---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In[9], line 1
----> 1 viewer_json = msm.convert(molecular_system, to_form='molsysmt.ViewerJSON')
File ~/repos@uibcdf/molsysmt/molsysmt/_private/digestion/digest.py:122, in digest.<locals>.digestor.<locals>.wrapper(*args, **kwargs)
120 return func(all_args['self'], **final_args)
121 else:
--> 122 return func(**final_args)
File ~/repos@uibcdf/molsysmt/molsysmt/basic/convert.py:515, in convert(molecular_system, to_form, selection, structure_indices, syntax, skip_digestion, **kwargs)
513 # If one to one
514 if not isinstance(from_form, (list, tuple)):
--> 515 output = _convert_one_to_one(molecular_system, from_form, to_form=to_form, selection=selection, structure_indices=structure_indices,
516 syntax=syntax, skip_digestion=True, **kwargs)
518 # If multiple to one
519
520 else:
521
522 # conversions in private shortcuts
523 if tuple(sorted(from_form)) in _multiple_conversion_shortcuts:
File ~/repos@uibcdf/molsysmt/molsysmt/basic/convert.py:93, in _convert_one_to_one(molecular_system, from_form, to_form, selection, structure_indices, syntax, **kwargs)
90 if len(missing_arguments)>0:
91 raise NotCompatibleConversionError(from_form, to_form, missing_arguments)
---> 93 output = function(molecular_system, **conversion_arguments, **kwargs)
95 elif ('molsysmt.MolSys' in _dict_modules[from_form]._convert_to) and (to_form in _dict_modules['molsysmt.MolSys']._convert_to):
97 output = _convert_one_to_one(molecular_system, from_form, to_form='molsysmt.MolSys', selection=selection,
98 structure_indices=structure_indices, syntax=syntax, **kwargs)
File ~/repos@uibcdf/molsysmt/molsysmt/_private/digestion/digest.py:52, in digest.<locals>.digestor.<locals>.wrapper(*args, **kwargs)
48 @functools.wraps(func)
49 def wrapper(*args, **kwargs):
51 if kwargs.get('skip_digestion', False):
---> 52 return func(*args, **kwargs)
54 # Define caller
56 caller = func.__module__+'.'+func.__name__
File ~/repos@uibcdf/molsysmt/molsysmt/form/molsysmt_MolSys/to_molsysmt_ViewerJSON.py:12, in to_molsysmt_ViewerJSON(item, skip_digestion)
9 """Convert a native MolSys into a ViewerJSON container."""
11 topo_vjson = topology_to_viewer(item.topology, skip_digestion=True)
---> 12 struct_vjson = structures_to_viewer(item.structures, skip_digestion=True)
14 data = {
15 "version": topo_vjson.data.get("version", "0.1"),
16 "atoms": topo_vjson.data.get("atoms", {}),
17 "bonds": topo_vjson.data.get("bonds", {}),
18 "estructures": struct_vjson.data.get("estructures", struct_vjson.data.get("frames", [])),
19 }
21 return ViewerJSON(data=data)
File ~/repos@uibcdf/molsysmt/molsysmt/_private/digestion/digest.py:52, in digest.<locals>.digestor.<locals>.wrapper(*args, **kwargs)
48 @functools.wraps(func)
49 def wrapper(*args, **kwargs):
51 if kwargs.get('skip_digestion', False):
---> 52 return func(*args, **kwargs)
54 # Define caller
56 caller = func.__module__+'.'+func.__name__
File ~/repos@uibcdf/molsysmt/molsysmt/form/molsysmt_Structures/to_molsysmt_ViewerJSON.py:58, in to_molsysmt_ViewerJSON(item, skip_digestion)
56 frame["time"] = float(time_values[ii])
57 if box_values is not None:
---> 58 frame["box"] = _box_from_matrix(np.asarray(box_values[ii]))
59 frames.append(frame)
61 data = {
62 "version": "0.1",
63 "atoms": atoms_block,
64 "bonds": bonds_block,
65 "estructures": frames,
66 }
File ~/repos@uibcdf/molsysmt/molsysmt/form/molsysmt_Structures/to_molsysmt_ViewerJSON.py:10, in _box_from_matrix(box)
8 def _box_from_matrix(box):
9 """Return box lengths (nm) and angles (rad) from a 3x3 matrix."""
---> 10 lengths, angles = get_lengths_and_angles_from_box(
11 puw.quantity(np.asarray(box), "nanometer"), skip_digestion=True
12 )
13 lengths_val = puw.get_value(lengths, to_unit="nanometer")
14 angles_val = puw.get_value(angles, to_unit="radian")
File ~/repos@uibcdf/molsysmt/molsysmt/_private/digestion/digest.py:52, in digest.<locals>.digestor.<locals>.wrapper(*args, **kwargs)
48 @functools.wraps(func)
49 def wrapper(*args, **kwargs):
51 if kwargs.get('skip_digestion', False):
---> 52 return func(*args, **kwargs)
54 # Define caller
56 caller = func.__module__+'.'+func.__name__
File ~/repos@uibcdf/molsysmt/molsysmt/pbc/get_lengths_and_angles_from_box.py:29, in get_lengths_and_angles_from_box(box, skip_digestion)
7 """Return box lengths and angles from a 3x3 box matrix or an array of boxes.
8
9 Parameters
(...) 25 beta between a and c, gamma between a and b).
26 """
28 box_value, box_unit = puw.get_value_and_unit(box)
---> 29 lengths_value, angles_value = msmlib.pbc.get_lengths_and_angles_from_box(box_value)
30 lengths = puw.quantity(lengths_value.round(6), box_unit)
31 lengths = puw.standardize(lengths)
File ~/Myopt/miniconda3/envs/molsysmt@uibcdf_3.12/lib/python3.12/site-packages/numba/core/dispatcher.py:659, in _DispatcherBase._explain_matching_error(self, *args, **kws)
656 args = [self.typeof_pyval(a) for a in args]
657 msg = ("No matching definition for argument type(s) %s"
658 % ', '.join(map(str, args)))
--> 659 raise TypeError(msg)
TypeError: No matching definition for argument type(s) array(float64, 2d, C)
