from __future__ import print_function
import unittest
import pytraj as pt
from pytraj.testing import aa_eq, tempfolder
from pytraj import cluster
from pytraj.utils.context import capture_stdout
# local
from utils import fn
tz2_trajin = fn('tz2.nc')
tz2_top = fn('tz2.parm7')
def test_ClusteringDataset():
traj = pt.load(tz2_trajin, tz2_top)
x = pt.cluster.kmeans(traj, n_clusters=5, metric='rms', mask='@CA')
assert x.n_frames == 101
assert list(x.centroids) == [24, 101, 76, 13, 9]
aa_eq(x.fraction, [0.485, 0.238, 0.139, 0.079, 0.059], decimal=3)
def test_cluster_kmeans():
kmeans = cluster.kmeans
traj = pt.iterload(tz2_trajin, tz2_top)
cm = 'cluster kmeans clusters 10 @CA rms randompoint kseed 2 {0} noinfo'
for sieve in [2, 3, 4]:
sieve_str = "sieve {0} sieveseed 12".format(sieve)
import pytest
import pytraj as pt
from pytraj import TrajectoryWriter
from pytraj.testing import aa_eq
from pytraj.utils import tempfolder
# local
from utils import fn
tc5b_trajin = fn('Tc5b.x')
tc5b_top = fn('Tc5b.top')
def test_write_CRYST1():
traj = pt.datafiles.load_tz2_ortho()[:1]
print(traj.unitcells)
with tempfolder():
fn = "test.pdb"
traj.save(fn)
traj2 = pt.load(fn)
aa_eq(traj.unitcells, traj2.unitcells, decimal=3)
def test_trajectory_writer():
traj = pt.iterload(tc5b_trajin, tc5b_top)
with tempfolder():
pt.write_traj("test_1.pdb", traj[:1], overwrite=True)
pt.write_traj("test_1.dcd", traj[:1], overwrite=True)
with TrajectoryWriter("test_1") as trajout:
def test_0(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
for xyz0 in traj.xyz:
frame = pt.Frame(traj.n_atoms, xyz0, _as_ptr=True)
aa_eq(frame.xyz, xyz0)
def setUp(self):
self.traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
def test_rdf(self):
traj = pt.iterload(fn("tz2.truncoct.nc"),
fn("tz2.truncoct.parm7"),
frame_slice=(0, 10))
command = '''
radial Radial.agr 0.5 10.0 :5@CD :WAT@O
radial cRadial.agr 0.5 10.0 :5 :WAT@O center1
radial cRadial.agr 0.5 10.0 :5 :WAT@O center2
radial cRadial.agr 0.5 20.0 :3 :WAT@O
radial cRadial.agr 0.5 20.0 :3 :WAT@O noimage
radial radial.dat 0.5 10.0 :5@CD :WAT@O
radial radial2.dat 0.25 10.0 :5@CD :WAT@O
radial radial2.dat 0.25 10.0 :5@CD :WAT@O volume
'''
state = pt.load_batch(traj, command)
with tempfolder():
# get data directly from cpptraj
state.run()
# get data from pytraj
data0 = pt.rdf(traj,
solute_mask=':WAT@O',
bin_spacing=0.5,
maximum=10.0,
solvent_mask=':5@CD')
data01 = pt.rdf(traj,
solvent_mask=':5@CD',
solute_mask=':WAT@O',
bin_spacing=0.5,
maximum=10.0)
data1 = pt.rdf(traj,
solvent_mask=':5',
solute_mask=':WAT@O',
bin_spacing=0.5,
maximum=10.0,
center_solvent=True)
data2 = pt.rdf(traj,
solvent_mask=':5',
solute_mask=':WAT@O',
bin_spacing=0.5,
maximum=10.0,
center_solute=True)
data3 = pt.rdf(traj,
solvent_mask=':3',
solute_mask=':WAT@O',
bin_spacing=0.5,
maximum=20.0,
center_solute=False)
data4 = pt.rdf(traj,
solvent_mask=':3',
solute_mask=':WAT@O',
bin_spacing=0.5,
maximum=20.0,
center_solute=False,
image=False)
data5 = pt.rdf(traj,
solute_mask=':WAT@O',
bin_spacing=0.25,
maximum=10.0,
solvent_mask=':5@CD')
# solvent_mask is array
solvent_indices = pt.select(':WAT@O', traj.top)
data6 = pt.rdf(traj,
solvent_mask=':5@CD',
solute_mask=solvent_indices,
bin_spacing=0.25,
maximum=10.0)
# volume
data7 = pt.rdf(traj,
solvent_mask=':5@CD',
solute_mask=':WAT@O',
bin_spacing=0.25,
maximum=10.0,
volume=True)
# do assertion
aa_eq(data0[1], state.data[1], decimal=7)
aa_eq(data1[1], state.data[2], decimal=7)
aa_eq(data2[1], state.data[3], decimal=7)
aa_eq(data3[1], state.data[4], decimal=7)
aa_eq(data4[1], state.data[5], decimal=7)
aa_eq(data7[1], state.data[8], decimal=7)
# default solvent mask :WAT@O
aa_eq(data01[1], state.data[1], decimal=7)
steps = np.loadtxt('radial.dat').T[0]
aa_eq(data0[0], steps)
steps2 = np.loadtxt('radial2.dat').T[0]
aa_eq(data5[0], steps2)
aa_eq(data6[0], steps2)
def test_pbc(self):
traj = pt.load(fn('small_pbc.pdb'))
aa_eq(traj.unitcells[0], [51.263, 51.263, 51.263, 90.00, 90.00, 90.00])
assert traj.top.has_box() == True, 'Topology must has box'
assert traj.top.box.type == 'ortho', 'must be ortho box'
def test_0(self):
arr = pt.tools.read_to_array(fn('floBF-resp.chg'))
assert arr.shape == (84, )
aa_eq(arr, expected_result)
def setUp(self):
self.traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
self.mask = '@C,N,CA,O'
def test_volmap_RuntimeError(self):
# raise RuntimeError
dry_traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
self.assertRaises(RuntimeError, lambda: pt.volmap(dry_traj, mask=':WAT@O',
grid_spacing=(0.5, 0.5, 0.5)))
