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_pytraj_do():
traj = pt.iterload(fn("tz2.nc"), fn("tz2.parm7"))
ref0 = pt.autoimage(traj[0], top=traj.top)
ref1 = pt.autoimage(traj[1], top=traj.top)
data = pt.tools.dict_to_ndarray(pt.compute(
['autoimage', 'radgyr nomax @CA', 'rms refindex 0',
'rms refindex 1'],
traj,
ref=[ref0, ref1]))
t0 = pt.autoimage(traj[:])
aa_eq(pt.radgyr(t0, '@CA'), data[0])
aa_eq(pt.rmsd(t0, ref=ref0), data[1])
aa_eq(pt.rmsd(t0, ref=ref1), data[2])
aa_eq(pt.compute(pt.radgyr, t0, '@CA'), data[0])
def test_pytraj_do(self):
traj = pt.iterload("./data/tz2.nc", "./data/tz2.parm7")
ref0 = pt.autoimage(traj[0], top=traj.top)
ref1 = pt.autoimage(traj[1], top=traj.top)
data = pt.tools.dict_to_ndarray(pt.compute(
['autoimage', 'radgyr nomax @CA', 'rms refindex 0',
'rms refindex 1'],
traj,
ref=[ref0, ref1]))
t0 = pt.autoimage(traj[:])
aa_eq(pt.radgyr(t0, '@CA'), data[0])
aa_eq(pt.rmsd(t0, ref=ref0), data[1])
aa_eq(pt.rmsd(t0, ref=ref1), data[2])
# pytraj's method
aa_eq(pt.compute(pt.radgyr, t0, '@CA'), data[0])
def test_nativecontacts(tmpdir):
with tmpdir.as_cwd():
traj_fname = fn('DPDP.nc')
top_fname = fn('DPDP.parm7')
traj = pt.iterload(traj_fname, top_fname)
c_raw = pt.compute(
"""
nativecontacts name NC3 :1-21&!@H= byresidue out nc.all.res.dat distance 3.0
""", traj)
data = pt.nativecontacts(traj,
mask=':1-21&!@H=',
byres=True,
distance=3.0,
options='name NC3',
dtype='dict')
print(c_raw, data)
aa_eq(c_raw['NC3[native]'], data['NC3[native]'])
import pytraj as pt refname = '../tests/data/Tc5b.nat.inpcrd' fn = '../tests/data/Tc5b.x' prmtop = '../tests/data/Tc5b.prmtop' traj = pt.iterload(fn, top=prmtop) ref = pt.iterload(refname, top=prmtop) cm = """ rms reference @CA distance :3 :7 angle :3 :8 :12 multidihedral phi psi molsurf @CA """ # need to specify ref=ref # TODO: reflist data = pt.compute(cm, traj, ref=ref) print(data)
def test_raising_error(self):
traj = pt.datafiles.load_tz2()
with pytest.raises(ValueError, match="ERROR: radgyr myrms @CA nomax"):
pt.compute(['rms myrms @CA','radgyr myrms @CA nomax'], traj)