def parseMap(self):
# append to log file for this eTrack run
logfileName = '{}output/{}_log.txt'.format(self.where,self.pdbName)
logfile = open(logfileName,'a')
# define 'rho' electron map object
rho = electron_map_info()
# open electron density .map file here
binarymapfile = open(self.where+self.mapFileName,'rb')
# start adding header information into electron_map_info class format.
# Note the unpacking of a struct for each byte, read as a long 'l'
rho.nx = struct.unpack('=l',binarymapfile.read(4))[0]
rho.ny = struct.unpack('=l',binarymapfile.read(4))[0]
rho.nz = struct.unpack('=l',binarymapfile.read(4))[0]
rho.type = struct.unpack('=l',binarymapfile.read(4))[0]
print 'Num. Col, Row, Sec: '
print '{} {} {}'.format(rho.nx,rho.ny,rho.nz)
logfile.write('Num. Col, Row, Sec: {} {} {}\n'.format(rho.nx,rho.ny,rho.nz))
rho.start1 = struct.unpack('=l',binarymapfile.read(4))[0]
rho.start2 = struct.unpack('=l',binarymapfile.read(4))[0]
rho.start3 = struct.unpack('=l',binarymapfile.read(4))[0]
print 'Start positions: '
print '{} {} {}'.format(rho.start1,rho.start2,rho.start3)
logfile.write('Start positions: {} {} {}\n'.format(rho.start1,rho.start2,rho.start3))
rho.gridsamp1 = struct.unpack('=l',binarymapfile.read(4))[0]
rho.gridsamp2 = struct.unpack('=l',binarymapfile.read(4))[0]
rho.gridsamp3 = struct.unpack('=l',binarymapfile.read(4))[0]
print 'Grid sampling:'
print '{} {} {}'.format(rho.gridsamp1,rho.gridsamp2,rho.gridsamp3)
logfile.write('Grid sampling: {} {} {}\n'.format(rho.gridsamp1,rho.gridsamp2,rho.gridsamp3))
# for cell dimensions, stored in header file as float not long
# integer so must account for this
rho.celldim_a = struct.unpack('f',binarymapfile.read(4))[0]
rho.celldim_b = struct.unpack('f',binarymapfile.read(4))[0]
rho.celldim_c = struct.unpack('f',binarymapfile.read(4))[0]
rho.celldim_alpha = struct.unpack('f',binarymapfile.read(4))[0]
rho.celldim_beta = struct.unpack('f',binarymapfile.read(4))[0]
rho.celldim_gamma = struct.unpack('f',binarymapfile.read(4))[0]
print 'Cell dimensions:'
print '{} {} {}'.format(rho.celldim_a,rho.celldim_b,rho.celldim_c)
print '{} {} {}'.format(rho.celldim_alpha,rho.celldim_beta,rho.celldim_gamma)
logfile.write('Cell dimensions: {} {} {} {} {} {}\n'.format(rho.celldim_a,rho.celldim_b,
rho.celldim_c,rho.celldim_alpha,
rho.celldim_beta,rho.celldim_gamma))
rho.fast_axis = struct.unpack('=l',binarymapfile.read(4))[0]
rho.med_axis = struct.unpack('=l',binarymapfile.read(4))[0]
rho.slow_axis = struct.unpack('=l',binarymapfile.read(4))[0]
print 'Fast,med,slow axes: '
print '{} {} {}'.format(rho.fast_axis,rho.med_axis,rho.slow_axis)
logfile.write('Fast,med,slow axes: {} {} {}\n'.format(rho.fast_axis,rho.med_axis,rho.slow_axis))
rho.mindensity = struct.unpack('f',binarymapfile.read(4))[0]
rho.maxdensity = struct.unpack('f',binarymapfile.read(4))[0]
rho.meandensity = struct.unpack('f',binarymapfile.read(4))[0]
print 'Density values: '
print '{} {} {}'.format(rho.mindensity,rho.maxdensity,rho.meandensity)
logfile.write('Density values: {} {} {}\n'.format(rho.mindensity,rho.maxdensity,rho.meandensity))
# next find .map file size, to calculate the last nx*ny*nz bytes of
# file (corresponding to the position of the 3D electron density
# array). Note factor of 4 is included since 4-byte floats used for
# electron density array values.
filesize = os.path.getsize(self.where+self.mapFileName)
densitystart = filesize - 4*(rho.nx*rho.ny*rho.nz)
# next seek start of electron density data
binarymapfile.seek(densitystart,0)
# if electron density written in shorts (I don't think it will be
# but best to have this case)
if rho.type is 1:
print 'Untested .map type --> 1 (type 2 expected). Values read'
+ 'as int16 ("i2?") - consult .map header in MAPDUMP(CCP4) to check'
struct_fmt = '=i2'
struct_len = struct.calcsize(struct_fmt)
density = []
while True:
data = binarymapfile.read(struct_len)
if not data: break
s = struct.unpack(struct_fmt,data)[0]
density.append(s)
# if electron density written in floats (which is to be expected
# from FFT-CCP4 outputted .map file of electron density)
if rho.type is 2:
struct_fmt = '=f4'
struct_len = struct.calcsize(struct_fmt)
density = []
appenddens = density.append
if self.mapType in ('atom_map'):
self.atomIndices = []
appendindex = self.atomIndices.append
counter = -1
while True:
data = binarymapfile.read(struct_len)
if not data: break
s = struct.unpack(struct_fmt,data)[0]
counter += 1
if int(s) == 0:
continue
else:
appenddens(s)
appendindex(counter)
# efficient way to read through density map file using indices of atoms
# from atom map file above
elif self.mapType in ('density_map'):
for i in range(0,len(self.atomIndices)):
if i != 0:
binarymapfile.read(struct_len*(self.atomIndices[i]-self.atomIndices[i-1] - 1))
else:
binarymapfile.read(struct_len*(self.atomIndices[0]))
data = binarymapfile.read(struct_len)
s = struct.unpack(struct_fmt,data)[0]
appenddens(s)
else:
print 'Unknown map type --> terminating script'
sys.exit()
logfile.close()
binarymapfile.close()
