diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 45c97af79..fa40e3e73 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,12 +13,18 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
+    # set up conda
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: ${{ matrix.python-version }}
+        auto-activate-base: true
+        activate-environment: ""
+    # install rdkit and openbabel
+    - name: Install rdkit
+      run: conda create -c conda-forge -n my-rdkit-env python=${{ matrix.python-version }} rdkit openbabel;
     - name: Install dependencies
-      run: pip install .[amber] coverage codecov
+      run: source $CONDA/bin/activate my-rdkit-env && pip install .[amber] coverage codecov
     - name: Test
-      run: cd tests && coverage run --source=../dpdata -m unittest && cd .. && coverage combine tests/.coverage && coverage report
-    - run: codecov
+      run: source $CONDA/bin/activate my-rdkit-env && cd tests && coverage run --source=../dpdata -m unittest && cd .. && coverage combine tests/.coverage && coverage report
+    - name: Run codecov
+      run: source $CONDA/bin/activate my-rdkit-env && codecov
diff --git a/README.md b/README.md
index fd1532990..66333f824 100644
--- a/README.md
+++ b/README.md
@@ -78,6 +78,7 @@ The `System` or `LabeledSystem` can be constructed from the following file forma
 | PWmat   | movement    | True         | True    | LabeledSystem | 'pwmat/movement'     |
 | PWmat   | OUT.MLMD    | True         | True    | LabeledSystem | 'pwmat/out.mlmd'     |
 | Amber   | multi       | True         | True    | LabeledSystem | 'amber/md'           |
+| Amber/sqm | sqm.out   | False        | False   | System        | 'sqm/out'            |
 | Gromacs | gro         | True         | False   | System        | 'gromacs/gro'        |
 
 
@@ -206,4 +207,48 @@ s.replace('Hf', 'Zr', 8)
 s.to_vasp_poscar('POSCAR.P42nmc.replace')
 ```
 
+# BondOrderSystem
+A new class `BondOrderSystem` which inherits from class `System` is introduced in dpdata. This new class contains information of chemical bonds and formal charges (stored in `BondOrderSystem.data['bonds']`, `BondOrderSystem.data['formal_charges']`). Now BondOrderSystem can only read from .mol/.sdf formats, because of its dependency on rdkit (which means rdkit must be installed if you want to use this function). Other formats, such as pdb, must be converted to .mol/.sdf format (maybe with software like open babel). 
+```python
+import dpdata
+system_1 = dpdata.BondOrderSystem("tests/bond_order/CH3OH.mol", fmt="mol") # read from .mol file
+system_2 = dpdata.BondOrderSystem("tests/bond_order/methane.sdf", fmt="sdf") # read from .sdf file
+```
+In sdf file, all molecules must be of the same topology (i.e. conformers of the same molecular configuration).
+`BondOrderSystem` also supports initialize from a `rdkit.Chem.rdchem.Mol` object directly.
+```python
+from rdkit import Chem
+from rdkit.Chem import AllChem
+import dpdata
+
+mol = Chem.MolFromSmiles("CC")
+mol = Chem.AddHs(mol)
+AllChem.EmbedMultipleConfs(mol, 10)
+system = dpdata.BondOrderSystem(rdkit_mol=mol)
+```
+
+## Bond Order Assignment
+The `BondOrderSystem` implements a more robust sanitize procedure for rdkit Mol, as defined in `dpdata.rdkit.santizie.Sanitizer`. This class defines 3 level of sanitization process by: low, medium and high. (default is medium).
++ low: use `rdkit.Chem.SanitizeMol()` function to sanitize molecule.
++ medium: before using rdkit, the programm will first assign formal charge of each atom to avoid inappropriate valence exceptions. However, this mode requires the rightness of the bond order information in the given molecule.
++ high: the program will try to fix inappropriate bond orders in aromatic hetreocycles, phosphate, sulfate, carboxyl, nitro, nitrine, guanidine groups. If this procedure fails to sanitize the given molecule, the program will then try to call `obabel` to pre-process the mol and repeat the sanitization procedure. **That is to say, if you wan't to use this level of sanitization, please ensure `obabel` is installed in the environment.**
+According to our test, our sanitization procedure can successfully read 4852 small molecules in the PDBBind-refined-set. It is necessary to point out that the in the molecule file (mol/sdf), the number of explicit hydrogens has to be correct. Thus, we recommend to use
+ `obabel xxx -O xxx -h` to pre-process the file. The reason why we do not implement this hydrogen-adding procedure in dpdata is that we can not ensure its correctness.
+
+```python
+import dpdata
+    
+for sdf_file in glob.glob("bond_order/refined-set-ligands/obabel/*sdf"):
+    syst = dpdata.BondOrderSystem(sdf_file, sanitize_level='high', verbose=False)
+```
+## Formal Charge Assignment
+BondOrderSystem implement a method to assign formal charge for each atom based on the 8-electron rule (see below). Note that it only supports common elements in bio-system: B,C,N,O,P,S,As
+```python
+import dpdata
+
+syst = dpdata.BondOrderSystem("tests/bond_order/CH3NH3+.mol", fmt='mol')
+print(syst.get_formal_charges()) # return the formal charge on each atom
+print(syst.get_charge()) # return the total charge of the system
+```
 
+If a valence of 3 is detected on carbon, the formal charge will be assigned to -1. Because for most cases (in alkynyl anion, isonitrile, cyclopentadienyl anion), the formal charge on 3-valence carbon is -1, and this is also consisent with the 8-electron rule.
diff --git a/dpdata/__init__.py b/dpdata/__init__.py
index 3923f70e5..bd8fd8c02 100644
--- a/dpdata/__init__.py
+++ b/dpdata/__init__.py
@@ -9,3 +9,15 @@
     from ._version import version as __version__
 except ImportError:
     from .__about__ import __version__
+
+# BondOrder System has dependency on rdkit
+try:
+    import rdkit
+    USE_RDKIT = True
+except ModuleNotFoundError:
+    USE_RDKIT = False
+
+if USE_RDKIT:
+    from .bond_order_system import BondOrderSystem
+
+
diff --git a/dpdata/amber/__init__.py b/dpdata/amber/__init__.py
new file mode 100644
index 000000000..8b1378917
--- /dev/null
+++ b/dpdata/amber/__init__.py
@@ -0,0 +1 @@
+
diff --git a/dpdata/amber/sqm.py b/dpdata/amber/sqm.py
new file mode 100644
index 000000000..6d5843126
--- /dev/null
+++ b/dpdata/amber/sqm.py
@@ -0,0 +1,54 @@
+import numpy as np
+
+
+START = 0
+READ_CHARGE = 1
+READ_CHARGE_SUCCESS = 2
+READ_COORDS_START = 3
+READ_COORDS = 6
+
+def parse_sqm_out(fname):
+    '''
+        Read atom symbols, charges and coordinates from ambertools sqm.out file
+    '''
+    atom_symbols = []
+    coords = []
+    charges = []
+    with open(fname) as f:
+        flag = 0
+        for line in f:
+            if line.startswith("  Atom    Element       Mulliken Charge"):
+                flag = READ_CHARGE
+            elif line.startswith(" Total Mulliken Charge"):
+                flag = READ_CHARGE_SUCCESS
+            elif line.startswith(" Final Structure"):
+                flag = READ_COORDS_START
+            elif flag == READ_CHARGE:
+                ls = line.strip().split()
+                atom_symbols.append(ls[-2])
+                charges.append(float(ls[-1]))
+            elif READ_COORDS_START <= flag < READ_COORDS:
+                flag += 1
+            elif flag == READ_COORDS:
+                ls = line.strip()
+                if not ls:
+                    break
+                else:
+                    symbol = line.strip().split()[-4]
+                    coord = list(map(float, line.strip().split()[-3:]))
+                    coords.append(coord)
+    return atom_symbols, charges, np.array(coords)
+
+
+def to_system_data(fname):
+    data = {}
+    atom_symbols, charges, coords = parse_sqm_out(fname)
+    atom_names, data['atom_types'], atom_numbs = np.unique(atom_symbols, return_inverse=True, return_counts=True)
+    data['atom_names'] = list(atom_names)
+    data['atom_numbs'] = list(atom_numbs)
+    data['charges'] = np.array([charges])
+    data['coords'] = np.array([coords])
+    data['orig'] = np.array([0, 0, 0])
+    data['cells'] = np.array([[[100., 0., 0.], [0., 100., 0.], [0., 0., 100.]]])
+    data['nopbc'] = True
+    return data
diff --git a/dpdata/bond_order_system.py b/dpdata/bond_order_system.py
new file mode 100644
index 000000000..b590f1fcf
--- /dev/null
+++ b/dpdata/bond_order_system.py
@@ -0,0 +1,199 @@
+#%%
+# Bond Order System
+from dpdata.system import Register, System, LabeledSystem, check_System
+import rdkit.Chem
+import dpdata.rdkit.utils
+from dpdata.rdkit.sanitize import Sanitizer, SanitizeError
+from copy import deepcopy
+# import dpdata.rdkit.mol2
+
+def check_BondOrderSystem(data):
+    check_System(data)
+    assert ('bonds' in data.keys())
+    
+class BondOrderSystem(System):
+    '''
+    The system with chemical bond and formal charges information
+
+    For example, a labeled methane system named `d_example` has one molecule (5 atoms, 4 bonds) and `n_frames` frames. The bond order and formal charge information can be accessed by
+        - `d_example['bonds']` : a numpy array of size 4 x 3, and
+                                    the first column represents the index of begin atom,
+                                    the second column represents the index of end atom, 
+                                    the third columen represents the bond order:
+                                        1 - single bond, 2 - double bond, 3 - triple bond, 1.5 - aromatic bond
+        - `d_example['formal_charges']` : a numpy array of size 5 x 1
+    '''
+    def __init__(self,
+                 file_name = None,
+                 fmt = 'auto',
+                 type_map = None,
+                 begin = 0,
+                 step = 1,
+                 data = None,
+                 rdkit_mol = None,
+                 sanitize_level = "medium",
+                 raise_errors = True,
+                 verbose = False,
+                 **kwargs):
+        """
+        Constructor
+
+        Parameters
+        ----------
+        file_name : str
+            The file to load the system
+        fmt : str
+            Format of the file, supported formats are
+                - ``auto`` : inferred from `file_name`'s extention
+                - ``mol`` : .mol file
+                - ``sdf`` : .sdf file
+        type_map : list of str
+            Needed by formats deepmd/raw and deepmd/npy. Maps atom type to name. The atom with type `ii` is mapped to `type_map[ii]`.
+            If not provided the atom names are assigned to `'Type_1'`, `'Type_2'`, `'Type_3'`...
+        begin : int
+            The beginning frame when loading MD trajectory.
+        step : int
+            The number of skipped frames when loading MD trajectory.
+        data : dict
+            System data dict.
+        rdkit_mol : rdkit.Chem.rdchem.Mol
+            If `file_name` is None, you must init with a rdkit Mol type.
+        sanitize_level : str
+            The level of sanitizer, 'low', 'medium' or 'high'.
+        raise_errors : bool
+            whether to raise an Exception if sanitization procedure fails.
+        verbose : bool
+            whether to print information in the sanitization procedure.
+        """
+
+        System.__init__(self)
+        self.sanitizer = Sanitizer(sanitize_level, raise_errors, verbose)
+
+        if data:
+            mol = dpdata.rdkit.utils.system_data_to_mol(data)
+            self.from_rdkit_mol(mol)
+        if file_name:
+            self.from_fmt(file_name, 
+                          fmt,
+                          type_map=type_map,
+                          begin=begin, 
+                          step=step,
+                          **kwargs)
+        elif rdkit_mol:
+            self.from_rdkit_mol(rdkit_mol)
+        else:
+            raise ValueError("Please specify a mol/sdf file or a rdkit Mol object")
+
+        if type_map:
+            self.apply_type_map(type_map)
+
+    register_from_funcs = Register()
+    register_to_funcs = System.register_to_funcs + Register()
+
+    def __repr__(self):
+        return self.__str__()
+
+    def __str__(self):
+        '''
+            A brief summary of the system
+        '''
+        ret = "Data Summary"
+        ret += "\nBondOrder System"
+        ret += "\n-------------------"
+        ret += f"\nFrame Numbers      : {self.get_nframes()}"
+        ret += f"\nAtom Numbers       : {self.get_natoms()}"
+        ret += f"\nBond Numbers       : {self.get_nbonds()}"
+        ret += "\nElement List       :"
+        ret += "\n-------------------"
+        ret += "\n"+"  ".join(map(str,self.get_atom_names()))
+        ret += "\n"+"  ".join(map(str,self.get_atom_numbs()))
+        return ret
+
+    def get_nbonds(self):
+        '''
+            Return the number of bonds
+        '''
+        return len(self.data['bonds'])
+    
+    def get_charge(self):
+        '''
+            Return the total formal charge of the moleclue
+        '''
+        return sum(self.data['formal_charges'])
+    
+    def get_mol(self):
+        '''
+            Return the rdkit.Mol object
+        '''
+        return self.rdkit_mol
+    
+    def get_bond_order(self, begin_atom_idx, end_atom_idx):
+        '''
+            Return the bond order between given atoms
+        '''
+        return self.data['bond_dict'][f'{int(begin_atom_idx)}-{int(end_atom_idx)}']
+    
+    def get_formal_charges(self):
+        '''
+            Return the formal charges on each atom
+        '''
+        return self.data['formal_charges']
+    
+    def copy(self):
+        new_mol = deepcopy(self.rdkit_mol)
+        self.__class__(data=deepcopy(self.data),
+                       rdkit_mol=new_mol)
+    
+    # def __add__(self, other):
+    #     '''
+    #         magic method "+" operation
+    #     '''
+    #     if isinstance(other, BondOrderSystem):
+    #         if dpdata.rdkit.utils.check_same_molecule(self.rdkit_mol, other.rdkit_mol):
+    #             self.__class__(self, data=other.data)
+    #         else:
+    #             raise RuntimeError("The two systems are not of the same topology.")
+    #     else:
+    #         raise RuntimeError(f"Unsupported data structure: {type(other)}")
+
+    def from_rdkit_mol(self, rdkit_mol):
+        '''
+            Initialize from a rdkit.Chem.rdchem.Mol object
+        '''
+        rdkit_mol = self.sanitizer.sanitize(rdkit_mol)
+        self.data = dpdata.rdkit.utils.mol_to_system_data(rdkit_mol)
+        self.data['bond_dict'] = dict([(f'{int(bond[0])}-{int(bond[1])}', bond[2]) for bond in self.data['bonds']])
+        self.rdkit_mol = rdkit_mol
+
+    @register_from_funcs.register_funcs('mol')
+    def from_mol_file(self, file_name):
+        mol = rdkit.Chem.MolFromMolFile(file_name, sanitize=False, removeHs=False)
+        self.from_rdkit_mol(mol)
+
+    @register_to_funcs.register_funcs("mol")
+    def to_mol_file(self, file_name, frame_idx=0):
+        assert (frame_idx < self.get_nframes())
+        rdkit.Chem.MolToMolFile(self.rdkit_mol, file_name, confId=frame_idx)
+    
+    @register_from_funcs.register_funcs("sdf")
+    def from_sdf_file(self, file_name):
+        '''
+        Note that it requires all molecules in .sdf file must be of the same topology
+        '''
+        mols = [m for m in rdkit.Chem.SDMolSupplier(file_name, sanitize=False, removeHs=False)]
+        if len(mols) > 1:
+            mol = dpdata.rdkit.utils.combine_molecules(mols)
+        else:
+            mol = mols[0]
+        self.from_rdkit_mol(mol)
+    
+    @register_to_funcs.register_funcs("sdf")
+    def to_sdf_file(self, file_name, frame_idx=-1):
+        sdf_writer = rdkit.Chem.SDWriter(file_name)
+        if frame_idx == -1:
+            for ii in self.get_nframes():
+                sdf_writer.write(self.rdkit_mol, confId=ii)
+        else:
+            assert (frame_idx < self.get_nframes())
+            sdf_writer.write(self.rdkit_mol, confId=frame_idx)
+        sdf_writer.close()
diff --git a/dpdata/deepmd/comp.py b/dpdata/deepmd/comp.py
index f8a367f8e..1cd2b055a 100644
--- a/dpdata/deepmd/comp.py
+++ b/dpdata/deepmd/comp.py
@@ -71,6 +71,11 @@ def dump(folder,
     # dump raw 
     np.savetxt(os.path.join(folder, 'type.raw'), data['atom_types'], fmt = '%d')    
     np.savetxt(os.path.join(folder, 'type_map.raw'),    data['atom_names'], fmt = '%s')
+    # BondOrder System
+    if "bonds" in data:
+        np.savetxt(os.path.join(folder, "bonds.raw"), data['bonds'], header="begin_atom, end_atom, bond_order")
+    if "formal_charges" in data:
+        np.savetxt(os.path.join(folder, "formal_charges.raw"), data['formal_charges'])
     # reshape frame properties and convert prec
     nframes = data['cells'].shape[0]
     cells  = np.reshape(data['cells'],    [nframes,  9]).astype(comp_prec)
diff --git a/dpdata/deepmd/raw.py b/dpdata/deepmd/raw.py
index c897f377c..ab3290f61 100644
--- a/dpdata/deepmd/raw.py
+++ b/dpdata/deepmd/raw.py
@@ -63,6 +63,12 @@ def dump (folder, data) :
     np.savetxt(os.path.join(folder, 'type_map.raw'),    data['atom_names'], fmt = '%s')
     np.savetxt(os.path.join(folder, 'box.raw'),     np.reshape(data['cells'],    [nframes,  9]))
     np.savetxt(os.path.join(folder, 'coord.raw'),   np.reshape(data['coords'],   [nframes, -1]))
+    # BondOrder System
+    if "bonds" in data:
+        np.savetxt(os.path.join(folder, "bonds.raw"), data['bonds'], header="begin_atom, end_atom, bond_order")
+    if "formal_charges" in data:
+        np.savetxt(os.path.join(folder, "formal_charges.raw"), data['formal_charges'])
+    # Labeled System
     if 'energies' in data :
         np.savetxt(os.path.join(folder, 'energy.raw'),  np.reshape(data['energies'], [nframes,  1]))
     if 'forces' in data :
diff --git a/dpdata/pwmat/__init__.py b/dpdata/pwmat/__init__.py
new file mode 100644
index 000000000..8b1378917
--- /dev/null
+++ b/dpdata/pwmat/__init__.py
@@ -0,0 +1 @@
+
diff --git a/dpdata/rdkit/__init__.py b/dpdata/rdkit/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/dpdata/rdkit/sanitize.py b/dpdata/rdkit/sanitize.py
new file mode 100644
index 000000000..7e40fa7b4
--- /dev/null
+++ b/dpdata/rdkit/sanitize.py
@@ -0,0 +1,572 @@
+from copy import deepcopy
+from rdkit import Chem
+from rdkit.Chem.rdchem import Atom, Bond, Mol, BondType
+import os
+import time
+# openbabel
+try:
+    from openbabel import openbabel
+    USE_OBABEL = True
+except ModuleNotFoundError as e:
+    USE_OBABEL = False
+
+def get_explicit_valence(atom, verbose=False):
+    exp_val_calculated_from_bonds = int(sum([bond.GetBondTypeAsDouble() for bond in atom.GetBonds()]))
+    try:
+        exp_val = atom.GetExplicitValence()
+        if exp_val != exp_val_calculated_from_bonds:
+            if verbose:
+                print(f"Explicit valence given by GetExplicitValence() and sum of bond order are inconsistent on {atom.GetSymbol()}{atom.GetIdx()+1}, using sum of bond order.")
