from __future__ import print_function
import numpy as np
import mdtraj as md
from mdtraj.testing import eq
from mdtraj.nmr.shift_wrappers import find_executable, SPARTA_PLUS, PPM, SHIFTX2
from mdtraj.utils import six
import pytest
import os
@pytest.mark.skipif(not find_executable(SPARTA_PLUS),
reason='SPARTA+ binary not found')
def test_spartaplus(get_fn):
t = md.load(get_fn('2EQQ.pdb'))
result = md.chemical_shifts_spartaplus(t)
print(result)
eq(result.shape[1], 20) # 2EQQ is NMR structure with 20 frames
eq(float(result.ix[(1, "HA")][0]), 4.378, decimal=4)
# 4.378 taken from first entry in pred.tab, which looks like the following:
# 1 E HA 0.000 4.378 4.350 0.047 0.000 0.291
@pytest.mark.skipif(not find_executable(PPM), reason='PPM binary not found')
def test_ppm(get_fn):
t = md.load(get_fn('2EQQ.pdb'))
result = md.chemical_shifts_ppm(t)
print(result)
eq(result.shape[1], 20) # 2EQQ is NMR structure with 20 frames
from __future__ import print_function
import mdtraj as md
from mdtraj.testing import get_fn, eq, DocStringFormatTester, skipif
from mdtraj.nmr.shift_wrappers import find_executable, SPARTA_PLUS, PPM, SHIFTX2
from mdtraj.utils import six
@skipif(not find_executable(SPARTA_PLUS), 'SPARTA+ binary not found')
def test_spartaplus():
t = md.load(get_fn('2EQQ.pdb'))
result = md.chemical_shifts_spartaplus(t)
print(result)
eq(result.shape[1], 20) # 2EQQ is NMR structure with 20 frames
eq(float(result.ix[(1, "HA")][0]), 4.378, decimal=4)
# 4.378 taken from first entry in pred.tab, which looks like the following:
# 1 E HA 0.000 4.378 4.350 0.047 0.000 0.291
@skipif(not find_executable(PPM), 'PPM binary not found')
def test_ppm():
t = md.load(get_fn('2EQQ.pdb'))
result = md.chemical_shifts_ppm(t)
print(result)
eq(result.shape[1], 20) # 2EQQ is NMR structure with 20 frames
eq(float(result.ix[(2, "CA")][0]), 53.004, decimal=4)
# taken from first entry in bb_details.dat, which looks like the following:
# 2 ASN CA 999.000 53.004 51.168 51.802 53.081 54.098 52.820 52.379 51.856 53.034 52.754 54.134 54.222 51.210 52.207 50.824 54.459 53.605 54.211 53.688 52.344 53.004 51.168 51.802 53.081 54.098 52.820 52.379 51.856 53.034 52.754 54.134 54.222 51.210 52.207 50.824 54.459 53.605 54.211 53.688 52.344
from __future__ import print_function
import mdtraj as md
from mdtraj.testing import get_fn, eq, DocStringFormatTester, skipif
from mdtraj.nmr.shift_wrappers import find_executable, SPARTA_PLUS, PPM, SHIFTX2
from mdtraj.utils import six
@skipif(not find_executable(SPARTA_PLUS), 'SPARTA+ binary not found')
def test_spartaplus():
t = md.load(get_fn('2EQQ.pdb'))
result = md.chemical_shifts_spartaplus(t)
print(result)
eq(result.shape[1], 20) # 2EQQ is NMR structure with 20 frames
eq(float(result.ix[(1, "HA")][0]), 4.378, decimal=4)
# 4.378 taken from first entry in pred.tab, which looks like the following:
# 1 E HA 0.000 4.378 4.350 0.047 0.000 0.291
@skipif(not find_executable(PPM), 'PPM binary not found')
def test_ppm():
t = md.load(get_fn('2EQQ.pdb'))
result = md.chemical_shifts_ppm(t)
print(result)
eq(result.shape[1], 20) # 2EQQ is NMR structure with 20 frames
eq(float(result.ix[(2, "CA")][0]), 53.004, decimal=4)
