def test_nupars(self):
pdb_fn = fn('Test_NAstruct/adh026.3.pdb')
traj = pt.iterload(pdb_fn, pdb_fn)
data = pt.nastruct(traj)
# default
text = '''
parm {}
trajin {}
nastruct groovecalc 3dna
'''.format(fn('Test_NAstruct/adh026.3.pdb'),
fn('Test_NAstruct/adh026.3.pdb'))
state = pt.load_cpptraj_state(text)
state.run()
for key in ['major', 'minor', 'twist']:
cpp_data = np.array(
[x.values for x in state.data if x.aspect == key])
# need to transpose to get shape=(n_frames, n_pairs)
cpp_data = cpp_data.T
aa_eq(data[key][1], cpp_data)
# TODO: assert
data._summary(np.mean, indices=None)
data._summary(np.mean, indices=[
1,
])
data._summary(np.mean, keys=['major', 'twist'], indices=[
1,
])
data._summary(np.mean, keys='major', indices=[
1,
])
data._summary(np.std, indices=[
1,
])
data._summary([np.std, np.mean], indices=[
1,
])
data._explain()
dir(data)
# pickle
pt.to_pickle(data, 'na.pk')
na2 = pt.read_pickle('na.pk')
for key in data.keys():
aa_eq(data[key][1], na2[key][1])
# raise
self.assertRaises(ValueError,
lambda: pt.nastruct(traj, dtype='ndarray'))
def test_baseref(self):
pdb_fn = fn('Test_NAstruct/adh026.3.pdb')
baseref_fn = fn('Test_NAstruct/Atomic_G.pdb.nastruct')
traj = pt.iterload(pdb_fn, pdb_fn)
data = pt.nastruct(traj, baseref=baseref_fn)
saved_data = """
# major minor 3 frames
19.9015, 15.8085,
20.7510, 15.8180,
19.9822, 15.4856,
19.5528, 15.9407,
20.6965, 16.2324,
19.6335, 16.3369,
19.2871, 15.9514,
21.2010, 16.7085,
19.9055, 16.6283
"""
aa_eq(data.major[1][0], [19.9015, 20.7510, 19.9822], decimal=3)
aa_eq(data.major[1][1], [19.5528, 20.6965, 19.6335], decimal=3)
aa_eq(data.major[1][2], [19.2871, 21.2010, 19.9055], decimal=3)
aa_eq(data.minor[1][0], [15.8085, 15.8180, 15.4856], decimal=3)
def test_nab_arna():
with tempfolder():
filename = 'nuc.pdb'
traj = builder.build_arna('AAAAAAAAAA')
nu = pt.nastruct(traj)
aa_eq(np.mean(nu.major[1]), [15.183,], decimal=3)
aa_eq(np.mean(nu.minor[1]), [18.804,], decimal=3)
def _compute_major_groove(builder):
with tempfolder():
pdb_out = 'out.pdb'
builder.write_pdb(pdb_out)
traj = pytraj.load(pdb_out)
data = pytraj.nastruct(traj)
return data.major[1][0]
def test_nupars(self):
fn = "./data/Test_NAstruct/adh026.3.pdb"
traj = pt.iterload(fn, fn)
data = pt.nastruct(traj)
# default
text = '''
parm "./data/Test_NAstruct/adh026.3.pdb"
trajin "./data/Test_NAstruct/adh026.3.pdb"
nastruct groovecalc 3dna
'''
state = pt.load_cpptraj_state(text)
state.run()
for key in ['major', 'minor', 'twist']:
cpp_data = np.array([x.values for x in state.data if x.aspect ==
key])
# need to transpose to get shape=(n_frames, n_pairs)
cpp_data = cpp_data.T
aa_eq(data[key][1], cpp_data)
# TODO: assert
data._summary(np.mean, indices=None)
data._summary(np.mean, indices=[1, ])
data._summary(np.mean, keys=['major', 'twist'], indices=[1, ])
data._summary(np.mean, keys='major', indices=[1, ])
data._summary(np.std, indices=[1, ])
data._summary([np.std, np.mean], indices=[1, ])
data._explain()
dir(data)
# pickle
pt.to_pickle(data, 'data/na.pk')
na2 = pt.read_pickle('data/na.pk')
for key in data.keys():
aa_eq(data[key][1], na2[key][1])
# raise
self.assertRaises(ValueError, lambda: pt.nastruct(traj, dtype='ndarray'))
def test_nupars_vs_x3dna(self):
traj = pt.iterload(fn('Test_NAstruct/x3dna/rna.pdb'))
ref = pt.iterload(fn('Test_NAstruct/x3dna/rna_nab.pdb'))
nu = pt.nastruct(traj, ref=ref, groove_3dna=True)
root = fn('Test_NAstruct/x3dna/')
# helical pars
saved_helical_pars = np.loadtxt(root + 'bp_helical.par',
skiprows=3,
usecols=range(1, 13)).T