+        return exp_val_calculated_from_bonds
+    except:
+        return exp_val_calculated_from_bonds
+
+def regularize_formal_charges(mol, sanitize=True, verbose=False):
+    """
+    Regularize formal charges of atoms
+    """
+    assert isinstance(mol, Chem.rdchem.Mol)
+    for atom in mol.GetAtoms():
+        assign_formal_charge_for_atom(atom, verbose)
+    if sanitize:
+        try:
+            Chem.SanitizeMol(mol)
+            return mol
+        except:
+            return None
+    else:
+        return mol
+
+def assign_formal_charge_for_atom(atom, verbose=False):
+    """
+        assigen formal charge according to 8-electron rule for element B,C,N,O,S,P,As
+    """
+    assert isinstance(atom, Chem.rdchem.Atom)
+    valence = get_explicit_valence(atom, verbose)
+    if atom.GetSymbol() == "B":
+        atom.SetFormalCharge(3 - valence)
+    elif atom.GetSymbol() == "C":
+        atom.SetFormalCharge(valence - 4)
+        if valence == 3:
+            print(f"Detect a valence of 3 on #C{atom.GetIdx()+1}, the formal charge of this atom will be assigned to -1")
+        elif valence > 4:
+            raise ValueError(f"#C{atom.GetIdx()+1} has a valence larger than 4")
+    elif atom.GetSymbol() == "N":
+        if valence > 4:
+            raise ValueError(f"#N{atom.GetIdx()+1} has a valence larger than 4")
+        else:
+            atom.SetFormalCharge(valence - 3)
+    elif atom.GetSymbol() == "O":
+        atom.SetFormalCharge(valence - 2)
+    elif atom.GetSymbol() == "S":
+        if valence == 1:
+            atom.SetFormalCharge(-1)
+        elif valence == 3:
+            atom.SetFormalCharge(1)
+        elif valence > 6:
+            raise ValueError(f"#S{atom.GetIdx()+1} has a valence larger than 6")
+        else:
+            atom.SetFormalCharge(0)
+    elif atom.GetSymbol() == "P" or atom.GetSymbol() == "As":
+        if valence == 5:
+            atom.SetFormalCharge(0)
+        elif valence > 5:
+            raise ValueError(f"#{atom.GetSymbol()}{atom.GetIdx()+1} has a valence larger than 5")
+        else:
+            atom.SetFormalCharge(valence - 3)
+
+# print bond and atom information (for debugger)
+def print_bonds(mol):
+    for bond in mol.GetBonds():
+        begin_atom = bond.GetBeginAtom()
+        end_atom = bond.GetEndAtom()
+        print(f'{begin_atom.GetSymbol()}{begin_atom.GetIdx()+1} {end_atom.GetSymbol()}{end_atom.GetIdx()+1} {bond.GetBondType()}')
+
+def print_atoms(mol):
+    for atom in mol.GetAtoms():
+        print(f'{atom.GetSymbol()}{atom.GetIdx()+1} {atom.GetFormalCharge()} {get_explicit_valence(atom)}')
+
+
+def is_terminal_oxygen(O_atom):
+    if len(O_atom.GetNeighbors()) == 1:
+        return True
+    else:
+        return False
+
+def get_terminal_oxygens(atom):
+    terminal_oxygens = []
+    for nei in atom.GetNeighbors():
+        if nei.GetSymbol() == "O" or nei.GetSymbol() == "S":
+            if is_terminal_oxygen(nei):
+                terminal_oxygens.append(nei)
+    return terminal_oxygens
+
+def sanitize_phosphate_Patom(P_atom, verbose=True):
+    if P_atom.GetSymbol() == "P":
+        terminal_oxygens = get_terminal_oxygens(P_atom)
+        mol = P_atom.GetOwningMol()
+        if len(terminal_oxygens) > 1:
+            if verbose:
+                print("Phospate group detected, sanitizing it...")
+            # set one P=O and two P-O
+            bond1 = mol.GetBondBetweenAtoms(P_atom.GetIdx(), terminal_oxygens[0].GetIdx())
+            bond1.SetBondType(Chem.rdchem.BondType.DOUBLE)
+            for ii in range(1, len(terminal_oxygens)):
+                bond = mol.GetBondBetweenAtoms(P_atom.GetIdx(), terminal_oxygens[ii].GetIdx())
+                bond.SetBondType(Chem.rdchem.BondType.SINGLE)
+                terminal_oxygens[ii].SetFormalCharge(-1)
+
+def sanitize_phosphate(mol):
+    for atom in mol.GetAtoms():
+        sanitize_phosphate_Patom(atom)
+    return mol
+
+def sanitize_sulfate_Satom(S_atom, verbose=True):
+    if S_atom.GetSymbol() == "S":
+        terminal_oxygens = get_terminal_oxygens(S_atom)
+        mol = S_atom.GetOwningMol()
+        if len(terminal_oxygens) == 3:
+            if verbose:
+                print("Sulfate group detected, sanitizing it...")
+            # set one S-O and two S=O
+            bond1 = mol.GetBondBetweenAtoms(S_atom.GetIdx(), terminal_oxygens[0].GetIdx())
+            bond1.SetBondType(Chem.rdchem.BondType.SINGLE)
+            terminal_oxygens[0].SetFormalCharge(-1)
+            for ii in range(1, len(terminal_oxygens)):
+                bond = mol.GetBondBetweenAtoms(S_atom.GetIdx(), terminal_oxygens[ii].GetIdx())
+                bond.SetBondType(Chem.rdchem.BondType.DOUBLE)
+
+def sanitize_sulfate(mol):
+    for atom in mol.GetAtoms():
+        sanitize_sulfate_Satom(atom)
+    return mol
+
+def sanitize_carboxyl_Catom(C_atom, verbose=True):
+    if C_atom.GetSymbol() == "C":
+        terminal_oxygens = get_terminal_oxygens(C_atom)
+        mol = C_atom.GetOwningMol()
+        if len(terminal_oxygens) == 2:
+            if verbose:
+                print("Carbonxyl group detected, sanitizing it...")
+            # set one C-O and one C=O
+            bond1 = mol.GetBondBetweenAtoms(C_atom.GetIdx(), terminal_oxygens[0].GetIdx())
+            bond1.SetBondType(Chem.rdchem.BondType.SINGLE)
+            terminal_oxygens[0].SetFormalCharge(-1)
+
+            bond2 = mol.GetBondBetweenAtoms(C_atom.GetIdx(), terminal_oxygens[1].GetIdx())
+            bond2.SetBondType(Chem.rdchem.BondType.DOUBLE)
+            terminal_oxygens[1].SetFormalCharge(0)
+
+def sanitize_carboxyl(mol):
+    for atom in mol.GetAtoms():
+        sanitize_carboxyl_Catom(atom)
+    return mol
+
+def sanitize_nitro_Natom(N_atom, verbose=True):
+    if N_atom.GetSymbol() == "N":
+        terminal_oxygens = get_terminal_oxygens(N_atom)
+        mol = N_atom.GetOwningMol()
+        if len(terminal_oxygens) == 2:
+            if verbose:
+                print("Nitro group detected, sanitizing it...")
+            # set one N-O and one N=O
+            bond1 = mol.GetBondBetweenAtoms(N_atom.GetIdx(), terminal_oxygens[0].GetIdx())
+            bond1.SetBondType(Chem.rdchem.BondType.SINGLE)
+            terminal_oxygens[0].SetFormalCharge(-1)
+
+            bond2 = mol.GetBondBetweenAtoms(N_atom.GetIdx(), terminal_oxygens[1].GetIdx())
+            bond2.SetBondType(Chem.rdchem.BondType.DOUBLE)
+            terminal_oxygens[1].SetFormalCharge(0)
+
+def sanitize_nitro(mol):
+    for atom in mol.GetAtoms():
+        sanitize_nitro_Natom(atom)
+    return mol
+
+def is_terminal_nitrogen(N_atom):
+    if N_atom.GetSymbol() == 'N' and len(N_atom.GetNeighbors()) == 1:
+        return True
+    else:
+        return False
+
+def sanitize_nitrine_Natom(atom, verbose=True):
+    if atom.GetSymbol() == "N" and len(atom.GetNeighbors()) == 2:
+        mol = atom.GetOwningMol()
+        nei1, nei2 = atom.GetNeighbors()[0], atom.GetNeighbors()[1]
+        if nei1.GetSymbol() == "N" and nei2.GetSymbol() == "N":
+            if is_terminal_nitrogen(nei1):
+                N_terminal = nei1
+                N_non_terminal = nei2
+            elif is_terminal_nitrogen(nei2):
+                N_terminal = nei2
+                N_non_terminal = nei1
+            else:
+                N_terminal = None
+                N_non_terminal = None
+            if (N_terminal is not None) and (N_non_terminal is not None):
+                # set X-N=[N+]=[N-]
+                if verbose:
+                    print("Detecting nitrine group, fixing it...")
+                bond = mol.GetBondBetweenAtoms(atom.GetIdx(), N_terminal.GetIdx())
+                bond.SetBondType(Chem.rdchem.BondType.DOUBLE)
+                N_terminal.SetFormalCharge(-1)
+
+                bond = mol.GetBondBetweenAtoms(atom.GetIdx(), N_non_terminal.GetIdx())
+                bond.SetBondType(Chem.rdchem.BondType.DOUBLE)
+                atom.SetFormalCharge(1)                
+
+def contain_hetero_aromatic(mol):
+    flag = False
+    for atom in mol.GetAtoms():
+        if atom.GetSymbol() != "C" and atom.GetIsAromatic():
+            flag = True
+            break
+    return flag
+
+# for carbon with explicit valence > 4
+def regularize_carbon_bond_order(atom, verbose=True):
+    if atom.GetSymbol() == "C" and get_explicit_valence(atom) > 4:
+        if verbose:
+            print("Detecting carbon with explicit valence > 4, fixing it...")
+        mol = atom.GetOwningMol()
+        double_bond_idx = -1
+        for nei in atom.GetNeighbors():
+            bond = mol.GetBondBetweenAtoms(atom.GetIdx(), nei.GetIdx())
+            if bond.GetBondTypeAsDouble() == 2:
+                double_bond_idx = bond.GetIdx()
+                break
+        if double_bond_idx != -1:
+            for bond in atom.GetBonds():
+                if bond.GetIdx() != double_bond_idx:
+                    bond.SetBondType(Chem.rdchem.BondType.SINGLE)
+
+# for nitrogen with explicit valence > 4
+def regularize_nitrogen_bond_order(atom, verbose=True):
+    mol = atom.GetOwningMol()
+    if atom.GetSymbol() == "N" and get_explicit_valence(atom) > 4:
+        O_atoms = get_terminal_oxygens(atom)
+        for O_atom in O_atoms:
+            bond = mol.GetBondBetweenAtoms(atom.GetIdx(), O_atom.GetIdx())
+            if bond.GetBondTypeAsDouble() == 2:
+                bond.SetBondType(Chem.rdchem.BondType.SINGLE)
+                O_atom.SetFormalCharge(-1)
+
+
+def sanitize_mol(mol, verbose=False):
+    for atom in mol.GetAtoms():
+        sanitize_carboxyl_Catom(atom, verbose)
+        sanitize_phosphate_Patom(atom, verbose)
+        sanitize_sulfate_Satom(atom, verbose)
+        sanitize_nitro_Natom(atom, verbose)
+        sanitize_nitrine_Natom(atom, verbose)
+        regularize_carbon_bond_order(atom, verbose)
+        regularize_nitrogen_bond_order(atom, verbose)
+    return mol
+
+
+# copy from FEprep
+def mol_edit_log(mol, i, j):
+    if not mol.HasProp("edit"):
+        mol.SetProp("edit", "%d_%d" % (i, j))
+    else:
+        edited = mol.GetProp("edit")
+        mol.SetProp("edit", edited + ",%d_%d" % (i, j))
+
+def kekulize_aromatic_heterocycles(mol_in, assign_formal_charge=True, sanitize=True):
+    mol = Chem.RWMol(mol_in)
+    rings = Chem.rdmolops.GetSymmSSSR(mol)
+    rings = [list(i) for i in list(rings)]
+    rings.sort(key=lambda r: len(r))
+
+    def search_and_assign_ring(mol, ring, hetero, start, forward=True, start_switch=True):
+        j = start
+        switch = start_switch
+        lring = len(ring)
+        delta = 1 if forward else -1
+        n_edit = 0
+        n_double = 0
+        while not ((j in hetero) & (not switch)):
+            btype = BondType.SINGLE if switch else BondType.DOUBLE
+            bond = mol.GetBondBetweenAtoms(ring[j], ring[(j + delta) % lring])
+            if bond.GetBondType() == BondType.AROMATIC:
+                bond.SetBondType(btype)
+                mol_edit_log(mol, ring[j], ring[(j + delta) % lring])
+                # print(ring[j], ring[(j + delta) % lring], bond.GetBondType())
+                if btype == BondType.DOUBLE:
+                    n_double += 1
+                n_edit += 1
+            else:
+                break
+            j = (j + delta) % lring
+            switch = not switch
+        return n_edit, n_double
+
+    def print_bondtypes(mol, rings):
+        for ring in rings:
+            lring = len(ring)
+            btype = []
+            for i in range(lring):
+                btype.append(mol.GetBondBetweenAtoms(ring[i], ring[(i + 1) % lring]).GetBondType())
+            atoms = [mol.GetAtomWithIdx(i).GetSymbol() for i in ring]
+            print(ring)
+            print(atoms)
+            print(btype)
+
+    def hetero_priority(idx, mol):
+        atom = mol.GetAtomWithIdx(idx)
+        sym = atom.GetSymbol()
+        valence = len(atom.GetBonds())
+
+        if (sym in ['O', 'S']) & (valence == 2):
+            return 0
+        elif (sym in ['N', 'P', 'As', 'B']):
+            if valence == 3:
+                return 1
+            elif valence == 2:
+                return 2
+
+    # save carbon/hetero aromatic rings
+    CAr = []
+    HAr = []
+    for ring in rings:
+        lring = len(ring)
+        bAllAr = True
+        bAllC = True
+        for i in range(lring):
+            atom = mol.GetAtomWithIdx(ring[i])
+            if atom.GetSymbol() != 'C':
+                bAllC = False
+
+            bond = mol.GetBondBetweenAtoms(ring[i], ring[(i + 1) % lring])
+            if bond.GetBondType() != BondType.AROMATIC:
+                bAllAr = False
+        if bAllAr and bAllC:
+            CAr.append(ring)
+        elif bAllAr and not bAllC:
+            HAr.append(ring)
+
+    if len(HAr) == 0: 
+        # no hetrerocycles
+        return mol_in
+    else:
+        # edit heterocycles
+        for ring in HAr:
+            lring = len(ring)
+            cring = len(CAr)
+            hetero = []
+            hasDouble = []
+            fuseCAr = []
+            fuseDouble = []
+            for i in range(lring):
+                fuseCAr.append(-1)
+                for j in range(cring):
+                    if ring[i] in CAr[j]:
+                        fuseCAr[i] = j
+                        break
+                if i > 1:
+                    if (fuseCAr[i] == fuseCAr[i-1]) & (fuseCAr[i] >= 0):
+                        fuseDouble.append(i)
+                atom = mol.GetAtomWithIdx(ring[i])
+                if atom.GetSymbol() != 'C':
+                    hetero.append(i)
+                atom_bonds = atom.GetBonds()
+                btype = [bond.GetBondType() for bond in atom_bonds]
+                # print(btype)
+                if BondType.DOUBLE in btype:
+                    hasDouble.append(i)
+                bond = mol.GetBondBetweenAtoms(ring[i], ring[(i + 1) % lring])
+
+            if (fuseCAr[0] == fuseCAr[lring-1]) & (fuseCAr[0] >= 0):
+                fuseDouble.append(0)
+
+            if (len(hetero) > 0) | (len(hasDouble) > 0):
+                n_targetDouble = lring // 2
+                n_targetEdit = lring
+                hetero_prior = {i: hetero_priority(ring[i], mol) for i in hetero}
+                hetero.sort(key=lambda i: hetero_prior[i])
+                for i in hasDouble:
+                    d1, e1 = search_and_assign_ring(mol, ring, hetero, i, forward=True)
+                    d2, e2 = search_and_assign_ring(mol, ring, hetero, i, forward=False)
+                    n_targetDouble -= (d1 + d2 + 1)
+                    n_targetEdit -= (e1 + e2)
+                for i in fuseDouble:
+                    bond = mol.GetBondBetweenAtoms(ring[i], ring[(i - 1) % lring])
+                    if bond.GetBondType() == BondType.AROMATIC:
+                        bond.SetBondType(BondType.DOUBLE)
+                        mol_edit_log(mol, ring[i], ring[(i - 1) % lring])
+                    d1, e1 = search_and_assign_ring(mol, ring, hetero, i, forward=True)
+                    d2, e2 = search_and_assign_ring(mol, ring, hetero, (i - 1) % lring, forward=False)
+                    n_targetDouble -= (d1 + d2 + 1)
+                    n_targetEdit -= (e1 + e2 + 1)
+                for i in hetero:
+                    atom = mol.GetAtomWithIdx(ring[i])
+                    if (hetero_prior[i] == 2) | (n_targetDouble * 2 >= n_targetEdit):
+                        forward_btype = mol.GetBondBetweenAtoms(ring[i], ring[(i + 1) % lring]).GetBondType()
+                        backward_btype = mol.GetBondBetweenAtoms(ring[i], ring[(i - 1) % lring]).GetBondType()
+                        if forward_btype != BondType.AROMATIC:
+                            switch = forward_btype == BondType.DOUBLE
+                            d1, e1 = search_and_assign_ring(mol, ring, hetero, i, forward=False, start_switch=switch)
+                            d2 = e2 = 0
+                        elif backward_btype != BondType.AROMATIC:
+                            switch = backward_btype == BondType.DOUBLE
+                            d1, e1 = search_and_assign_ring(mol, ring, hetero, i, forward=True, start_switch=switch)
+                            d2 = e2 = 0
+                        else:
+                            d1, e1 = search_and_assign_ring(mol, ring, hetero, i, forward=True, start_switch=True)
+                            d2, e2 = search_and_assign_ring(mol, ring, hetero, i, forward=False, start_switch=False)
+                        n_targetDouble -= (d1 + d2)
+                        n_targetEdit -= (e1 + e2)
+                    else:
+                        d1, e1 = search_and_assign_ring(mol, ring, hetero, i, forward=True, start_switch=True)
+                        d2, e2 = search_and_assign_ring(mol, ring, hetero, i, forward=False, start_switch=True)
+                        n_targetDouble -= (d1 + d2)
+                        n_targetEdit -= (e1 + e2)
+
+        for ring in CAr:
+            lring = len(ring)
+            for i in range(lring):
+                bond = mol.GetBondBetweenAtoms(ring[i], ring[(i + 1) % lring])
+                bond.SetBondType(BondType.AROMATIC)
+        print("Manual kekulization for aromatic heterocycles:")
+        print_bondtypes(mol, rings)
+
+        atoms = mol.GetAtoms()
+        for i in range(len(atoms)):
+            mol.ReplaceAtom(i, Chem.Atom(atoms[i].GetSymbol()))
+        mol_edited = mol.GetMol()
+        # charge assignment
+        if assign_formal_charge:
+            mol_edited = regularize_formal_charges(mol_edited, sanitize=False)
+        if not sanitize:
+            return mol_edited
+        else:
+            try:
+                Chem.SanitizeMol(mol_edited)
+                return mol_edited
+            except Exception as e:
+                raise RuntimeError(f"Manual kekulization for aromatic heterocycles failed, below are errors:\n\t {e}")
+
+def convert_by_obabel(mol, cache_dir=os.path.join(os.getcwd(), '.cache'), obabel_path="obabel"):
+    if not os.path.exists(cache_dir):
+        os.mkdir(cache_dir)
+    if mol.HasProp("_Name"):
+        name = mol.GetProp("_Name")
+    else:
+        name = f"mol{int(time.time())}"
+    mol_file_in = os.path.join(cache_dir, f'{name}.mol')
+    mol_file_out = os.path.join(cache_dir, f'{name}_obabel.mol')
+    Chem.MolToMolFile(mol, mol_file_in, kekulize=False)
+    obConversion = openbabel.OBConversion()
+    obConversion.SetInAndOutFormats("mol", "mol")
+    mol = openbabel.OBMol()
+    obConversion.ReadFile(mol, mol_file_in)
+    obConversion.WriteFile(mol, mol_file_out)
+    mol_obabel = Chem.MolFromMolFile(mol_file_out, removeHs=False, sanitize=False)
+    return mol_obabel
+
+def super_sanitize_mol(mol, name=None, verbose=True):
+    if name is None:
+        if mol.HasProp("_Name"):
+            name = mol.GetProp("_Name")
+        else:
+            name = "mol"
+    try:
+        if verbose:
+            print("=====Stage 1: use Hermite procedure=====")
+        # use our procedure
+        mol = sanitize_mol(mol, verbose)
+        mol = regularize_formal_charges(mol, sanitize=False)
+        mol_copy = deepcopy(mol)
+        Chem.SanitizeMol(mol_copy)
+        if verbose:
+            print(name, "Success.")