# taken from first entry in bb_details.dat, which looks like the following:
# 2 ASN CA 999.000 53.004 51.168 51.802 53.081 54.098 52.820 52.379 51.856 53.034 52.754 54.134 54.222 51.210 52.207 50.824 54.459 53.605 54.211 53.688 52.344 53.004 51.168 51.802 53.081 54.098 52.820 52.379 51.856 53.034 52.754 54.134 54.222 51.210 52.207 50.824 54.459 53.605 54.211 53.688 52.344
from __future__ import print_function
import numpy as np
import mdtraj as md
from mdtraj.testing import eq
from mdtraj.nmr.shift_wrappers import find_executable, SPARTA_PLUS, PPM, SHIFTX2
from mdtraj.utils import six
import pytest
import os
@pytest.mark.skipif(not find_executable(SPARTA_PLUS),
reason='SPARTA+ binary not found')
def test_spartaplus(get_fn):
t = md.load(get_fn('2EQQ.pdb'))
result = md.chemical_shifts_spartaplus(t)
print(result)
eq(result.shape[1], 20) # 2EQQ is NMR structure with 20 frames
eq(float(result.ix[(1, "HA")][0]), 4.378, decimal=4)
# 4.378 taken from first entry in pred.tab, which looks like the following:
# 1 E HA 0.000 4.378 4.350 0.047 0.000 0.291
@pytest.mark.skipif(not find_executable(PPM),
reason='PPM binary not found')
def test_ppm(get_fn):
t = md.load(get_fn('2EQQ.pdb'))
result = md.chemical_shifts_ppm(t)
print(result)
from __future__ import print_function
import mdtraj as md
from mdtraj.testing import get_fn, eq, DocStringFormatTester, skipif
from mdtraj.nmr.shift_wrappers import find_executable, SPARTA_PLUS
@skipif(not find_executable(SPARTA_PLUS), 'SPARTA+ binary not found')
def test_1():
t = md.load(get_fn('2EQQ.pdb'))
result = md.chemical_shifts_spartaplus(t)
print(result)
def test_2_scalar_couplings():
t = md.load(get_fn('frame0.h5')) # This is Alanine dipeptide
for model in ["Ruterjans1999", "Bax2007", "Bax1997"]:
indices, J = md.compute_J3_HN_HA(t)
eq(indices.shape, (1, 4))
eq(J.shape, (501, 1))
J = J.mean()
assert abs(J - 6.06) <= 2.0, "Value is far from experimental value."
# 6.06 [Hz] is the value from Baldwin PNAS 2006 Table 1.
# We expect the models to give something comparable to this
# If it doesn't, something is fishy.
# Typical ranges are between 1 and 9.
# Obviously this isn't a perfect test, but it's still a useful sanity check.
def test_3_scalar_couplings():
t = md.load(get_fn('1bpi.pdb'))
from __future__ import print_function
import mdtraj as md
from mdtraj.testing import get_fn, eq, DocStringFormatTester, skipif
from mdtraj.nmr.shift_wrappers import find_executable, SPARTA_PLUS
@skipif(not find_executable(SPARTA_PLUS), 'SPARTA+ binary not found')
def test_1():
t = md.load(get_fn('2EQQ.pdb'))
result = md.chemical_shifts_spartaplus(t)
print(result)
def test_2_scalar_couplings():
t = md.load(get_fn('frame0.h5')) # This is Alanine dipeptide
for model in ["Ruterjans1999", "Bax2007", "Bax1997"]:
indices, J = md.compute_J3_HN_HA(t)
eq(indices.shape, (1, 4))
eq(J.shape, (501, 1))
J = J.mean()
assert abs(J - 6.06) <= 2.0, "Value is far from experimental value."
# 6.06 [Hz] is the value from Baldwin PNAS 2006 Table 1.
# We expect the models to give something comparable to this
# If it doesn't, something is fishy.
# Typical ranges are between 1 and 9.
# Obviously this isn't a perfect test, but it's still a useful sanity check.
def test_3_scalar_couplings():
t = md.load(get_fn('1bpi.pdb'))
for model in ["Ruterjans1999", "Bax2007", "Bax1997"]:
indices, J = md.compute_J3_HN_HA(t)