def mlp_map(session, atoms, method, spacing, max_dist, nexp, name, open_map):
data, bounds = calculatefimap(atoms, method, spacing, max_dist, nexp)
# m.pot is 1-dimensional if m.writedxfile() was called. Has indices in x,y,z order.
origin = tuple(xmin for xmin, xmax in bounds)
s = spacing
step = (s, s, s)
from chimerax.map_data import ArrayGridData
g = ArrayGridData(data, origin, step, name=name)
g.polar_values = True
from chimerax.map import volume_from_grid_data
v = volume_from_grid_data(g,
session,
open_model=open_map,
show_dialog=open_map)
if open_map:
v.update_drawings() # Compute surface levels
v.set_parameters(
surface_colors=[(0, 139 / 255, 139 / 255,
1), (184 / 255, 134 / 255, 11 / 255, 1)])
return v
def laplacian(v, step=None, subregion=None, model_id=None):
m = v.matrix(step=step, subregion=subregion)
from numpy import float32, multiply, add
lm = m.astype(float32) # Copy array
multiply(lm, -6.0, lm)
add(lm[:-1, :, :], m[1:, :, :], lm[:-1, :, :])
add(lm[1:, :, :], m[:-1, :, :], lm[1:, :, :])
add(lm[:, :-1, :], m[:, 1:, :], lm[:, :-1, :])
add(lm[:, 1:, :], m[:, :-1, :], lm[:, 1:, :])
add(lm[:, :, :-1], m[:, :, 1:], lm[:, :, :-1])
add(lm[:, :, 1:], m[:, :, :-1], lm[:, :, 1:])
lm[0, :, :] = 0
lm[-1, :, :] = 0
lm[:, 0, :] = 0
lm[:, -1, :] = 0
lm[:, :, 0] = 0
lm[:, :, -1] = 0
origin, step = v.data_origin_and_step(subregion=subregion, step=step)
d = v.data
from chimerax.map_data import ArrayGridData
ld = ArrayGridData(lm,
origin,
step,
d.cell_angles,
d.rotation,
name=v.name + ' Laplacian')
ld.polar_values = True
from chimerax.map import volume_from_grid_data
lv = volume_from_grid_data(ld, v.session, model_id=model_id)
lv.copy_settings_from(v, copy_thresholds=False, copy_colors=False)
lv.set_parameters(cap_faces=False)
v.display = False # Hide original map
return lv