+        return mol_copy
+    except Exception as e:
+        try:
+            if verbose:
+                print("Hermite procedure failed, maybe due to unsupported representation of hetero aromatic rings, re-try with obabel")
+                print("=====Stage 2: re-try with obabel=====")
+            mol = convert_by_obabel(mol)
+            mol = sanitize_mol(mol, verbose)
+            mol = kekulize_aromatic_heterocycles(mol, assign_formal_charge=False, sanitize=False)    # aromatic heterocycles
+            mol = regularize_formal_charges(mol, sanitize=False)
+            mol_copy = deepcopy(mol)
+            Chem.SanitizeMol(mol_copy)
+            if verbose:
+                print(name, "Success.")
+            return mol_copy
+        except Exception as e:
+            if verbose:
+                print(e)
+                print(name, "Failed!")
+            return None
+
+class Sanitizer(object):
+    def __init__(self, level='medium', raise_errors=True, verbose=False):
+        '''
+            Set up sanitizer.
+            --------
+            Parameters:
+                level : 'low', 'medium' or 'high'.
+                    `low`    - use rdkit.Chem.SanitizeMol() to sanitize
+                    `medium` - before using rdkit, assign formal charges of each atom first, which requires
+                                the rightness of bond order information
+                    `high`   - try to regularize bond order of nitro, phosphate, sulfate, nitrine, guanidine, 
+                                pyridine-oxide function groups and aromatic heterocycles. If failed, the program
+                                will call obabel to pre-process the mol object and re-try the procedure.
+        '''
+        self._check_level(level)
+        self.level = level
+        self.raise_errors = raise_errors
+        self.verbose = verbose
+
+    def _check_level(self, level):
+        if level not in ['low', 'medium', 'high']:
+            raise ValueError(f"Invalid level '{level}', please set to 'low', 'medium' or 'high'")
+        else:
+            if level == 'high' and not USE_OBABEL:
+                raise ModuleNotFoundError("obabel not installed, high level sanitizer cannot work")
+    
+    def _handle_exception(self, error_info):
+        if self.raise_errors:
+            raise SanitizeError(error_info)
+        elif self.verbose:
+            print(error_info)
+
+    def sanitize(self, mol):
+        '''
+            Sanitize mol according to `self.level`. If failed, return None.
+        '''
+        if self.level == "low":
+            try:
+                Chem.SanitizeMol(mol)
+                return mol
+            except Exception as e:
+                error_info = f"Sanitization Failed, please use more strict sanitizer by setting 'level' to 'medium' or 'high'. The error occurs:\n\t{e}"
+                self._handle_exception(error_info)
+                return None
+        elif self.level == "medium":
+            try:
+                mol = regularize_formal_charges(mol, sanitize=False)
+                Chem.SanitizeMol(mol)
+                return mol
+            except Exception as e:
+                error_info = f"Sanitization Failed, please use more strict sanitizer by setting 'level' to 'high'. The error occurs:\n\t{e}"
+                self._handle_exception(error_info)
+                return None
+        elif self.level == "high":
+            mol = super_sanitize_mol(mol, verbose=self.verbose)
+            error_info = "Sanitization Failed. Please check your molecule file."
+            if mol is None:
+                self._handle_exception(error_info)
+            return mol
+
+class SanitizeError(Exception):
+    def __init__(self, content="Sanitization Failed."):
+        self.content = content
+
+    def __str__(self):
+        return self.content
+
+    def __repr__(self):
+        return self.__str__()
diff --git a/dpdata/rdkit/utils.py b/dpdata/rdkit/utils.py
new file mode 100644
index 000000000..a8a52be86
--- /dev/null
+++ b/dpdata/rdkit/utils.py
@@ -0,0 +1,108 @@
+from rdkit import Chem
+from rdkit.Chem import AllChem
+import numpy as np
+
+def mol_to_system_data(mol):
+    if not isinstance(mol, Chem.rdchem.Mol):
+        raise TypeError(f"rdkit.Chem.Mol required, not {type(mol)}")
+
+    num_confs = mol.GetNumConformers()
+    if num_confs:
+        atom_symbols = [at.GetSymbol() for at in mol.GetAtoms()]
+        atom_names, atom_types, atom_numbs = np.unique(atom_symbols, return_inverse=True, return_counts=True)
+        coords = np.array([conf.GetPositions() for conf in mol.GetConformers()])
+        bonds = np.array([[bond.GetBeginAtomIdx(),
+                           bond.GetEndAtomIdx(),
+                           bond.GetBondTypeAsDouble()] for bond in mol.GetBonds()])
+        formal_charges = np.array([at.GetFormalCharge() for at in mol.GetAtoms()], dtype=np.int32)
+        data = {}
+        data['atom_numbs'] = list(atom_numbs)
+        data['atom_names'] = list(atom_names)
+        data['atom_types'] = atom_types
+        data['cells'] = np.array([[[100., 0., 0.],
+                                   [0., 100., 0.],
+                                   [0., 0., 100.]] for _ in range(num_confs)])
+        data['coords'] = coords
+        data['bonds'] = bonds
+        data['formal_charges'] = formal_charges
+        data['orig'] = np.array([0., 0., 0.])
+        # other properties
+        if mol.HasProp("_Name"):
+            data['_name'] = mol.GetProp('_Name')
+        return data
+    else:
+        raise ValueError("The moleclue does not contain 3-D conformers")
+
+def system_data_to_mol(data):
+    mol_ed = Chem.RWMol()
+    atom_symbols = [data['atom_names'][i] for i in data['atom_types']]
+    # add atoms
+    for atom_type in data['atom_types']:
+        symbol = data['atom_names'][atom_type]
+        atom = Chem.Atom(symbol)
+        mol_ed.AddAtom(atom)
+    # add bonds
+    for bond_info in data['bonds']:
+        if bond_info[2] == 1:
+            mol_ed.AddBond(int(bond_info[0]), int(bond_info[1]), Chem.BondType.SINGLE)
+        elif bond_info[2] == 2:
+            mol_ed.AddBond(int(bond_info[0]), int(bond_info[1]), Chem.BondType.DOUBLE)
+        elif bond_info[2] == 3:
+            mol_ed.AddBond(int(bond_info[0]), int(bond_info[1]), Chem.BondType.TRIPLE)
+        elif bond_info[2] == 1.5:
+            mol_ed.AddBond(int(bond_info[0]), int(bond_info[1]), Chem.BondType.AROMATIC)
+    # set conformers
+    for frame_idx in range(data['coords'].shape[0]):
+        conf = Chem.rdchem.Conformer(len(data['atom_types']))
+        for atom_idx in range(len(data['atom_types'])):
+            conf.SetAtomPosition(atom_idx, data['coords'][frame_idx][atom_idx])
+        mol_ed.AddConformer(conf, assignId=True)
+    mol = mol_ed.GetMol()
+    # set formal charges
+    for idx, atom in enumerate(mol.GetAtoms()):
+        atom.SetFormalCharge(data['formal_charges'][idx])
+    # set mol name
+    if '_name' in list(data.keys()):
+        mol.SetProp("_Name", data['_name'])
+    # sanitize
+    Chem.SanitizeMol(mol_ed)
+    return mol        
+
+
+def check_same_atom(atom_1, atom_2):
+    if atom_1.GetIdx() != atom_2.GetIdx():
+        return False
+    elif atom_1.GetSymbol() != atom_2.GetSymbol():
+        return False
+    else:
+        return True
+
+def check_same_molecule(mol_1, mol_2):
+    flag = True
+    for bond_1, bond_2 in zip(mol_1.GetBonds(), mol_2.GetBonds()):
+        begin_atom_1, end_atom_1 = bond_1.GetBeginAtom(), bond_1.GetEndAtom()
+        begin_atom_2, end_atom_2 = bond_2.GetBeginAtom(), bond_2.GetEndAtom()
+        if not check_same_atom(begin_atom_1, begin_atom_2):
+            flag = False
+            break
+        elif not check_same_atom(end_atom_1, end_atom_2):
+            flag = False
+            break
+    return flag
+
+def check_molecule_list(mols):
+    flag = True
+    for mol in mols[1:]:
+        if not check_same_molecule(mol, mols[0]):
+            flag = False
+            break
+    return flag
+
+def combine_molecules(mols):
+    if check_molecule_list(mols):
+        for mol in mols[1:]:
+            for conf in mol.GetConformers():
+                mols[0].AddConformer(conf, assignId=True)
+        return mols[0]
+    else:
+        raise ValueError("molecules are not of the same topology.")
\ No newline at end of file
diff --git a/dpdata/siesta/__init__.py b/dpdata/siesta/__init__.py
new file mode 100644
index 000000000..8b1378917
--- /dev/null
+++ b/dpdata/siesta/__init__.py
@@ -0,0 +1 @@
+
diff --git a/dpdata/system.py b/dpdata/system.py
index 298f4e8fd..1bd509d67 100644
--- a/dpdata/system.py
+++ b/dpdata/system.py
@@ -17,6 +17,7 @@
 import dpdata.md.pbc
 import dpdata.gaussian.log
 import dpdata.amber.md
+import dpdata.amber.sqm
 import dpdata.cp2k.output
 from dpdata.cp2k.output import Cp2kSystems
 import dpdata.pwmat.movement
@@ -696,6 +697,13 @@ def to_deepmd_raw(self, folder) :
         Dump the system in deepmd raw format to `folder`
         """
         dpdata.deepmd.raw.dump(folder, self.data)
+    
+    @register_from_funcs.register_funcs('sqm/out')
+    def from_sqm_out(self, fname):
+        '''
+        Read from ambertools sqm.out
+        '''
+        self.data = dpdata.amber.sqm.to_system_data(fname)
 
     @register_from_funcs.register_funcs('siesta/output')
     def from_siesta_output(self, fname):
@@ -1849,7 +1857,4 @@ def elements_index_map(elements,standard=False,inverse=False):
         return dict(zip(range(len(elements)),elements))
     else:
         return dict(zip(elements,range(len(elements))))
-
-
-
 # %%
diff --git a/setup.py b/setup.py
index 4f831fd4a..ae2e4e049 100644
--- a/setup.py
+++ b/setup.py
@@ -37,7 +37,8 @@
               'dpdata/pwmat', 
               'dpdata/amber',
               'dpdata/fhi_aims',
-              'dpdata/gromacs'
+              'dpdata/gromacs',
+              'dpdata/rdkit'
     ],
     package_data={'dpdata':['*.json']},
     classifiers=[
diff --git a/tests/amber/sqm.out b/tests/amber/sqm.out
new file mode 100644
index 000000000..764dc8649
--- /dev/null
+++ b/tests/amber/sqm.out
@@ -0,0 +1,138 @@
+            --------------------------------------------------------
+                             AMBER SQM VERSION 19
+ 
+                                     By
+              Ross C. Walker, Michael F. Crowley, Scott Brozell,
+                         Tim Giese, Andreas W. Goetz,
+                        Tai-Sung Lee and David A. Case
+ 
+            --------------------------------------------------------
+ 
+
+--------------------------------------------------------------------------------
+  QM CALCULATION INFO
+--------------------------------------------------------------------------------
+
+| QMMM: Citation for AMBER QMMM Run:
+| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
+
+QMMM: SINGLET STATE CALCULATION
+QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 18
+
+| QMMM: *** Selected Hamiltonian *** 
+| QMMM: AM1         
+
+| QMMM: *** Parameter sets in use ***
+| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
+| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
+| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
+
+| QMMM: *** SCF convergence criteria ***
+| QMMM: Energy change                :  0.1D-09 kcal/mol
+| QMMM: Error matrix |FP-PF|         :  0.1D+00 au
+| QMMM: Density matrix change        :  0.5D-06
+| QMMM: Maximum number of SCF cycles :     1000
+
+| QMMM: *** Diagonalization Routine Information ***
+| QMMM: Pseudo diagonalizations are allowed.
+| QMMM: Auto diagonalization routine selection is in use.
+| QMMM:
+| QMMM: Timing diagonalization routines:
+| QMMM:                              norbs =       34
+| QMMM:    diag iterations used for timing =       20
+| QMMM:
+| QMMM:              Internal diag routine = 0.002953 seconds
+| QMMM:                 Dspev diag routine = 0.174916 seconds
+| QMMM:                Dspevd diag routine = 0.002847 seconds
+| QMMM:                Dspevx diag routine = 0.018112 seconds
+| QMMM:                 Dsyev diag routine = 0.016637 seconds
+| QMMM:                Dsyevd diag routine = 0.002183 seconds
+| QMMM:                Dsyevr diag routine = 0.003551 seconds
+| QMMM:
+| QMMM:                Pseudo diag routine = 0.000901 seconds
+| QMMM:
+| QMMM: Using dsyevd routine (diag_routine=6).
+
+  QMMM: QM Region Cartesian Coordinates (*=link atom) 
+  QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
+  QMMM:     1        1      C        0.0090    2.0020    2.9920
+  QMMM:     2        2      N       -0.5270    2.5050    4.1370
+  QMMM:     3        3      C       -0.5300    0.8560    2.3840
+  QMMM:     4        4      N        1.0500    2.6460    2.4950
+  QMMM:     5        5      H       -0.1200    3.3160    4.5380
+  QMMM:     6        6      H       -1.3090    2.0860    4.5790
+  QMMM:     7        7      C        0.0580    0.4000    1.2310
+  QMMM:     8        8      H       -1.3780    0.3570    2.8170
+  QMMM:     9        9      C        1.1550    1.0720    0.6990
+  QMMM:    10       10      H       -0.3330   -0.4760    0.7420
+  QMMM:    11       11      C        1.5970    2.1840    1.3810
+  QMMM:    12       12      H        1.6400    0.7440   -0.2010
+  QMMM:    13       13      H        2.4420    2.7430    1.0170
+
+--------------------------------------------------------------------------------
+  RESULTS
+--------------------------------------------------------------------------------
+
+      iter         sqm energy              rms gradient
+      ----    -------------------    -----------------------
+xmin    10       33.5359 kcal/mol        0.0648 kcal/(mol*A)
+xmin    20       33.3605 kcal/mol        2.9126 kcal/(mol*A)
+xmin    30       32.8935 kcal/mol        0.2527 kcal/(mol*A)
+xmin    40       32.8838 kcal/mol        0.0537 kcal/(mol*A)
+xmin    50       32.8834 kcal/mol        0.0102 kcal/(mol*A)
+xmin    60       32.8833 kcal/mol        0.0020 kcal/(mol*A)
+  ... geometry converged !
