/
load_grid.py
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/
load_grid.py
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from chempy.brick import Brick
from pymol import cmd
import h5py
import numpy as np
def load_grid(fname, prefix='aa', ramp='jet'):
cmd.volume_ramp_new('ramp_DA', [
0.00, 1.00, 1.00, 1.00, 0.00,
25.00, 1.00, 0.77, 0.77, 0.02,
50.00, 1.00, 0.54, 0.54, 0.06,
75.00, 1.00, 0.38, 0.38, 0.18,
90.00, 0.93, 0.00, 0.00, 0.60,
100.00, 0.70, 0.00, 0.00, 1.00,
])
cmd.volume_ramp_new('ramp_DG', [
0.00, 1.00, 1.00, 1.00, 0.00,
25.00, 0.77, 0.77, 1.00, 0.02,
50.00, 0.54, 0.54, 1.00, 0.06,
75.00, 0.38, 0.38, 1.00, 0.18,
90.00, 0.00, 0.00, 0.93, 0.60,
100.00, 0.00, 0.00, 0.70, 1.00,
])
cmd.volume_ramp_new('ramp_DC', [
0.00, 1.00, 1.00, 1.00, 0.00,
25.00, 0.64, 1.00, 0.61, 0.02,
50.00, 0.48, 1.00, 0.47, 0.06,
75.00, 0.26, 1.00, 0.28, 0.18,
90.00, 0.04, 0.85, 0.00, 0.44,
100.00, 0.00, 0.52, 0.06, 1.00,
])
cmd.volume_ramp_new('ramp_DT', [
0.00, 1.00, 1.00, 1.00, 0.00,
25.00, 1.00, 0.99, 0.55, 0.02,
50.00, 1.00, 0.98, 0.46, 0.06,
75.00, 1.00, 0.99, 0.37, 0.19,
90.00, 0.92, 0.92, 0.00, 0.39,
100.00, 0.76, 0.73, 0.00, 1.00,
])
cmd.volume_ramp_new('ramp_P', [
0.00, 1.00, 1.00, 1.00, 0.00,
25.00, 1.00, 0.95, 0.93, 0.02,
50.00, 1.00, 0.85, 0.69, 0.06,
75.00, 1.00, 0.78, 0.55, 0.19,
90.00, 1.00, 0.66, 0.30, 0.39,
100.00, 0.97, 0.50, 0.00, 1.00,
])
cmd.volume_ramp_new('ramp_jet', [
0.00, 0.00, 0.00, 1.00, 0.00,
25.00, 0.06, 0.93, 1.00, 0.05,
50.00, 0.49, 0.51, 1.00, 0.15,
75.00, 1.00, 1.00, 0.00, 0.23,
90.00, 0.80, 0.18, 1.00, 0.48,
100.00, 0.98, 0.01, 1.00, 1.00,
])
cmd.volume_ramp_new('ramp_delta', [
-1.0, 1.00, 0.00, 0.00, 0.00,
-0.4, 1.00, 1.00, 0.00, 1.0,
-0.2, 1.00, 0.00, 0.00, 0.00,
0.2, 0.00, 0.00, 1.00, 0.00,
0.4, 0.00, 1.00, 1.00, 1.0,
1.0, 0.00, 0.00, 1.00, 0.00])
F = h5py.File(fname, 'r')
# load step along every axis
# step = np.array([1.0, 1.0, 1.0])
step = F['step'][()]
# load origin of grid
# origin = np.array([0.0, 0.0, 0.0])
origin = F['origin'][()]
NUCS = set(F.keys())
protected = set(['origin', 'step', 'atypes'])
NUCS -= protected
for i in NUCS:
# load data: 3D array
data = F[i][()]
# Create brick
b = Brick.from_numpy(data, step, origin)
bname = prefix + '_' + i
# load brick into pymol
cmd.load_brick(b, bname)
volname = bname + '_volume'
# assign ramp to the brick
cmd.volume(volname, bname)
if ramp == 'nuc':
cmd.volume_color(volname, 'ramp_' + i)
elif ramp == 'delta':
cmd.volume_color(volname, 'ramp_delta')
else:
cmd.volume_color(volname, 'ramp_jet')
# The extend command makes this runnable as a command, from PyMOL.
cmd.extend("load_grid", load_grid)
def load_meta_grid(fname, prefix='meta'):
F = h5py.File(fname, 'r')
step = F['step'][()]
origin = F['origin'][()]
NUCS = set(F.keys())
protected = set(['origin', 'step', 'atypes'])
NUCS -= protected
for i in NUCS:
data = F[i][()]
b = Brick.from_numpy(data, step, origin)
bname = prefix + '_' + i
cmd.load_brick(b, bname)
volname = bname + '_volume'
d_min = np.min(data)
d_max = np.max(data)
v = np.linspace(d_min, d_max, 6)
cmd.volume(volname, bname)
print('ramp_%s' % i)
cmd.volume_ramp_new('ramp_grid', [
v[0], 0.00, 0.00, 1.00, 0.70,
v[1], 0.06, 0.93, 1.00, 0.50,
v[2], 0.49, 0.51, 1.00, 0.30,
v[3], 1.00, 1.00, 0.00, 0.10,
v[4], 0.80, 0.18, 1.00, 0.05,
v[5], 0.98, 0.01, 1.00, 0.00,
])
cmd.volume_color(volname, 'ramp_grid')
# The extend command makes this runnable as a command, from PyMOL.
cmd.extend("load_meta_grid", load_meta_grid)