def test_0(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
from pytraj.utils import convert as cv
arange = cv.array_to_cpptraj_range(range(7))
a0 = pt.multidihedral(traj, resrange='1-7').values
a1 = pt.multidihedral(traj, resrange=range(7)).values
aa_eq(a0.flatten(), a1.flatten())
def test_0(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
from pytraj.utils import convert as cv
cv.array_to_cpptraj_range(range(7))
a0 = pt.multidihedral(traj, resrange='1-7').values
a1 = pt.multidihedral(traj, resrange=range(7)).values
aa_eq(a0.flatten(), a1.flatten())
def calculate_angles(traj, residues=[], angles='phi psi'):
if residues:
data = list(
pt.multidihedral(traj, dihedral_types=angles, resrange=residues))
else:
# get all residues numbers
residues = [int(l[4:]) for l in list(pt.dssp(traj)[0])]
data = pt.multidihedral(traj, dihedral_types=angles, resrange=residues)
return data
def test():
fname = 'data/nogit/remd/remd.x.000'
topname = 'data/nogit/remd/myparm.parm7'
traj = pt.trajectory.Trajectory(fname, top=topname)
print(traj.xyz.dtype)
for f in traj:
pass
pt.radgyr(traj)
pt.molsurf(traj, '@CA')
pt.rmsd(traj, mask='@CA')
pt.multidihedral(traj)
def getdihedrals(self, s='phi psi', stride=2):
print('reading dihedral angles from trajectories....')
self.dih = dict()
for tt, t in enumerate(self.trajs):
traj = pt.iterload(t, self.top, stride=stride)
#read dihedral angles
self.dih[tt] = pt.multidihedral(traj, s)
def test_multidihedral():
trajin = fn('Tc5b.x')
topin = fn('Tc5b.top')
traj = pt.iterload(trajin, top=topin)
command = "resrange 2-19 phi psi"
state = pt.load_cpptraj_state('''
parm {}
trajin {}
multidihedral resrange 2-19 phi psi
'''.format(topin, trajin))
state.run()
cpp_out = state.data[1:].to_dict()
out = pt.multidihedral(traj, command, dtype='dict')
for key, value in out.items():
aa_eq(value, cpp_out.get(key))
def calcS2(self, s='phi', stride=2):
print('calculating order parameters of ' + s + ' angles....')
S2 = dict()
for tt, t in enumerate(self.trajs):
traj = pt.iterload(t, self.top, stride=stride)
#read dihedral angles
dih = pt.multidihedral(traj, s)
#get residues
labels = dih.keys()
residues = sorted([int(l[len(s) + 1:]) for l in labels])
S2[tt] = dict()
for r in residues:
lab = s + ':' + str(r)
vals = np.array(dih[lab])
S2[tt][r] = (np.sum(np.cos(vals * np.pi / 180.))**2 + np.sum(
np.sin(vals * np.pi / 180.))**2) / len(vals)**2
return S2
def test_extra_coverage(self):
'''all kind of tests that do not belong to anywhere else
'''
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
# show_versions
pt.show_versions()
pt._verbose()
pt._verbose(False)
# info
pt.info()
pt.info('parallel')
misc.parallel_info('pmap')
misc.parallel_info('openmp')
misc.parallel_info(None)
eq([2, 3], [2, 3])
dslist = pt.multidihedral(traj)
str(dslist[0])
def test_extra_coverage(self):
'''all kind of tests that do not belong to anywhere else
'''
traj = pt.iterload("./data/tz2.nc", "./data/tz2.parm7")
# show_versions
pt.show_versions()
pt._verbose()
pt._verbose(False)
print(version)
# info
pt.info()
pt.info('parallel')
pt.misc.parallel_info('pmap')
pt.misc.parallel_info('openmp')
pt.misc.parallel_info(None)
eq([2, 3], [2, 3])
# raise if comparing NaN
self.assertRaises(ValueError, lambda: aa_eq(np.nan, np.nan))
dslist = pt.multidihedral(traj)
string_ = str(dslist[0])
def test_extra_coverage(self):
