def run(project, atom_indices=None, traj_fn = 'all'):
n_atoms = project.load_conf()['XYZList'].shape[1]
if traj_fn.lower() == 'all':
SASA = np.ones((project.n_trajs, np.max(project.traj_lengths), n_atoms)) * -1
for traj_ind in xrange(project.n_trajs):
traj_asa = []
logger.info("Working on Trajectory %d", traj_ind)
traj_fn = project.traj_filename(traj_ind)
chunk_ind = 0
for traj_chunk in Trajectory.enum_chunks_from_lhdf( traj_fn, AtomIndices=atom_indices ):
#print chunk_ind
traj_asa.extend(asa.calculate_asa(traj_chunk, n_sphere_points = 24))
chunk_ind += 1
SASA[traj_ind, 0:project.traj_lengths[traj_ind]] = traj_asa
else:
traj_asa = []
for traj_chunk in Trajectory.enum_chunks_from_lhdf( traj_fn, AtomIndices=atom_indices ):
traj_asa.extend( asa.calculate_asa( traj_chunk ) )
SASA = np.array(traj_asa)
return SASA
def run(project, atom_indices=None, traj_fn='all'):
n_atoms = project.load_conf()['XYZList'].shape[1]
if traj_fn.lower() == 'all':
SASA = np.ones(
(project.n_trajs, np.max(project.traj_lengths), n_atoms)) * -1
for traj_ind in xrange(project.n_trajs):
traj_asa = []
logger.info("Working on Trajectory %d", traj_ind)
traj_fn = project.traj_filename(traj_ind)
chunk_ind = 0
for traj_chunk in Trajectory.enum_chunks_from_lhdf(
traj_fn, AtomIndices=atom_indices):
#print chunk_ind
traj_asa.extend(
asa.calculate_asa(traj_chunk, n_sphere_points=24))
chunk_ind += 1
SASA[traj_ind, 0:project.traj_lengths[traj_ind]] = traj_asa
else:
traj_asa = []
for traj_chunk in Trajectory.enum_chunks_from_lhdf(
traj_fn, AtomIndices=atom_indices):
traj_asa.extend(asa.calculate_asa(traj_chunk))
SASA = np.array(traj_asa)
return SASA
def test_asa_2():
t = Trajectory.load_trajectory_file(os.path.join(fixtures_dir(), 'trj0.lh5'))
val1 = np.sum(calculate_asa(t[0])) # calculate only frame 0
val2 = np.sum(calculate_asa(t)[0]) # calculate on all frames
true_frame_0_asa = 2.859646797180176
npt.assert_approx_equal(true_frame_0_asa, val1)
npt.assert_approx_equal(true_frame_0_asa, val2)
def test_asa_2():
t = get("Trajectories/trj0.lh5")
val1 = np.sum(calculate_asa(t[0])) # calculate only frame 0
val2 = np.sum(calculate_asa(t)[0]) # calculate on all frames
true_frame_0_asa = 2.859646797180176
assert_approx_equal(true_frame_0_asa, val1)
assert_approx_equal(true_frame_0_asa, val2)
def test_asa_0():
# make one atom at the origin
traj = {"XYZList": np.zeros((1, 1, 3)), "AtomNames": ["H"]}
probe_radius = 0.14
calc_area = np.sum(calculate_asa(traj, probe_radius=probe_radius))
true_area = 4 * np.pi * (ATOMIC_RADII["H"] + probe_radius) ** 2
assert_approx_equal(calc_area, true_area)
def test_asa_0():
# make one atom at the origin
traj = {'XYZList': np.zeros((1,1,3)),
'AtomNames': ['H']}
probe_radius = 0.14
calc_area = np.sum(calculate_asa(traj, probe_radius=probe_radius))
true_area = 4 * np.pi * (ATOMIC_RADII['H'] + probe_radius)**2
npt.assert_approx_equal(calc_area, true_area)
def test_asa_3():
traj_ref = get("g_sas_ref.dat")
traj = get("Trajectories/trj0.lh5")
traj_asa = calculate_asa(traj, probe_radius=0.14, n_sphere_points=960)
# the algorithm used by gromacs' g_sas is slightly different than the one
# used here, so the results are not exactly the same -- see the comments
# in src/python/geomtry/asa.py or the readme file src/ext/asa/README.txt
# for details
assert_array_almost_equal(traj_asa, traj_ref, decimal=2)
def test_asa_3():
traj_ref = np.loadtxt( os.path.join(reference_dir(),'g_sas_ref.dat'))
Conf = Trajectory.load_from_pdb(os.path.join( fixtures_dir(), 'native.pdb'))
traj = Trajectory.load_trajectory_file( os.path.join(fixtures_dir(), 'trj0.xtc') , Conf=Conf)
traj_asa = calculate_asa(traj, probe_radius=0.14, n_sphere_points = 960)
# the algorithm used by gromacs' g_sas is slightly different than the one
# used here, so the results are not exactly the same -- see the comments
# in src/python/geomtry/asa.py or the readme file src/ext/asa/README.txt
# for details
npt.assert_array_almost_equal(traj_asa, traj_ref, decimal=2)
def test_asa_1():
# two atoms
traj = {"XYZList": np.zeros((1, 2, 3)), "AtomNames": ["H", "H"]}
probe_radius = 0.14
true = 4 * np.pi * (ATOMIC_RADII["H"] + probe_radius) ** 2
# when atoms are closer than 2e-5, there seems to be a bug.
# note that you should never actually have a case where atoms are this close
# but nonetheless I'm adding a check for this in the implementation -- to make
# it crash if the atoms are too close, as opposed to giving you wrong results
separations = np.linspace(2.0e-5, probe_radius * 2 + ATOMIC_RADII["H"] * 2, 10)
areas = np.zeros_like(separations)
# check the asa as we vary the separation
for i, sep in enumerate(separations):
traj["XYZList"][0, 0, 1] = sep
areas[i] = np.sum(calculate_asa(traj, probe_radius=probe_radius))
assert_approx_equal(areas[0], true)
assert_approx_equal(areas[-1], 2 * true)
# make sure that areas is increasing
assert_array_less(areas[0:8], areas[1:9])
def test_asa_1():
# two atoms
traj = {'XYZList': np.zeros((1,2,3)),
'AtomNames': ['H', 'H']}
probe_radius = 0.14
true = 4 * np.pi * (ATOMIC_RADII['H'] + probe_radius)**2
# when atoms are closer than 2e-5, there seems to be a bug.
# note that you should never actually have a case where atoms are this close
# but nonetheless I'm adding a check for this in the implementation -- to make
# it crash if the atoms are too close, as opposed to giving you wrong results
separations = np.linspace(2.0e-5, probe_radius*2 + ATOMIC_RADII['H']*2, 10)
areas = np.zeros_like(separations)
# check the asa as we vary the separation
for i, sep in enumerate(separations):
traj['XYZList'][0, 0, 1] = sep
areas[i] = np.sum(calculate_asa(traj, probe_radius=probe_radius))
npt.assert_approx_equal(areas[0], true)
npt.assert_approx_equal(areas[-1], 2*true)
# make sure that areas is increasing
npt.assert_array_less(areas[0:8], areas[1:9])
from msmbuilder.geometry import asa
from msmbuilder import Trajectory
from msmbuilder import io
import numpy as np
p=Trajectory.load_from_pdb('barstarH.pdb')
sasa = asa.calculate_asa(p, n_sphere_points=150)
io.saveh('sasa.h5', sasa=sasa)