def readMap(dirIn='./', dirOut='./', mapName='untitled.map',
mapType='atom_map', atomInds=[], log='',
standardise=False, fixMaxMapVal=''):
# a function to read in a .map file of either density or atom-tagged type
# define 'rho' electron map object
rho = MapInfo()
mapName = dirIn + mapName
filesize = os.path.getsize(mapName)
log.writeToLog(str='Map file of size {} bytes to be read'.format(filesize))
# open electron density .map file here (bmf for binary map file)
if os.name != 'nt':
with open(mapName) as f:
bmf = mmap.mmap(
f.fileno(), 0, prot=mmap.PROT_READ, flags=mmap.MAP_PRIVATE)
else:
with open(mapName, "r+b") as f:
bmf = mmap.mmap(f.fileno(), 0)
# start adding header information into MapInfo class format.
# Note the unpacking of a struct for each byte, read as a long 'l'
for n in ('nx', 'ny', 'nz'):
rho.nxyz[n] = unpack('=l', bmf.read(4))[0]
rho.type = unpack('=l', bmf.read(4))[0]
for s in ('fast', 'med', 'slow'):
rho.start[s] = unpack('=l', bmf.read(4))[0]
for g in ('1', '2', '3'):
rho.gridsamp[g] = unpack('=l', bmf.read(4))[0]
for d in ('a', 'b', 'c', 'alpha', 'beta', 'gamma'):
# cell dims stored as float not long int
rho.celldims[d] = unpack('f', bmf.read(4))[0]
for a in ('fast', 'med', 'slow'):
rho.axis[a] = unpack('=l', bmf.read(4))[0]
for d in ('min', 'max', 'mean'):
rho.density[d] = unpack('f', bmf.read(4))[0]
s = rho.getHeaderInfo(tab=True)
# write to log file if specified
if log != '':
if os.path.exists(log.logFile):
for l in s.split('\n'):
log.writeToLog(l, priority='minor')
else:
print(s)
# 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.
densitystart = filesize - 4*(reduce(lambda x, y: x*y, list(rho.nxyz.values())))
# if sys.version_info[0] >= 3:
# import functools
# densitystart = filesize - 4*(functools.reduce(lambda x, y: x*y, list(rho.nxyz.values())))
# else:
# densitystart = filesize - 4*(reduce(lambda x, y: x*y, list(rho.nxyz.values())))
# get symmetry operations from map header
for j in range(23, 58):
if j != 53 and j < 57:
if j != 55:
val = unpack('=l', bmf.read(4))[0]
else:
val = unpack('=f', bmf.read(4))[0]
if j == 24:
numSymBytes = val
if j == 55:
mapStdev = round(val, 5)
elif j < 57:
for i in range(4):
val = unpack('c', bmf.read(1))[0]
else:
for i in range(10):
for k in range(80):
char = unpack('c', bmf.read(1))[0]
symOps = []
for j in range(numSymBytes // 80):
line = ''
for k in range(80):
char = unpack('=c', bmf.read(1))[0].decode("utf-8")
line += char
symOps.append(line)
rho.curateSymOps(symOps)
# next seek start of electron density data
bmf.seek(densitystart, 0)
# if electron density written in shorts this is not
# currently expected, so program will halt
if rho.type == 1:
error(text='Untested .map type --> 1 (type 2 expected). ' +
'Values read as int16 ("i2?") - consult .map header in ' +
'MAPDUMP(CCP4) to check', log=log, type='error')
# if electron density written in floats (which is to be expected
# from FFT-CCP4 outputted .map file of electron density)
if rho.type == 2:
# the length of the each data chunk to read map voxels below
struct_fmt = '=f'
struct_len = calcsize(struct_fmt)
# should get struct_len = 4
if struct_len != 4:
error(text='Bad data chunk length assigned when reading map',
log=log, type='error')
density = []
appenddens = density.append
if mapType in ('atom_map'):
atomInds = []
appendindex = atomInds.append
counter = -1
while True:
data = bmf.read(struct_len)
if not data:
break
s = unpack(struct_fmt, data)[0]
