cart, atom) for atom in AtomPositions]).flatten().tolist()
         chemJSON['atoms']['coords']['3d'] = CartPosition
 
-    chemJSON['atoms']['PartialCharges'] = PartialCharges
+    if PartialCharges != {}:
+        chemJSON['atoms']['PartialCharges'] = PartialCharges
+
+    bond_indexes = [[i[0], i[1]] for i in BondIndexes]
+    bond_indexes = [item for row in bond_indexes for item in row]
+
+    bond_orders = BondOrders if BondOrders != [] else [1] * len(bond_indexes)
 
-    chemJSON['bonds']['connections']['index'] = Bonds
-    chemJSON['bonds']['order'] = BondOrders
+    chemJSON['bonds']['connections']['index'] = bond_indexes
+    chemJSON['bonds']['order'] = bond_orders
 
     return chemJSON
 
diff --git a/build/lib/pycofbuilder/tools.py b/build/lib/pycofbuilder/tools.py
index 14f74f17..95563552 100644
--- a/build/lib/pycofbuilder/tools.py
+++ b/build/lib/pycofbuilder/tools.py
@@ -1004,3 +1004,65 @@ def cell_to_ibrav(cell):
                   'celldm(6)': np.cos(np.deg2rad(gamma))}
 
     return celldm
+
+
+def is_bonded(atom1: str, atom2: str, dist: float, cutoff: float = 1.3):
+    """
+    Determine if two atoms are bonded based on the distance between them.
+    Two atoms are considered bonded if the distance between them is less than
+    the sum of their covalent radii multiplied by a cutoff factor.
+
+    Parameters
+    ----------
+    atom1 : str
+        Label of the first atom
+    atom2 : str
+        Label of the second atom
+    dist : float
+        Distance between the two atoms
+    cutoff : float
+        Cutoff factor for the covalent radii. Default: 1.3
+    """
+
+    periodic_table = elements_dict(property='covalent_radius')
+
+    # Get the covalent radii of the two atoms
+    cr_1 = periodic_table[atom1]
+    cr_2 = periodic_table[atom2]
+
+    # Calculate max bond distance
+    max_bond_distance = (cr_1 + cr_2) * cutoff
+
+    if dist < 0.6:
+        print('Distance between atoms is less than 0.6 Å. Check if the structure is correct.')
+
+    # Check if the distance is less than the cutoff
+    if 0.6 < dist <= max_bond_distance:
+        return True
+    else:
+        return False
+
+
+def get_bonds(structure, cutoff=1.3):
+    """
+    Get the bonded atoms in a structure based on the distance between them.
+
+    Parameters
+    ----------
+    structure : pymatgen.Structure
+        Structure object of pymatgen
+    cutoff : float
+        Cutoff factor for the covalent radii. Default: 1.3 Å
+    """
+
+    atom_types = [i.as_dict()['species'][0]['element'] for i in structure.sites]
+
+    # Get bonded atoms
+    center_indices, points_indies, _, bond_distances = structure.get_neighbor_list(5)
+    bonded_atoms = np.array([center_indices, points_indies, bond_distances]).T
+
+    bonded_atoms = [i for i in bonded_atoms if is_bonded(atom_types[int(i[0])], atom_types[int(i[1])], i[2], cutoff)]
+
+    bonded_atoms = [[int(i[0]), int(i[1]), i[2]] for i in bonded_atoms]
+
+    return bonded_atoms
diff --git a/dist/pycofbuilder-0.0.7.6.tar.gz b/dist/pycofbuilder-0.0.7.6.tar.gz
deleted file mode 100644
index aae2e51d..00000000
Binary files a/dist/pycofbuilder-0.0.7.6.tar.gz and /dev/null differ
diff --git a/dist/pycofbuilder-0.0.7.6-py3-none-any.whl b/dist/pycofbuilder-0.0.8-py3-none-any.whl
similarity index 57%
rename from dist/pycofbuilder-0.0.7.6-py3-none-any.whl
rename to dist/pycofbuilder-0.0.8-py3-none-any.whl
index b0612149..e5be3fa9 100644
Binary files a/dist/pycofbuilder-0.0.7.6-py3-none-any.whl and b/dist/pycofbuilder-0.0.8-py3-none-any.whl differ
diff --git a/dist/pycofbuilder-0.0.8.tar.gz b/dist/pycofbuilder-0.0.8.tar.gz
new file mode 100644
index 00000000..0a095566
Binary files /dev/null and b/dist/pycofbuilder-0.0.8.tar.gz differ
diff --git a/pyproject.toml b/pyproject.toml
index 21bc3627..1ef003c0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,7 +2,7 @@
 
