def test_write_gromacs():
water = Molecule(
[
Atom("O", [0.0, 0.0, 0.0], export={"grotype": "OW"}),
Atom("H", [0.1, 0.0, 0.0], export={"grotype": "HW1"}),
Atom("H", [-0.03333, 0.09428, 0.0], export={"grotype": "HW2"}),
],
export={"groname": "SOL"},
)
sys = System.empty(200, 3 * 200, box_vectors=np.eye(3) * 2.0)
for i in range(200):
sys.add(water.copy())
df = datafile("/tmp/dummy.gro", mode="w")
df.write("system", sys)
with assert_raises(Exception):
df = datafile("/tmp/dummy.gro")
df.write("system", sys)
df = datafile("/tmp/dummy.gro")
sread = df.read("system")
assert all(sread.type_array == sys.type_array)
def test_bond_guessing():
from chemlab.db import ChemlabDB, CirDB
from chemlab.graphics import display_molecule
from chemlab.io import datafile
mol = datafile('tests/data/3ZJE.pdb').read('molecule')
print(mol.r_array)
mol.guess_bonds()
assert mol.bonds.size > 0
# We should find the bond guessing also for systems
# System Made of two benzenes
bz = datafile("tests/data/benzene.mol").read('molecule')
bzbonds = bz.bonds
bz.bonds = np.array([])
# Separating the benzenes by large amount
bz2 = bz.copy()
bz2.r_array += 2.0
s = System([bz, bz2])
s.guess_bonds()
assert_eqbonds(s.bonds, np.concatenate((bzbonds, bzbonds + 6)))
# Separating benzenes by small amount
bz2 = bz.copy()
bz2.r_array += 0.15
s = System([bz, bz2])
s.guess_bonds()
assert_eqbonds(s.bonds, np.concatenate((bzbonds, bzbonds + 6)))
def rdffunc(args):
import multiprocessing
type_a, type_b = args.selection.split('-')
syst = datafile(args.filename).read("system")
sel_a = syst.type_array == type_a
sel_b = syst.type_array == type_b
df = datafile(args.trajectory)
t, coords = df.read("trajectory")
boxes = df.read("boxes")
times = [int(tim) for tim in args.t.split(',')]
ind = np.searchsorted(t, times)
arguments = ((coords[i][sel_a], coords[i][sel_b], boxes[i]) for i in ind)
rds = map(get_rdf, arguments)
for rd in rds:
plot(rd[0], rd[1])
ticklabel_format(style='sci', axis='y', scilimits=(0,0))
xlabel('Time(ps)')
ylabel(args.selection)
grid()
show()
def rdffunc(args):
import multiprocessing
type_a, type_b = args.selection.split('-')
syst = datafile(args.filename).read("system")
sel_a = syst.type_array == type_a
sel_b = syst.type_array == type_b
df = datafile(args.trajectory)
t, coords = df.read("trajectory")
boxes = df.read("boxes")
times = [int(tim) for tim in args.t.split(',')]
ind = np.searchsorted(t, times)
arguments = ((coords[i][sel_a], coords[i][sel_b], boxes[i]) for i in ind)
rds = map(get_rdf, arguments)
for rd in rds:
plot(rd[0], rd[1])
ticklabel_format(style='sci', axis='y', scilimits=(0, 0))
xlabel('Time(ps)')
ylabel(args.selection)
grid()
show()
def test_write_cml():
df = datafile('tests/data/mol.cml')
mol = df.read("molecule")
df = datafile('/tmp/sadf.cml', 'w')
df.write('molecule', mol)
def test_bond_guessing():
from chemlab.db import ChemlabDB, CirDB
from chemlab.graphics import display_molecule
from chemlab.io import datafile
mol = datafile('tests/data/3ZJE.pdb').read('molecule')
print(mol.r_array)
mol.guess_bonds()
assert mol.bonds.size > 0
# We should find the bond guessing also for systems
# System Made of two benzenes
bz = datafile("tests/data/benzene.mol").read('molecule')
bzbonds = bz.bonds
bz.bonds = np.array([])
# Separating the benzenes by large amount
bz2 = bz.copy()
bz2.r_array += 2.0
s = System([bz, bz2])
s.guess_bonds()
assert_eqbonds(s.bonds, np.concatenate((bzbonds, bzbonds + 6)))
# Separating benzenes by small amount
bz2 = bz.copy()
bz2.r_array += 0.15
s = System([bz, bz2])
s.guess_bonds()
assert_eqbonds(s.bonds, np.concatenate((bzbonds, bzbonds + 6)))
def test_read_xyz():
df = datafile("tests/data/sulphoxide.xyz")
mol1 = df.read("molecule")
df = datafile("/tmp/t.xyz", mode="w")
df.write("molecule", mol1)
df = datafile("/tmp/t.xyz", mode="rb")
mol2 = df.read("molecule")
assert np.allclose(mol1.r_array, mol2.r_array)
