Can I handle BuildingBlock during ConstructedMolecule process?

[KeDUCK00]

Hi, thanks a lot for your excellent tutorial for stk.

Because some buildingblocks are asymmetrical, I want to rotate them during construction to list all the possibilities.
I tried with_rotation_between_vectors() and with_rotation_between_vectors(), but it doesn't work.
How can I rotate the buildingblock during construction ?
Any suggestions would be helpful for me !

[andrewtarzia]

Hey @KeDUCK00 , welcome and thank you!

So, the main way to do this in stk is to set the vertex_alignments argument when initialising a topology graph, like in this example (in https://stk.readthedocs.io/en/stable/stk.molecular.topology_graphs.cage.cage.html):

import stk

bb1 = stk.BuildingBlock('NCCN', [stk.PrimaryAminoFactory()])
bb2 = stk.BuildingBlock(
    smiles='O=CC(C=O)C=O',
    functional_groups=[stk.AldehydeFactory()],
)

cage = stk.ConstructedMolecule(
    topology_graph=stk.cage.FourPlusSix(
        building_blocks=(bb1, bb2),
        vertex_alignments={0: 1, 1: 1, 2: 2},
    ),
)

In this instance, you are changing the orientation of the 0th, 1st and 2nd building blocks in this topology.

You can change the values here to any number associated with any functional group in your building blocks. Lines 171 to 176 in this file https://github.com/andrewtarzia/unsymm_match/blob/master/cage_building.py shows how to do this to build 4 distinct isomers of Pd2L4 cages in my recent paper.

Basically, the process I take is to start from the default orientations, then change one "vertex_alignment" value at a time and check the structure until you get the desired isomer. There is currently no way to know in advance what orientation you will get because it depends on the order of the functional groups in the building blocks and the order of vertices in the topology graph.

Hope this helps, please let us know!

[KeDUCK00]

The way to define vertex_alignments rotates the molecule with 2-functional groups effectively and your code in building 4 distinct isomers of Pd2L4 cages gives some idea for me !
Thanks a lot for your suggestion !

[andrewtarzia]

Excellent! Just note that vertex_alignments can be used for building blocks with more than 2 FGs.

[KeDUCK00]

I've used vertex_alignment for 4 FGs. It also works perfectly through the definition of {vertex_index : range(num_fgs)} . So, I can list all of the conformations in this way.
It's very useful for me, thanks a lot for your help!