 [project]
 name = "pycofbuilder"
-version = '0.0.7.6'
+version = '0.0.8'
 authors = [
   { name="Felipe Lopes", email="felipe.lopes@nano.ufrj.br" },
 ]
diff --git a/setup.py b/setup.py
index 8006fe8c..0cc663a5 100644
--- a/setup.py
+++ b/setup.py
@@ -6,7 +6,7 @@
     license = f.read()
 
 
-VERSION = '0.0.7.6'
+VERSION = '0.0.8'
 DESCRIPTION = 'A package for Covalent Organic Frameworks sturcture assembly.'
 
 setup(
diff --git a/src/pycofbuilder.egg-info/PKG-INFO b/src/pycofbuilder.egg-info/PKG-INFO
index 72fda503..46994799 100644
--- a/src/pycofbuilder.egg-info/PKG-INFO
+++ b/src/pycofbuilder.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pycofbuilder
-Version: 0.0.7.6
+Version: 0.0.8
 Summary: A package for Covalent Organic Frameworks sturcture creation based on the reticular approach.
 Home-page: https://github.com/lipelopesoliveira/pyCOFBuilder
 Author: Felipe Lopes Oliveira
diff --git a/src/pycofbuilder.egg-info/SOURCES.txt b/src/pycofbuilder.egg-info/SOURCES.txt
index e7897012..f1ce56f6 100644
--- a/src/pycofbuilder.egg-info/SOURCES.txt
+++ b/src/pycofbuilder.egg-info/SOURCES.txt
@@ -19,7 +19,9 @@ src/pycofbuilder.egg-info/top_level.txt
 src/pycofbuilder/data/__init__.py
 src/pycofbuilder/data/periodic_table.json
 src/pycofbuilder/data/topology.py
+src/pycofbuilder/data/__pycache__/__init__.cpython-311.pyc
 src/pycofbuilder/data/__pycache__/topology.cpython-311.pyc
+src/pycofbuilder/data/__pycache__/topology.cpython-39.pyc
 src/pycofbuilder/data/conector/BOH2.cjson
 src/pycofbuilder/data/conector/Br.cjson
 src/pycofbuilder/data/conector/CH2CN.cjson
diff --git a/src/pycofbuilder/__init__.py b/src/pycofbuilder/__init__.py
index 41a33dea..b9c040ca 100644
--- a/src/pycofbuilder/__init__.py
+++ b/src/pycofbuilder/__init__.py
@@ -43,6 +43,6 @@
 
 __author__ = "Felipe Lopes de Oliveira"
 __license__ = "MIT"
-__version__ = '0.0.6'
+__version__ = '0.0.8'
 __email__ = "felipe.lopes@nano.ufrj.br"
 __status__ = "Development"
diff --git a/src/pycofbuilder/framework.py b/src/pycofbuilder/framework.py
index 20376e51..958802de 100644
--- a/src/pycofbuilder/framework.py
+++ b/src/pycofbuilder/framework.py
@@ -33,11 +33,11 @@
                                 rotation_matrix_from_vectors,
                                 unit_vector,
                                 angle,
-                                get_framework_symm_text)
+                                get_framework_symm_text,
+                                get_bonds)
 
