def test_compute_at_cpptraj_level(self):
from pytraj.testing import get_fn
fn, tn = get_fn('tz2') # ortho
traj_on_disk0 = pt.iterload([
fn,
] * 2, tn)
traj_on_disk1 = pt.iterload([
fn,
] * 2, tn)
traj_on_mem = pt.load([
fn,
] * 2, tn)
traj_on_mem2 = pt.load([
fn,
] * 2, tn)
traj_on_disk0.autoimage().superpose()
traj_on_disk1.autoimage().superpose()
traj_on_mem.autoimage().superpose()
aa_eq(traj_on_disk0.xyz, traj_on_disk1.xyz)
aa_eq(traj_on_disk0.xyz, traj_on_mem.xyz)
data0 = pt.rmsd(traj_on_disk0, mask='@CA', ref=0, nofit=True)
data1 = pt.compute(['rms @CA first nofit'],
traj_on_disk1)['RMSD_00000']
data2 = pt.rmsd(traj_on_mem, mask='@CA', ref=0, nofit=True)
aa_eq(data0, data2)
aa_eq(data0, data1)
def test_reset_dataset_that_hold_rmsd(self):
from pytraj.testing import get_fn
fn, tn = get_fn('tz2_dry')
traj_on_disk = pt.iterload([
fn,
] * 10, tn) # 1010 frames
assert traj_on_disk.n_frames == 1010
ref = traj_on_disk[:1]
traj_on_disk.superpose(mask='@CA', ref=ref)
traj_on_disk._max_count_to_reset = 100
for _ in range(10):
for frame in traj_on_disk:
pass
#!/usr/bin/env python
import numpy as np
import pytraj as pt
from memory_profiler import profile
from pytraj.testing import get_fn
fn, tn = get_fn('tz2')
traj = pt.iterload([
fn,
] * 100, tn)
print(traj)
ref = traj[:1]
@profile
def do_it(traj=traj, n_times=1):
# memory leaking
traj.superpose(ref=ref, mask='@CA')
# memory not leaking
# traj.autoimage().center()
for _ in range(n_times):
for frame in traj:
pass
print(traj._cdslist)
import pytraj as pt
from pytraj.testing import get_fn, aa_eq
fn, tn = get_fn('tz2_dry')
traj0 = pt.load(fn, tn)
traj1 = pt.load(fn, tn)
traj2 = pt.load(fn, tn)
print(traj0.xyz[0, 0], traj1.xyz[0, 0], traj2.xyz[0, 0])
# Use ActionList for traj0
actlist = pt.ActionList(top=traj0.top)
actlist.add("translate", "x 1.2")
actlist.add("center", "origin")
actlist.add("rotate", "x 45.")
for frame in traj0:
actlist.compute(frame)
# use transformation
itertraj = pt.transform(
traj1, by=['translate x 1.2', 'center origin', 'rotate x 45.'])
for frame in itertraj:
pass
aa_eq(traj0.xyz, traj1.xyz)
print(traj0.xyz[0, 0], traj1.xyz[0, 0], traj2.xyz[0, 0])
# use API
traj2.translate('x 1.2')
traj2.center('origin')