assert all(mol1.type_array == mol2.type_array)
def test_read_xyz():
df = datafile('tests/data/sulphoxide.xyz')
mol1 = df.read('molecule')
df = datafile('/tmp/t.xyz', mode="w")
df.write('molecule', mol1)
df = datafile('/tmp/t.xyz', mode="r")
mol2 = df.read('molecule')
assert np.allclose(mol1.r_array, mol2.r_array)
assert all(mol1.type_array == mol2.type_array)
def make_gromacs(simulation, directory, clean=False):
"""Create gromacs directory structure"""
if clean is False and os.path.exists(directory):
raise ValueError(
'Cannot override {}, use option clean=True'.format(directory))
else:
shutil.rmtree(directory, ignore_errors=True)
os.mkdir(directory)
# Check custom simulation potential
if simulation.potential.intermolecular.type == 'custom':
for pair in simulation.potential.intermolecular.special_pairs:
table = to_table(
simulation.potential.intermolecular.pair_interaction(*pair),
simulation.cutoff)
fname1 = os.path.join(directory,
'table_{}_{}.xvg'.format(pair[0], pair[1]))
fname2 = os.path.join(directory,
'table_{}_{}.xvg'.format(pair[1], pair[0]))
with open(fname1, 'w') as fd:
fd.write(table)
with open(fname2, 'w') as fd:
fd.write(table)
ndx = {'System': np.arange(simulation.system.n_atoms, dtype='int')}
for particle in simulation.potential.intermolecular.particles:
idx = simulation.system.where(
atom_name=particle)['atom'].nonzero()[0]
ndx[particle] = idx
with open(os.path.join(directory, 'index.ndx'), 'w') as fd:
fd.write(to_ndx(ndx))
# Parameter file
mdpfile = to_mdp(simulation)
with open(os.path.join(directory, 'grompp.mdp'), 'w') as fd:
fd.write(mdpfile)
# Topology file
topfile = to_top(simulation.system, simulation.potential)
with open(os.path.join(directory, 'topol.top'), 'w') as fd:
fd.write(topfile)
# Simulation file
datafile(os.path.join(directory, 'conf.gro'),
'w').write('system', simulation.system)
return directory
def test_read_xyz():
df = datafile('tests/data/sulphoxide.xyz')
mol1 = df.read('molecule')
df = datafile('/tmp/t.xyz', mode="w")
df.write('molecule', mol1)
df = datafile('/tmp/t.xyz', mode="r")
mol2 = df.read('molecule')
assert np.allclose(mol1.r_array, mol2.r_array)
assert all(mol1.type_array == mol2.type_array)
def test_traj_viewer():
tv = QtTrajectoryViewer()
s = datafile('tests/data/water.gro').read('system')
ar = tv.add_renderer(BallAndStickRenderer, s.r_array, s.type_array, find_bonds(s))
times, frames = datafile('tests/data/trajout.xtc').read('trajectory')
def update(index):
f = frames[index]
ar.update_positions(f)
tv.set_text(format_time(times[index]))
tv.widget.update()
tv.update_function(update, len(frames))
tv.run()
def test_read_cclib():
try:
import cclib
except:
raise SkipTest
df = datafile('tests/data/cclib/water_mp2.out', format='gamess')
# Reading a properties that does exist
result1 = df.read('gbasis')
result2 = [[
('S', [(130.7093214, 0.154328967295), (23.8088661, 0.535328142282),
(6.4436083, 0.444634542185)]),
('S', [(5.0331513, -0.099967229187), (1.1695961, 0.399512826089),
(0.380389, 0.70011546888)]),
('P', [(5.0331513, 0.155916274999), (1.1695961, 0.607683718598),
(0.380389, 0.391957393099)])
],
[('S', [(3.4252509, 0.154328967295),
(0.6239137, 0.535328142282),
(0.1688554, 0.444634542185)])],
[('S', [(3.4252509, 0.154328967295),
(0.6239137, 0.535328142282),
(0.1688554, 0.444634542185)])]]
assert result1 == result2
def energy(args, output=None):
ens = args.e
fns = args.filenames
datafiles = [datafile(fn) for fn in fns]
quants = datafiles[0].read('avail quantities')
for i,e in enumerate(ens):
if e not in quants:
match = difflib.get_close_matches(e, quants)
print 'Quantity %s not present, taking close match: %s' % (e, match[0])
ens[i] = match[0]
toplot = []
for df in datafiles:
for e in ens:
plotargs = {}
plotargs['points'] = df.read('quantity', e)
plotargs['filename'] = df.fd.name
plotargs['quantity'] = e
toplot.append(plotargs)
plots = []
legends = []
for arg in toplot:
p, = plot(arg['points'][0], arg['points'][1])
plots.append(p)
legends.append(arg['filename'])
xlabel('Time(ps)')
ylabel(ens[0])
ticklabel_format(style='sci', axis='y', scilimits=(0,0))
grid()
figlegend(plots, legends, 'upper right')
show()
def test_toon_shading():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
from chemlab.graphics import colors
from chemlab.core.molecule import guess_bonds
cdb = ChemlabDB()
#mol = cdb.get('molecule', 'example.norbornene')
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
#v.widget.post_processing = FXAAEffect(v.widget)
#v.widget.post_processing = SSAOEffect(v.widget, kernel_size=64, kernel_radius=1.0, ssao_power=2.0)
v.widget.camera.autozoom(mol.r_array)
#sr = v.add_renderer(AtomRenderer, mol.r_array,
# mol.type_array, 'impostors',
# shading='toon')
#sr = v.add_renderer(AtomRenderer, mol.r_array,
# mol.type_array, 'polygons',
# shading='toon')
ar = v.add_renderer(BallAndStickRenderer,
mol.r_array, mol.type_array,
guess_bonds(mol.r_array, mol.type_array),
shading='toon')
v.run()
def test_ball_and_stick_renderer():
from collections import defaultdict
from chemlab.io import datafile
from chemlab.db.cirdb import CirDB
v = QtViewer()
v.add_post_processing(SSAOEffect, kernel_radius=0.15)
#v.widget.background_color = black
#mol = Molecule([Atom("O", [-0.499, 0.249, 0.0]),
# Atom("H", [-0.402, 0.249, 0.0]),
# Atom("H", [-0.532, 0.198, 0.10])])
#mol.bonds = np.array([[0, 1],[0, 2]])
#mol = CirDB().get("molecule", "moronic acid")
mol = datafile('tests/data/3ZJE.pdb').read('molecule')
mol.bonds = find_bonds(mol)
ar = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array,
mol.bonds)
# Try without bonds
# ar2 = v.add_renderer(BallAndStickRenderer, mol.r_array + 0.5, mol.type_array, np.array([]))
v.run()
def test_merge_system():
# take a protein
from chemlab.io import datafile
from chemlab.graphics import display_system
from chemlab.db import ChemlabDB
water = ChemlabDB().get("molecule", "example.water")
prot = datafile("tests/data/3ZJE.pdb").read("system")
# Take a box of water
NWAT = 50000
bsize = 20.0
pos = np.random.random((NWAT, 3)) * bsize
wat = water.copy()
s = System.empty(NWAT, NWAT*3, box_vectors=np.eye(3)*bsize)
for i in range(NWAT):
wat.move_to(pos[i])
s.add(wat)
prot.r_array += 10
s = merge_systems(s, prot, 0.5)
display_system(s, 'ball-and-stick')
def test_outline():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
from chemlab.graphics.postprocessing.outline import OutlineEffect
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
mol = datafile('tests/data/3ZJE.pdb').read('system')
#mol = datafile('tests/data/water.gro').read('system')
#mol = datafile('tests/data/benzene.mol').read('molecule')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(AtomRenderer,
mol.r_array,
mol.type_array,
'impostors',
shading='toon')
v.add_post_processing(OutlineEffect, 'depthnormal')
v.add_post_processing(SSAOEffect, ssao_power=4.0)
v.add_post_processing(FXAAEffect)
v.add_post_processing(GammaCorrectionEffect)
v.run()
def test_newrdf():
from chemlab.molsim.rdf import distance_histogram
system = datafile("tests/data/rdf/cry.gro").read('system')
#system = datafile("/home/gabriele/projects/LiCl/molfrac-0.39-48668/opt.gro").read('system')
size = system.box_vectors[0,0]/2
timer.start()
rdf_old = rdf(system.r_array[system.type_array == 'Cl'],
system.r_array[system.type_array == 'Li'],
binsize=0.2,
cutoff=size,
periodic=system.box_vectors, normalize=False)
timer.stop()
timer.start()
rdf_new = distance_histogram(system.r_array[system.type_array == 'Cl'],
system.r_array[system.type_array == 'Li'],
binsize=0.2,
cutoff=size,
periodic=system.box_vectors)
timer.stop()
1/0
plot(rdf_new, 'r')
plot(rdf_old[1], 'b')
show()
def test_bonds():
# TODO: deprecate this shit
from chemlab.io import datafile
bz = datafile("tests/data/benzene.mol").read('molecule')
na = Molecule([