 # Import pycofbuilder io_tools
-from pycofbuilder.io_tools import (save_json,
-                                   save_chemjson,
+from pycofbuilder.io_tools import (save_chemjson,
                                    save_cif,
                                    save_xyz,
                                    save_turbomole,
@@ -120,6 +120,7 @@ def __init__(self, name: str = None, **kwargs):
         self.symm_tol = kwargs.get('symm_tol', 0.1)
         self.angle_tol = kwargs.get('angle_tol', 0.5)
         self.dist_threshold = kwargs.get('dist_threshold', 0.8)
+        self.bond_threshold = kwargs.get('bond_threshold', 1.3)
 
         self.bb1_name = None
         self.bb2_name = None
@@ -132,6 +133,7 @@ def __init__(self, name: str = None, **kwargs):
         self.atom_labels = []
         self.cellMatrix = np.eye(3)
         self.cellParameters = np.array([1, 1, 1, 90, 90, 90]).astype(float)
+        self.bonds = []
 
         self.lattice_sgs = None
         self.space_group = None
@@ -368,9 +370,24 @@ def from_building_blocks(self,
 
         result = net_build_dict[net](bb1, bb2, stacking, **kwargs)
 
+        structure = Structure(
+            self.cellMatrix,
+            self.atom_types,
+            self.atom_pos,
+            coords_are_cartesian=True,
+            site_properties={'source': self.atom_labels}
+        )
+
+        self.bonds = get_bonds(structure, self.bond_threshold)
+
         return result
 
-    def save(self, fmt: str = 'cif', supercell: list = [1, 1, 1], save_dir=None, primitive=False) -> None:
+    def save(self, 
+             fmt: str = 'cif',
+             supercell: list = [1, 1, 1],
+             save_dir=None,
+             primitive=False,
+             save_bonds=True) -> None:
         '''
         Save the structure in a specif file format.
 
@@ -392,7 +409,6 @@ def save(self, fmt: str = 'cif', supercell: list = [1, 1, 1], save_dir=None, pri
         '''
 
         save_dict = {
-            'json': save_json,
             'cjson': save_chemjson,
             'cif': save_cif,
             'xyz': save_xyz,
@@ -422,6 +438,11 @@ def save(self, fmt: str = 'cif', supercell: list = [1, 1, 1], save_dir=None, pri
 
         final_structure = structure.make_supercell(supercell, in_place=False)
 
+        if save_bonds:
+            bonds = get_bonds(final_structure, self.bond_threshold)
+        else:
+            bonds = []
+
         structure_dict = final_structure.as_dict()
 
         cell = structure_dict['lattice']['matrix']
@@ -440,7 +461,8 @@ def save(self, fmt: str = 'cif', supercell: list = [1, 1, 1], save_dir=None, pri
                        cell=cell,
                        atom_types=atom_types,
                        atom_labels=atom_labels,
-                       atom_pos=atom_pos)
+                       atom_pos=atom_pos,
+                       bonds=bonds)
 
 # --------------- Net creation methods -------------------------- #
 
diff --git a/src/pycofbuilder/io_tools.py b/src/pycofbuilder/io_tools.py
index e0d79d2c..3cf4c8f0 100644
--- a/src/pycofbuilder/io_tools.py
+++ b/src/pycofbuilder/io_tools.py
@@ -237,28 +237,39 @@ def read_cif(path, file_name):
         return None
 
 
-def save_xsf(path: str = None,
-             file_name: str = None,
-             cell: np.ndarray = np.eye(3),
-             atom_types: list = None,
-             atom_pos: list = None,
-             atom_labels: list = None,
-             frac_coords: bool = False):
+def save_xsf(path: str,
+             file_name: str,
+             cell: list,
+             atom_types: list,
+             atom_labels: list,
+             atom_pos: list,
+             atom_charges: list = None,
+             bonds: list = None,
+             bond_orders: list = None,
+             frac_coords=False):
     """
     Save a file in format `.xsf` on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.xsf` extention.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom label.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     file_name = file_name.split('.')[0]
@@ -290,31 +301,39 @@ def save_xsf(path: str = None,
     xsf_file.close()
 