aa_eq(nu.shear[1][0], saved_helical_pars[0], decimal=3)
aa_eq(nu.stretch[1][0], saved_helical_pars[1], decimal=3)
aa_eq(nu.stagger[1][0], saved_helical_pars[2], decimal=3)
aa_eq(nu.buckle[1][0], saved_helical_pars[3], decimal=3)
aa_eq(nu.prop[1][0], saved_helical_pars[4], decimal=3)
aa_eq(nu.open[1][0], saved_helical_pars[5], decimal=3)
aa_eq(nu.xdisp[1][0], saved_helical_pars[6][1:], decimal=3)
aa_eq(nu.ydisp[1][0], saved_helical_pars[7][1:], decimal=3)
aa_eq(nu.hrise[1][0], saved_helical_pars[8][1:], decimal=3)
aa_eq(nu.incl[1][0], saved_helical_pars[9][1:], decimal=3)
aa_eq(nu.tip[1][0], saved_helical_pars[10][1:], decimal=3)
aa_eq(nu.htwist[1][0], saved_helical_pars[11][1:], decimal=3)
# bp_step
saved_helical_pars = np.loadtxt(root + 'bp_step.par',
skiprows=3,
usecols=range(1, 13)).T
aa_eq(nu.shift[1][0], saved_helical_pars[6][1:], decimal=3)
aa_eq(nu.slide[1][0], saved_helical_pars[7][1:], decimal=3)
aa_eq(nu.tilt[1][0], saved_helical_pars[9][1:], decimal=3)
aa_eq(nu.roll[1][0], saved_helical_pars[10][1:], decimal=3)
aa_eq(nu.twist[1][0], saved_helical_pars[11][1:], decimal=3)
# grove
aa_eq(nu.minor[1][0], [15.8, 15.8, 15.5], decimal=1)
aa_eq(nu.major[1][0], [19.9, 20.8, 20.0], decimal=1)
def test_nupars_vs_x3dna(self):
traj = pt.iterload('data/Test_NAstruct/x3dna/rna.pdb')
ref = pt.iterload('data/Test_NAstruct/x3dna/rna_nab.pdb')
nu = pt.nastruct(traj, ref=ref, groove_3dna=True)
root = 'data/Test_NAstruct/x3dna/'
# helical pars
saved_helical_pars = np.loadtxt(root + 'bp_helical.par',
skiprows=3,
usecols=range(1, 13)).T
aa_eq(nu.shear[1], saved_helical_pars[0], decimal=3)
aa_eq(nu.stretch[1], saved_helical_pars[1], decimal=3)
aa_eq(nu.stagger[1], saved_helical_pars[2], decimal=3)
aa_eq(nu.buckle[1], saved_helical_pars[3], decimal=3)
aa_eq(nu.prop[1], saved_helical_pars[4], decimal=3)
aa_eq(nu.open[1], saved_helical_pars[5], decimal=3)
aa_eq(nu.xdisp[1], saved_helical_pars[6][1:], decimal=3)
aa_eq(nu.ydisp[1], saved_helical_pars[7][1:], decimal=3)
aa_eq(nu.hrise[1], saved_helical_pars[8][1:], decimal=3)
aa_eq(nu.incl[1], saved_helical_pars[9][1:], decimal=3)
aa_eq(nu.tip[1], saved_helical_pars[10][1:], decimal=3)
aa_eq(nu.htwist[1], saved_helical_pars[11][1:], decimal=3)
# bp_step
saved_helical_pars = np.loadtxt(root + 'bp_step.par',
skiprows=3,
usecols=range(1, 13)).T
aa_eq(nu.shift[1], saved_helical_pars[6][1:], decimal=3)
aa_eq(nu.slide[1], saved_helical_pars[7][1:], decimal=3)
aa_eq(nu.tilt[1], saved_helical_pars[9][1:], decimal=3)
aa_eq(nu.roll[1], saved_helical_pars[10][1:], decimal=3)
aa_eq(nu.twist[1], saved_helical_pars[11][1:], decimal=3)
# grove
aa_eq(nu.minor[1][0], [15.8, 15.8, 15.5], decimal=1)
aa_eq(nu.major[1][0], [19.9, 20.8, 20.0], decimal=1)
def worker(rank, frame, traj):
pt.nastruct(traj, ref=frame)
def worker(rank, frame, traj):
pt.nastruct(traj, ref=frame)
import pytraj as pt
from jamber.builder import build_bdna
seq = 'AAAAAAAAAA'
traj = build_bdna(seq)
nupar = pt.nastruct(traj)
print('major groove width', nupar.major[1])
print('minor groove width', nupar.minor[1])
def test_nab_bdna():
with tempfolder():
traj = builder.build_bdna('AAAAAAAAAA')
nu = pt.nastruct(traj)
aa_eq(np.mean(nu.major[1]), [17.246,], decimal=3)
aa_eq(np.mean(nu.minor[1]), [11.459,], decimal=3)
import pytraj as pt fn = "../tests/data/Test_NAstruct/adh026.3.pdb" traj = pt.load(fn, fn) d = pt.nastruct(traj) print(d) # get major groove print(d.major) # get minor groove print(d.minor) print(d.minor[1].mean(axis=0)) # get inclination print(d.incl) # get all supported keys print(d.keys())