Atom('O', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]),
])
# Adding bonds
s = System()
with s.batch() as b:
b.append(bz)
assert_npequal(s.bonds, bz.bonds)
assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2])
assert_npequal(s.bond_orders, bz.bond_orders)
s.add(bz)
assert_npequal(
s.type_array,
['C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C'])
eq_(s.dimensions['atom'], 12)
assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 7)))
# Reordering
s.bonds = np.array([[0, 1], [6, 8]])
s.reorder_molecules([1, 0])
assert_eqbonds(s.bonds, np.array([[6, 7], [0, 2]]))
# Selection
ss = subsystem_from_molecules(s, [1])
assert_npequal(ss.bonds, np.array([[0, 1]]))
def test_pickers():
from chemlab.graphics.pickers import SpherePicker
from chemlab.io import datafile
mol = datafile('/home/gabriele/projects/LiCl/interface/loafintjc-heat/equilibrium.gro').read('system')
centers = [[0.0, 0.0, 0.0], [1.0, 0.0, 1.0]]
radii = np.array([1.0, 0.5])
colors = [[0, 255, 255, 100], [255, 255, 0, 100]]
centers = mol.r_array
radii = np.array([0.2]*mol.n_atoms)
colors = np.array([[0, 255, 255, 255]]*mol.n_atoms)
v = QtViewer()
sr = v.add_renderer(SphereImpostorRenderer, centers, radii, colors, transparent=False)
#sr = v.add_renderer(SphereImpostorRenderer, centers,
# radii*1.5, [[255, 255, 255, 50]]*mol.n_atoms, transparent=True)
sp = SpherePicker(v.widget, centers, radii)
def on_click(evt):
x, y = v.widget.screen_to_normalized(evt.x(), evt.y())
print sp.pick(x, y)
v.widget.clicked.connect(on_click)
v.run()
def test_bonds():
# TODO: deprecate this shit
from chemlab.io import datafile
bz = datafile("tests/data/benzene.mol").read('molecule')
na = Molecule([Atom('O', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]), ])
# Adding bonds
s = System()
with s.batch() as b:
b.append(bz)
assert_npequal(s.bonds, bz.bonds)
assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2])
assert_npequal(s.bond_orders, bz.bond_orders)
s.add(bz)
assert_npequal(s.type_array, ['C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
'C', 'C', 'C'])
eq_(s.dimensions['atom'], 12)
assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 7)))
# Reordering
s.bonds = np.array([[0, 1], [6, 8]])
s.reorder_molecules([1, 0])
assert_eqbonds(s.bonds, np.array([[6, 7], [0, 2]]))
# Selection
ss = subsystem_from_molecules(s, [1])
assert_npequal(ss.bonds, np.array([[0, 1]]))
def test_ball_and_stick_renderer():
from collections import defaultdict
from chemlab.io import datafile
from chemlab.db.cirdb import CirDB
v = QtViewer()
v.add_post_processing(SSAOEffect, kernel_radius = 0.15)
#v.widget.background_color = black
#mol = Molecule([Atom("O", [-0.499, 0.249, 0.0]),
# Atom("H", [-0.402, 0.249, 0.0]),
# Atom("H", [-0.532, 0.198, 0.10])])
#mol.bonds = np.array([[0, 1],[0, 2]])
#mol = CirDB().get("molecule", "moronic acid")
mol = datafile('tests/data/3ZJE.pdb').read('molecule')
mol.bonds = find_bonds(mol)
ar = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array, mol.bonds)
# Try without bonds
# ar2 = v.add_renderer(BallAndStickRenderer, mol.r_array + 0.5, mol.type_array, np.array([]))
v.run()
def test_merge_system():
# take a protein
from chemlab.io import datafile
from chemlab.graphics import display_system
from chemlab.db import ChemlabDB
water = ChemlabDB().get("molecule", "example.water")
prot = datafile("tests/data/3ZJE.pdb").read("system")
# Take a box of water
NWAT = 50000
bsize = 20.0
pos = np.random.random((NWAT, 3)) * bsize
wat = water.copy()
s = System.empty(NWAT, NWAT * 3, box_vectors=np.eye(3) * bsize)
for i in range(NWAT):
wat.move_to(pos[i])
s.add(wat)
prot.r_array += 10
s = merge_systems(s, prot, 0.5)
display_system(s, 'ball-and-stick')
def load_trajectory(name, skip=1, format=None):
'''Load a trajectory file into chemlab. You should call this
command after you load a `~chemlab.core.System` through
load_system or load_remote_system.