 
-def save_pqr(path: str = None,
-             file_name: str = None,
-             cell: np.ndarray = np.eye(3),
-             atom_types: list = None,
-             atom_pos: list = None,
-             atom_labels: list = None,
-             partial_charges: list = None,
-             frac_coords: bool = False):
+def save_pqr(path: str,
+             file_name: str,
+             cell: list,
+             atom_types: list,
+             atom_labels: list,
+             atom_pos: list,
+             atom_charges: list = None,
+             bonds: list = None,
+             bond_orders: list = None,
+             frac_coords=False):
     """
     Save a file in format `.pqr` on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.pqr` extention.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom partial charges.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
-    partial_charges: list
+    atom_charges : list
         List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     file_name = file_name.split('.')[0]
@@ -337,7 +356,7 @@ def save_pqr(path: str = None,
                                                                                         cell[4],
                                                                                         cell[5]))
 
-    if partial_charges is None:
+    if atom_charges is None:
         atom_line = 'ATOM   {:>4} {:>2}   MOL A   0    {:>8.3f}{:>8.3f}{:>8.3f}   {:>15}\n'
         for i in range(len(atom_pos)):
             pqr_file.write(atom_line.format(i + 1,
@@ -354,34 +373,53 @@ def save_pqr(path: str = None,
                                             atom_pos[i][0],
                                             atom_pos[i][1],
                                             atom_pos[i][2],
-                                            partial_charges[i],
+                                            atom_charges[i],
                                             atom_types[i]))
 
+    if bonds and not bond_orders:
+        bond_orders = [1 for i in range(len(bonds))]
+
+    if bonds:
+        for i in range(len(bonds)):
+            for j in range(bond_orders[i]):
+                pqr_file.write(f'CONECT {bonds[i][0] + 1:4} {bonds[i][1] + 1:4}\n')
+
     pqr_file.close()
 
 
-def save_pdb(path: str = None,
-             file_name: str = None,
-             cell: np.ndarray = np.eye(3),
-             atom_types: list = None,
-             atom_pos: list = None,
-             atom_labels: list = None,
-             frac_coords: bool = False):
+def save_pdb(path: str,
+             file_name: str,
+             cell: list,
+             atom_types: list,
+             atom_labels: list,
+             atom_pos: list,
+             atom_charges: list = None,
+             bonds: list = None,
+             bond_orders: list = None,
+             frac_coords=False):
     """
     Save a file in format `.pdb` on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.pdb` extention.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom partial charges.
+        List of strings containing containg the N atom labels
     atom_pos : list
-        Nx3 array contaning the atoms coordinates in cartesian form.
+        Nx3 array contaning the atoms coordinates.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     file_name = file_name.split('.')[0]
@@ -414,37 +452,54 @@ def save_pdb(path: str = None,
                                         atom_pos[i][2],
                                         atom_types[i]))
 
-    pdb_file.close()
+    if bonds and not bond_orders:
+        bond_orders = [1 for i in range(len(bonds))]
+
+    if bonds:
+        for i in range(len(bonds)):
+            for j in range(bond_orders[i]):
+                pdb_file.write(f'CONECT {bonds[i][0] + 1:4} {bonds[i][1] + 1:4}\n')
 
+    pdb_file.close()
 
-def save_gjf(path: str = None,
-             file_name: str = None,
-             cell: list = None,
-             atom_types: list = None,
-             atom_pos: list = None,
-             atom_labels: list = None,
-             frac_coords: bool = False,
-             text: str = 'opt pm6'):
 
+def save_gjf(path: str,
+             file_name: str,
+             cell: list,
+             atom_types: list,
+             atom_labels: list,
+             atom_pos: list,
+             atom_charges: list = None,
+             bonds: list = None,
+             bond_orders: list = None,
+             frac_coords=False,
+             header: str = 'opt pm6'):
     """
-    Save a file in format `.gjf` on the `path`.
+    Save a file in format `.pqr` on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.gjf` extention.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom partial charges.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
-    text : str
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
+    header : str
         Parameters for Gaussian calculations.
     """
-
     if len(cell) == 6:
         cell = cellpar_to_cell(cell)
 