+ 
+ Final MO eigenvalues (eV):
+ -39.9239  -35.3153  -32.8895  -29.5926  -24.0617  -23.2695  -18.1247  -17.8391
+ -16.8615  -15.5408  -14.8743  -14.4815  -13.8252  -12.8035  -11.7649  -10.5917
+ -10.5457   -8.8383    0.3220    0.4382    2.6389    2.8672    3.6975    3.8711
+   4.0454    4.1744    4.4373    4.7364    4.9688    5.3485    5.5584    5.8794
+   6.1725    6.9900
+
+ Heat of formation   =         32.88333532 kcal/mol  (        1.42592842 eV)
+
+ Total SCF energy    =     -26203.17173278 kcal/mol  (    -1136.25479089 eV)
+ Electronic energy   =    -102669.26620941 kcal/mol  (    -4452.07346643 eV)
+ Core-core repulsion =      76466.09447663 kcal/mol  (     3315.81867554 eV)
+ 
+    Atomic Charges for Step       1 :
+  Atom    Element       Mulliken Charge
+     1      C                  0.105
+     2      N                 -0.324
+     3      C                 -0.235
+     4      N                 -0.198
+     5      H                  0.204
+     6      H                  0.193
+     7      C                 -0.059
+     8      H                  0.141
+     9      C                 -0.230
+    10      H                  0.135
+    11      C                 -0.031
+    12      H                  0.143
+    13      H                  0.156
+ Total Mulliken Charge =      -0.000
+ 
+                  X        Y        Z     TOTAL  
+  QM DIPOLE    -1.768   -0.338   -0.580    1.891
+ 
+ Final Structure
+
+  QMMM: QM Region Cartesian Coordinates (*=link atom) 
+  QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
+  QMMM:     1        1      C        0.0389    2.0017    3.0427
+  QMMM:     2        2      N       -0.4634    2.4081    4.2873
+  QMMM:     3        3      C       -0.5107    0.8424    2.4126
+  QMMM:     4        4      N        1.0975    2.6846    2.4920
+  QMMM:     5        5      H       -0.1848    3.3129    4.5972
+  QMMM:     6        6      H       -1.4313    2.2158    4.4122
+  QMMM:     7        7      C        0.0594    0.3846    1.2306
+  QMMM:     8        8      H       -1.3621    0.3152    2.8622
+  QMMM:     9        9      C        1.1460    1.0651    0.6800
+  QMMM:    10       10      H       -0.3464   -0.5099    0.7348
+  QMMM:    11       11      C        1.6183    2.2039    1.3541
+  QMMM:    12       12      H        1.6200    0.7291   -0.2494
+  QMMM:    13       13      H        2.4726    2.7815    0.9546
+
+           --------- Calculation Completed ----------
+
diff --git a/tests/bond_order/BOH4-.mol b/tests/bond_order/BOH4-.mol
new file mode 100644
index 000000000..714b24173
--- /dev/null
+++ b/tests/bond_order/BOH4-.mol
@@ -0,0 +1,22 @@
+
+     RDKit          3D
+
+  9  8  0  0  0  0  0  0  0  0999 V2000
+   -0.3467   -1.1124   -1.0725 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.1774   -0.0704   -0.1870 B   0  0  0  0  0  4  0  0  0  0  0  0
+   -0.0524    1.2169   -0.8307 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.6395   -0.2656   -0.1144 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.3605   -0.1491    1.1664 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1946   -1.4561   -0.7105 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.5414    1.8645   -0.2943 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.9678   -0.2364    0.8123 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2892    0.2085    1.2308 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  2  3  1  0
+  2  4  1  0
+  2  5  1  0
+  1  6  1  0
+  3  7  1  0
+  4  8  1  0
+  5  9  1  0
+M  END
diff --git a/tests/bond_order/C5H5-.mol b/tests/bond_order/C5H5-.mol
new file mode 100644
index 000000000..4a9640062
--- /dev/null
+++ b/tests/bond_order/C5H5-.mol
@@ -0,0 +1,25 @@
+
+     RDKit          3D
+
+ 10 10  0  0  0  0  0  0  0  0999 V2000
+    1.1589    0.0289    0.0218 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.3434    1.1375    0.0950 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.9573    0.6854    0.0376 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.9237   -0.6963   -0.0702 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.3941   -1.1202   -0.0812 C   0  0  0  0  0  3  0  0  0  0  0  0
+    2.2384    0.0086    0.0384 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.6427    2.1738    0.1813 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.8629    1.2749    0.0686 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.7894   -1.3506   -0.1361 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7559   -2.1420   -0.1553 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0
+  2  3  1  0
+  3  4  2  0
+  4  5  1  0
+  5  1  1  0
+  1  6  1  0
+  2  7  1  0
+  3  8  1  0
+  4  9  1  0
+  5 10  1  0
+M  END
diff --git a/tests/bond_order/CH3CC-.mol b/tests/bond_order/CH3CC-.mol
new file mode 100644
index 000000000..494c8331f
--- /dev/null
+++ b/tests/bond_order/CH3CC-.mol
@@ -0,0 +1,16 @@
+
+     RDKit          3D
+
+  6  5  0  0  0  0  0  0  0  0999 V2000
+   -0.4942    0.0244   -0.0265 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.9626   -0.0132    0.0194 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.1608   -0.0420    0.0394 C   0  0  0  0  0  3  0  0  0  0  0  0
+   -0.9042   -0.0082    1.0068 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8567    0.9445   -0.5170 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8683   -0.9055   -0.5221 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  2  3  3  0
+  1  4  1  0
+  1  5  1  0
+  1  6  1  0
+M  END
diff --git a/tests/bond_order/CH3NC.mol b/tests/bond_order/CH3NC.mol
new file mode 100644
index 000000000..7a042a3df
--- /dev/null
+++ b/tests/bond_order/CH3NC.mol
@@ -0,0 +1,16 @@
+
+     RDKit          3D
+
+  6  5  0  0  0  0  0  0  0  0999 V2000
+    2.1029   -0.0145    0.0170 C   0  0  0  0  0  3  0  0  0  0  0  0
+    0.9414   -0.0028    0.0122 N   0  0  0  0  0  4  0  0  0  0  0  0
+   -0.4788   -0.0102    0.0055 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8341   -0.6533   -0.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8681   -0.3314    0.9923 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8632    1.0123   -0.2052 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  3  0
+  2  3  1  0
+  3  4  1  0
+  3  5  1  0
+  3  6  1  0
+M  END
diff --git a/tests/bond_order/CH3NH3+.mol b/tests/bond_order/CH3NH3+.mol
new file mode 100644
index 000000000..5dc06ed99
--- /dev/null
+++ b/tests/bond_order/CH3NH3+.mol
@@ -0,0 +1,20 @@
+
+     RDKit          3D
+
+  8  7  0  0  0  0  0  0  0  0999 V2000
+   -0.7380   -0.0104    0.0504 N   0  0  0  0  0  4  0  0  0  0  0  0
+    0.7029   -0.0301   -0.0070 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.0863   -0.1569   -0.9255 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.0283    0.9546    0.3163 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1542   -0.7528    0.6281 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0120    0.9177   -0.5299 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.1838    0.0069    0.9852 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.1082   -0.9290   -0.5177 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  1  3  1  0
+  1  4  1  0
+  1  5  1  0
+  2  6  1  0
+  2  7  1  0
+  2  8  1  0
+M  END
diff --git a/tests/bond_order/CH3NO2.mol b/tests/bond_order/CH3NO2.mol
new file mode 100644
index 000000000..dd2d49115
--- /dev/null
+++ b/tests/bond_order/CH3NO2.mol
@@ -0,0 +1,18 @@
+
+     RDKit          3D
+
+  7  6  0  0  0  0  0  0  0  0999 V2000
+    1.4472   -1.1105   -0.0946 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7839   -0.0803   -0.0649 N   0  0  0  0  0  4  0  0  0  0  0  0
+   -0.6616   -0.0203    0.0443 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.4357    1.1273   -0.1393 O   0  0  0  0  0  1  0  0  0  0  0  0
+   -1.1321   -1.0057   -0.1374 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.9987    0.7548   -0.6870 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8746    0.3346    1.0787 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0
+  2  3  1  0
+  2  4  1  0
+  3  5  1  0
+  3  6  1  0
+  3  7  1  0
+M  END
diff --git a/tests/bond_order/CH3OAsO3_2-.mol b/tests/bond_order/CH3OAsO3_2-.mol
new file mode 100644
index 000000000..7be918e67
--- /dev/null
+++ b/tests/bond_order/CH3OAsO3_2-.mol
@@ -0,0 +1,22 @@
+
+     RDKit          3D
+
+  9  8  0  0  0  0  0  0  0  0999 V2000
+   -1.3508    1.6206   -1.1478 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2517    0.2899   -0.2069 As  0  0  0  0  0  5  0  0  0  0  0  0
+    0.4866    0.0891    0.3296 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.3447   -0.2336   -0.6923 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.3455    0.4600    1.2300 O   0  0  0  0  0  1  0  0  0  0  0  0
+   -1.7369   -1.2000   -1.1526 O   0  0  0  0  0  1  0  0  0  0  0  0
+    2.3628    0.1527   -0.4480 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.4364   -1.3299   -0.7847 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0544    0.1512   -1.6814 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0
+  2  3  1  0
+  3  4  1  0
+  2  5  1  0
+  2  6  1  0
+  4  7  1  0
+  4  8  1  0
+  4  9  1  0
+M  END
diff --git a/tests/bond_order/CH3OH.mol b/tests/bond_order/CH3OH.mol
new file mode 100644
index 000000000..ae2647120
--- /dev/null
+++ b/tests/bond_order/CH3OH.mol
@@ -0,0 +1,16 @@
+
+     RDKit          3D
+
+  6  5  0  0  0  0  0  0  0  0999 V2000
+   -0.3858    0.0121   -0.0046 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.9338    0.3744   -0.2961 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.4710   -0.6137    0.8940 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7417   -0.5863   -0.8591 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.9359    0.9788    0.1119 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.6006   -0.1653    0.1539 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  1  3  1  0
+  1  4  1  0
+  1  5  1  0
+  2  6  1  0
+M  END
diff --git a/tests/bond_order/CH3OPO3_2-.mol b/tests/bond_order/CH3OPO3_2-.mol
new file mode 100644
index 000000000..f80862180
--- /dev/null
+++ b/tests/bond_order/CH3OPO3_2-.mol
@@ -0,0 +1,22 @@
+
+     RDKit          3D
+
+  9  8  0  0  0  0  0  0  0  0999 V2000
+   -2.2229    0.2615   -1.3314 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2337    0.0923   -0.1748 P   0  0  0  0  0  5  0  0  0  0  0  0
+    0.2863   -0.0815   -0.8472 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.3111   -0.1138    0.0645 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.3507    1.4785    0.8042 O   0  0  0  0  0  1  0  0  0  0  0  0
+   -1.7333   -1.2840    0.6728 O   0  0  0  0  0  1  0  0  0  0  0  0
+    2.1323    0.5613   -0.3070 H   0  0  0  0  0  0  0  0  0  0  0  0
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diff --git a/tests/bond_order/CH3PH3+.mol b/tests/bond_order/CH3PH3+.mol
new file mode 100644
index 000000000..066e9d454
--- /dev/null
+++ b/tests/bond_order/CH3PH3+.mol
@@ -0,0 +1,20 @@
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diff --git a/tests/bond_order/CH3SH.mol b/tests/bond_order/CH3SH.mol
new file mode 100644
index 000000000..5a566c758
--- /dev/null
+++ b/tests/bond_order/CH3SH.mol
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diff --git a/tests/bond_order/CH3SO3-.mol b/tests/bond_order/CH3SO3-.mol
new file mode 100644
index 000000000..2b5fd7bf8
--- /dev/null
+++ b/tests/bond_order/CH3SO3-.mol
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new file mode 100644
index 000000000..fd8d12a3d
--- /dev/null
+++ b/tests/bond_order/CH3_2SO.mol
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diff --git a/tests/bond_order/CH3_2SO2.mol b/tests/bond_order/CH3_2SO2.mol
new file mode 100644
index 000000000..09bda6b70
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+++ b/tests/bond_order/CH3_2SO2.mol
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diff --git a/tests/bond_order/OCH3+.mol b/tests/bond_order/OCH3+.mol
new file mode 100644
index 000000000..29c5ce1d5
--- /dev/null
+++ b/tests/bond_order/OCH3+.mol
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new file mode 100644
index 000000000..ff7649600
--- /dev/null
+++ b/tests/bond_order/arg.mol
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diff --git a/tests/bond_order/formal_charge.mol b/tests/bond_order/formal_charge.mol
new file mode 100644
index 000000000..141f5f81d
--- /dev/null
+++ b/tests/bond_order/formal_charge.mol
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+M  END
diff --git a/tests/bond_order/gly.mol b/tests/bond_order/gly.mol
new file mode 100644
index 000000000..2a47b76b3
--- /dev/null
+++ b/tests/bond_order/gly.mol
@@ -0,0 +1,24 @@
+
+     RDKit          3D
+
+ 10  9  0  0  0  0  0  0  0  0999 V2000
+   -0.8847   -0.5545   -0.2953 N   0  0  0  0  0  4  0  0  0  0  0  0
+   -0.1362    0.5745    0.1710 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2865    0.2167    0.2432 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.6871   -1.0450   -0.1141 O   0  0  0  0  0  1  0  0  0  0  0  0
+    2.1175    1.0591    0.6274 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1118   -0.5249   -1.3170 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.7699   -0.6403    0.2808 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.3737   -1.4584   -0.1502 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.3181    1.3969   -0.5839 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.4968    0.9759    1.1382 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  1  0
+  3  5  2  0
+  1  6  1  0
+  1  7  1  0
+  1  8  1  0
+  2  9  1  0
+  2 10  1  0
+M  END
diff --git a/tests/bond_order/methane.sdf b/tests/bond_order/methane.sdf
new file mode 100644
index 000000000..a096aafae
--- /dev/null
+++ b/tests/bond_order/methane.sdf
@@ -0,0 +1,60 @@
+
+     RDKit          3D
+
+  5  4  0  0  0  0  0  0  0  0999 V2000
+    0.0059   -0.0002   -0.0049 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   -0.4899    0.9882   -0.0754 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.1439   -0.2888    1.0478 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.9894    0.0336   -0.4842 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  1  3  1  0
+  1  4  1  0
+  1  5  1  0
+M  END
+$$$$
+
+     RDKit          3D
+
+  5  4  0  0  0  0  0  0  0  0999 V2000
+    0.0043    0.0012   -0.0253 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.6943   -0.7305   -0.4680 H   0  0  0  0  0  0  0  0  0  0  0  0
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+    0.0543    0.9582   -0.5765 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.9921   -0.4633    0.0767 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  1  3  1  0
+  1  4  1  0
+  1  5  1  0
+M  END
+$$$$
+
+     RDKit          3D
+
+  5  4  0  0  0  0  0  0  0  0999 V2000
+    0.0071   -0.0179   -0.0048 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.6733   -0.6435   -0.6095 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1825    1.0482   -0.2270 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.2116   -0.1471    1.0799 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0603   -0.2397   -0.2386 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  1  3  1  0