'''
df = datafile(name, format=format)
dt, coords = df.read('trajectory', skip=skip)
boxes = df.read('boxes')
viewer.current_traj = coords
viewer.frame_times = dt
viewer.traj_controls.set_ticks(len(dt))
def update(index):
f = coords[index]
for fp in _frame_processors:
f = fp(coords, index)
# update the current representation
viewer.representation.update_positions(f)
viewer.representation.update_box(boxes[index])
current_system().r_array = f
current_system().box_vectors = boxes[index]
viewer.traj_controls.set_time(dt[index])
viewer.update()
viewer.traj_controls.show()
viewer.traj_controls.frame_changed.connect(update)
def test_toon_shading():
from chemlab.core.molecule import guess_bonds
cdb = ChemlabDB()
#mol = cdb.get('molecule', 'example.norbornene')
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
#v.widget.post_processing = FXAAEffect(v.widget)
#v.widget.post_processing = SSAOEffect(v.widget, kernel_size=64, kernel_radius=1.0, ssao_power=2.0)
v.widget.camera.autozoom(mol.r_array)
#sr = v.add_renderer(AtomRenderer, mol.r_array,
# mol.type_array, 'impostors',
# shading='toon')
#sr = v.add_renderer(AtomRenderer, mol.r_array,
# mol.type_array, 'polygons',
# shading='toon')
ar = v.add_renderer(BallAndStickRenderer,
mol.r_array,
mol.type_array,
guess_bonds(mol.r_array, mol.type_array),
shading='toon')
v.run()
def test_traj_viewer():
tv = QtTrajectoryViewer()
s = datafile('tests/data/water.gro').read('system')
ar = tv.add_renderer(BallAndStickRenderer, s.r_array, s.type_array, find_bonds(s))
times, frames = datafile('tests/data/trajout.xtc').read('trajectory')
def update(index):
f = frames[index]
ar.update_positions(f)
tv.set_text(format_time(times[index]))
tv.widget.update()
tv.update_function(update, len(frames))
tv.run()
def load_trajectory(name, skip=1, format=None):
'''Load a trajectory file into chemlab. You should call this
command after you load a `~chemlab.core.System` through
load_system or load_remote_system.
'''
df = datafile(name, format=format)
dt, coords = df.read('trajectory', skip=skip)
boxes = df.read('boxes')
viewer.current_traj = coords
viewer.frame_times = dt
viewer.traj_controls.set_ticks(len(dt))
def update(index):
f = coords[index]
for fp in _frame_processors:
f = fp(coords, index)
# update the current representation
viewer.representation.update_positions(f)
viewer.representation.update_box(boxes[index])
current_system().r_array = f
current_system().box_vectors = boxes[index]
viewer.traj_controls.set_time(dt[index])
viewer.update()
viewer.traj_controls.show()
viewer.traj_controls.frame_changed.connect(update)
def test_read_cclib():
try:
import cclib
except:
raise SkipTest
df = datafile('tests/data/cclib/water_mp2.out', format='gamess')
# Reading a properties that does exist
result1 = df.read('gbasis')
result2 = [[('S',
[(130.7093214, 0.154328967295),
(23.8088661, 0.535328142282),
(6.4436083, 0.444634542185)]),
('S',
[(5.0331513, -0.099967229187),
(1.1695961, 0.399512826089),
(0.380389, 0.70011546888)]),
('P',
[(5.0331513, 0.155916274999),
(1.1695961, 0.607683718598),
(0.380389, 0.391957393099)])],
[('S',
[(3.4252509, 0.154328967295),
(0.6239137, 0.535328142282),
(0.1688554, 0.444634542185)])],
[('S',
[(3.4252509, 0.154328967295),
(0.6239137, 0.535328142282),
(0.1688554, 0.444634542185)])]]
assert result1 == result2
def load_molecule(name, format=None):
'''Read a `~chemlab.core.Molecule` from a file.
.. seealso:: `chemlab.io.datafile`
'''
mol = datafile(name, format=format).read('molecule')
display_system(System([mol]))
def load_system(name, format=None):
'''Read a `~chemlab.core.System` from a file.
.. seealso:: `chemlab.io.datafile`
'''
mol = datafile(name).read('system')
display_system(mol)
def load_molecule(name, format=None):
'''Read a `~chemlab.core.Molecule` from a file.