@@ -457,7 +512,7 @@ def save_gjf(path: str = None,
 
     temp_file = open(os.path.join(path, file_name + '.gjf'), 'w')
     temp_file.write(f'%chk={file_name}.chk \n')
-    temp_file.write(f'# {text}\n')
+    temp_file.write(f'# {header}\n')
     temp_file.write('\n')
     temp_file.write(f'{file_name}\n')
     temp_file.write('\n')
@@ -476,28 +531,39 @@ def save_gjf(path: str = None,
     temp_file.close()
 
 
-def save_xyz(path: str = None,
-             file_name: str = None,
-             cell: np.ndarray = np.eye(3),
-             atom_types: list = None,
-             atom_pos: list = None,
-             atom_labels: list = None,
-             frac_coords: bool = False):
+def save_xyz(path: str,
+             file_name: str,
+             cell: list,
+             atom_types: list,
+             atom_labels: list,
+             atom_pos: list,
+             atom_charges: list = None,
+             bonds: list = None,
+             bond_orders: list = None,
+             frac_coords=False):
     """
     Save a file in format `.xyz` on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.xyz` extention.
+        Name of the file. Does not neet to contain the extention.
+    cell : numpy array
+        Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
     atom_types : list
         List of strings containing containg the N atom types
+    atom_label : list
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
-    cell : numpy array
-        Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     if len(cell) == 3:
@@ -527,27 +593,39 @@ def save_xyz(path: str = None,
     temp_file.close()
 
 
-def save_turbomole(path: str = None,
-                   file_name: str = None,
-                   cell: np.ndarray = np.eye(3),
-                   atom_types: list = None,
-                   atom_pos: list = None,
-                   atom_labels: list = None,
-                   frac_coords: bool = False):
-    """Save the structure in Turbomole .coord format
+def save_turbomole(path: str,
+                   file_name: str,
+                   cell: list,
+                   atom_types: list,
+                   atom_labels: list,
+                   atom_pos: list,
+                   atom_charges: list = None,
+                   bonds: list = None,
+                   bond_orders: list = None,
+                   frac_coords=False):
+    """
+    Save the structure in Turbomole .coord format on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.coord` extention.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom partial charges.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     if cell.shape == (3, 3):
@@ -575,29 +653,39 @@ def save_turbomole(path: str = None,
         temp_file.write('$end\n')
 
 
-def save_vasp(path: str = None,
-              file_name: str = None,
-              cell: np.ndarray = np.eye(3),
-              atom_types: list = None,
-              atom_pos: list = None,
-              atom_labels: list = None,
-              frac_coords: bool = False):
-    """Save the structure in VASP .vasp format
+def save_vasp(path: str,
+              file_name: str,
+              cell: list,
+              atom_types: list,
+              atom_labels: list,
+              atom_pos: list,
+              atom_charges: list = None,
+              bonds: list = None,
+              bond_orders: list = None,
+              frac_coords=False):
+    """
+    Save the structure in VASP .vasp format on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.vasp` extention.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom partial charges.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
-    coords_are_cartesian : bool
-        If True, the coordinates are in cartesian coordinates.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     if cell.shape == 6:
@@ -634,15 +722,19 @@ def save_vasp(path: str = None,
                                                                             atom_types[i]))
 
 
-def save_qe(path: str = None,
-            file_name: str = None,
-            cell: np.ndarray = np.eye(3),
-            atom_types: list = None,
-            atom_pos: list = None,
-            atom_labels: list = None,
-            frac_coords: bool = False,
-            calc_type: str = 'scf'):
-    '''
+def save_qe(path: str,
+            file_name: str,
+            cell: list,
+            atom_types: list,
+            atom_labels: list,
+            atom_pos: list,
+            atom_charges: list = None,
+            bonds: list = None,
+            bond_orders: list = None,
+            frac_coords=False,
+            calc_type: str = 'scf',
+            kspacing: float = 0.3):
+    """
     Save the structure in Quantum Espresso .pwscf format.
 
