/usr/lib/python2.7/dist-packages/chempy/brick.py is in pymol 1.8.4.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information.
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-*
#-*
#-*
#Z* -------------------------------------------------------------------
import numpy
class Brick(object):
'''
Map object to load into PyMOL with
>>> pymol.importing.load_brick(brickinstance, "name")
'''
def __init__(self):
self.valid = None
@classmethod
def from_numpy(cls, data, grid, origin=(0.0, 0.0, 0.0)):
'''
@param data: numpy float array with len(data.shape) == 3
@param range: 3f sequence
@param origin: 3f sequence
'''
data = numpy.asfarray(data)
assert len(data.shape) == 3
self = cls()
self.lvl = data
self.grid = list(grid)
self.origin = list(origin)
# redundant information
self.dim = list(data.shape)
self.range = [g * (d - 1) for (g, d) in zip(self.grid, self.dim)]
return self
def setup_from_min_max(self,mn,mx,grid,buffer=0.0):
self.origin = [
mn[0]-buffer,
mn[1]-buffer,
mn[2]-buffer
]
self.range = [
(mx[0]-mn[0])+2*buffer,
(mx[1]-mn[1])+2*buffer,
(mx[2]-mn[2])+2*buffer
]
self.dim = [
1 + int(self.range[0]/grid[0]),
1 + int(self.range[1]/grid[1]),
1 + int(self.range[2]/grid[2])
]
self.grid = list(grid)
self.lvl = numpy.zeros(self.dim,float)
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