.. seealso:: `chemlab.io.datafile`
'''
mol = datafile(name, format=format).read('molecule')
display_system(System([mol]))
def test_rdf_multi():
gro_rdf = np.loadtxt("examples/gromacs_tutorial/rdf.xvg",
skiprows=13,
unpack=True)
syst = datafile("examples/gromacs_tutorial/confout.gro").read('system')
df = datafile("examples/gromacs_tutorial/traj.xtc")
t, coords = df.read("trajectory")
boxes = df.read("boxes")
rd = rdf_multi(coords[:30], coords[:30], syst.type_array == 'O',
syst.type_array == 'O', boxes)
plot(gro_rdf[0], gro_rdf[1], color='blue')
#print len(rd[0]), len(rd[1])
plot(rd[0], rd[1], 'red')
show()
def load_system(name, format=None):
'''Read a `~chemlab.core.System` from a file.
.. seealso:: `chemlab.io.datafile`
'''
mol = datafile(name).read('system')
display_system(mol)
def test_write_gromacs():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'grotype': 'OW'}),
Atom('H', [0.1, 0.0, 0.0], export={'grotype': 'HW1'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'grotype': 'HW2'})],
export={'groname': 'SOL'})
sys = System.empty(200, 3*200, box_vectors = np.eye(3)*2.0)
for i in range(200):
sys.add(water.copy())
df = datafile('/tmp/dummy.gro', mode="w")
df.write('system', sys)
df = datafile('/tmp/dummy.gro')
sread = df.read('system')
assert all(sread.type_array == sys.type_array)
def make_gromacs(simulation, directory, clean=False):
"""Create gromacs directory structure"""
if clean is False and os.path.exists(directory):
raise ValueError("Cannot override {}, use option clean=True".format(directory))
else:
shutil.rmtree(directory, ignore_errors=True)
os.mkdir(directory)
# Check custom simulation potential
if simulation.potential.intermolecular.type == "custom":
for pair in simulation.potential.intermolecular.special_pairs:
table = to_table(simulation.potential.intermolecular.pair_interaction(*pair), simulation.cutoff)
fname1 = os.path.join(directory, "table_{}_{}.xvg".format(pair[0], pair[1]))
fname2 = os.path.join(directory, "table_{}_{}.xvg".format(pair[1], pair[0]))
with open(fname1, "w") as fd:
fd.write(table)
with open(fname2, "w") as fd:
fd.write(table)
ndx = {"System": np.arange(simulation.system.n_atoms, dtype="int")}
for particle in simulation.potential.intermolecular.particles:
idx = simulation.system.where(atom_name=particle)["atom"].nonzero()[0]
ndx[particle] = idx
with open(os.path.join(directory, "index.ndx"), "w") as fd:
fd.write(to_ndx(ndx))
# Parameter file
mdpfile = to_mdp(simulation)
with open(os.path.join(directory, "grompp.mdp"), "w") as fd:
fd.write(mdpfile)
# Topology file
topfile = to_top(simulation.system, simulation.potential)
with open(os.path.join(directory, "topol.top"), "w") as fd:
fd.write(topfile)
# Simulation file
datafile(os.path.join(directory, "conf.gro"), "w").write("system", simulation.system)
return directory
def test_rdf_multi():
gro_rdf = np.loadtxt("examples/gromacs_tutorial/rdf.xvg",
skiprows=13,unpack=True)
syst = datafile("examples/gromacs_tutorial/confout.gro").read('system')
df = datafile("examples/gromacs_tutorial/traj.xtc")
t, coords = df.read("trajectory")
boxes = df.read("boxes")
rd = rdf_multi(coords[:30], coords[:30],
syst.type_array == 'O',
syst.type_array == 'O',
boxes)
plot(gro_rdf[0], gro_rdf[1], color='blue')
#print len(rd[0]), len(rd[1])
plot(rd[0], rd[1], 'red')
show()
def test_read_pdb_secondary():
system = datafile('tests/data/pdb1g8p.ent', format='pdb').read('system')
# assert np.all(system.secondary_structure[106:109] == 'S')
eq_(system.sub(secondary_id=1).residue_name[0], 'VAL')
assert_npequal(system.sub(secondary_id=1).residue_name, ['VAL', 'VAL', 'ASP', 'LEU'])
helices = system.sub(secondary_structure='H')
helix = helices.sub(secondary_id=helices.secondary_id[0])
assert_npequal(helix.residue_name, ['PRO', 'PHE', 'SER', 'ALA', "ILE"])
def test_write_gromacs():
water = Molecule([
Atom('O', [0.0, 0.0, 0.0], export={'grotype': 'OW'}),
Atom('H', [0.1, 0.0, 0.0], export={'grotype': 'HW1'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'grotype': 'HW2'})
],
export={'groname': 'SOL'})
sys = System.empty(200, 3 * 200, box_vectors=np.eye(3) * 2.0)
for i in range(200):
sys.add(water.copy())
df = datafile('/tmp/dummy.gro', mode="w")
df.write('system', sys)
df = datafile('/tmp/dummy.gro')
sread = df.read('system')
assert all(sread.type_array == sys.type_array)