     The `input_dict` can be used to specify the input parameters for the
@@ -657,20 +749,28 @@ def save_qe(path: str = None,
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.pwscf` extention.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom labels.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
     frac_coords : bool
         If True, the coordinates are in fractional coordinates.
     calc_type : str
-       Type of pw.x calculation. Can be 'scf', 'nscf', 'bands', and 'vc-relax'.
-    '''
+        Type of calculation. Can be 'scf', 'vc-relax', 'relax', 'md', 'vc-md', 'vc-tddft', 'tddft'.
+    kspacing : float
+        Kpoints spacing in 1/Angstrom.
+    """
 
     if len(cell) == 6:
         cell_matrix = cellpar_to_cell(cell)
@@ -721,7 +821,7 @@ def save_qe(path: str = None,
     # If the kpoints grid is not specified, calculate it automatically
     if 'k_points' not in input_dict.keys():
         if 'kspacing' not in input_dict.keys():
-            input_dict['kspacing'] = 0.3
+            input_dict['kspacing'] = kspacing
         input_dict['kpoints'] = get_kgrid(cell_matrix, input_dict['kspacing'])
 
     with open(os.path.join(path, file_name + '.pwscf'), 'w') as f:
@@ -809,68 +909,38 @@ def convert_cif_2_qe(out_path, file_name):
             k_dist=0.3)
 
 
-def save_json(path, file_name, cell, atom_types, atom_pos, atom_labels, frac_coords=False):
+def save_chemjson(path: str,
+                  file_name: str,
+                  cell: list,
+                  atom_types: list,
+                  atom_labels: list,
+                  atom_pos: list,
+                  atom_charges: list = None,
+                  bonds: list = None,
+                  frac_coords=False):
     """
     Save a file in format `.json` on the `path`.
 
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.cif` extention.
-    atom_label : list
-        List of strings containing containg the N atom partial charges.
-    atom_pos : list
-        Nx3 array contaning the atoms coordinates.
+        Name of the file. Does not neet to contain the extention.
     cell : numpy array
         Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
-    """
-
-    file_name = file_name.split('.')[0]
-
-    cof_json = create_COF_json(file_name)
-
-    if len(cell) == 3:
-        cell_par = cell_to_cellpar(np.array(cell)).tolist()
-        cell_matrix = np.array(cell).astype(float).tolist()
-
-    if len(cell) == 6:
-        cell_par = np.array(cell).astype(float).tolist()
-        cell_matrix = cellpar_to_cell(cell_par).tolist()
-
-    cof_json['system']['geo_opt'] = False
-
-    cof_json['geometry']['cell_matrix'] = cell_matrix
-    cof_json['geometry']['cell_parameters'] = cell_par
-    cof_json['geometry']['atom_labels'] = list(atom_types)
-    cof_json['geometry']['atom_pos'] = list(atom_pos)
-
-    write_json(path, file_name, cof_json)
-
-
-def save_chemjson(path,
-                  file_name,
-                  cell,
-                  atom_types,
-                  atom_pos,
-                  atom_labels,
-                  frac_coords=False):
-    """
-    Save a file in format `.json` on the `path`.
-
-    Parameters
-    ----------
-    path : str
-        Path to the file.
-    file_name : str
-        Name of the file. Does not neet to contain the `.cif` extention.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom partial charges.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
-    cell : numpy array
-        Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     file_name = file_name.split('.')[0]
@@ -887,18 +957,20 @@ def save_chemjson(path,
                                       AtomTypes=atom_types,
                                       AtomPositions=atom_pos,
                                       AtomLabels=atom_labels,
-                                      CartesianPositions=not frac_coords)
+                                      CartesianPositions=not frac_coords,
+                                      BondIndexes=bonds)
 
     write_json(path, file_name, chemJSON)
 