+  1  4  1  0
+  1  5  1  0
+M  END
+$$$$
+
+     RDKit          3D
+
+  5  4  0  0  0  0  0  0  0  0999 V2000
+    0.0032    0.0117   -0.0013 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.5479   -0.8736   -0.3523 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.5265    0.9173   -0.3244 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0523   -0.0248    1.0966 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0189   -0.0306   -0.4186 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  1  3  1  0
+  1  4  1  0
+  1  5  1  0
+M  END
+$$$$
diff --git a/tests/bond_order/methane_ethane.sdf b/tests/bond_order/methane_ethane.sdf
new file mode 100644
index 000000000..7d3b91dfa
--- /dev/null
+++ b/tests/bond_order/methane_ethane.sdf
@@ -0,0 +1,72 @@
+
+     RDKit          3D
+
+  5  4  0  0  0  0  0  0  0  0999 V2000
+    0.0059   -0.0002   -0.0049 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.6493   -0.7327   -0.4834 H   0  0  0  0  0  0  0  0  0  0  0  0
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+    0.9894    0.0336   -0.4842 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  1  3  1  0
+  1  4  1  0
+  1  5  1  0
+M  END
+$$$$
+
+     RDKit          3D
+
+  5  4  0  0  0  0  0  0  0  0999 V2000
+    0.0043    0.0012   -0.0253 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.6943   -0.7305   -0.4680 H   0  0  0  0  0  0  0  0  0  0  0  0
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+    0.0543    0.9582   -0.5765 H   0  0  0  0  0  0  0  0  0  0  0  0
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+  1  2  1  0
+  1  3  1  0
+  1  4  1  0
+  1  5  1  0
+M  END
+$$$$
+
+     RDKit          3D
+
+  8  7  0  0  0  0  0  0  0  0999 V2000
+    0.7590    0.0236   -0.0560 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7547    0.0313    0.0718 C   0  0  0  0  0  0  0  0  0  0  0  0
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+    1.1419    0.9856   -0.3997 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.9785   -0.8255   -0.7489 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2457   -0.3097   -0.8758 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.0093   -0.7228    0.8325 H   0  0  0  0  0  0  0  0  0  0  0  0
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+  1  2  1  0
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+  1  4  1  0
+  1  5  1  0
+  2  6  1  0
+  2  7  1  0
+  2  8  1  0
+M  END
+$$$$
+
+     RDKit          3D
+
+  8  7  0  0  0  0  0  0  0  0999 V2000
+    0.7754   -0.0463    0.0099 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7512   -0.0348   -0.0031 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.1943   -1.0095   -0.2808 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0852    0.6964   -0.7578 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0697    0.2302    1.0328 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.0271    1.0589    0.0390 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1664   -0.4112   -0.9429 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1799   -0.4837    0.9029 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  1  3  1  0
+  1  4  1  0
+  1  5  1  0
+  2  6  1  0
+  2  7  1  0
+  2  8  1  0
+M  END
+$$$$
diff --git a/tests/bond_order/oxpy.mol b/tests/bond_order/oxpy.mol
new file mode 100644
index 000000000..e6ef61022
--- /dev/null
+++ b/tests/bond_order/oxpy.mol
@@ -0,0 +1,29 @@
+
+     RDKit          3D
+
+ 12 12  0  0  0  0  0  0  0  0999 V2000
+    2.5787    0.8944   -0.0838 O   0  0  0  0  0  1  0  0  0  0  0  0
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+   -1.8826    1.5654    0.0465 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.4307    2.4107   -0.0290 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  2  3  2  0
+  3  4  1  0
+  4  5  2  0
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+  3  8  1  0
+  4  9  1  0
+  5 10  1  0
+  6 11  1  0
+  7 12  1  0
+M  END
diff --git a/tests/bond_order/refined-set-ligands/obabel/1a4r_ligand_obabel.sdf b/tests/bond_order/refined-set-ligands/obabel/1a4r_ligand_obabel.sdf
new file mode 100644
index 000000000..efbacb0fc
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/obabel/1a4r_ligand_obabel.sdf
@@ -0,0 +1,107 @@
+1a4r_ligand
+ OpenBabel05112116033D
+Created by X-TOOL on Fri Nov 18 12:31:18 2016
+ 42 44  0  0  0  0  0  0  0  0999 V2000
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+ 26 41  1  0  0  0  0
+ 26 42  1  0  0  0  0
+ 27 28  1  0  0  0  0
+M  END
+>  <MOLECULAR_FORMULA>
+C10H14N6O10P2
+
+>  <MOLECULAR_WEIGHT>
+440.1
+
+>  <NUM_HB_ATOMS>
+16
+
+>  <NUM_ROTOR>
+6
+
+>  <XLOGP2>
+-4.52
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/obabel/1ai5_ligand_obabel.sdf b/tests/bond_order/refined-set-ligands/obabel/1ai5_ligand_obabel.sdf
new file mode 100644
index 000000000..1c195a771
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/obabel/1ai5_ligand_obabel.sdf
@@ -0,0 +1,60 @@
+1ai5_ligand
+ OpenBabel05112116033D
+Created by X-TOOL on Fri Nov 18 12:05:44 2016
+ 19 19  0  0  0  0  0  0  0  0999 V2000
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+   13.1143   37.1575   33.5351 H   0  0  0  0  0  0  0  0  0  0  0  0
+    9.4089   34.9506   33.3483 H   0  0  0  0  0  0  0  0  0  0  0  0
+    9.9166   33.9016   35.5428 H   0  0  0  0  0  0  0  0  0  0  0  0
+   11.9468   34.6054   36.7760 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1 13  2  0  0  0  0
+  1 12  2  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+  2 14  1  0  0  0  0
+  2 15  1  0  0  0  0
+  3 11  2  0  0  0  0
+  3  4  1  0  0  0  0
+  4  5  2  0  0  0  0
+  4 16  1  0  0  0  0
+  5  9  1  0  0  0  0
+  5  6  1  0  0  0  0
+  6  8  2  0  0  0  0
+  6  7  2  0  0  0  0
+  9 10  2  0  0  0  0
+  9 17  1  0  0  0  0
+ 10 11  1  0  0  0  0
+ 10 18  1  0  0  0  0
+ 11 19  1  0  0  0  0
+M  CHG  1   1  -1
+M  END
+>  <MOLECULAR_FORMULA>
+C8H6NO4
+
+>  <MOLECULAR_WEIGHT>
+180.1
+
+>  <NUM_HB_ATOMS>
+4
+
+>  <NUM_ROTOR>
+1
+
+>  <XLOGP2>
+1.08
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/obabel/1f5l_ligand_obabel.sdf b/tests/bond_order/refined-set-ligands/obabel/1f5l_ligand_obabel.sdf
new file mode 100644
index 000000000..aae7d264c
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/obabel/1f5l_ligand_obabel.sdf
@@ -0,0 +1,70 @@
+1f5l_ligand
+ OpenBabel05112116043D
+Created by X-TOOL on Fri Nov 18 12:50:13 2016
+ 24 24  0  0  0  0  0  0  0  0999 V2000
+   31.1120    7.6690   27.6830 N   0  0  0  0  0  0  0  0  0  0  0  0
+   30.5020    6.7410   28.4320 C   0  0  0  0  0  0  0  0  0  0  0  0
+   31.2400    5.3550   28.6010 C   0  0  0  0  0  0  0  0  0  0  0  0
+   32.5550    5.2790   28.1310 N   0  0  0  0  0  4  0  0  0  0  0  0
+   33.2510    4.1770   28.0800 C   0  3  0  0  0  0  0  0  0  0  0  0
+   32.7670    3.0180   28.4620 N   0  0  0  0  0  4  0  0  0  0  0  0
+   34.4700    4.2400   27.6300 N   0  0  0  0  0  4  0  0  0  0  0  0
+   30.6520    4.3960   29.1150 O   0  0  0  0  0  0  0  0  0  0  0  0
+   29.2610    7.0260   29.0190 C   0  0  0  0  0  0  0  0  0  0  0  0
+   28.5730    6.0860   29.8140 N   0  0  0  0  0  0  0  0  0  0  0  0
+   28.6930    8.2380   28.8250 N   0  0  0  0  0  0  0  0  0  0  0  0
+   29.3140    9.1790   28.0650 C   0  0  0  0  0  0  0  0  0  0  0  0
+   28.6660   10.4360   27.8950 N   0  0  0  0  0  0  0  0  0  0  0  0
+   30.5610    8.8800   27.4780 C   0  0  0  0  0  0  0  0  0  0  0  0
+   31.4320   10.0160   26.4870 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+   32.9889    6.1224   27.8142 H   0  0  0  0  0  0  0  0  0  0  0  0
+   33.3514    2.1718   28.4049 H   0  0  0  0  0  0  0  0  0  0  0  0
+   31.8028    2.9549   28.8188 H   0  0  0  0  0  0  0  0  0  0  0  0
+   34.8612    5.1435   27.3272 H   0  0  0  0  0  0  0  0  0  0  0  0
+   35.0440    3.3864   27.5765 H   0  0  0  0  0  0  0  0  0  0  0  0
+   27.6628    6.3308   30.2293 H   0  0  0  0  0  0  0  0  0  0  0  0
+   28.9808    5.1547   29.9793 H   0  0  0  0  0  0  0  0  0  0  0  0
+   29.1091   11.1710   27.3254 H   0  0  0  0  0  0  0  0  0  0  0  0
+   27.7543   10.6100   28.3417 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  9  2  0  0  0  0
+  2  3  1  0  0  0  0
+  3  8  2  0  0  0  0
+  3  4  1  0  0  0  0
+  4  5  2  0  0  0  0
+  4 16  1  0  0  0  0
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+  5  6  2  0  0  0  0
+  6 17  1  0  0  0  0
+  6 18  1  0  0  0  0
+  7 19  1  0  0  0  0
+  7 20  1  0  0  0  0
+  9 11  1  0  0  0  0
+  9 10  1  0  0  0  0
+ 10 21  1  0  0  0  0
+ 10 22  1  0  0  0  0
+ 11 12  2  0  0  0  0
+ 12 14  1  0  0  0  0
+ 12 13  1  0  0  0  0
+ 13 23  1  0  0  0  0
+ 13 24  1  0  0  0  0
+ 14  1  2  0  0  0  0
+ 14 15  1  0  0  0  0
+M  CHG  1   5   1
+M  END
+>  <MOLECULAR_FORMULA>
+C6H9N7OCl
+
+>  <MOLECULAR_WEIGHT>
+230.6
+
+>  <NUM_HB_ATOMS>
+8
+
+>  <NUM_ROTOR>
+0
+
+>  <XLOGP2>
+-1.11
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/obabel/1m1b_ligand_obabel.sdf b/tests/bond_order/refined-set-ligands/obabel/1m1b_ligand_obabel.sdf
new file mode 100644
index 000000000..3df7b55c6
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/obabel/1m1b_ligand_obabel.sdf
@@ -0,0 +1,45 @@
+1m1b_ligand
+ OpenBabel05112116043D
+Created by X-TOOL on Fri Nov 18 12:58:40 2016
+ 12 11  0  0  0  0  0  0  0  0999 V2000
+   30.3110   69.4470   73.1140 C   0  5  0  0  0  0  0  0  0  0  0  0
+   30.8240   68.4790   72.4320 O   0  0  0  0  0  0  0  0  0  0  0  0
+   30.9770   70.3480   73.5750 O   0  0  0  0  0  0  0  0  0  0  0  0
+   28.7920   69.3220   73.2920 C   0  0  0  0  0  0  0  0  0  0  0  0
+   28.0660   68.2870   73.7790 C   0  0  0  0  0  0  0  0  0  0  0  0
+   28.1120   70.3400   72.9260 O   0  0  0  0  0  0  0  0  0  0  0  0
+   28.4660   67.9240   75.5260 S   0  0  0  0  0  0  0  0  0  0  0  0
+   28.2630   69.1270   76.2210 O   0  0  0  0  0  0  0  0  0  0  0  0
+   29.8230   67.4780   75.5040 O   0  0  0  0  0  0  0  0  0  0  0  0
+   27.5120   67.0010   75.9560 O   0  0  0  0  0  0  0  0  0  0  0  0
+   28.2752   67.3921   73.1745 H   0  0  0  0  0  0  0  0  0  0  0  0
+   26.9976   68.5380   73.7051 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  4  1  0  0  0  0
+  1  3  2  0  0  0  0
+  1  2  2  0  0  0  0
+  4  6  2  0  0  0  0
+  4  5  1  0  0  0  0
+  5  7  1  0  0  0  0
+  5 11  1  0  0  0  0
+  5 12  1  0  0  0  0
+  7 10  2  0  0  0  0
+  7  9  2  0  0  0  0
+  7  8  2  0  0  0  0
+M  CHG  1   1  -1
+M  END
+>  <MOLECULAR_FORMULA>
+C3H2O6S
+
+>  <MOLECULAR_WEIGHT>
+166.1
+
+>  <NUM_HB_ATOMS>
+6
+
+>  <NUM_ROTOR>
+1
+
+>  <XLOGP2>
+-1.66
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/obabel/1mue_ligand_obabel.sdf b/tests/bond_order/refined-set-ligands/obabel/1mue_ligand_obabel.sdf
new file mode 100644
index 000000000..883df756e
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/obabel/1mue_ligand_obabel.sdf
@@ -0,0 +1,121 @@
+1mue_ligand
+ OpenBabel05112116053D
+Created by X-TOOL on Fri Nov 18 13:41:51 2016
+ 49 51  0  0  0  0  0  0  0  0999 V2000
+   22.0800  -15.7580   25.0900 C   0  0  0  0  0  0  0  0  0  0  0  0
+   20.9530  -16.4530   25.2050 N   0  0  0  0  0  0  0  0  0  0  0  0
+   19.8510  -15.8890   25.7250 C   0  0  0  0  0  0  0  0  0  0  0  0
+   19.8360  -14.5630   26.1210 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   18.6030  -16.7060   25.9480 C   0  0  0  0  0  0  0  0  0  0  0  0
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+ 15 29  1  0  0  0  0
+ 16 17  1  0  0  0  0
+ 16 40  1  0  0  0  0
+ 18 19  1  0  0  0  0
+ 18 41  1  0  0  0  0
+ 18 42  1  0  0  0  0
+ 19 20  1  0  0  0  0
+ 19 30  2  0  0  0  0
+ 20 21  1  0  0  0  0
+ 20 43  1  0  0  0  0
+ 21 22  1  0  0  0  0
+ 21 44  1  0  0  0  0
+ 21 45  1  0  0  0  0
+ 22 23  2  0  0  0  0
+ 22 27  1  0  0  0  0
+ 23 24  1  0  0  0  0
+ 23 46  1  0  0  0  0
+ 24 25  2  0  0  0  0
+ 24 47  1  0  0  0  0
+ 25 26  1  0  0  0  0
+ 25 48  1  0  0  0  0
+ 26 27  2  0  0  0  0
+ 26 49  1  0  0  0  0
+ 27 31  1  0  0  0  0
+M  END
+>  <MOLECULAR_FORMULA>
+C20H17N5O3F3Cl
+
+>  <MOLECULAR_WEIGHT>
+467.7
+
+>  <NUM_HB_ATOMS>
+6
+
+>  <NUM_ROTOR>
+7
+
+>  <XLOGP2>
+2.89
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/obabel/1w4q_ligand_obabel.sdf b/tests/bond_order/refined-set-ligands/obabel/1w4q_ligand_obabel.sdf
new file mode 100644
index 000000000..8e2aacc2a
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/obabel/1w4q_ligand_obabel.sdf
@@ -0,0 +1,84 @@
+1w4q_ligand
+ OpenBabel05112116053D
+Created by X-TOOL on Fri Nov 18 14:04:08 2016
+ 31 32  0  0  0  0  0  0  0  0999 V2000
+   36.2250   -2.3660   12.1580 N   0  0  0  0  0  0  0  0  0  0  0  0
+   35.0290   -2.5550   11.4210 C   0  0  0  0  0  0  0  0  0  0  0  0
+   34.7000   -1.7980   10.5870 O   0  0  0  0  0  0  0  0  0  0  0  0
+   34.3270   -3.7120   11.7940 N   0  0  0  0  0  0  0  0  0  0  0  0
+   34.6750   -4.6670   12.7960 C   0  0  0  0  0  0  0  0  0  0  0  0
+   33.9250   -5.6050   12.9580 O   0  0  0  0  0  0  0  0  0  0  0  0
+   35.9240   -4.3900   13.5180 C   0  0  0  0  0  0  0  0  0  0  0  0
+   36.6450   -3.2830   13.1940 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   40.0020   -0.1650   14.2100 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   36.2460    1.3130   11.5430 F   0  0  0  0  0  0  0  0  0  0  0  0
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+   38.6832   -1.2469   15.4099 H   0  0  0  0  0  0  0  0  0  0  0  0
+   40.5932   -1.0175   13.8445 H   0  0  0  0  0  0  0  0  0  0  0  0
+   40.6528    0.7160   14.3113 H   0  0  0  0  0  0  0  0  0  0  0  0
+   39.3186    0.4879   12.4253 H   0  0  0  0  0  0  0  0  0  0  0  0
+   37.2659    1.0391   14.2348 H   0  0  0  0  0  0  0  0  0  0  0  0
+   35.5930    0.0715   12.8703 H   0  0  0  0  0  0  0  0  0  0  0  0
+   37.5145   -1.1206   10.8241 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  8  1  0  0  0  0
+  2  3  2  0  0  0  0
+  2  4  1  0  0  0  0
+  4  5  1  0  0  0  0
+  4 22  1  0  0  0  0
+  5  6  2  0  0  0  0
+  7  5  1  0  0  0  0
+  7 23  1  0  0  0  0
+  8  7  2  0  0  0  0
+  8 24  1  0  0  0  0
+  9 25  1  0  0  0  0
+ 10  9  1  0  0  0  0
+ 10 26  1  0  0  0  0
+ 10 27  1  0  0  0  0
+ 11 10  1  0  0  0  0
+ 11 13  1  0  0  0  0
+ 11 28  1  6  0  0  0
+ 12 11  1  0  0  0  0
+ 12 17  1  0  0  0  0
+ 13 14  1  0  0  0  0
+ 13 15  1  0  0  0  0
+ 13 29  1  1  0  0  0
+ 14 19  1  0  0  0  0
+ 15 16  1  0  0  0  0
+ 15 17  1  0  0  0  0
+ 15 30  1  1  0  0  0
+ 17  1  1  0  0  0  0
+ 17 31  1  6  0  0  0
+ 19 18  2  0  0  0  0
+ 19 20  2  0  0  0  0
+ 19 21  2  0  0  0  0
+M  END
+>  <MOLECULAR_FORMULA>
+C9H10N2O8PF
+
+>  <MOLECULAR_WEIGHT>
+324.1
+
+>  <NUM_HB_ATOMS>
+9
+
+>  <NUM_ROTOR>
+3
+
+>  <XLOGP2>
+-2.27
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/obabel/2e94_ligand_obabel.sdf b/tests/bond_order/refined-set-ligands/obabel/2e94_ligand_obabel.sdf
new file mode 100644
index 000000000..8bbcbf9ef