def run_gromacs(simulation, directory, clean=False):
if clean is False and os.path.exists(directory):
raise ValueError(
'Cannot override {}, use option clean=True'.format(directory))
else:
shutil.rmtree(directory, ignore_errors=True)
os.mkdir(directory)
# Parameter file
mdpfile = to_mdp(simulation)
with open(os.path.join(directory, 'grompp.mdp'), 'w') as fd:
fd.write(mdpfile)
# Topology file
topfile = to_top(simulation.system, simulation.potential)
with open(os.path.join(directory, 'topol.top'), 'w') as fd:
fd.write(topfile)
# Simulation file
datafile(os.path.join(directory, 'conf.gro'),
'w').write('system', simulation.system)
process = subprocess.Popen(
'cd {} && grompp_d && exec mdrun_d -v'.format(directory),
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True)
output_box = Textarea()
output_box.height = '200px'
output_box.font_family = 'monospace'
output_box.color = '#AAAAAA'
output_box.background_color = 'black'
output_box.width = '800px'
display(output_box)
def output_function(text, output_box=output_box):
output_box.value += text.decode('utf8')
output_box.scroll_to_bottom()
return AsyncCalculation(process, simulation, directory, output_function)
def test_read_edr():
df = datafile('tests/data/ener.edr')
#df.read('frames')
dt, temp = df.read('quantity', 'Temperature')
unit = df.read('units', 'Temperature')
try:
df.read('quantity', 'NonExistent')
except:
pass
def test_read_edr():
df = datafile("tests/data/ener.edr")
# df.read('frames')
dt, temp = df.read("quantity", "Temperature")
unit = df.read("units", "Temperature")
try:
df.read("quantity", "NonExistent")
except:
pass
def run_gromacs(simulation, directory, clean=False):
if clean is False and os.path.exists(directory):
raise ValueError("Cannot override {}, use option clean=True".format(directory))
else:
shutil.rmtree(directory, ignore_errors=True)
os.mkdir(directory)
# Parameter file
mdpfile = to_mdp(simulation)
with open(os.path.join(directory, "grompp.mdp"), "w") as fd:
fd.write(mdpfile)
# Topology file
topfile = to_top(simulation.system, simulation.potential)
with open(os.path.join(directory, "topol.top"), "w") as fd:
fd.write(topfile)
# Simulation file
datafile(os.path.join(directory, "conf.gro"), "w").write("system", simulation.system)
process = subprocess.Popen(
"cd {} && grompp_d && exec mdrun_d -v".format(directory),
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
)
output_box = Textarea()
output_box.height = "200px"
output_box.font_family = "monospace"
output_box.color = "#AAAAAA"
output_box.background_color = "black"
output_box.width = "800px"
display(output_box)
def output_function(text, output_box=output_box):
output_box.value += text.decode("utf8")
output_box.scroll_to_bottom()
return AsyncCalculation(process, simulation, directory, output_function)
def test_write_pdb():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'grotype': 'OW'}),
Atom('H', [0.1, 0.0, 0.0], export={'grotype': 'HW1'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'grotype': 'HW2'})],
export={'groname': 'SOL'})
sys = System.empty(200, 3*200, box_vectors = np.eye(3) * 2.0)
for i in range(200):
sys.add(water.copy())
df = datafile('/tmp/dummy.gro', mode="w")
df.write("system", sys)
def test_ssao():
cdb = ChemlabDB()
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
v.widget.post_processing.append(SSAOEffect(v.widget, kernel_size=16,
kernel_radius=3.0, ssao_power=2.7))
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array, 'impostors')
#ar = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array, [])
v.widget.camera.orbit_y(90)
v.run()
def test_ball_and_stick_renderer():
v = QtViewer()
v.add_post_processing(SSAOEffect, kernel_radius=0.15)
mol = datafile('tests/data/3ZJE.pdb').read('molecule')
mol.bonds = find_bonds(mol)
ar = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array,
mol.bonds)
# ar2 = v.add_renderer(BallAndStickRenderer, mol.r_array + 0.5, mol.type_array, np.array([]))
v.run()
def test_write_gromacs():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], name="OW"),
Atom('H', [0.1, 0.0, 0.0], name='HW1'),
Atom('H', [-0.03333, 0.09428, 0.0], name='HW2')],
name='SOL')
sys = System.empty()
with sys.batch() as b:
for i in range(200):
b.append(water.copy())
sys.box_vectors = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