 
-def save_cif(path,
-             file_name,
-             cell,
-             atom_types,
-             atom_pos,
-             atom_labels=None,
-             partial_charges=False,
+def save_cif(path: str,
+             file_name: str,
+             cell: list,
+             atom_types: list,
+             atom_labels: list,
+             atom_pos: list,
+             atom_charges: list = None,
+             bonds: list = None,
              frac_coords=False):
     """
     Save a file in format `.cif` on the `path`.
@@ -906,15 +978,23 @@ def save_cif(path,
     Parameters
     ----------
     path : str
-        Path to the file.
+        Path to the save the file.
     file_name : str
-        Name of the file. Does not neet to contain the `.cif` extention.
+        Name of the file. Does not neet to contain the extention.
+    cell : numpy array
+        Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_types : list
+        List of strings containing containg the N atom types
     atom_label : list
-        List of strings containing containg the N atom partial charges.
+        List of strings containing containg the N atom labels
     atom_pos : list
         Nx3 array contaning the atoms coordinates.
-    cell : numpy array
-        Can be a 3x3 array contaning the cell vectors or a list with the 6 cell parameters.
+    atom_charges : list
+        List of strings containing containg the N atom partial charges.
+    bonds : list
+        List of lists containing the index of the bonded atoms and the bond length.
+    frac_coords : bool
+        If True, the coordinates are in fractional coordinates.
     """
 
     file_name = file_name.split('.')[0]
@@ -932,7 +1012,7 @@ def save_cif(path,
 
 _audit_creation_date     {date.today().strftime("%Y-%d-%m")}
 _audit_creation_method   pyCOFBuilder
-_audit_author_name       'Felipe Lopes de Oliveira'
+_audit_author_name       '{os.getlogin()}'
 
 _chemical_name_common                  '{file_name}'
 _cell_length_a                          {a:>10.6f}
@@ -956,7 +1036,7 @@ def save_cif(path,
    _atom_site_fract_z
 """
 
-    if partial_charges is not False:
+    if atom_charges:
         cif_text += '   _atom_site_charge\n'
 
     if frac_coords is False:
@@ -966,22 +1046,33 @@ def save_cif(path,
 
     for i in range(len(atom_pos)):
         u, v, w = atom_pos[i][0], atom_pos[i][1], atom_pos[i][2]
-        if partial_charges is not False:
-            cif_text += '{:<7}    {} {:>15.9f} {:>15.9f} {:>15.9f} {:>10.5f}\n'.format(
+        if atom_charges:
+            atom_labels[i] = f"{atom_types[i]}{str(i + 1)}_{atom_labels[i]}"
+            cif_text += '{:<15}    {} {:>15.9f} {:>15.9f} {:>15.9f} {:>10.5f}\n'.format(
                 f"{atom_types[i]}{str(i + 1)}_{atom_labels[i]}",
                 atom_types[i],
                 u,
                 v,
                 w,
-                partial_charges[i])
+                atom_charges[i])
         else:
-            cif_text += '{:<7}    {} {:>15.9f} {:>15.9f} {:>15.9f}\n'.format(
+            atom_labels[i] = f"{atom_types[i]}{str(i + 1)}_{atom_labels[i]}"
+            cif_text += '{:<15}    {} {:>15.9f} {:>15.9f} {:>15.9f}\n'.format(
                 f"{atom_types[i]}{str(i + 1)}_{atom_labels[i]}",
                 atom_types[i],
                 u,
                 v,
                 w)
 
+    if bonds:
+        cif_text += '\nloop_\n'
+        cif_text += '_geom_bond_atom_site_label_1\n'
+        cif_text += '_geom_bond_atom_site_label_2\n'
+        cif_text += '_geom_bond_distance\n'
+
+        for bond in bonds:
+            cif_text += f'{atom_labels[bond[0]]:10} {atom_labels[bond[1]]:10} {bond[2]:.5f}\n'
+
     # Write cif_text to file
     cif_file = open(os.path.join(path, file_name + '.cif'), 'w')
     cif_file.write(cif_text)
@@ -1189,10 +1280,10 @@ def create_structure_CJSON(StructureName: str,
                            CellParameters: list = None,
                            CellMatrix: list = None,
                            AtomTypes: list = None,
+                           AtomLabels: list = [],
                            AtomPositions: list = None,
                            CartesianPositions: bool = False,
-                           AtomLabels: list = [],
-                           Bonds: list = [],
+                           BondIndexes: list = [],
                            BondOrders: list = [],
                            PartialCharges: dict = {},
                            ) -> dict:
@@ -1208,11 +1299,20 @@ def create_structure_CJSON(StructureName: str,
         List with the cell parameters.
     CellMatrix : list
         List with the cell matrix. Optional
+    AtomTypes : list
+        List with the atom types.
     AtomLabels : list
         List with the atom labels.
     AtomPositions : list
         List with the atom positions.
-
+    CartesianPositions : bool
+        If True, the coordinates are in cartesian coordinates.
+    BondIndexes : list
+        List with the bonds indexes and bond length.
+    BondOrders : list
+        List with the bond orders.
+    PartialCharges : dict
+        Dictionary with the partial charges.
     """
 