'''all kind of tests that do not belong to anywhere else
'''
traj = pt.iterload("./data/tz2.nc", "./data/tz2.parm7")
# show_versions
pt.show_versions()
pt._verbose()
pt._verbose(False)
print(version)
# info
pt.info()
pt.info('parallel')
pt.misc.parallel_info('pmap')
pt.misc.parallel_info('openmp')
pt.misc.parallel_info(None)
eq([2, 3], [2, 3])
# raise if comparing NaN
self.assertRaises(ValueError, lambda: aa_eq(np.nan, np.nan))
dslist = pt.multidihedral(traj)
string_ = str(dslist[0])
def test_pickle_datasetlist(self):
traj = pt.iterload("data/Tc5b.x", "data/Tc5b.top")
dslist = pt.multidihedral(traj)
pt.to_pickle(dslist, 'output/ds.pk')
dslist2 = pt.read_pickle('output/ds.pk')
aa_eq(dslist.values, dslist2.values)
# require pytraj, pysander and parmed
import pytraj as pt
import numpy as np
traj = pt.iterload("../tests/data/Ala3/Ala3.crd",
"../tests/data/Ala3/Ala3.top")
print(traj.n_atoms, traj.top.n_residues)
print(pt.multidihedral(traj).to_dict())
t0 = traj[:1]
deg_ene = []
flist = []
try:
import sander
import parmed
# scan from -180 to 180, every 5 deg
# calculate dihedral energy for each conformation
#
for deg in range(-180, 180, 5):
pt.rotate_dihedral(t0, "custom:3:omega:" + str(deg))
flist.append(t0[0].copy())
en = pt.energy_decomposition(t0,
igb=8,
verbose=False,
parm=traj.top.filename)['dihedral'][0]
import pytraj as pt
# use `iterload` to save memory
traj = pt.iterload("../tests/data/tz2.ortho.nc",
"../tests/data/tz2.ortho.parm7")
try:
import pandas as pd
# search all possible dihedral types supported by cpptraj
dset = pt.multidihedral(traj, dtype='dataframe')
print(dset)
except ImportError:
pass
def test_pickle_datasetlist(self):
traj = pt.iterload("data/Tc5b.x", "data/Tc5b.top")
dslist = pt.multidihedral(traj)
pt.to_pickle(dslist, 'output/ds.pk')
dslist2 = pt.read_pickle('output/ds.pk')
aa_eq(dslist.values, dslist2.values)
import pytraj as pt from jamber.builder import build_protein seq = ' '.join(['ALA'] * 10) print(seq) traj = build_protein(seq, command=['alpha:1-10']) print(traj) print(pt.multidihedral(traj, dihedral_types='phi psi', dtype='dict'))
import pytraj as pt
import numpy as np
try:
import sander
traj = pt.iterload("./data/Ala3/Ala3.crd", "./data/Ala3/Ala3.top")
print(traj.n_atoms, traj.top.n_residues)
print(pt.multidihedral(traj).to_dict())
t0 = traj[:1]
deg_ene = []
flist = []
for deg in range(-180, 180, 5):
pt.rotate_dihedral(t0, "custom:3:omega:" + str(deg))
flist.append(t0[0].copy())
en = pt.energy_decomposition(t0, igb=8,
prmtop=traj.top.filename)['dihedral'][0]
deg_ene.append((deg, en))
arr = np.array(deg_ene).T
pt.write_traj("test.pdb",
flist,
top=traj.top,
overwrite=True,
options='model')
def test_pickle_datasetlist(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
dslist = pt.multidihedral(traj)
pt.to_pickle(dslist, 'ds.pk')
dslist2 = pt.read_pickle('ds.pk')
aa_eq(dslist.values, dslist2.values)
import pytraj as pt
# use `iterload` to save memory
traj = pt.iterload("../tests/data/tz2.ortho.nc",
"../tests/data/tz2.ortho.parm7")
# search all possible dihedral types supported by cpptraj
dset = pt.multidihedral(traj)
print(dset)
# residue 3 to 7, skip every 2
dset2 = pt.multidihedral(traj, resrange='3-7')
print(dset2)
# residue 3 to 7, skip every 2
# use `range360`
dset = pt.multidihedral(traj, resrange='3-7', range360=True)
print(dset)
