MDA rhombic dodecahedron PBC testing

calc_center.py

import MDAnalysis
import numpy as np
from scipy.spatial.distance import euclidean

u = MDAnalysis.Universe('split_rhombic_small.gro')
residue = u.atoms.residues[0]
residue_centroid_no_pbc = residue.atoms.centroid(pbc=False)
residue_centroid = residue.atoms.centroid(pbc=True)
head_centroid_distance = euclidean(residue.atoms.positions[0],
        residue_centroid)
tail_centroid_distance = euclidean(residue.atoms.positions[-1],
        residue_centroid)
print 'residue_centroid no pbc:', residue_centroid_no_pbc
print 'residue_centroid:', residue_centroid
print 'head_centroid_distance:', head_centroid_distance
print 'tail_centroid_distance:', tail_centroid_distance

split_rhombic_small.gro

Written by MDAnalysis
   11
  103DPSM   NC3    1 155.979  49.482 111.613
  103DPSM   PO4    2 156.020  49.525 112.036
  103DPSM   AM1    3 156.415  49.583 112.314
  103DPSM   AM2    4 156.475  49.321 112.323
  103DPSM   T1A    5 156.609  49.813 112.506
  103DPSM   C2A    6  77.101 129.440   0.078
  103DPSM   C3A    7  77.319 129.514   0.372
  103DPSM   C1B    8 156.766  49.182 112.460
  103DPSM   C2B    9  77.142 128.918   0.021
  103DPSM   C3B   10  77.443 128.974   0.249
  103DPSM   C4B   11  77.641 129.136   0.581
 159.47252 159.47252 112.76409   0.00000   0.00000  -0.00001   0.00000  79.73627  79.73626