# as a check that file has been read correctly, check that the min
# and max electron density stated in .map file header correspond to
# calculated min and max here
# Note for the case of atom map, the min voxel val will be 0 (no atom present)
# --> since these voxels are removed during the filtering of the map, only
# the map value is tested.
# For density map, cannot currently perform a check, since there is no
# guarantee that the max and min voxel values may be non atom voxels and
# thus removed
if self.mapType in ('atom_map'):
if max(density) == rho.maxdensity:
print 'calculated max voxel value match value stated in file header'
else:
print 'calculated max voxel value does NOT match value stated in file header'
print 'have now calculated max voxel value to be: %s'\
%str(max(density))
sys.exit()
# if each voxel value is an atom number, then want to convert to integer
if self.mapType in ('atom_map'):
density_final = [int(dens)/100 for dens in density]
elif self.mapType in ('density_map'):
density_final = density
else:
print 'Unknown map type --> terminating script'
sys.exit()
rho.vxls_val = density_final
self.rho = rho
def densmap2class_readheader(mapfilename):
# define 'rho' electron map object
rho = electron_map_info()
# open electron density .map file here
binarymapfile = open(mapfilename,'rb')
# start adding header information into electron_map_info class format.
# Note the unpacking of a struct for each byte, read as a long 'l'
rho.nx = struct.unpack('=l',binarymapfile.read(4))[0]
rho.ny = struct.unpack('=l',binarymapfile.read(4))[0]
rho.nz = struct.unpack('=l',binarymapfile.read(4))[0]
rho.type = struct.unpack('=l',binarymapfile.read(4))[0]
print 'Num. Col, Row, Sec: '
print '%s %s %s' %(rho.nx,rho.ny,rho.nz)
# currently can't handle type 1 maps:
if rho.type == 1:
print 'Map type 1 found... can only handle type 2'
print '---> terminating script...'
sys.exit()
rho.start1 = struct.unpack('=l',binarymapfile.read(4))[0]
rho.start2 = struct.unpack('=l',binarymapfile.read(4))[0]
rho.start3 = struct.unpack('=l',binarymapfile.read(4))[0]
print 'Start positions: '
print '%s %s %s' %(rho.start1,rho.start2,rho.start3)
rho.gridsamp1 = struct.unpack('=l',binarymapfile.read(4))[0]
rho.gridsamp2 = struct.unpack('=l',binarymapfile.read(4))[0]
rho.gridsamp3 = struct.unpack('=l',binarymapfile.read(4))[0]
print 'Grid sampling:'
print '%s %s %s' %(rho.gridsamp1,rho.gridsamp2,rho.gridsamp3)
# for cell dimensions, stored in header file as float not long
# integer so must account for this
rho.celldim_a = struct.unpack('f',binarymapfile.read(4))[0]
rho.celldim_b = struct.unpack('f',binarymapfile.read(4))[0]
rho.celldim_c = struct.unpack('f',binarymapfile.read(4))[0]
rho.celldim_alpha = struct.unpack('f',binarymapfile.read(4))[0]
rho.celldim_beta = struct.unpack('f',binarymapfile.read(4))[0]
rho.celldim_gamma = struct.unpack('f',binarymapfile.read(4))[0]
print 'Cell dimensions:'
print '%s %s %s' %(rho.celldim_a,rho.celldim_b,rho.celldim_c)
print '%s %s %s' %(rho.celldim_alpha,rho.celldim_beta,rho.celldim_gamma)
rho.fast_axis = struct.unpack('=l',binarymapfile.read(4))[0]
rho.med_axis = struct.unpack('=l',binarymapfile.read(4))[0]
rho.slow_axis = struct.unpack('=l',binarymapfile.read(4))[0]
print 'Fast,med,slow axes: '
print '%s %s %s' %(rho.fast_axis,rho.med_axis,rho.slow_axis)
rho.mindensity = struct.unpack('f',binarymapfile.read(4))[0]
rho.maxdensity = struct.unpack('f',binarymapfile.read(4))[0]
rho.meandensity = struct.unpack('f',binarymapfile.read(4))[0]
print 'Density values: '
print '%s %s %s' %(rho.mindensity,rho.maxdensity,rho.meandensity)
# next find .map file size, to calculate the last nx*ny*nz bytes of
# file (corresponding to the position of the 3D electron density
# array). Note factor of 4 is included since 4-byte floats used for
# electron density array values.
filesize = os.path.getsize(mapfilename)
densitystart = filesize - 4*(rho.nx*rho.ny*rho.nz)
return rho, densitystart