def random_ellipsoid(box, size, min_axis):
# return a random ellipsoid record of the form:
# [ ELLIPSOID, x_pos, y_pos, z_pos, size, x0, y0, z0, x1, y1, z2, x2, y2, z2 ]
# where the xyz vectors are orthogonal and of length 1.0 or less.
box = box - size
tmp0 = cpv.random_vector()
tmp1 = cpv.random_vector()
tmp2 = cpv.cross_product(tmp1, tmp0)
tmp3 = cpv.cross_product(tmp1, tmp2)
tmp4 = cpv.cross_product(tmp2, tmp3)
tmp2 = cpv.normalize(tmp2)
tmp3 = cpv.normalize(tmp3)
tmp4 = cpv.normalize(tmp4)
primary = cpv.scale(tmp2, random())
secondary = cpv.scale(tmp3,random())
tertiary = cpv.scale(tmp4,random())
factor = 1.0 / max( cpv.length(primary), cpv.length(secondary), cpv.length(tertiary))
primary = cpv.scale(primary, factor)
secodary = cpv.scale(secondary, factor)
tertiary = cpv.scale(tertiary, factor)
return [ ELLIPSOID,
size + random() * box, size + random() * box, size + random() * box,
max(random() * size, min_axis),
] + primary + secondary + tertiary
def random_conic(box, size, min_axis):
# return a random ellipsoid record of the form:
# [ ELLIPSOID, x_pos, y_pos, z_pos, size, x0, y0, z0, x1, y1, z2, x2, y2, z2 ]
# where the xyz vectors are orthogonal and of length 1.0 or less.
box = box - size
tmp0 = [
size + random() * box, size + random() * box, size + random() * box
]
tmp1 = cpv.random_vector()
tmp2 = cpv.scale(tmp1, box / 10)
tmp1 = cpv.add(tmp2, tmp0)
return [
CONE,
tmp0[0],
tmp0[1],
tmp0[2], # coordinates
tmp1[0],
tmp1[1],
tmp1[2],
(abs(random()) * 0.4 + 0.2) * size, # radii
(abs(random()) * 0.1 + 0.01) * size,
random(),
random(),
random(), # colors
random(),
random(),
random(),
1.0,
1.0
]
def random_conic(box, size, min_axis):
# return a random ellipsoid record of the form:
# [ ELLIPSOID, x_pos, y_pos, z_pos, size, x0, y0, z0, x1, y1, z2, x2, y2, z2 ]
# where the xyz vectors are orthogonal and of length 1.0 or less.
box = box - size
tmp0 = [ size + random() * box, size + random() * box, size + random() * box ]
tmp1 = cpv.random_vector()
tmp2 = cpv.scale(tmp1,box/10)
tmp1 = cpv.add(tmp2,tmp0)
return [ CONE,
tmp0[0], tmp0[1], tmp0[2], # coordinates
tmp1[0], tmp1[1], tmp1[2],
(abs(random())*0.4+0.2) * size, # radii
(abs(random())*0.1+0.01) * size,
random(), random(), random(), # colors
random(), random(), random(),
1.0, 1.0 ]
def obscure(selection, hiding="medium", keep=0, state=-1, name_map='', name_iso='', quiet=0, _self=cmd):
"""
DESCRIPTION
Given an object or selection, usually a small molecule, obscure it
to protect its exact identity.
USAGE
obscure selection [, hiding [, keep ]]
ARGUMENTS
selection = str: atom selection to hide
hiding = low|medium|high: level to which PyMOL obscures the object {default: medium}
keep = 0/1: by default, PyMOL removes the obscured atoms from your file,
this flag will keep the atoms in the file. Be careful!
NOTES
Large molecules are very slow.
"""
from chempy.cpv import add, scale, random_vector
keep = bool(keep) if not keep else int(keep)
quiet = int(quiet)
hiding = hiding_sc.auto_err(hiding, 'hiding level')
hiding = ['low', 'medium', 'high'].index(hiding)
# these parameters are fine-tuned for a good visual experience
resolution, grid, level = [
[2.00, 0.18, 2.00], # low
[3.75, 0.25, 2.50], # medium
[4.00, 0.33, 2.00], # high
][hiding]
# detect if we're hiding a subset of a molecule, then add one bond, so ensure that what sticks out looks good
tmp_sele = _self.get_unused_name("_target")
natoms = _self.select(tmp_sele, "(%s) extend 1" % (selection), 0)
if not quiet:
print(' Obscuring %d atoms' % natoms)
# get a new name for the map/surf
if not name_map:
name_map = _self.get_unused_name("obsc_map")
if not name_iso:
name_iso = _self.get_unused_name("obsc_surf")
if not keep:
# randomize the coordinates
_self.alter_state(state, tmp_sele, "(x,y,z)=perturb([x,y,z])", space={'perturb':
lambda v: add(v, scale(random_vector(), 0.4))})
# clear out charge and b-factor
_self.alter(tmp_sele, "(b,q) = (10.0, 1.0)")
# make the gaussian map and draw its surface
_self.map_new(name_map, "gaussian", grid, tmp_sele, resolution=resolution, quiet=quiet)
_self.isosurface(name_iso, name_map, level, quiet=quiet)
if not keep:
if natoms == _self.count_atoms('byobject (%s)' % (tmp_sele)):
names = ' '.join(_self.get_object_list('(%s)' % (selection)))
if not quiet:
print(' Deleting object:', names)
_self.delete(names)
else:
_self.remove(selection, quiet=quiet)
_self.delete(tmp_sele)