parm {}
trajin {}
rms first !@H=
average crdset AVG
run
# Step two. RMS-Fit to average structure. Calculate covariance matrix.
# Save the fit coordinates.
rms ref AVG !@H=
matrix covar name MyMatrix !@H=
createcrd CRD1
run
# Step three. Diagonalize matrix.
runanalysis diagmatrix MyMatrix vecs 2 name MyEvecs
# Step four. Project saved fit coordinates along eigenvectors 1 and 2
crdaction CRD1 projection evecs MyEvecs !@H= out project.dat beg 1 end 2
'''.format(fn('tz2.parm7'), fn('tz2.nc'))
class TestCpptrajDatasetWithMathLib(unittest.TestCase):
def setUp(self):
self.state = pt.datafiles.load_cpptraj_state(txt)
self.state.run()
self.traj = pt.iterload(tz2_trajin, tz2_top)
def test_call_values(self):
for d in self.state.data:
d.values
def test_dataset_coords_ref(self):
traj = pt.iterload(tz2_trajin, tz2_top)
avg_frame = pt.mean_structure(traj(rmsfit=(0, '!@H=')))
def setUp(self):
self.traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
self.traj_ortho = pt.iterload(fn('tz2.ortho.nc'),
fn('tz2.ortho.parm7'))
self.traj_nu = pt.iterload(fn('Test_NAstruct/adh026.3.pdb'))
import pytraj as pt
from pytraj.testing import aa_eq, tempfolder
from pytraj import *
# local
from utils import fn
farray = pt.load(fn("Tc5b.x"), fn("Tc5b.top"), frame_indices=list(range(10)))
def test_trajectory_writer_open_close():
farray = pt.load(fn("Tc5b.x"),
fn("Tc5b.top"),
frame_indices=list(range(10)))
frame0 = farray[0]
with tempfolder():
trajout = TrajectoryWriter()
trajout.open(filename="test.x", top=farray.top, overwrite=True)
trajout.write(frame0)
# add more frames
for i in range(5, 8):
trajout.write(farray[i])
trajout.close()
farray = Trajectory()
farray.top = pt.load_topology(fn('Tc5b.top'))
farray.load("test.x")
import pytraj as pt
from utils import fn
import numpy as np
try:
traj = pt.iterload("./data/Ala3/Ala3.crd", fn('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_1(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
count = 0
for farray in traj.iterchunk(chunksize=4):
count += 1
def test_short_save():
with tempfolder():
(pt.iterload(fn('tz2.nc'), fn('tz2.parm7')).save('mini.nc',
overwrite=True))
assert pt.iterload(
'mini.nc', fn('tz2.parm7')).n_frames == 101, 'must be 101 frames'
from __future__ import print_function
import unittest
import pytraj as pt
from utils import fn
from pytraj.externals.six import zip
from pytraj.trajectory.shared_methods import iterframe_master
from pytraj import dihedral_analysis as da
"""
try not to get segmentation fault error (due to whatever freaking reason)
"""
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
class Test(unittest.TestCase):
def test_0(self):
it = iterframe_master(traj)
for idx, frame in enumerate(it):
pass
# Status: don't need to fix since "it" and "traj" share the same iterator
fa = traj[:]
for idx, frame in enumerate(fa):
fa[idx]
def test_1(self):
pt.search_hbonds(traj)
pt.search_hbonds(traj, 'series')
pt.search_hbonds(traj, 'series, nointramol')
def test_load_url():
url = 'https://raw.githubusercontent.com/Amber-MD/pytraj/master/tests/data/1L2Y.pdb'
local_traj = pt.load(fn('1L2Y.pdb'))
github_traj = pt.io.load_url(url)
aa_eq(local_traj.xyz, github_traj.xyz)
def test_hbonds_with_image(self):
traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
hbonds_0 = pt.search_hbonds(traj(autoimage=True))
hbonds_1 = pt.search_hbonds(traj, image=True)
aa_eq(hbonds_0.values, hbonds_1.values)
def test_3_indexing(self):
top = pt.load_topology(fn('Tc5b.top'))
atm = AtomMask("@CA")
top._set_integer_mask(atm)
def test_raises(self):
frame = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))[0]
with pytest.raises(ValueError):
pt.pca(frame, mask='@CA')
def setUp(self):
self.traj = pt.iterload(fn('Test_NAstruct/x3dna/rna.pdb'))
def test():
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
frame0 = traj[0]