counter += 1
if int(s) == 0:
continue
else:
appenddens(s)
appendindex(counter)
log.writeToLog(str='# voxels in total : {}'.format(counter + 1))
# efficient way to read through density map file
# using indices of atoms from atom map file above
elif mapType in ('density_map'):
for i in range(0, len(atomInds)):
if i != 0:
bmf.read(struct_len*(atomInds[i]-atomInds[i-1] - 1))
else:
bmf.read(struct_len*(atomInds[0]))
data = bmf.read(struct_len)
s = unpack(struct_fmt, data)[0]
appenddens(s)
# check that resulting list of same length as atomInds
if len(density) != len(atomInds):
error(text='Failure to process the density map ' +
'using atom-tagged map', log=log, type='error')
# UNCOMMENT TO INSTEAD READ IN ALL VOXELS
# while True:
# data = bmf.read(struct_len)
# if not data: break
# s = unpack(struct_fmt,data)[0]
# appenddens(s)
else:
error(text='Unknown map type!', log=log, type='error')
bmf.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 mapType in ('atom_map'):
if max(density) == rho.density['max']:
log.writeToLog(
str='calculated max voxel value match value ' +
'stated in file header')
else:
error(
text='Calculated max voxel value:{} does NOT '.format(
max(density)) +
'match value stated in file header:{}'.format(
rho.density['max']),
log=log, type='error')
# if each voxel value is an atom number, then want to convert to integer
if mapType in ('atom_map'):
density_final = [int(dens // 100) for dens in density]
elif mapType in ('density_map'):
density_final = density
else:
error(text='Unknown map type!', log=log, type='error')
# provide option to standardise density to map mean and standard deviation
if standardise and mapType in ('density_map'):
density_final = (np.array(density_final)-rho.density['mean'])/mapStdev
if fixMaxMapVal != '':
density_final /= np.max(np.absolute(density_final))
if fixMaxMapVal == 'rand':
fixMaxMapVal = np.random.uniform(6, 10)
log.writeToLog(
str='Random max map value chosen to be {}'.format(
fixMaxMapVal))
density_final *= fixMaxMapVal
density_final = density_final.tolist()
rho.vxls_val = density_final
if mapType in ('atom_map'):
return rho, atomInds
else:
return rho
def readMap(where,pdbname,mapfilename,maptype,atom_indices):
# append to log file for this eTrack run
logfileName = '{}output/{}_log.txt'.format(where,pdbname)
logfile = open(logfileName,'a')
# define 'rho' electron map object
rho = MapInfo()
# open electron density .map file here (bmf for binary map file)
bmf = open(where+mapfilename,'rb')
# start adding header information into MapInfo class format.
# Note the unpacking of a struct for each byte, read as a long 'l'
for n in ('nx','ny','nz'):
rho.nxyz[n] = struct.unpack('=l',bmf.read(4))[0]
print 'Num. Col, Row, Sec: '
print '{} {} {}'.format(*rho.nxyz.values())
logfile.write('Num. Col, Row, Sec: {} {} {}\n'.format(*rho.nxyz.values()))
rho.type = struct.unpack('=l',bmf.read(4))[0]
for s in ('1','2','3'):
rho.start[s] = struct.unpack('=l',bmf.read(4))[0]
print 'Start positions: '
print '{} {} {}'.format(*rho.start.values())
logfile.write('Start positions: {} {} {}\n'.format(*rho.start.values()))
for g in ('1','2','3'):
rho.gridsamp[g] = struct.unpack('=l',bmf.read(4))[0]
print 'Grid sampling:'
print '{} {} {}'.format(*rho.gridsamp.values())
logfile.write('Grid sampling: {} {} {}\n'.format(*rho.gridsamp.values()))
# for cell dimensions, stored in header file as float not long
# integer so must account for this
for d in ('a','b','c','alpha','beta','gamma'):