     chemJSON = create_empty_CJSON()
@@ -1252,10 +1352,16 @@ def create_structure_CJSON(StructureName: str,
         CartPosition = np.array([np.dot(V_cart, atom) for atom in AtomPositions]).flatten().tolist()
         chemJSON['atoms']['coords']['3d'] = CartPosition
 
-    chemJSON['atoms']['PartialCharges'] = PartialCharges
+    if PartialCharges != {}:
+        chemJSON['atoms']['PartialCharges'] = PartialCharges
+
+    bond_indexes = [[i[0], i[1]] for i in BondIndexes]
+    bond_indexes = [item for row in bond_indexes for item in row]
+
+    bond_orders = BondOrders if BondOrders != [] else [1] * len(bond_indexes)
 
-    chemJSON['bonds']['connections']['index'] = Bonds
-    chemJSON['bonds']['order'] = BondOrders
+    chemJSON['bonds']['connections']['index'] = bond_indexes
+    chemJSON['bonds']['order'] = bond_orders
 
     return chemJSON
 
diff --git a/src/pycofbuilder/tools.py b/src/pycofbuilder/tools.py
index 14f74f17..95563552 100644
--- a/src/pycofbuilder/tools.py
+++ b/src/pycofbuilder/tools.py
@@ -1004,3 +1004,65 @@ def cell_to_ibrav(cell):
                   'celldm(6)': np.cos(np.deg2rad(gamma))}
 
     return celldm
+
+
+def is_bonded(atom1: str, atom2: str, dist: float, cutoff: float = 1.3):
+    """
+    Determine if two atoms are bonded based on the distance between them.
+    Two atoms are considered bonded if the distance between them is less than
+    the sum of their covalent radii multiplied by a cutoff factor.
+
+    Parameters
+    ----------
+    atom1 : str
+        Label of the first atom
+    atom2 : str
+        Label of the second atom
+    dist : float
+        Distance between the two atoms
+    cutoff : float
+        Cutoff factor for the covalent radii. Default: 1.3
+    """
+
+    periodic_table = elements_dict(property='covalent_radius')
+
+    # Get the covalent radii of the two atoms
+    cr_1 = periodic_table[atom1]
+    cr_2 = periodic_table[atom2]
+
+    # Calculate max bond distance
+    max_bond_distance = (cr_1 + cr_2) * cutoff
+
+    if dist < 0.6:
+        print('Distance between atoms is less than 0.6 Å. Check if the structure is correct.')
+
+    # Check if the distance is less than the cutoff
+    if 0.6 < dist <= max_bond_distance:
+        return True
+    else:
+        return False
+
+
+def get_bonds(structure, cutoff=1.3):
+    """
+    Get the bonded atoms in a structure based on the distance between them.
+
+    Parameters
+    ----------
+    structure : pymatgen.Structure
+        Structure object of pymatgen
+    cutoff : float
+        Cutoff factor for the covalent radii. Default: 1.3 Å
+    """
+
+    atom_types = [i.as_dict()['species'][0]['element'] for i in structure.sites]
+
+    # Get bonded atoms
+    center_indices, points_indies, _, bond_distances = structure.get_neighbor_list(5)
+    bonded_atoms = np.array([center_indices, points_indies, bond_distances]).T
+
+    bonded_atoms = [i for i in bonded_atoms if is_bonded(atom_types[int(i[0])], atom_types[int(i[1])], i[2], cutoff)]
+
+    bonded_atoms = [[int(i[0]), int(i[1]), i[2]] for i in bonded_atoms]
+
+    return bonded_atoms