def test_range(u):
ags = sels(u)
rmin, rmax = 1.0, 13.0
rdf = InterRDF_s(u, ags, range=(rmin, rmax)).run()
assert rdf.edges[0] == rmin
assert rdf.edges[-1] == rmax
def test_density(u, sels, density, value):
kwargs = {'density': density} if density is not None else {}
rdf = InterRDF_s(u, sels, **kwargs).run()
assert_almost_equal(max(rdf.rdf[0][0][0]), value)
if not density:
s1 = u.select_atoms('name ZND and resid 289')
s2 = u.select_atoms(
'name OD1 and resid 51 and sphzone 5.0 (resid 289)')
rdf_ref = InterRDF(s1, s2).run()
assert_almost_equal(rdf_ref.rdf, rdf.rdf[0][0][0])
def test_nbins(u, sels):
rdf = InterRDF_s(u, sels, nbins=412).run()
assert len(rdf.bins) == 412
def rdf(u, sels):
return InterRDF_s(u, sels).run()
def test_density(u, sels, density, value):
rdf = InterRDF_s(u, sels, density=density).run()
assert_almost_equal(max(rdf.rdf[0][0][0]), value)
import MDAnalysis as mda
from MDAnalysis.analysis.rdf import InterRDF_s
import numpy as np
u = mda.Universe('step6.6.part0001.gro', 'step7_1000ns_dt_500_center.xtc')
Zn1 = u.select_atoms('name ZND and resid 24905')
Zn2 = u.select_atoms('name ZND and resid 24900')
Zn3 = u.select_atoms('name ZND')
Bsites1 = u.select_atoms(
'((name O* and resname ASP) or (name N* and resname HSD)) and around 4.0 (name ZND and resid 24905)'
)
Bsites2 = u.select_atoms(
'((name O* and resname ASP) or (name N* and resname HSD)) and around 4.0 (name ZND and resid 24900)'
)
ags = [[Zn1, Bsites1], [Zn2, Bsites2]]
rdf = InterRDF_s(u, ags, nbins=200, range=(1.0, 4.0), density=False)
rdf.run()
rdf.get_cdf()
np.savetxt('bins.dat', rdf.bins)
np.save('rdf', rdf.rdf)
np.save('indices', rdf.indices)
np.save('cdf', rdf.cdf)
def test_nbins(u):
ags = sels(u)
rdf = InterRDF_s(u, ags, nbins=412).run()
assert len(rdf.bins) == 412