rho.celldims[d] = struct.unpack('f',bmf.read(4))[0]
print 'Cell dimensions:'
print '{} {} {}'.format(*rho.gridsamp.values()[0:3])
print '{} {} {}'.format(*rho.gridsamp.values()[3:6])
logfile.write('Cell dimensions: {} {} {} {} {} {}\n'.format(*rho.gridsamp.values()))
for a in ('fast','med','slow'):
rho.axis[a] = struct.unpack('=l',bmf.read(4))[0]
print 'Fast,med,slow axes: '
print '{} {} {}'.format(*rho.axis.values())
logfile.write('Fast,med,slow axes: {} {} {}\n'.format(*rho.axis.values()))
for d in ('min','max','mean'):
rho.density[d] = struct.unpack('f',bmf.read(4))[0]
print 'Density values: '
print '{} {} {}'.format(*rho.density.values())
logfile.write('Density values: {} {} {}\n'.format(*rho.density.values()))
# 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(where+mapfilename)
densitystart = filesize - 4*(rho.nx*rho.ny*rho.nz)
# next seek start of electron density data
bmf.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 = bmf.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 maptype in ('atom_map'):
atom_indices = []
appendindex = atom_indices.append
counter = -1
while True:
data = bmf.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 maptype in ('density_map'):
for i in range(0,len(atom_indices)):
if i != 0:
bmf.read(struct_len*(atom_indices[i]-atom_indices[i-1] - 1))
else:
bmf.read(struct_len*(atom_indices[0]))
data = bmf.read(struct_len)
s = struct.unpack(struct_fmt,data)[0]
appenddens(s)
else:
print 'Unknown map type --> terminating script'
sys.exit()
logfile.close()
bmf.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 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 maptype in ('atom_map'):
density_final = [int(dens)/100 for dens in density]
elif maptype in ('density_map'):
density_final = density
else:
print 'Unknown map type --> terminating script'
sys.exit()
rho.vxls_val = density_final
if maptype in ('atom_map'):
return rho,atom_indices
else:
return rho
def readMap(dirIn = './',
dirOut = './',
mapName = 'untitled.map',
mapType = 'atom_map',
atomInds = [],
log = ''):
# define 'rho' electron map object
rho = MapInfo()
mapName = dirIn + mapName
filesize = os.path.getsize(mapName)
ln = 'Map file of size {} bytes to be read'.format(filesize)
log.writeToLog(str = ln)
# open electron density .map file here (bmf for binary map file)
if os.name != 'nt': # if not windows
with open( mapName ) as f:
bmf = mmap.mmap( f.fileno(), 0, prot = mmap.PROT_READ, flags = mmap.MAP_PRIVATE )
else:
with open( mapName ,"r+b") as f:
bmf = mmap.mmap( f.fileno(), 0)
# start adding header information into MapInfo class format.
# Note the unpacking of a struct for each byte, read as a long 'l'
for n in ('nx','ny','nz'):
rho.nxyz[n] = unpack('=l',bmf.read(4))[0]
rho.type = unpack('=l',bmf.read(4))[0]
for s in ('fast','med','slow'):
rho.start[s] = unpack('=l',bmf.read(4))[0]
for g in ('1','2','3'):
rho.gridsamp[g] = unpack('=l',bmf.read(4))[0]
for d in ('a','b','c','alpha','beta','gamma'):
rho.celldims[d] = unpack('f',bmf.read(4))[0] # cell dims stored as float not long int
for a in ('fast','med','slow'):
rho.axis[a] = unpack('=l',bmf.read(4))[0]
for d in ('min','max','mean'):
rho.density[d] = unpack('f',bmf.read(4))[0]
s = rho.getHeaderInfo(tab = True)
# write to log file if specified
if log != '':
if os.path.exists(log.logFile):
for l in s.split('\n'): log.writeToLog(l)
else:
