[cctbxbb] convert an arbitrary point to one inside the asymmetric unit

Tijskens Engelbert Engelbert.Tijskens at uantwerpen.be
Fri Nov 18 05:06:01 PST 2016


Hi,

I am an experienced C++ and Python programmer, but new to cctbx.

Can any tell me if there is an algorithm in cctbx available  to convert an arbritrary point in direct space to the corresponding point in the asymmetric unit of a given space group? i can figure out how to convert it to the corresponding point in the unit cell at the origin, but from there to the asymmetric unit is unclear to me.

I found the brick class which gives me the assymmetric unit
from cctbx import crystal,sgtbx

if __name__=='__main__':
    crystal_symmetry = crystal.symmetry( unit_cell=(3.5093,3.5093,3.5093,90,90,90)
                                       , space_group_symbol="229" # = "I m -3 m"
                                       )
    sg = crystal_symmetry.space_group()
    brick = sgtbx.brick( sg.type() )
    print brick

I also found cctbx::sgtbx::asu and the classes therein, but they are largely undocumented.

For the interested, this is the problem i want to solve:
I have a (scalar) physical property P(r), depending on spatial position, presented as a 3D array on a regular grid over the unit cell (space group is known). I need to integrate P(r)*f(r), f(r) being an arbitrary function over a region of direct space, which typically comprises several unit cells. In order to reduce the memory footprint of the P array, i would like to restrict it to the space group’s asymmetric unit.

All help is greatly appreciated.
kindest regards,

Dr [Engel]bert Tijskens
HPC Analyst/Consultant

Flemish Supercomputer Center vscentrum.be<http://vscentrum.be>
HPC core facility CalcUA uantwerp.be/calcua<http://uantwerp.be/calcua>
Computational mathematics www.uantwerpen.be/en/rg/cma<http://www.uantwerpen.be/en/rg/cma>

University of Antwerp
Middelheimlaan1 G.309, B-2020 Antwerp, Belgium

engelbert.tijskens at uantwerpen.be<mailto:engelbert.tijskens at uantwerpen.be>
++32 3 265 3879

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