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/obabel/2e94_ligand_obabel.sdf
@@ -0,0 +1,113 @@
+2e94_ligand
+ OpenBabel05112116063D
+Created by X-TOOL on Fri Nov 18 14:45:46 2016
+ 45 47  0  0  0  0  0  0  0  0999 V2000
+   35.3180   53.0670   10.5620 C   0  0  0  0  0  0  0  0  0  0  0  0
+   36.1370   53.5310   11.5840 C   0  0  0  0  0  0  0  0  0  0  0  0
+   36.4880   52.6820   12.6290 C   0  0  0  0  0  0  0  0  0  0  0  0
+   36.0170   51.3740   12.6480 C   0  0  0  0  0  0  0  0  0  0  0  0
+   35.1970   50.9120   11.6240 C   0  0  0  0  0  0  0  0  0  0  0  0
+   34.8460   51.7570   10.5760 C   0  0  0  0  0  0  0  0  0  0  0  0
+   34.0920   51.2750    9.5140 C   0  0  0  0  0  0  0  0  0  0  0  0
+   33.0200   50.4150    9.7350 C   0  0  0  0  0  0  0  0  0  0  0  0
+   34.4090   51.6590    8.2140 C   0  0  0  0  0  0  0  0  0  0  0  0
+   33.6640   51.1810    7.1430 C   0  0  0  0  0  0  0  0  0  0  0  0
+   32.5970   50.3180    7.3690 C   0  0  0  0  0  0  0  0  0  0  0  0
+   32.2710   49.9350    8.6650 C   0  0  0  0  0  0  0  0  0  0  0  0
+   31.1760   49.1050    8.8820 C   0  0  0  0  0  0  0  0  0  0  0  0
+   30.9280   48.0420    8.0190 C   0  0  0  0  0  3  0  0  0  0  0  0
+   30.3640   49.2900    9.9960 C   0  0  0  0  0  0  0  0  0  0  0  0
+   29.3100   48.4230   10.2570 C   0  0  0  0  0  0  0  0  0  0  0  0
+   29.0600   47.3550    9.4030 C   0  0  0  0  0  0  0  0  0  0  0  0
+   29.8730   47.1580    8.2800 N   0  0  0  0  0  0  0  0  0  0  0  0
+   29.6790   45.9550    7.4370 C   0  0  0  0  0  0  0  0  0  0  0  0
+   29.2480   46.2370    5.9940 C   0  0  0  0  0  0  0  0  0  0  0  0
+   29.2590   44.5910    5.1110 P   0  0  0  0  0  0  0  0  0  0  0  0
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+   26.4770   46.0170    6.5000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   27.6150   48.2790    6.9420 O   0  0  0  0  0  0  0  0  0  0  0  0
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+   30.1860   47.1170    5.3640 O   0  0  0  0  0  0  0  0  0  0  0  0
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+   37.1279   53.0400   13.4274 H   0  0  0  0  0  0  0  0  0  0  0  0
+   36.2895   50.7128   13.4627 H   0  0  0  0  0  0  0  0  0  0  0  0
+   34.8308   49.8919   11.6425 H   0  0  0  0  0  0  0  0  0  0  0  0
+   32.7673   50.1175   10.7463 H   0  0  0  0  0  0  0  0  0  0  0  0
+   35.2394   52.3328    8.0368 H   0  0  0  0  0  0  0  0  0  0  0  0
+   33.9143   51.4806    6.1317 H   0  0  0  0  0  0  0  0  0  0  0  0
+   32.0182   49.9431    6.5326 H   0  0  0  0  0  0  0  0  0  0  0  0
+   31.5516   47.8978    7.1441 H   0  0  0  0  0  0  0  0  0  0  0  0
+   30.5554   50.1191   10.6675 H   0  0  0  0  0  0  0  0  0  0  0  0
+   28.6824   48.5795   11.1269 H   0  0  0  0  0  0  0  0  0  0  0  0
+   28.2387   46.6772    9.6056 H   0  0  0  0  0  0  0  0  0  0  0  0
+   28.9061   45.3297    7.9077 H   0  0  0  0  0  0  0  0  0  0  0  0
+   30.6297   45.4025    7.4071 H   0  0  0  0  0  0  0  0  0  0  0  0
+   30.1822   47.9550    5.8115 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0  0  0  0
+  1  6  1  0  0  0  0
+  1 30  1  0  0  0  0
+  2  3  1  0  0  0  0
+  2 31  1  0  0  0  0
+  3  4  2  0  0  0  0
+  3 32  1  0  0  0  0
+  4  5  1  0  0  0  0
+  4 33  1  0  0  0  0
+  5  6  2  0  0  0  0
+  5 34  1  0  0  0  0
+  6  7  1  0  0  0  0
+  7  8  2  0  0  0  0
+  7  9  1  0  0  0  0
+  8 12  1  0  0  0  0
+  8 35  1  0  0  0  0
+  9 10  2  0  0  0  0
+  9 36  1  0  0  0  0
+ 10 11  1  0  0  0  0
+ 10 37  1  0  0  0  0
+ 11 12  2  0  0  0  0
+ 11 38  1  0  0  0  0
+ 12 13  1  0  0  0  0
+ 13 14  1  0  0  0  0
+ 13 15  2  0  0  0  0
+ 14 18  1  0  0  0  0
+ 14 39  1  0  0  0  0
+ 15 16  1  0  0  0  0
+ 15 40  1  0  0  0  0
+ 16 17  2  0  0  0  0
+ 16 41  1  0  0  0  0
+ 17 18  1  0  0  0  0
+ 17 42  1  0  0  0  0
+ 18 19  1  0  0  0  0
+ 19 20  1  0  0  0  0
+ 19 43  1  0  0  0  0
+ 19 44  1  0  0  0  0
+ 20 21  1  0  0  0  0
+ 20 25  1  0  0  0  0
+ 20 29  1  0  0  0  0
+ 21 22  2  0  0  0  0
+ 21 23  2  0  0  0  0
+ 21 24  2  0  0  0  0
+ 25 26  2  0  0  0  0
+ 25 27  2  0  0  0  0
+ 25 28  2  0  0  0  0
+ 29 45  1  0  0  0  0
+M  END
+>  <MOLECULAR_FORMULA>
+C19H16NO7P2
+
+>  <MOLECULAR_WEIGHT>
+432.1
+
+>  <NUM_HB_ATOMS>
+8
+
+>  <NUM_ROTOR>
+2
+
+>  <XLOGP2>
+1.94
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/obabel/4xaq_ligand_obabel.sdf b/tests/bond_order/refined-set-ligands/obabel/4xaq_ligand_obabel.sdf
new file mode 100644
index 000000000..758b75773
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/obabel/4xaq_ligand_obabel.sdf
@@ -0,0 +1,69 @@
+4xaq_ligand
+ OpenBabel05112116113D
+Created by X-TOOL on Fri Nov 18 18:00:48 2016
+ 23 24  0  0  0  0  0  0  0  0999 V2000
+   -5.5750   35.7600   26.9370 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -8.1450   37.0440   27.8960 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -9.2460   32.3630   29.3640 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.7210   36.5030   29.3140 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -8.0470   35.8370   26.9130 C   0  0  1  0  0  0  0  0  0  0  0  0
+   -7.9940   35.0120   29.2480 C   0  0  1  0  0  0  0  0  0  0  0  0
+  -10.0660   33.3980   29.0580 C   0  5  0  0  0  0  0  0  0  0  0  0
+   -9.3880   34.6630   28.7190 C   0  0  2  0  0  0  0  0  0  0  0  0
+   -8.2120   34.6260   27.7880 C   0  0  1  0  0  0  0  0  0  0  0  0
+  -11.2780   33.2560   29.0670 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -9.0700   35.8490   25.8450 N   0  3  0  0  0  0  0  0  0  0  0  0
+   -6.6190   35.7900   26.3010 C   0  5  0  0  0  0  0  0  0  0  0  0
+   -6.5010   35.8060   24.9570 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.4661   37.8489   27.5780 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -9.1763   37.4252   27.9277 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -8.3223   36.9738   30.1057 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.6541   36.6951   29.5006 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.4560   34.4093   29.9945 H   0  0  0  0  0  0  0  0  0  0  0  0
+  -10.1400   35.4606   28.6279 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.8481   33.6937   27.3314 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -8.9446   36.6665   25.2688 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -9.9885   35.8680   26.2597 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -8.9741   35.0208   25.2785 H   0  0  0  0  0  0  0  0  0  0  0  0
+  2 14  1  0  0  0  0
+  2 15  1  0  0  0  0
+  4  2  1  0  0  0  0
+  4 16  1  0  0  0  0
+  4 17  1  0  0  0  0
+  5  2  1  0  0  0  0
+  5 11  1  0  0  0  0
+  5 12  1  6  0  0  0
+  6  4  1  0  0  0  0
+  6  9  1  0  0  0  0
+  6 18  1  1  0  0  0
+  7  3  2  0  0  0  0
+  7  8  1  0  0  0  0
+  7 10  2  0  0  0  0
+  8  6  1  0  0  0  0
+  8  9  1  0  0  0  0
+  8 19  1  6  0  0  0
+  9  5  1  0  0  0  0
+  9 20  1  6  0  0  0
+ 11 21  1  0  0  0  0
+ 11 22  1  0  0  0  0
+ 11 23  1  0  0  0  0
+ 12  1  2  0  0  0  0
+ 12 13  2  0  0  0  0
+M  CHG  3   7  -1  11   1  12  -1
+M  END
+>  <MOLECULAR_FORMULA>
+C8H10NO4
+
+>  <MOLECULAR_WEIGHT>
+184.1
+
+>  <NUM_HB_ATOMS>
+5
+
+>  <NUM_ROTOR>
+0
+
+>  <XLOGP2>
+-3.47
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/obabel/4xtw_ligand_obabel.sdf b/tests/bond_order/refined-set-ligands/obabel/4xtw_ligand_obabel.sdf
new file mode 100644
index 000000000..09af162a2
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/obabel/4xtw_ligand_obabel.sdf
@@ -0,0 +1,161 @@
+4xtw_ligand
+ OpenBabel05112116113D
+Created by X-TOOL on Fri Nov 18 18:00:31 2016
+ 68 72  0  0  0  0  0  0  0  0999 V2000
+   -4.7030    1.6350    5.9630 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.6630   -0.3240   11.3830 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.3580   -0.7620   13.6240 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.1170  -10.0370   13.8260 C   0  0  1  0  0  0  0  0  0  0  0  0
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+   -0.0190   -9.3280   14.5020 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   -0.4310  -10.1590   15.4430 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.7740  -10.6600   15.1950 C   0  0  1  0  0  0  0  0  0  0  0  0
+   -2.6150  -10.0570   16.3170 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.3090   -8.6030   15.6260 S   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.3050   -9.0820   13.9370 C   0  0  1  0  0  0  0  0  0  0  0  0
+   -3.2130   -7.8700   13.0160 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   -3.9373   -7.1097   13.3436 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.4644   -8.8392   11.5648 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.7056   -8.9086   11.2063 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.7111   -6.5166   10.6216 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.4565   -6.4060   11.0317 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.8533   -8.2560    9.3183 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.1460   -8.0336    8.8062 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.6760   -6.4740    7.3626 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.1792   -3.2369    7.4621 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.2600   -2.9263    6.8449 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.6593   -3.1291    8.5844 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.6831   -0.9704    6.6837 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.6764   -0.9510    8.9492 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8273    0.6549    7.5182 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5391    1.0381    9.8190 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.2279    0.8174    8.9350 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.4547   -0.0435   11.3357 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -8.9540   -0.6447   11.5654 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.8471   -1.1378   15.6020 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.1071   -0.9299   15.2672 H   0  0  0  0  0  0  0  0  0  0  0  0
+  2 34  2  0  0  0  0
+  2 35  1  0  0  0  0
+  3 37  2  0  0  0  0
+  3 38  1  0  0  0  0
+  4  5  1  0  0  0  0
+  4  9  1  0  0  0  0
+  4 41  1  6  0  0  0
+  5  6  1  0  0  0  0
+  5 42  1  0  0  0  0
+  6  7  2  0  0  0  0
+  8  6  1  0  0  0  0
+  8 43  1  0  0  0  0
+  9  8  1  0  0  0  0
+  9 44  1  6  0  0  0
+ 10  9  1  0  0  0  0
+ 10 45  1  0  0  0  0
+ 10 46  1  0  0  0  0
+ 11 10  1  0  0  0  0
+ 12  4  1  0  0  0  0
+ 12 11  1  0  0  0  0
+ 12 47  1  6  0  0  0
+ 13 12  1  0  0  0  0
+ 13 48  1  0  0  0  0
+ 13 49  1  0  0  0  0
+ 14 13  1  0  0  0  0
+ 14 50  1  0  0  0  0
+ 14 51  1  0  0  0  0
+ 15 14  1  0  0  0  0
+ 15 52  1  0  0  0  0
+ 15 53  1  0  0  0  0
+ 16 15  1  0  0  0  0
+ 16 54  1  0  0  0  0
+ 16 55  1  0  0  0  0
+ 17 16  1  0  0  0  0
+ 17 18  2  0  0  0  0
+ 19 17  1  0  0  0  0
+ 19 56  1  0  0  0  0
+ 20 19  1  0  0  0  0
+ 20 21  2  0  0  0  0
+ 20 22  2  0  0  0  0
+ 23 20  1  0  0  0  0
+ 23 57  1  0  0  0  0
+ 24 23  1  0  0  0  0
+ 24 58  1  0  0  0  0
+ 24 59  1  0  0  0  0
+ 25 24  1  0  0  0  0
+ 25 60  1  6  0  0  0
+ 26 25  1  0  0  0  0
+ 27 25  1  0  0  0  0
+ 27 28  1  0  0  0  0
+ 27 61  1  1  0  0  0
+ 28 62  1  0  0  0  0
+ 29 27  1  0  0  0  0
+ 29 30  1  0  0  0  0
+ 29 63  1  1  0  0  0
+ 30 26  1  0  0  0  0
+ 30 31  1  0  0  0  0
+ 30 64  1  6  0  0  0
+ 31  2  1  0  0  0  0
+ 31 32  1  0  0  0  0
+ 32 33  2  0  0  0  0
+ 32 65  1  0  0  0  0
+ 33 34  1  0  0  0  0
+ 34  3  1  0  0  0  0
+ 35 36  2  0  0  0  0
+ 36 37  1  0  0  0  0
+ 36 66  1  0  0  0  0
+ 38 67  1  0  0  0  0
+ 38 68  1  0  0  0  0
+ 39  1  3  0  0  0  0
+ 39 40  2  0  0  0  0
+ 40 29  1  0  0  0  0
+M  END
+>  <MOLECULAR_FORMULA>
+C20H28N12O6S2
+
+>  <MOLECULAR_WEIGHT>
+596.5
+
+>  <NUM_HB_ATOMS>
+17
+
+>  <NUM_ROTOR>
+9
+
+>  <XLOGP2>
+-2.69
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/origin/1a4r_ligand.sdf b/tests/bond_order/refined-set-ligands/origin/1a4r_ligand.sdf
new file mode 100644
index 000000000..72429c370
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/origin/1a4r_ligand.sdf
@@ -0,0 +1,107 @@
+1a4r_ligand
+
+Created by X-TOOL on Fri Nov 18 12:31:18 2016
+ 42 44  0  0  0  0  0  0  0  0999 V2000
+  102.4860   24.8700   -2.9090  N 0  0  0  3  0  3
+  101.5220   25.8860   -2.4280  P 0  0  0  1  0  4
+  100.9830   25.4700   -1.0790  O 0  0  0  1  0  1
+  100.3500   26.2500   -3.2730  O 0  0  0  1  0  1
+  102.4090   27.1490   -2.1360  O 0  0  0  1  0  2
+  102.9800   27.8190   -0.7750  P 0  0  0  1  0  4
+  103.9320   26.8730   -0.1570  O 0  0  0  1  0  1
+  101.8500   28.3180    0.0570  O 0  0  0  1  0  1
+  103.7180   29.0170   -1.4980  O 0  0  0  1  0  2
+  104.8640   28.8490   -2.3670  C 0  0  0  3  0  4
+  105.9930   29.8990   -2.1000  C 0  0  0  2  0  4
+  105.4820   31.1830   -2.4390  O 0  0  0  1  0  2
+  106.4630   30.0620   -0.6570  C 0  0  0  2  0  4
+  107.8730   30.1930   -0.5940  O 0  0  0  2  0  2
+  105.7350   31.2660   -0.0960  C 0  0  0  2  0  4
+  106.2980   31.8890    1.0590  O 0  0  0  2  0  2
+  105.5820   32.1390   -1.3490  C 0  0  0  2  0  4
+  104.3150   32.9430   -1.5100  N 0  0  0  1  0  3
+  103.0000   32.5360   -1.3540  C 0  0  0  2  0  3
+  102.0730   33.4460   -1.5560  N 0  0  0  1  0  2
+  102.8070   34.5960   -1.8890  C 0  0  0  1  0  3
+  102.3660   35.9710   -2.2360  C 0  0  0  1  0  3
+  101.2060   36.3850   -2.3060  O 0  0  0  1  0  1
+  103.4480   36.8880   -2.5220  N 0  0  0  2  0  3
+  104.8390   36.5560   -2.4810  C 0  0  0  1  0  3
+  105.7330   37.5170   -2.7670  N 0  0  0  3  0  3
+  105.2800   35.2710   -2.1570  N 0  0  0  1  0  2
+  104.2050   34.3230   -1.8660  C 0  0  0  1  0  3
+  102.1650   23.9586   -3.1665  H 0  0  0  1  0  1
+  103.4580   25.0953   -2.9763  H 0  0  0  1  0  1
+  104.5306   28.9505   -3.4103  H 0  0  0  1  0  1
+  105.2779   27.8419   -2.2106  H 0  0  0  1  0  1
+  106.8572   29.6421   -2.7302  H 0  0  0  1  0  1
+  106.1769   29.1711   -0.0788  H 0  0  0  1  0  1
+  108.1405   30.2929    0.3121  H 0  0  0  1  0  1
+  104.7318   30.9403    0.2163  H 0  0  0  1  0  1
+  107.1751   32.1932    0.8575  H 0  0  0  1  0  1
+  106.4561   32.8002   -1.4424  H 0  0  0  1  0  1
+  102.7469   31.5134   -1.0779  H 0  0  0  1  0  1
+  103.2047   37.8264   -2.7673  H 0  0  0  1  0  1
+  106.7409   37.3058   -2.7451  H 0  0  0  1  0  1
+  105.4106   38.4650   -3.0082  H 0  0  0  1  0  1
+  2  1  1  0  0  2
+  2  3  2  0  0  2
+  2  4  2  0  0  2
+  2  5  1  0  0  2
+  5  6  1  0  0  2
+  6  7  2  0  0  2
+  6  8  2  0  0  2
+  6  9  1  0  0  2
+  9 10  1  0  0  2
+ 10 11  1  0  0  2
+ 11 12  1  0  0  1
+ 11 13  1  0  0  1
+ 12 17  1  0  0  1
+ 13 14  1  0  0  2
+ 13 15  1  0  0  1
+ 15 16  1  0  0  2
+ 17 15  1  0  0  1
+ 17 18  1  0  0  2
+ 18 19  1  0  0  1
+ 18 28  1  0  0  1
+ 19 20  2  0  0  1
+ 20 21  1  0  0  1
+ 21 22  1  0  0  1
+ 21 28  2  0  0  1
+ 22 23  2  0  0  2
+ 22 24  1  0  0  1
+ 24 25  1  0  0  1
+ 25 26  1  0  0  2
+ 25 27  2  0  0  1