df = datafile('/tmp/dummy.gro', mode="w")
df.write('system', sys)
with assert_raises(Exception):
df = datafile('/tmp/dummy.gro')
df.write('system', sys)
df = datafile('/tmp/dummy.gro')
sread = df.read('system')
assert all(sread.type_array == sys.type_array)
def test_camera_autozoom():
v = QtViewer()
mol = Molecule([Atom("O", [-0.499, 0.249, 0.0]),
Atom("H", [-0.402, 0.249, 0.0]),
Atom("H", [-0.532, 0.198, 0.10])])
s = datafile('tests/data/3ZJE.pdb').read('system')
# To add some interaction to it
ar = v.add_renderer(AtomRenderer, s.r_array, s.type_array, "impostors")
v.widget.camera.autozoom(s.r_array)
v.run()
def test_write_pdb():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'pdb.type': 'O'}),
Atom('H', [0.1, 0.0, 0.0], export={'pdb.type': 'H'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'pdb.type': 'H'})],
export={'groname': 'SOL'})
sys = System.empty(200, 3*200, box_vectors = np.eye(3) * 2.0)
for i in range(200):
water.r_array += 0.1
sys.add(water.copy())
df = datafile('/tmp/dummy.pdb', mode="w")
df.write("system", sys)
def test_ssao():
cdb = ChemlabDB()
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
v.widget.post_processing.append(SSAOEffect(v.widget, kernel_size=16,
kernel_radius=3.0, ssao_power=2.7))
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array, 'impostors')
#ar = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array, [])
v.widget.camera.orbit_y(90)
v.run()
def test_camera_autozoom():
v = QtViewer()
mol = Molecule([Atom("O", [-0.499, 0.249, 0.0]),
Atom("H", [-0.402, 0.249, 0.0]),
Atom("H", [-0.532, 0.198, 0.10])])
from chemlab.io import datafile
s = datafile('tests/data/3ZJE.pdb').read('system')
# To add some interaction to it
ar = v.add_renderer(AtomRenderer, s.r_array, s.type_array, "impostors")
v.widget.camera.autozoom(s.r_array)
v.run()
def test_geom_cartoon():
# For this test we need chemlab
from chemlab.io import datafile
system = datafile('tests/data/pdb1g8p.ent', format='pdb').read('system')
cartoon = GeomProteinCartoon(Aes(xyz=system.r_array,
types=system.atom_name,
secondary_id=system.secondary_id,
secondary_type=system.secondary_structure))
reps = cartoon.produce(Aes())
eq_(reps[0]['rep_type'], 'ribbon')
def test_write_gromacs():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], name="OW"),
Atom('H', [0.1, 0.0, 0.0], name='HW1'),
Atom('H', [-0.03333, 0.09428, 0.0], name='HW2')],
name='SOL')
sys = System.empty()
with sys.batch() as b:
for i in range(200):
b.append(water.copy())
sys.box_vectors = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
df = datafile('/tmp/dummy.gro', mode="w")
df.write('system', sys)
with assert_raises(Exception):
df = datafile('/tmp/dummy.gro')
df.write('system', sys)
df = datafile('/tmp/dummy.gro')
sread = df.read('system')
assert all(sread.type_array == sys.type_array)
def test_gamma():
cdb = ChemlabDB()
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
v.widget.camera.orbit_y(3.14/3)
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array,
'impostors', shading='phong')
v.add_post_processing(SSAOEffect, ssao_power=4.0)
v.add_post_processing(GammaCorrectionEffect)
v.run()
def test_geom_cartoon():
# For this test we need chemlab
from chemlab.io import datafile
system = datafile('tests/data/pdb1g8p.ent', format='pdb').read('system')
cartoon = GeomProteinCartoon(
Aes(xyz=system.r_array,
types=system.atom_name,
secondary_id=system.secondary_id,
secondary_type=system.secondary_structure))
reps = cartoon.produce(Aes())
eq_(reps[0]['rep_type'], 'ribbon')
def add_molecule(self,
path,
renderer='ballandstick',
color='default',
cache=True):
try:
mol = self.molecules[path]
except KeyError:
mol = self.molecules[path] = datafile(path).read('molecule')
mol.renderer = self.RENDERERS[renderer](self, mol.r_array,
mol.type_array, mol.bonds)
# color_scheme=self.COLORS[color])
self.renderers.append(mol.renderer)
self.update()
def test_write_pdb():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'pdb.type': 'O'}),
Atom('H', [0.1, 0.0, 0.0], export={'pdb.type': 'H'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'pdb.type': 'H'})],
export={'groname': 'SOL'})
sys = System.empty()
with sys.batch() as b:
for i in range(200):
water.r_array += 0.1
b.append(water.copy())
df = datafile('/tmp/dummy.pdb', mode="w")
df.write("system", sys)