assert frame0.has_box() == False
frame0.box
assert frame0.box.type == 'no_shape'
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)
def test_velocityautocorr(self):
# usecoords = False
traj = pt.iterload(fn('issue807/trunc.nc'),
fn("issue807/system.prmtop"),
frame_slice=(0, 3))
data0 = pt.all_actions.velocityautocorr(traj,
tstep=2,
norm=True,
direct=True)
cm = """
parm {}
trajin {} 1 3
velocityautocorr mydata * tstep 2 norm direct
""".format(fn('issue807/system.prmtop'), fn('issue807/trunc.nc'))
state = pt.load_cpptraj_state(cm)
state.run()
aa_eq(data0[0], state.data[-2].values)
# usecoords = True
data = pt.all_actions.velocityautocorr(traj,
tstep=1,
norm=False,
direct=True,
usecoords=True)
cm = """
parm {}
trajin {} 1 3
velocityautocorr mydata * tstep 1 direct usecoords
""".format(fn('issue807/system.prmtop'), fn('issue807/trunc.nc'))
state = pt.load_cpptraj_state(cm)
state.run()
aa_eq(data[0], state.data[-2].values)
# try on memory Trajectory, usecoords = False
traj_on_mem = traj[:]
data2 = pt.all_actions.velocityautocorr(traj_on_mem,
tstep=2,
norm=True,
direct=True)
aa_eq(data0[0], data2[0])
# try on memory Trajectory, usecoords = True
# need to raise if no `velocity_arr` is given
traj_on_mem = traj[:]
# try on memory Trajectory, usecoords = True
traj_on_disk = traj
velocity_arr = pt.get_velocity(traj_on_disk)
data3 = pt.all_actions.velocityautocorr(traj_on_mem,
tstep=2,
norm=True,
direct=True,
usecoords=True,
velocity_arr=velocity_arr)
data4 = pt.all_actions.velocityautocorr(traj_on_disk,
tstep=2,
norm=True,
direct=True,
usecoords=True)
# raise if velocity_arr has wrong shape
velocity_arr_2 = velocity_arr.flatten()
with pytest.raises(ValueError):
pt.all_actions.velocityautocorr(traj_on_mem,
usecoords=True,
velocity_arr=velocity_arr_2)
from __future__ import print_function
import numpy as np
import pytraj as pt
from utils import fn
import unittest
from pytraj import io as mdio
from pytraj.testing import aa_eq
from pytraj.datasets.datasetlist import stack
from pytraj.datasets.datasetlist import stack as stack
import pytest
traj = mdio.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
class Test(unittest.TestCase):
def test_0(self):
_ds1 = pt.calc_dssp(traj[:5], dtype='dataset')
ds1 = _ds1.grep('LYS')
_ds2 = pt.calc_dssp(traj[5:], dtype='dataset')
ds2 = _ds2.grep('LYS')
dstack = stack((ds1, ds2))
_d12 = pt.calc_dssp(traj, dtype='dataset')
d12 = _d12.grep("LYS")
dstack_dict = dstack.to_dict()
d12_dict = d12.to_dict()
assert sorted(dstack_dict.keys()) == sorted(d12_dict)
for key in dstack_dict.keys():
def test_0(self):
with Timer() as t:
pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
def test_0(self):
traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
frame0 = traj[0]
frame0.box
from pytraj.testing import cpptraj_test_dir
from pytraj.testing import get_remd_fn
from pytraj.testing import tempfolder
from pytraj.io import _get_amberhome
# local
from utils import fn
try:
has_scipy = True
except ImportError:
has_scipy = False
amberhome = os.getenv('AMBERHOME', '')
tleap = amberhome + '/bin/tleap'
traj_tz2_ortho = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7"))
tc5b_trajin = fn('Tc5b.x')
tc5b_top = fn('Tc5b.top')
def test_iterload_comprehensive():
trajin, tn = fn("tz2.ortho.nc"), fn("tz2.ortho.parm7")
# frame_slice
t0 = pt.iterload(trajin, tn, frame_slice=(0, -1, 0))
aa_eq(traj_tz2_ortho.xyz, t0.xyz)
t0 = pt.iterload(trajin, tn, frame_slice=(0, -1, 2))
aa_eq(traj_tz2_ortho.xyz[::2], t0.xyz)
# stride
def test_0(self):
traj = mdio.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
frame = traj[0].copy()
frame.set_mass(traj.top)
Frame(frame, traj.top("@CA"))
def main():
global count
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
boring_list = [traj[0], traj[1], traj, traj(1, 6, 2),
traj.iterchunk(chunksize=4)]
count_frames(boring_list)