def drawIsoSurface(values3d, resolution=1., plot_center=None, viewer=None):
from htmd.vmdviewer import getCurrentViewer
from htmd.molecule.util import writeVoxels
# plot_center should be - molecule.get_center() + 12
if len(values3d.shape) != 3:
raise ValueError("Your provided a box of {} dimensions."
"\nThis only works with dimension of 3".format(
len(values3d.shape)))
from htmd.util import tempname
if viewer is None:
viewer = getCurrentViewer()
mincoor = np.zeros(3, dtype=np.float64)
maxcoor = np.array(values3d.shape, dtype=np.float64)
rescoor = np.array([resolution] * 3)
# Adjust the plotting center
if plot_center is None:
plot_center = maxcoor / 2.
else:
plot_center = np.array(plot_center)
mincoor -= (plot_center + 0.5
) # TODO: Fix so it will work in case resolution != 1.
maxcoor -= (plot_center + 0.5)
outf = tempname(suffix='.cube')
writeVoxels(values3d, outf, mincoor, maxcoor, rescoor)
viewer.send(
'mol new {} type cube first 0 last -1 step 1 waitfor 1 volsets {{0 }}'.
format(outf))
viewer.send('mol modstyle 0 top Isosurface 0.75 0 2 0 1 1')
def drawIsoSurface(values3d, resolution=1., plot_center=None, viewer=None):
from htmd.vmdviewer import getCurrentViewer
from htmd.molecule.util import writeVoxels
# plot_center should be - molecule.get_center() + 12
if len(values3d.shape) != 3:
raise ValueError("Your provided a box of {} dimensions."
"\nThis only works with dimension of 3".format(len(values3d.shape)))
from htmd.util import tempname
if viewer is None:
viewer = getCurrentViewer()
mincoor = np.zeros(3, dtype=np.float64)
maxcoor = np.array(values3d.shape, dtype=np.float64)
rescoor = np.array([resolution] * 3)
# Adjust the plotting center
if plot_center is None:
plot_center = maxcoor / 2.
else:
plot_center = np.array(plot_center)
mincoor -= (plot_center + 0.5) # TODO: Fix so it will work in case resolution != 1.
maxcoor -= (plot_center + 0.5)
outf = tempname(suffix='.cube')
writeVoxels(values3d, outf, mincoor, maxcoor, rescoor)
viewer.send('mol new {} type cube first 0 last -1 step 1 waitfor 1 volsets {{0 }}'.format(outf))
viewer.send('mol modstyle 0 top Isosurface 0.75 0 2 0 1 1')
def volumetric_map():
sims = simlist(glob('data/*/'), glob('data/*/structure.pdb'),
glob('input/*/'))
sim_num = len(sims)
for s in sims:
print("\nSimulation", s.simid + 1, "of", sim_num)
if s.simid == 0:
(traj, traj_wat, ref_traj) = prepare_traject(s)
(min_d, max_d) = define_extremes(traj_wat)
else:
(traj, traj_wat, ref_traj) = prepare_traject(s, ref_traj)
traj_wat.moveBy([max_d / 2, max_d / 2, max_d / 2])
w_count = create_count_dict(min_d, max_d)
avg_wat = calculate_occupancy(traj_wat, w_count, min_d, max_d)
try:
occup_all += avg_wat
except NameError:
occup_all = avg_wat
occup_all = occup_all / sim_num
occup_all += 1e-40
pot = chemical_pot(occup_all)
writeVoxels(pot, "cubefile.cube", np.array([min_d, min_d, min_d]),
np.array([max_d, max_d, max_d]), np.array([1, 1, 1]))
print("\nVolumetric file created.\n")
view_vmd(traj, max_d)
def isosurface_generator(grid, cubedistance,output):
for x,y,z in itertools.product(*map(range, (grid.shape[0], grid.shape[1],grid.shape[2]))):
prob = grid[x][y][z]
if prob == 0:
continue
else:
grid[x][y][z] = (np.log(grid[x][y][z])) * 0.001987191 * 298 * -1
print("Energy calculated!")
min_vec= np.array([0,0,0])
max_vec=np.array([cubedistance,cubedistance,cubedistance])
res_vec=np.array([1,1,1])
writeVoxels(grid, output+'.cube', min_vec, max_vec, res_vec)
print("Output file "+output+".cube generated on the current directory")
def isosurface_generator(grid, cubedistance, output):
for x, y, z in itertools.product(
*map(range, (grid.shape[0], grid.shape[1], grid.shape[2]))):
prob = grid[x][y][z]
if prob == 0:
continue
else:
grid[x][y][z] = (np.log(grid[x][y][z])) * 0.001987191 * 298 * -1
print("Energy calculated!")
min_vec = np.array([0, 0, 0])
max_vec = np.array([cubedistance, cubedistance, cubedistance])
res_vec = np.array([1, 1, 1])
writeVoxels(grid, output + '.cube', min_vec, max_vec, res_vec)
print("Output file " + output + ".cube generated on the current directory")
def volumetric_map():
sims = simlist(glob('data/*/'), glob('data/*/structure.pdb'), glob('input/*/'))
sim_num=len(sims)
for s in sims:
print("\nSimulation", s.simid +1, "of", sim_num)
if s.simid == 0:
(traj,traj_wat,ref_traj)=prepare_traject(s)
(min_d,max_d)=define_extremes(traj_wat)
else:
(traj,traj_wat,ref_traj)=prepare_traject(s,ref_traj)
traj_wat.moveBy([max_d/2,max_d/2,max_d/2])
w_count=create_count_dict(min_d,max_d)
avg_wat = calculate_occupancy(traj_wat,w_count,min_d,max_d)
try:
occup_all += avg_wat
except NameError:
occup_all = avg_wat
occup_all=occup_all/sim_num
occup_all += 1e-40
pot=chemical_pot(occup_all)
writeVoxels(pot,"cubefile.cube",np.array([min_d,min_d,min_d]),np.array([max_d,max_d,max_d]),np.array([1,1,1]))
print("\nVolumetric file created.\n")
view_vmd(traj,max_d)