def test_rmsd():
n = 4
crds1 = [v3.random_vector() for i in range(n)]
random_m = v3.random_rotation()
crds2 = [v3.transform(random_m, c) for c in crds1]
rms, m = rmsd.calc_rmsd_rot(crds1, crds2)
assert v3.is_similar_mag(0, rms)
# test the two algorithms separately
rms, m = rmsd.pyqcprot_rmsd_rot(crds1, crds2)
assert v3.is_similar_mag(0, rms)
if rmsd.is_numpy:
rms, m = rmsd.numpy_svd_rmsd_rot(crds1, crds2)
assert v3.is_similar_mag(0, rms)
def test_rmsd():
n = 4
crds1 = [v3.random_vector() for i in range(n)]
random_m = v3.random_rotation()
crds2 = [v3.transform(random_m, c) for c in crds1]
rms, m = rmsd.calc_rmsd_rot(crds1, crds2)
assert v3.is_similar_mag(0, rms)
# test the two algorithms separately
rms, m = rmsd.pyqcprot_rmsd_rot(crds1, crds2)
assert v3.is_similar_mag(0, rms)
if rmsd.is_numpy:
rms, m = rmsd.numpy_svd_rmsd_rot(crds1, crds2)
assert v3.is_similar_mag(0, rms)
for i in range(0, len(indices), 2):
yield indices[i:i+2]
def get_crds(res_tags, soup):
crds = []
i_residues = [soup.get_i_residue(r) for r in res_tags]
for j, k in split_pairs(i_residues):
for i in range(j, k+1):
crds.append(soup.residue(i).atom('CA').pos)
center = v3.get_center(crds)
crds = [c-center for c in crds]
return crds
res_tags1 = "A:311 A:318 A:322 A:329 A:335 A:391".split()
res_tags2 = "A:158 A:165 A:171 A:178 A:194 A:250".split()
rmsd, rot = rmsd.pyqcprot_rmsd_rot(
get_crds(res_tags1, soup), get_crds(res_tags2, soup2))
print "RMSD:"
print rmsd
# select polar/charged residues using regular expresions
# and list comprehensions
residues = filter(
lambda r: re.match('(LY.|AR.|GL.|AS.).?', r.type),
soup.residues())
print "Charged residues:"
for res in residues:
print res.tag()+'-'+res.type
def get_crds(res_tags, soup):
crds = []
i_residues = [soup.get_i_residue(r) for r in res_tags]
for j, k in split_pairs(i_residues):
for i in range(j, k + 1):
crds.append(soup.residue(i).atom('CA').pos)
center = v3.get_center(crds)
crds = [c - center for c in crds]
return crds
res_tags1 = "A:311 A:318 A:322 A:329 A:335 A:391".split()
res_tags2 = "A:158 A:165 A:171 A:178 A:194 A:250".split()
rmsd, rot = rmsd.pyqcprot_rmsd_rot(get_crds(res_tags1, soup),
get_crds(res_tags2, soup2))
print "RMSD:"
print rmsd
# select polar/charged residues using regular expresions
# and list comprehensions
residues = filter(lambda r: re.match('(LY.|AR.|GL.|AS.).?', r.type),
soup.residues())
print "Charged residues:"
for res in residues:
print res.tag() + '-' + res.type
# find contact residue pairs by decomposing comparisons
# into functions that can be used later