+ 27 28  1  0  0  1
+  1 29  1  0  0  2
+  1 30  1  0  0  2
+ 10 31  1  0  0  2
+ 10 32  1  0  0  2
+ 11 33  1  0  0  2
+ 13 34  1  0  0  2
+ 14 35  1  0  0  2
+ 15 36  1  0  0  2
+ 16 37  1  0  0  2
+ 17 38  1  0  0  2
+ 19 39  1  0  0  2
+ 24 40  1  0  0  2
+ 26 41  1  0  0  2
+ 26 42  1  0  0  2
+M  END
+> <MOLECULAR_FORMULA>
+C10H14N6O10P2
+
+> <MOLECULAR_WEIGHT>
+440.1
+
+> <NUM_HB_ATOMS>
+16 
+
+> <NUM_ROTOR>
+6  
+
+> <XLOGP2>
+-4.52
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/origin/1ai5_ligand.sdf b/tests/bond_order/refined-set-ligands/origin/1ai5_ligand.sdf
new file mode 100644
index 000000000..fed1d2056
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/origin/1ai5_ligand.sdf
@@ -0,0 +1,59 @@
+1ai5_ligand
+
+Created by X-TOOL on Fri Nov 18 12:05:44 2016
+ 19 19  0  0  0  0  0  0  0  0999 V2000
+   14.0160   37.7680   36.3700  C 0  5  0  1  0  3
+   13.9490   36.3240   35.8790  C 0  0  0  3  0  4
+   12.6700   35.9080   35.2370  C 0  0  0  1  0  3
+   12.4280   36.4610   34.0030  C 0  0  0  2  0  3
+   11.2590   36.0710   33.4050  C 0  0  0  1  0  3
+   10.9480   36.5440   32.1190  N 0  0  0  1  0  3
+    9.7150   35.9000   31.8610  O 0  0  0  1  0  1
+   11.6460   37.4310   31.3120  O 0  0  0  1  0  1
+   10.3140   35.1870   33.8960  C 0  0  0  2  0  3
+   10.5900   34.6320   35.1090  C 0  0  0  2  0  3
+   11.7540   35.0150   35.7910  C 0  0  0  2  0  3
+   14.5840   37.9400   37.4320  O 0  0  0  1  0  1
+   13.5320   38.7810   35.9290  O 0  0  0  1  0  1
+   14.1200   35.6666   36.7442  H 0  0  0  1  0  1
+   14.7555   36.1810   35.1448  H 0  0  0  1  0  1
+   13.1143   37.1575   33.5351  H 0  0  0  1  0  1
+    9.4089   34.9506   33.3483  H 0  0  0  1  0  1
+    9.9166   33.9016   35.5428  H 0  0  0  1  0  1
+   11.9468   34.6054   36.7760  H 0  0  0  1  0  1
+  1 13  2  0  0  2
+  1 12  2  0  0  2
+  1  2  1  0  0  2
+  2  3  1  0  0  2
+  3 11  4  0  0  1
+  3  4  4  0  0  1
+  4  5  4  0  0  1
+  5  9  4  0  0  1
+  5  6  1  0  0  2
+  6  8  2  0  0  2
+  6  7  2  0  0  2
+  9 10  4  0  0  1
+ 10 11  4  0  0  1
+  2 14  1  0  0  2
+  2 15  1  0  0  2
+  4 16  1  0  0  2
+  9 17  1  0  0  2
+ 10 18  1  0  0  2
+ 11 19  1  0  0  2
+M  END
+> <MOLECULAR_FORMULA>
+C8H6NO4
+
+> <MOLECULAR_WEIGHT>
+180.1
+
+> <NUM_HB_ATOMS>
+4  
+
+> <NUM_ROTOR>
+1  
+
+> <XLOGP2>
+1.08 
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/origin/1f5l_ligand.sdf b/tests/bond_order/refined-set-ligands/origin/1f5l_ligand.sdf
new file mode 100644
index 000000000..6b10ee685
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/origin/1f5l_ligand.sdf
@@ -0,0 +1,69 @@
+1f5l_ligand
+
+Created by X-TOOL on Fri Nov 18 12:50:13 2016
+ 24 24  0  0  0  0  0  0  0  0999 V2000
+   31.1120    7.6690   27.6830  N 0  0  0  1  0  2
+   30.5020    6.7410   28.4320  C 0  0  0  1  0  3
+   31.2400    5.3550   28.6010  C 0  0  0  1  0  3
+   32.5550    5.2790   28.1310  N 0  0  0  2  0  3
+   33.2510    4.1770   28.0800  C 0  3  0  1  0  3
+   32.7670    3.0180   28.4620  N 0  0  0  3  0  3
+   34.4700    4.2400   27.6300  N 0  0  0  3  0  3
+   30.6520    4.3960   29.1150  O 0  0  0  1  0  1
+   29.2610    7.0260   29.0190  C 0  0  0  1  0  3
+   28.5730    6.0860   29.8140  N 0  0  0  3  0  3
+   28.6930    8.2380   28.8250  N 0  0  0  1  0  2
+   29.3140    9.1790   28.0650  C 0  0  0  1  0  3
+   28.6660   10.4360   27.8950  N 0  0  0  3  0  3
+   30.5610    8.8800   27.4780  C 0  0  0  1  0  3
+   31.4320   10.0160   26.4870 Cl 0  0  0  1  0  1
+   32.9889    6.1224   27.8142  H 0  0  0  1  0  1
+   33.3514    2.1718   28.4049  H 0  0  0  1  0  1
+   31.8028    2.9549   28.8188  H 0  0  0  1  0  1
+   34.8612    5.1435   27.3272  H 0  0  0  1  0  1
+   35.0440    3.3864   27.5765  H 0  0  0  1  0  1
+   27.6628    6.3308   30.2293  H 0  0  0  1  0  1
+   28.9808    5.1547   29.9793  H 0  0  0  1  0  1
+   29.1091   11.1710   27.3254  H 0  0  0  1  0  1
+   27.7543   10.6100   28.3417  H 0  0  0  1  0  1
+ 14  1  4  0  0  1
+  1  2  4  0  0  1
+  2  9  4  0  0  1
+  2  3  1  0  0  2
+  3  8  2  0  0  2
+  3  4  1  0  0  2
+  4  5  2  0  0  2
+  5  7  2  0  0  2
+  5  6  2  0  0  2
+  9 11  4  0  0  1
+  9 10  1  0  0  2
+ 11 12  4  0  0  1
+ 12 14  4  0  0  1
+ 12 13  1  0  0  2
+ 14 15  1  0  0  2
+  4 16  1  0  0  2
+  6 17  1  0  0  2
+  6 18  1  0  0  2
+  7 19  1  0  0  2
+  7 20  1  0  0  2
+ 10 21  1  0  0  2
+ 10 22  1  0  0  2
+ 13 23  1  0  0  2
+ 13 24  1  0  0  2
+M  END
+> <MOLECULAR_FORMULA>
+C6H9N7OCl
+
+> <MOLECULAR_WEIGHT>
+230.6
+
+> <NUM_HB_ATOMS>
+8  
+
+> <NUM_ROTOR>
+0  
+
+> <XLOGP2>
+-1.11
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/origin/1m1b_ligand.sdf b/tests/bond_order/refined-set-ligands/origin/1m1b_ligand.sdf
new file mode 100644
index 000000000..d8f376ba3
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/origin/1m1b_ligand.sdf
@@ -0,0 +1,44 @@
+1m1b_ligand
+
+Created by X-TOOL on Fri Nov 18 12:58:40 2016
+ 12 11  0  0  0  0  0  0  0  0999 V2000
+   30.3110   69.4470   73.1140  C 0  5  0  1  0  3
+   30.8240   68.4790   72.4320  O 0  0  0  1  0  1
+   30.9770   70.3480   73.5750  O 0  0  0  1  0  1
+   28.7920   69.3220   73.2920  C 0  0  0  1  0  3
+   28.0660   68.2870   73.7790  C 0  0  0  3  0  4
+   28.1120   70.3400   72.9260  O 0  0  0  1  0  1
+   28.4660   67.9240   75.5260  S 0  0  0  1  0  4
+   28.2630   69.1270   76.2210  O 0  0  0  1  0  1
+   29.8230   67.4780   75.5040  O 0  0  0  1  0  1
+   27.5120   67.0010   75.9560  O 0  0  0  1  0  1
+   28.2752   67.3921   73.1745  H 0  0  0  1  0  1
+   26.9976   68.5380   73.7051  H 0  0  0  1  0  1
+  1  4  1  0  0  2
+  1  3  2  0  0  2
+  1  2  2  0  0  2
+  4  6  2  0  0  2
+  4  5  1  0  0  2
+  5  7  1  0  0  2
+  7 10  2  0  0  2
+  7  9  2  0  0  2
+  7  8  2  0  0  2
+  5 11  1  0  0  2
+  5 12  1  0  0  2
+M  END
+> <MOLECULAR_FORMULA>
+C3H2O6S
+
+> <MOLECULAR_WEIGHT>
+166.1
+
+> <NUM_HB_ATOMS>
+6  
+
+> <NUM_ROTOR>
+1  
+
+> <XLOGP2>
+-1.66
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/origin/1mue_ligand.sdf b/tests/bond_order/refined-set-ligands/origin/1mue_ligand.sdf
new file mode 100644
index 000000000..6dbfe7a57
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/origin/1mue_ligand.sdf
@@ -0,0 +1,121 @@
+1mue_ligand
+
+Created by X-TOOL on Fri Nov 18 13:41:51 2016
+ 49 51  0  0  0  0  0  0  0  0999 V2000
+   22.0800  -15.7580   25.0900  C 0  0  0  2  0  3
+   20.9530  -16.4530   25.2050  N 0  0  0  1  0  3
+   19.8510  -15.8890   25.7250  C 0  0  0  1  0  3
+   19.8360  -14.5630   26.1210  C 0  0  0  2  0  3
+   20.9710  -13.8180   25.9770  C 0  0  0  2  0  3
+   22.1230  -14.4260   25.4800  C 0  0  0  2  0  3
+   18.6030  -16.7060   25.9480  C 0  0  0  1  0  4
+   17.9180  -17.0720   24.6620  C 0  0  0  3  0  4
+   18.9660  -17.8240   26.5990  F 0  0  0  1  0  1
+   17.7360  -16.0050   26.7280  F 0  0  0  1  0  1
+   17.1580  -15.9350   24.1360  N 0  0  0  2  0  3
+   17.9180  -15.2540   23.1780  C 0  0  0  1  0  3
+   17.2740  -14.0320   22.4940  C 0  0  0  1  0  3
+   18.0090  -13.4450   21.5160  N 0  0  0  1  0  3
+   19.3550  -13.9470   21.1720  C 0  0  0  1  0  3
+   19.9300  -15.0380   21.9380  C 0  0  0  2  0  3
+   19.1980  -15.6190   22.9100  N 0  0  0  1  0  2
+   17.5460  -12.2610   20.7780  C 0  0  0  3  0  4
+   16.0670  -12.3310   20.4100  C 0  0  0  1  0  3
+   15.2870  -11.4840   21.1270  N 0  0  0  2  0  3
+   13.8690  -11.4110   20.7680  C 0  0  0  3  0  4
+   12.9150  -11.4250   21.9620  C 0  0  0  1  0  3
+   12.9000  -10.3750   22.8950  C 0  0  0  2  0  3
+   12.0190  -10.4350   24.0000  C 0  0  0  2  0  3
+   11.1120  -11.4930   24.1370  C 0  0  0  2  0  3
+   11.1250  -12.5320   23.2100  C 0  0  0  2  0  3
+   12.0370  -12.4940   22.1420  C 0  0  0  1  0  3
+   16.1420  -13.6640   22.8260  O 0  0  0  1  0  1
+   20.2420  -13.2370   19.8930 Cl 0  0  0  1  0  1
+   15.6570  -13.1090   19.5420  O 0  0  0  1  0  1
+   12.1890  -13.5200   21.2880  F 0  0  0  1  0  1
+   20.9520  -17.7700   24.8070  O 0  0  0  1  0  1
+   22.9688  -16.2327   24.6903  H 0  0  0  1  0  1
+   18.9377  -14.1230   26.5387  H 0  0  0  1  0  1
+   20.9764  -12.7678   26.2455  H 0  0  0  1  0  1
+   23.0457  -13.8629   25.3986  H 0  0  0  1  0  1
+   17.2309  -17.9112   24.8454  H 0  0  0  1  0  1
+   18.6751  -17.3727   23.9229  H 0  0  0  1  0  1
+   16.2051  -15.6752   24.4281  H 0  0  0  1  0  1
+   20.9416  -15.3834   21.7298  H 0  0  0  1  0  1
+   18.1340  -12.1722   19.8526  H 0  0  0  1  0  1
+   17.7102  -11.3712   21.4036  H 0  0  0  1  0  1
+   15.6647  -10.9320   21.8704  H 0  0  0  1  0  1
+   13.6313  -12.2730   20.1274  H 0  0  0  1  0  1
+   13.7036  -10.4799   20.2062  H 0  0  0  1  0  1
+   13.5595   -9.5240   22.7689  H 0  0  0  1  0  1
+   12.0463   -9.6526   24.7498  H 0  0  0  1  0  1
+   10.4050  -11.5031   24.9586  H 0  0  0  1  0  1
+   10.4370  -13.3635   23.3116  H 0  0  0  1  0  1
+  1  2  4  0  0  1
+  1  6  4  0  0  1
+  2  3  4  0  0  1
+  2 32  2  0  0  2
+  3  4  4  0  0  1
+  3  7  1  0  0  2
+  4  5  4  0  0  1
+  5  6  4  0  0  1
+  7  8  1  0  0  2
+  7  9  1  0  0  2
+  7 10  1  0  0  2
+  8 11  1  0  0  2
+ 11 12  1  0  0  2
+ 12 13  1  0  0  1
+ 12 17  2  0  0  1
+ 13 14  1  0  0  1
+ 13 28  2  0  0  2
+ 14 15  1  0  0  1
+ 14 18  1  0  0  2
+ 15 16  2  0  0  1
+ 15 29  1  0  0  2
+ 16 17  1  0  0  1
+ 18 19  1  0  0  2
+ 19 20  1  0  0  2
+ 19 30  2  0  0  2
+ 20 21  1  0  0  2
+ 21 22  1  0  0  2
+ 22 23  4  0  0  1
+ 22 27  4  0  0  1
+ 23 24  4  0  0  1
+ 24 25  4  0  0  1
+ 25 26  4  0  0  1
+ 26 27  4  0  0  1
+ 27 31  1  0  0  2
+  1 33  1  0  0  2
+  4 34  1  0  0  2
+  5 35  1  0  0  2
+  6 36  1  0  0  2
+  8 37  1  0  0  2
+  8 38  1  0  0  2
+ 11 39  1  0  0  2
+ 16 40  1  0  0  2
+ 18 41  1  0  0  2
+ 18 42  1  0  0  2
+ 20 43  1  0  0  2
+ 21 44  1  0  0  2
+ 21 45  1  0  0  2
+ 23 46  1  0  0  2
+ 24 47  1  0  0  2
+ 25 48  1  0  0  2
+ 26 49  1  0  0  2
+M  END
+> <MOLECULAR_FORMULA>
+C20H17N5O3F3Cl
+
+> <MOLECULAR_WEIGHT>
+467.7
+
+> <NUM_HB_ATOMS>
+6  
+
+> <NUM_ROTOR>
+7  
+
+> <XLOGP2>
+2.89 
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/origin/1w4q_ligand.sdf b/tests/bond_order/refined-set-ligands/origin/1w4q_ligand.sdf
new file mode 100644
index 000000000..030d08824
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/origin/1w4q_ligand.sdf
@@ -0,0 +1,84 @@
+1w4q_ligand
+
+Created by X-TOOL on Fri Nov 18 14:04:08 2016
+ 31 32  0  0  0  0  0  0  0  0999 V2000
+   36.2250   -2.3660   12.1580  N 0  0  0  1  0  3
+   35.0290   -2.5550   11.4210  C 0  0  0  1  0  3
+   34.7000   -1.7980   10.5870  O 0  0  0  1  0  1
+   34.3270   -3.7120   11.7940  N 0  0  0  2  0  3
+   34.6750   -4.6670   12.7960  C 0  0  0  1  0  3
+   33.9250   -5.6050   12.9580  O 0  0  0  1  0  1
+   35.9240   -4.3900   13.5180  C 0  0  0  2  0  3
+   36.6450   -3.2830   13.1940  C 0  0  0  2  0  3
+   39.2530   -0.4990   15.5460  O 0  0  0  2  0  2
+   40.0020   -0.1650   14.2100  C 0  0  0  3  0  4
+   38.7750    0.1200   13.3080  C 0  0  0  2  0  4
+   38.4020   -1.1420   12.9600  O 0  0  0  1  0  2
+   37.6410    1.0610   13.2010  C 0  0  0  2  0  4
+   37.5420    2.5320   12.9110  O 0  0  0  1  0  2
+   36.5030    0.3120   12.3010  C 0  0  0  2  0  4
+   36.2460    1.3130   11.5430  F 0  0  0  1  0  1
+   37.1740   -1.1150   11.8700  C 0  0  0  2  0  4
+   35.4680    3.1250   13.5200  O 0  0  0  1  0  1
+   37.0160    3.5030   13.6300  P 0  0  0  1  0  4
+   37.3410    3.6810   15.0910  O 0  0  0  1  0  1
+   37.4710    4.6660   12.8340  O 0  0  0  1  0  1
+   33.4780   -3.8890   11.2961  H 0  0  0  1  0  1
+   36.2682   -5.0623   14.3025  H 0  0  0  1  0  1
+   37.5694   -3.0806   13.7329  H 0  0  0  1  0  1
+   38.6832   -1.2469   15.4099  H 0  0  0  1  0  1
+   40.5932   -1.0175   13.8445  H 0  0  0  1  0  1
+   40.6528    0.7160   14.3113  H 0  0  0  1  0  1
+   39.3186    0.4879   12.4253  H 0  0  0  1  0  1
+   37.2659    1.0391   14.2348  H 0  0  0  1  0  1
+   35.5930    0.0715   12.8703  H 0  0  0  1  0  1
+   37.5145   -1.1206   10.8241  H 0  0  0  1  0  1
+  1  2  1  0  0  1
+  1  8  1  0  0  1
+ 17  1  1  0  0  2
+  2  3  2  0  0  2
+  2  4  1  0  0  1
+  4  5  1  0  0  1
+  5  6  2  0  0  2
+  7  5  1  0  0  1
+  8  7  2  0  0  1
+ 10  9  1  0  0  2
+ 11 10  1  0  0  2
+ 12 11  1  0  0  1
+ 11 13  1  0  0  1
+ 12 17  1  0  0  1
+ 13 14  1  0  0  2
+ 13 15  1  0  0  1
+ 14 19  1  0  0  2
+ 15 16  1  0  0  2
+ 15 17  1  0  0  1
+ 19 18  2  0  0  2
+ 19 20  2  0  0  2
+ 19 21  2  0  0  2
+  4 22  1  0  0  2
+  7 23  1  0  0  2
+  8 24  1  0  0  2
+  9 25  1  0  0  2
+ 10 26  1  0  0  2
+ 10 27  1  0  0  2
+ 11 28  1  0  0  2
+ 13 29  1  0  0  2
+ 15 30  1  0  0  2
+ 17 31  1  0  0  2
+M  END
+> <MOLECULAR_FORMULA>
+C9H10N2O8PF
+
+> <MOLECULAR_WEIGHT>
+324.1
+
+> <NUM_HB_ATOMS>
+9  
+
+> <NUM_ROTOR>
+3  
+
+> <XLOGP2>
+-2.27
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/origin/2e94_ligand.sdf b/tests/bond_order/refined-set-ligands/origin/2e94_ligand.sdf
new file mode 100644
index 000000000..35de477f5
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/origin/2e94_ligand.sdf
@@ -0,0 +1,113 @@
+2e94_ligand
+
+Created by X-TOOL on Fri Nov 18 14:45:46 2016
+ 45 47  0  0  0  0  0  0  0  0999 V2000
+   35.3180   53.0670   10.5620  C 0  0  0  2  0  3
+   36.1370   53.5310   11.5840  C 0  0  0  2  0  3
+   36.4880   52.6820   12.6290  C 0  0  0  2  0  3
+   36.0170   51.3740   12.6480  C 0  0  0  2  0  3
+   35.1970   50.9120   11.6240  C 0  0  0  2  0  3
+   34.8460   51.7570   10.5760  C 0  0  0  1  0  3
+   34.0920   51.2750    9.5140  C 0  0  0  1  0  3
+   33.0200   50.4150    9.7350  C 0  0  0  2  0  3
+   34.4090   51.6590    8.2140  C 0  0  0  2  0  3
+   33.6640   51.1810    7.1430  C 0  0  0  2  0  3
+   32.5970   50.3180    7.3690  C 0  0  0  2  0  3
+   32.2710   49.9350    8.6650  C 0  0  0  1  0  3
+   31.1760   49.1050    8.8820  C 0  0  0  1  0  3
+   30.9280   48.0420    8.0190  C 0  0  0  2  0  3
+   30.3640   49.2900    9.9960  C 0  0  0  2  0  3
+   29.3100   48.4230   10.2570  C 0  0  0  2  0  3
+   29.0600   47.3550    9.4030  C 0  0  0  2  0  3
+   29.8730   47.1580    8.2800  N 0  0  0  1  0  3
+   29.6790   45.9550    7.4370  C 0  0  0  3  0  4
+   29.2480   46.2370    5.9940  C 0  0  0  1  0  4
+   29.2590   44.5910    5.1110  P 0  0  0  1  0  4
+   29.0390   44.8840    3.5440  O 0  0  0  1  0  1
+   30.7590   44.0240    5.2380  O 0  0  0  1  0  1
+   28.2570   43.6440    5.6500  O 0  0  0  1  0  1
+   27.5660   47.0450    5.9070  P 0  0  0  1  0  4
+   26.4770   46.0170    6.5000  O 0  0  0  1  0  1
+   27.6150   48.2790    6.9420  O 0  0  0  1  0  1
+   27.2420   47.5040    4.5380  O 0  0  0  1  0  1
+   30.1860   47.1170    5.3640  O 0  0  0  2  0  2
+   35.0447   53.7291    9.7484  H 0  0  0  1  0  1
+   36.5015   54.5517   11.5673  H 0  0  0  1  0  1
+   37.1279   53.0400   13.4274  H 0  0  0  1  0  1
+   36.2895   50.7128   13.4627  H 0  0  0  1  0  1
+   34.8308   49.8919   11.6425  H 0  0  0  1  0  1
+   32.7673   50.1175   10.7463  H 0  0  0  1  0  1
+   35.2394   52.3328    8.0368  H 0  0  0  1  0  1
