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[lukasturcani]

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[NguyenThiHoaiLinh]

I am new to stk. Trying to follow the examples on the Documentation. Whenever "stk.ConstructedMolecule" is called, the
AttributeError: type object 'Rotation' has no attribute 'from_matrix'
error happens.
What should I do to solve this?

import stk

bb1 = stk.BuildingBlock('NCCCN', [stk.PrimaryAminoFactory()])
bb2 = stk.BuildingBlock(
smiles='O=CC(C=O)CC=O',
functional_groups=[stk.AldehydeFactory()],
)
tetrahedron = stk.cage.FourPlusSix((bb1, bb2))
cage1 = stk.ConstructedMolecule(tetrahedron)

---

AttributeError Traceback (most recent call last)
in
7 )
8 tetrahedron = stk.cage.FourPlusSix((bb1, bb2))
----> 9 cage1 = stk.ConstructedMolecule(tetrahedron)

~/opt/anaconda3/lib/python3.7/site-packages/stk/molecular/molecules/constructed_molecule.py in init(self, topology_graph)
71 """
72
---> 73 construction_result = topology_graph.construct()
74 super().init(
75 atoms=construction_result.get_atoms(),

~/opt/anaconda3/lib/python3.7/site-packages/stk/molecular/topology_graphs/topology_graph/topology_graph/topology_graph.py in construct(self)
394
395 state = self._get_construction_state()
--> 396 state = self._place_building_blocks(state)
397 state = self._run_reactions(state)
398 return ConstructionResult(state)

~/opt/anaconda3/lib/python3.7/site-packages/stk/molecular/topology_graphs/topology_graph/topology_graph/topology_graph.py in _place_building_blocks(self, state)
449 """
450
--> 451 return self._implementation._place_building_blocks(state)
452
453 def _run_reactions(self, state):

~/opt/anaconda3/lib/python3.7/site-packages/stk/molecular/topology_graphs/topology_graph/topology_graph/implementations/serial.py in _place_building_blocks(self, state)
45 edges=edges,
46 building_blocks=building_blocks,
---> 47 results=placement_results,
48 )
49 return state

~/opt/anaconda3/lib/python3.7/site-packages/stk/molecular/topology_graphs/topology_graph/construction_state/construction_state.py in with_placement_results(self, vertices, edges, building_blocks, results)
125 edges=edges,
126 building_blocks=building_blocks,
--> 127 results=results,
128 )
129

~/opt/anaconda3/lib/python3.7/site-packages/stk/molecular/topology_graphs/cage/cage_construction_state.py in _with_placement_results(self, vertices, edges, building_blocks, results)
55 ):
56 # Need to iterate multiple times through results.
---> 57 results = tuple(results)
58 super()._with_placement_results(
59 vertices=vertices,

~/opt/anaconda3/lib/python3.7/site-packages/stk/molecular/topology_graphs/topology_graph/topology_graph/implementations/serial.py in (placement)
38 )
39 placement_results = map(
---> 40 lambda placement: placement.get_result(),
41 placements,
42 )

~/opt/anaconda3/lib/python3.7/site-packages/stk/molecular/topology_graphs/topology_graph/topology_graph/implementations/utilities.py in get_result(self)
66 position_matrix = self._vertex.place_building_block(
67 building_block=self._building_block,
---> 68 edges=self._edges,
69 )
70 position_matrix.setflags(write=False)

~/opt/anaconda3/lib/python3.7/site-packages/stk/molecular/topology_graphs/cage/vertices.py in place_building_block(self, building_block, edges)
239 ),
240 target=edge_normal,
--> 241 origin=self._position,
242 )
243 fg_bonder_centroid = building_block.get_centroid(

~/opt/anaconda3/lib/python3.7/site-packages/stk/molecular/molecules/molecule/molecule.py in with_rotation_between_vectors(self, start, target, origin)
260 start=start,
261 target=target,
--> 262 origin=origin,
263 )
264

~/opt/anaconda3/lib/python3.7/site-packages/stk/molecular/molecules/molecule/molecule.py in _with_rotation_between_vectors(self, start, target, origin)
156 # Set the origin of the rotation to "origin".
157 self._with_displacement(-origin)
--> 158 rot_mat = rotation_matrix(start, target)
159
160 # Apply the rotation matrix to the atomic positions to yield

~/opt/anaconda3/lib/python3.7/site-packages/stk/utilities/utilities.py in rotation_matrix(vector1, vector2)
547 # matrix and allows for returns as quaternion or alternative
548 # type in the future.
--> 549 return Rotation.from_matrix(
550 i + vx + np.multiply(np.dot(vx, vx), mult_factor)
551 ).as_matrix()

AttributeError: type object 'Rotation' has no attribute 'from_matrix'
​

[lukasturcani]

Hi there! What version of scipy are you using? from_matrix was added in version 1.4.0 so you may have to update.

Try running:

pip install scipy --ugprade

and let me know what you get when you run (before and after the update)

pip show scipy

For reference:
https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.transform.Rotation.from_matrix.html#scipy.spatial.transform.Rotation.from_matrix

[NguyenThiHoaiLinh]

Dear Lukas,
Thanks a lot for your quick response.
I updated scipy to 1.6.1 and now it works.

[lukasturcani]

Yay! Glad to hear :)