self.array.__setattr__(attr, value)
except AttributeError:
object.__setattr__(self, attr, value)
# Only called after other approaches fail.
def __getattr__(self, attr):
if (attr == 'array'):
return object.__getattribute__(self, attr)
return self.array.__getattribute__(attr)
#############################################################
# Test of class container
#############################################################
if __name__ == '__main__':
temp = reshape(arange(10000), (100, 100))
ua = container(temp)
# new object created begin test
print dir(ua)
print shape(ua), ua.shape # I have changed Numeric.py
ua_small = ua[:3, :5]
print ua_small
ua_small[
0, 0] = 10 # this did not change ua[0,0], which is not normal behavior
print ua_small[0, 0], ua[0, 0]
print sin(ua_small) / 3. * 6. + sqrt(ua_small**2)
print less(ua_small, 103), type(less(ua_small, 103))
print type(ua_small * reshape(arange(15), shape(ua_small)))
print reshape(ua_small, (5, 3))
def coarseMolSurface(molFrag,XYZd,isovalue=5.0,resolution=-0.4,padding=0.0, name='CoarseMolSurface',geom=None):
"""
Function adapted from the Vision network which compute a coarse molecular
surface in PMV
@type molFrag: MolKit.AtomSet
@param molFrag: the atoms selection
@type XYZd: array
@param XYZd: shape of the volume
@type isovalue: float
@param isovalue: isovalue for the isosurface computation
@type resolution: float
@param resolution: resolution of the final mesh
@type padding: float
@param padding: the padding
@type name: string
@param name: the name of the resultante geometry
@type geom: DejaVu.Geom
@param geom: update geom instead of creating a new one
@rtype: DejaVu.Geom
@return: the created or updated DejaVu.Geom
"""
import pdb
from MolKit.molecule import Atom
atoms = molFrag.findType(Atom)
coords = atoms.coords
radii = atoms.vdwRadius
from UTpackages.UTblur import blur
import numpy.core as Numeric
volarr, origin, span = blur.generateBlurmap(coords, radii, XYZd,resolution, padding = 0.0)
volarr.shape = (XYZd[0],XYZd[1],XYZd[2])
volarr = Numeric.ascontiguousarray(Numeric.transpose(volarr), 'f')
weights = Numeric.ones(len(radii), 'f')
h = {}
from Volume.Grid3D import Grid3DF
maskGrid = Grid3DF( volarr, origin, span , h)
h['amin'], h['amax'],h['amean'],h['arms']= maskGrid.stats()
from UTpackages.UTisocontour import isocontour
isocontour.setVerboseLevel(0)
data = maskGrid.data
origin = Numeric.array(maskGrid.origin).astype('f')
stepsize = Numeric.array(maskGrid.stepSize).astype('f')
if data.dtype.char!=Numeric.float32:
data = data.astype('f')#Numeric.Float32)
newgrid3D = Numeric.ascontiguousarray(Numeric.reshape( Numeric.transpose(data),
(1, 1)+tuple(data.shape) ), data.dtype.char)
ndata = isocontour.newDatasetRegFloat3D(newgrid3D, origin, stepsize)
isoc = isocontour.getContour3d(ndata, 0, 0, isovalue,
isocontour.NO_COLOR_VARIABLE)
vert = Numeric.zeros((isoc.nvert,3)).astype('f')
norm = Numeric.zeros((isoc.nvert,3)).astype('f')
col = Numeric.zeros((isoc.nvert)).astype('f')
tri = Numeric.zeros((isoc.ntri,3)).astype('i')
isocontour.getContour3dData(isoc, vert, norm, col, tri, 0)
if maskGrid.crystal:
vert = maskGrid.crystal.toCartesian(vert)
return (vert, tri)
try:
self.array.__setattr__(attr, value)
except AttributeError:
object.__setattr__(self, attr, value)
# Only called after other approaches fail.
def __getattr__(self,attr):
if (attr == 'array'):
return object.__getattribute__(self, attr)
return self.array.__getattribute__(attr)
#############################################################
# Test of class container
#############################################################
if __name__ == '__main__':
temp=reshape(arange(10000),(100,100))
ua=container(temp)
# new object created begin test
print dir(ua)
print shape(ua),ua.shape # I have changed Numeric.py
ua_small=ua[:3,:5]
print ua_small
ua_small[0,0]=10 # this did not change ua[0,0], which is not normal behavior
print ua_small[0,0],ua[0,0]
print sin(ua_small)/3.*6.+sqrt(ua_small**2)
print less(ua_small,103),type(less(ua_small,103))
print type(ua_small*reshape(arange(15),shape(ua_small)))
print reshape(ua_small,(5,3))
print transpose(ua_small)
def coarseMolSurface(molFrag,
XYZd,
isovalue=5.0,
resolution=-0.4,
padding=0.0,
name='CoarseMolSurface',
geom=None):
"""
Function adapted from the Vision network which compute a coarse molecular
surface in PMV
@type molFrag: MolKit.AtomSet
@param molFrag: the atoms selection
@type XYZd: array
@param XYZd: shape of the volume
@type isovalue: float
@param isovalue: isovalue for the isosurface computation
@type resolution: float
@param resolution: resolution of the final mesh
@type padding: float
@param padding: the padding
@type name: string
@param name: the name of the resultante geometry
@type geom: DejaVu.Geom
@param geom: update geom instead of creating a new one
@rtype: DejaVu.Geom
@return: the created or updated DejaVu.Geom
"""
import pdb
from MolKit.molecule import Atom
atoms = molFrag.findType(Atom)
coords = atoms.coords
radii = atoms.vdwRadius
from UTpackages.UTblur import blur
import numpy.core as Numeric
volarr, origin, span = blur.generateBlurmap(coords,
radii,
XYZd,
resolution,
padding=0.0)
volarr.shape = (XYZd[0], XYZd[1], XYZd[2])
volarr = Numeric.ascontiguousarray(Numeric.transpose(volarr), 'f')
weights = Numeric.ones(len(radii), 'f')
h = {}
from Volume.Grid3D import Grid3DF
maskGrid = Grid3DF(volarr, origin, span, h)
h['amin'], h['amax'], h['amean'], h['arms'] = maskGrid.stats()
from UTpackages.UTisocontour import isocontour
isocontour.setVerboseLevel(0)
data = maskGrid.data
origin = Numeric.array(maskGrid.origin).astype('f')
stepsize = Numeric.array(maskGrid.stepSize).astype('f')
if data.dtype.char != Numeric.float32:
data = data.astype('f') #Numeric.Float32)
newgrid3D = Numeric.ascontiguousarray(
Numeric.reshape(Numeric.transpose(data), (1, 1) + tuple(data.shape)),
data.dtype.char)
ndata = isocontour.newDatasetRegFloat3D(newgrid3D, origin, stepsize)
isoc = isocontour.getContour3d(ndata, 0, 0, isovalue,
isocontour.NO_COLOR_VARIABLE)
vert = Numeric.zeros((isoc.nvert, 3)).astype('f')
norm = Numeric.zeros((isoc.nvert, 3)).astype('f')
col = Numeric.zeros((isoc.nvert)).astype('f')
tri = Numeric.zeros((isoc.ntri, 3)).astype('i')
isocontour.getContour3dData(isoc, vert, norm, col, tri, 0)
if maskGrid.crystal:
vert = maskGrid.crystal.toCartesian(vert)
return (vert, tri)