+   33.9143   51.4806    6.1317  H 0  0  0  1  0  1
+   32.0182   49.9431    6.5326  H 0  0  0  1  0  1
+   31.5516   47.8978    7.1441  H 0  0  0  1  0  1
+   30.5554   50.1191   10.6675  H 0  0  0  1  0  1
+   28.6824   48.5795   11.1269  H 0  0  0  1  0  1
+   28.2387   46.6772    9.6056  H 0  0  0  1  0  1
+   28.9061   45.3297    7.9077  H 0  0  0  1  0  1
+   30.6297   45.4025    7.4071  H 0  0  0  1  0  1
+   30.1822   47.9550    5.8115  H 0  0  0  1  0  1
+  1  2  4  0  0  1
+  1  6  4  0  0  1
+  2  3  4  0  0  1
+  3  4  4  0  0  1
+  4  5  4  0  0  1
+  5  6  4  0  0  1
+  6  7  1  0  0  2
+  7  8  4  0  0  1
+  7  9  4  0  0  1
+  8 12  4  0  0  1
+  9 10  4  0  0  1
+ 10 11  4  0  0  1
+ 11 12  4  0  0  1
+ 12 13  1  0  0  2
+ 13 14  4  0  0  1
+ 13 15  4  0  0  1
+ 14 18  4  0  0  1
+ 15 16  4  0  0  1
+ 16 17  4  0  0  1
+ 17 18  4  0  0  1
+ 18 19  1  0  0  2
+ 19 20  1  0  0  2
+ 20 21  1  0  0  2
+ 20 25  1  0  0  2
+ 20 29  1  0  0  2
+ 21 22  2  0  0  2
+ 21 23  2  0  0  2
+ 21 24  2  0  0  2
+ 25 26  2  0  0  2
+ 25 27  2  0  0  2
+ 25 28  2  0  0  2
+  1 30  1  0  0  2
+  2 31  1  0  0  2
+  3 32  1  0  0  2
+  4 33  1  0  0  2
+  5 34  1  0  0  2
+  8 35  1  0  0  2
+  9 36  1  0  0  2
+ 10 37  1  0  0  2
+ 11 38  1  0  0  2
+ 14 39  1  0  0  2
+ 15 40  1  0  0  2
+ 16 41  1  0  0  2
+ 17 42  1  0  0  2
+ 19 43  1  0  0  2
+ 19 44  1  0  0  2
+ 29 45  1  0  0  2
+M  END
+> <MOLECULAR_FORMULA>
+C19H16NO7P2
+
+> <MOLECULAR_WEIGHT>
+432.1
+
+> <NUM_HB_ATOMS>
+8  
+
+> <NUM_ROTOR>
+2  
+
+> <XLOGP2>
+1.94 
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/origin/4xaq_ligand.sdf b/tests/bond_order/refined-set-ligands/origin/4xaq_ligand.sdf
new file mode 100644
index 000000000..e592942e1
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/origin/4xaq_ligand.sdf
@@ -0,0 +1,68 @@
+4xaq_ligand
+
+Created by X-TOOL on Fri Nov 18 18:00:48 2016
+ 23 24  0  0  0  0  0  0  0  0999 V2000
+   -5.5750   35.7600   26.9370  O 0  0  0  1  0  1
+   -8.1450   37.0440   27.8960  C 0  0  0  3  0  4
+   -9.2460   32.3630   29.3640  O 0  0  0  1  0  1
+   -7.7210   36.5030   29.3140  C 0  0  0  3  0  4
+   -8.0470   35.8370   26.9130  C 0  0  0  1  0  4
+   -7.9940   35.0120   29.2480  C 0  0  0  2  0  4
+  -10.0660   33.3980   29.0580  C 0  5  0  1  0  3
+   -9.3880   34.6630   28.7190  C 0  0  0  2  0  4
+   -8.2120   34.6260   27.7880  C 0  0  0  2  0  4
+  -11.2780   33.2560   29.0670  O 0  0  0  1  0  1
+   -9.0700   35.8490   25.8450  N 0  3  0  4  0  4
+   -6.6190   35.7900   26.3010  C 0  5  0  1  0  3
+   -6.5010   35.8060   24.9570  O 0  0  0  1  0  1
+   -7.4661   37.8489   27.5780  H 0  0  0  1  0  1
+   -9.1763   37.4252   27.9277  H 0  0  0  1  0  1
+   -8.3223   36.9738   30.1057  H 0  0  0  1  0  1
+   -6.6541   36.6951   29.5006  H 0  0  0  1  0  1
+   -7.4560   34.4093   29.9945  H 0  0  0  1  0  1
+  -10.1400   35.4606   28.6279  H 0  0  0  1  0  1
+   -7.8481   33.6937   27.3314  H 0  0  0  1  0  1
+   -8.9446   36.6665   25.2688  H 0  0  0  1  0  1
+   -9.9885   35.8680   26.2597  H 0  0  0  1  0  1
+   -8.9741   35.0208   25.2785  H 0  0  0  1  0  1
+ 12  1  2  0  0  2
+  4  2  1  0  0  1
+  5  2  1  0  0  1
+  7  3  2  0  0  2
+  6  4  1  0  0  1
+  9  5  1  0  0  1
+  5 11  1  0  0  2
+  5 12  1  0  0  2
+  8  6  1  0  0  1
+  6  9  1  0  0  1
+  7  8  1  0  0  2
+  7 10  2  0  0  2
+  8  9  1  0  0  1
+ 12 13  2  0  0  2
+  2 14  1  0  0  2
+  2 15  1  0  0  2
+  4 16  1  0  0  2
+  4 17  1  0  0  2
+  6 18  1  0  0  2
+  8 19  1  0  0  2
+  9 20  1  0  0  2
+ 11 21  1  0  0  2
+ 11 22  1  0  0  2
+ 11 23  1  0  0  2
+M  END
+> <MOLECULAR_FORMULA>
+C8H10NO4
+
+> <MOLECULAR_WEIGHT>
+184.1
+
+> <NUM_HB_ATOMS>
+5  
+
+> <NUM_ROTOR>
+0  
+
+> <XLOGP2>
+-3.47
+
+$$$$
diff --git a/tests/bond_order/refined-set-ligands/origin/4xtw_ligand.sdf b/tests/bond_order/refined-set-ligands/origin/4xtw_ligand.sdf
new file mode 100644
index 000000000..3099254f7
--- /dev/null
+++ b/tests/bond_order/refined-set-ligands/origin/4xtw_ligand.sdf
@@ -0,0 +1,161 @@
+4xtw_ligand
+
+Created by X-TOOL on Fri Nov 18 18:00:31 2016
+ 68 72  0  0  0  0  0  0  0  0999 V2000
+   -4.7030    1.6350    5.9630  N 0  0  0  1  0  1
+   -5.6630   -0.3240   11.3830  C 0  0  0  1  0  3
+   -6.3580   -0.7620   13.6240  C 0  0  0  1  0  3
+   -2.1170  -10.0370   13.8260  C 0  0  0  2  0  4
+   -0.9500   -9.2030   13.5700  N 0  0  0  2  0  3
+   -0.0190   -9.3280   14.5020  C 0  0  0  1  0  3
+    1.0640   -8.7620   14.4970  O 0  0  0  1  0  1
+   -0.4310  -10.1590   15.4430  N 0  0  0  2  0  3
+   -1.7740  -10.6600   15.1950  C 0  0  0  2  0  4
+   -2.6150  -10.0570   16.3170  C 0  0  0  3  0  4
+   -3.3090   -8.6030   15.6260  S 0  0  0  1  0  2
+   -3.3050   -9.0820   13.9370  C 0  0  0  2  0  4
+   -3.2130   -7.8700   13.0160  C 0  0  0  3  0  4
+   -3.5220   -8.2720   11.5780  C 0  0  0  3  0  4
+   -3.6630   -7.0670   10.6530  C 0  0  0  3  0  4
+   -4.0230   -7.5380    9.2480  C 0  0  0  3  0  4
+   -4.4420   -6.3980    8.3460  C 0  0  0  1  0  3
+   -5.5370   -5.8720    8.4720  O 0  0  0  1  0  1
+   -3.5630   -6.0160    7.4210  N 0  0  0  2  0  3
+   -3.8940   -4.8900    6.4520  S 0  0  0  1  0  4
+   -5.0320   -5.2610    5.6570  O 0  0  0  1  0  1
+   -2.7710   -4.6720    5.5860  O 0  0  0  1  0  1
+   -4.2490   -3.5330    7.2450  N 0  0  0  2  0  3
+   -3.0360   -2.7820    7.6110  C 0  0  0  3  0  4
+   -3.4150   -1.3070    7.6960  C 0  0  0  2  0  4
+   -4.5300   -1.1180    8.5710  O 0  0  0  1  0  2
+   -2.3120   -0.4110    8.2320  C 0  0  0  2  0  4
+   -1.5100    0.0980    7.1630  O 0  0  0  2  0  2
+   -3.0660    0.7150    8.9090  C 0  0  0  2  0  4
+   -4.4280    0.1340    9.2560  C 0  0  0  2  0  4
+   -4.5270   -0.1090   10.7160  N 0  0  0  1  0  3
+   -3.5070   -0.1720   11.5850  C 0  0  0  2  0  3
+   -3.9970   -0.4210   12.8210  N 0  0  0  1  0  2
+   -5.3390   -0.5200   12.7140  C 0  0  0  1  0  3
+   -6.9580   -0.3730   10.9940  N 0  0  0  1  0  2
+   -7.9210   -0.6080   11.8920  C 0  0  0  2  0  3
+   -7.6350   -0.7990   13.1870  N 0  0  0  1  0  2
+   -6.0820   -0.9590   14.9360  N 0  0  0  3  0  3
+   -4.0200    1.7320    6.8940  N 0  0  0  1  0  2
+   -3.2220    1.8460    8.0110  N 0  0  0  1  0  2
+   -2.2852  -10.7999   13.0516  H 0  0  0  1  0  1
+   -0.8622   -8.6014   12.7761  H 0  0  0  1  0  1
+    0.1194  -10.4152   16.2376  H 0  0  0  1  0  1
+   -1.8407  -11.7579   15.1794  H 0  0  0  1  0  1
+   -1.9846   -9.8109   17.1842  H 0  0  0  1  0  1
+   -3.4069  -10.7553   16.6256  H 0  0  0  1  0  1
+   -4.2328   -9.6221   13.6972  H 0  0  0  1  0  1
+   -2.1962   -7.4532   13.0655  H 0  0  0  1  0  1
+   -3.9373   -7.1097   13.3436  H 0  0  0  1  0  1
+   -4.4644   -8.8392   11.5648  H 0  0  0  1  0  1
+   -2.7056   -8.9086   11.2063  H 0  0  0  1  0  1
+   -2.7111   -6.5166   10.6216  H 0  0  0  1  0  1
+   -4.4565   -6.4060   11.0317  H 0  0  0  1  0  1
+   -4.8533   -8.2560    9.3183  H 0  0  0  1  0  1
+   -3.1460   -8.0336    8.8062  H 0  0  0  1  0  1
+   -2.6760   -6.4740    7.3626  H 0  0  0  1  0  1
+   -5.1792   -3.2369    7.4621  H 0  0  0  1  0  1
+   -2.2600   -2.9263    6.8449  H 0  0  0  1  0  1
+   -2.6593   -3.1291    8.5844  H 0  0  0  1  0  1
+   -3.6831   -0.9704    6.6837  H 0  0  0  1  0  1
+   -1.6764   -0.9510    8.9492  H 0  0  0  1  0  1
+   -0.8273    0.6549    7.5182  H 0  0  0  1  0  1
+   -2.5391    1.0381    9.8190  H 0  0  0  1  0  1
+   -5.2279    0.8174    8.9350  H 0  0  0  1  0  1
+   -2.4547   -0.0435   11.3357  H 0  0  0  1  0  1
+   -8.9540   -0.6447   11.5654  H 0  0  0  1  0  1
+   -6.8471   -1.1378   15.6020  H 0  0  0  1  0  1
+   -5.1071   -0.9299   15.2672  H 0  0  0  1  0  1
+ 39  1  3  0  0  2
+ 31  2  1  0  0  1
+  2 34  4  0  0  1
+  2 35  4  0  0  1
+ 34  3  4  0  0  1
+  3 37  4  0  0  1
+  3 38  1  0  0  2
+  4  5  1  0  0  1
+  4  9  1  0  0  1
+ 12  4  1  0  0  1
+  5  6  1  0  0  1
+  6  7  2  0  0  2
+  8  6  1  0  0  1
+  9  8  1  0  0  1
+ 10  9  1  0  0  1
+ 11 10  1  0  0  1
+ 12 11  1  0  0  1
+ 13 12  1  0  0  2
+ 14 13  1  0  0  2
+ 15 14  1  0  0  2
+ 16 15  1  0  0  2
+ 17 16  1  0  0  2
+ 17 18  2  0  0  2
+ 19 17  1  0  0  2
+ 20 19  1  0  0  2
+ 20 21  2  0  0  2
+ 20 22  2  0  0  2
+ 23 20  1  0  0  2
+ 24 23  1  0  0  2
+ 25 24  1  0  0  2
+ 26 25  1  0  0  1
+ 27 25  1  0  0  1
+ 30 26  1  0  0  1
+ 27 28  1  0  0  2
+ 29 27  1  0  0  1
+ 29 30  1  0  0  1
+ 40 29  1  0  0  2
+ 30 31  1  0  0  2
+ 31 32  1  0  0  1
+ 32 33  2  0  0  1
+ 33 34  1  0  0  1
+ 35 36  4  0  0  1
+ 36 37  4  0  0  1
+ 39 40  2  0  0  2
+  4 41  1  0  0  2
+  5 42  1  0  0  2
+  8 43  1  0  0  2
+  9 44  1  0  0  2
+ 10 45  1  0  0  2
+ 10 46  1  0  0  2
+ 12 47  1  0  0  2
+ 13 48  1  0  0  2
+ 13 49  1  0  0  2
+ 14 50  1  0  0  2
+ 14 51  1  0  0  2
+ 15 52  1  0  0  2
+ 15 53  1  0  0  2
+ 16 54  1  0  0  2
+ 16 55  1  0  0  2
+ 19 56  1  0  0  2
+ 23 57  1  0  0  2
+ 24 58  1  0  0  2
+ 24 59  1  0  0  2
+ 25 60  1  0  0  2
+ 27 61  1  0  0  2
+ 28 62  1  0  0  2
+ 29 63  1  0  0  2
+ 30 64  1  0  0  2
+ 32 65  1  0  0  2
+ 36 66  1  0  0  2
+ 38 67  1  0  0  2
+ 38 68  1  0  0  2
+M  END
+> <MOLECULAR_FORMULA>
+C20H28N12O6S2
+
+> <MOLECULAR_WEIGHT>
+596.5
+
+> <NUM_HB_ATOMS>
+17 
+
+> <NUM_ROTOR>
+9  
+
+> <XLOGP2>
+-2.69
+
+$$$$
diff --git a/tests/context.py b/tests/context.py
index c17ef0ea8..95257e195 100644
--- a/tests/context.py
+++ b/tests/context.py
@@ -3,3 +3,4 @@
 import dpdata
 import dpdata.md.water
 import dpdata.md.msd
+import dpdata.system
diff --git a/tests/test_amber_sqm.py b/tests/test_amber_sqm.py
new file mode 100644
index 000000000..48342c4cc
--- /dev/null
+++ b/tests/test_amber_sqm.py
@@ -0,0 +1,21 @@
+import os
+import unittest
+import shutil
+from context import dpdata
+from comp_sys import CompSys, IsNoPBC
+
+
+class TestAmberSqmOut(unittest.TestCase, CompSys, IsNoPBC):
+    def setUp (self) :
+        self.system_1 = dpdata.System('amber/sqm.out', fmt = 'sqm/out')
+        self.system_1.to('deepmd/npy','tmp.deepmd.npy')
+        self.system_2 = dpdata.System('tmp.deepmd.npy', fmt = 'deepmd/npy')
+        self.places = 5
+        self.e_places = 4
+        self.f_places = 6
+        self.v_places = 6
+
+    def tearDown(self) :
+        if os.path.exists('tmp.deepmd.npy'):
+            shutil.rmtree('tmp.deepmd.npy')
+
diff --git a/tests/test_bond_order_system.py b/tests/test_bond_order_system.py
new file mode 100644
index 000000000..086a90cad
--- /dev/null
+++ b/tests/test_bond_order_system.py
@@ -0,0 +1,99 @@
+import os
+import unittest
+from context import dpdata
+import glob
+from rdkit import Chem
+from rdkit.Chem import AllChem
+import shutil
+import numpy as np
+
+class TestBondOrderSystem(unittest.TestCase):
+
+    def test_from_rdkit_mol(self):
+        mol = Chem.MolFromSmiles("CC")
+        mol = Chem.AddHs(mol)
+        AllChem.EmbedMultipleConfs(mol, 10)
+        system = dpdata.BondOrderSystem(rdkit_mol=mol)
+        self.assertEqual(system.get_nframes(), 10)
+        self.assertEqual(system.get_nbonds(), 7)
+
+    def test_from_mol_file(self):
+        syst = dpdata.BondOrderSystem("bond_order/CH3OH.mol", fmt='mol', type_map=['O','C','H'])
+        self.assertEqual(syst.get_nframes(), 1)
+        self.assertEqual(syst.get_nbonds(), 5)
+        self.assertEqual(syst.get_natoms(), 6)
+        self.assertEqual(syst['atom_names'], ['O','C','H'])
+        self.assertAlmostEqual(syst['coords'][0][0][0], -0.3858)
+    
+    def test_from_sdf_file(self):
+        syst = dpdata.BondOrderSystem("bond_order/methane.sdf", type_map=['C','H'])
+        self.assertEqual(syst.get_nframes(), 4)
+        self.assertEqual(syst.get_nbonds(), 4)
+        self.assertEqual(syst.get_natoms(), 5)
+        self.assertEqual(syst['atom_names'], ['C','H'])
+        self.assertAlmostEqual(syst['coords'][0][0][0], 0.0059)
+        self.assertAlmostEqual(syst['coords'][1][0][0], 0.0043)
+        self.assertAlmostEqual(syst['coords'][2][0][0], 0.0071)
+        self.assertAlmostEqual(syst['coords'][3][0][0], 0.0032)
+    
+    def test_from_sdf_file_err(self):
+        self.assertRaises(ValueError, dpdata.BondOrderSystem, "bond_order/methane_ethane.sdf")
+
+    def test_regularize_formal_charges(self):
+        non_regular = Chem.MolFromMolFile("bond_order/formal_charge.mol", removeHs=False)
+        regular = dpdata.BondOrderSystem("bond_order/formal_charge.mol", fmt="mol")
+        self.assertFalse(non_regular)
+        self.assertTrue(isinstance(regular.rdkit_mol, Chem.rdchem.Mol))
+    
+    def test_formal_charge(self):
+        names = ["C5H5-", "CH3CC-", "CH3NC", "CH3NH3+", "CH3NO2", "OCH3+",
+                 "gly", "arg", "oxpy", "CH3OPO3_2-", "CH3PH3+", "CH3OAsO3_2-",
+                 "CH3SH", "CH3_2SO", "CH3_2SO2", "CH3SO3-", "BOH4-"]
+        charges = [-1, -1, 0, 1, 0, 1, 0, 1, 0, -2, 1, -2, 0, 0, 0, -1, -1]
+        mols = [dpdata.BondOrderSystem(f"bond_order/{name}.mol") for name in names]
+        self.assertEqual(charges, [mol.get_charge() for mol in mols])
+
+    def test_read_other_format_without_bond_info(self):
+        self.assertRaises(RuntimeError, dpdata.BondOrderSystem, "gromacs/1h.gro")
+    
+    def test_dump_to_deepmd_raw(self):
+        syst = dpdata.BondOrderSystem("bond_order/methane.sdf", fmt="sdf")
+        syst.to_deepmd_raw("bond_order/methane")
+        formal_charges = list(np.loadtxt("bond_order/methane/formal_charges.raw"))
+        self.assertTrue(formal_charges, [0 for _ in range(5)])
+        bonds = np.loadtxt("bond_order/methane/bonds.raw")
+        for bond_idx in range(4):
+            for ii in range(3):
+                self.assertEqual(syst['bonds'][bond_idx][ii], bonds[bond_idx][ii])
+        shutil.rmtree("bond_order/methane")
+    
+    def test_dump_to_deepmd_npy(self):
+        syst = dpdata.BondOrderSystem("bond_order/methane.sdf", fmt="sdf")
+        syst.to_deepmd_npy("bond_order/methane")
+        formal_charges = list(np.loadtxt("bond_order/methane/formal_charges.raw"))
+        self.assertTrue(formal_charges, [0 for _ in range(5)])
+        bonds = np.loadtxt("bond_order/methane/bonds.raw")
+        for bond_idx in range(4):
+            for ii in range(3):
+                self.assertEqual(syst['bonds'][bond_idx][ii], bonds[bond_idx][ii])
+        shutil.rmtree("bond_order/methane")
+    
+    def test_sanitize_mol_obabel(self):
+        cnt = 0
+        for sdf_file in glob.glob("bond_order/refined-set-ligands/obabel/*sdf"):
+            syst = dpdata.BondOrderSystem(sdf_file, sanitize_level='high', verbose=False)
+            if syst.rdkit_mol is None:
+                cnt += 1
+        self.assertEqual(cnt, 0)
+    
+    def test_sanitize_mol_origin(self):
+        cnt = 0
+        for sdf_file in glob.glob("bond_order/refined-set-ligands/origin/*sdf"):
+            syst = dpdata.BondOrderSystem(sdf_file, sanitize_level='high', verbose=False)
+            if syst.rdkit_mol is None:
+                cnt += 1
+        self.assertEqual(cnt, 0)
+    
+    def tearDown(self):
+        if os.path.exists("tests/.cache"):
+            shutil.rmtree("tests/.cache")