print s
# 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.
densitystart = filesize - 4*(reduce(lambda x, y: x*y, rho.nxyz.values()))
# get symmetry operations from map header
for j in range(23,58):
if j != 53 and j < 57:
val = unpack('=l',bmf.read(4))[0]
if j == 24:
numSymBytes = val
elif j < 57:
for i in range(4):
val = unpack('c',bmf.read(1))[0]
else:
for i in range(10):
for k in range(80):
char = unpack('c',bmf.read(1))[0]
symOps = []
for j in range(numSymBytes/80):
line = ''
for k in range(80):
char = unpack('c',bmf.read(1))[0]
line += char
symOps.append(line)
rho.curateSymOps(symOps)
# next seek start of electron density data
bmf.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:
err = 'Untested .map type --> 1 (type 2 expected). Values read'+\
'as int16 ("i2?") - consult .map header in MAPDUMP(CCP4) to check'
log.writeToLog(str = err)
struct_fmt = '=i2'
struct_len = calcsize(struct_fmt)
density = []
while True:
data = bmf.read(struct_len)
if not data: break
s = 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 = calcsize(struct_fmt)
density = []
appenddens = density.append
if mapType in ('atom_map'):
atomInds = []
appendindex = atomInds.append
counter = -1
while True:
data = bmf.read(struct_len)
if not data: break
s = unpack(struct_fmt,data)[0]
counter += 1
if int(s) == 0:
continue
else:
appenddens(s)
appendindex(counter)
ln = '# voxels in total : {}'.format(counter + 1)
log.writeToLog(str = ln)
# efficient way to read through density map file using indices of atoms
# from atom map file above
elif mapType in ('density_map'):
for i in range(0,len(atomInds)):
if i != 0:
bmf.read(struct_len*(atomInds[i]-atomInds[i-1] - 1))
else:
bmf.read(struct_len*(atomInds[0]))
data = bmf.read(struct_len)
s = unpack(struct_fmt,data)[0]
appenddens(s)
# check that resulting list of same length as atomInds
if len(density) != len(atomInds):
err = 'Error in processing of density map using atom-tagged map'
log.writeToLog(str = err)
sys.exit()
else:
err = 'Unknown map type --> terminating script'
log.writeToLog(str = err)
sys.exit()
bmf.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 mapType in ('atom_map'):
if max(density) == rho.density['max']:
ln = 'calculated max voxel value match value stated in file header'
log.writeToLog(str = ln)
else:
err = 'calculated max voxel value:{} does NOT '.format(max(density))+\
'match value stated in file header:{}'.format(rho.density['max'])
log.writeToLog(str = err)
sys.exit()
# if each voxel value is an atom number, then want to convert to integer
if mapType in ('atom_map'):
density_final = [int(dens)/100 for dens in density]
elif mapType in ('density_map'):
density_final = density
else:
err = 'Unknown map type --> terminating script'
log.writeToLog(str = err)
sys.exit()
rho.vxls_val = density_final
if mapType in ('atom_map'):
return rho,atomInds
else:
return rho
def readMap(dirIn,dirOut,pdbname,mapfilename,maptype,atom_indices):
# append to log file for this eTrack run
logfileName = '{}{}_log.txt'.format(dirOut,pdbname)
logfile = open(logfileName,'a')
# define 'rho' electron map object
rho = MapInfo()
# open electron density .map file here (bmf for binary map file)
# bmf = open(where+mapfilename,'rb')
mapName = dirIn+mapfilename
with open( mapName ) as f:
bmf = mmap.mmap( f.fileno(), 0, prot = mmap.PROT_READ, flags = mmap.MAP_PRIVATE )
# start adding header information into MapInfo class format.
# Note the unpacking of a struct for each byte, read as a long 'l'
for n in ('nx','ny','nz'):
rho.nxyz[n] = unpack('=l',bmf.read(4))[0]
rho.type = unpack('=l',bmf.read(4))[0]
for s in ('1','2','3'):
rho.start[s] = unpack('=l',bmf.read(4))[0]
for g in ('1','2','3'):
rho.gridsamp[g] = unpack('=l',bmf.read(4))[0]
for d in ('a','b','c','alpha','beta','gamma'):
rho.celldims[d] = unpack('f',bmf.read(4))[0] # cell dims stored as float not long int
for a in ('fast','med','slow'):
rho.axis[a] = unpack('=l',bmf.read(4))[0]
for d in ('min','max','mean'):
rho.density[d] = unpack('f',bmf.read(4))[0]
s = rho.getHeaderInfo()
logfile.write(s)
# 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(dirIn+mapfilename)
densitystart = filesize - 4*(reduce(lambda x, y: x*y, rho.nxyz.values()))
# next seek start of electron density data
bmf.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 = calcsize(struct_fmt)
density = []
while True:
data = bmf.read(struct_len)
if not data: break
s = 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 = calcsize(struct_fmt)
density = []
appenddens = density.append
if maptype in ('atom_map'):
atom_indices = []
appendindex = atom_indices.append
counter = -1
while True:
data = bmf.read(struct_len)
if not data: break
s = unpack(struct_fmt,data)[0]
counter += 1
if int(s) == 0:
continue
else:
appenddens(s)
appendindex(counter)
print '# voxels in total : {}'.format(counter+1)
# efficient way to read through density map file using indices of atoms
# from atom map file above
elif maptype in ('density_map'):
for i in range(0,len(atom_indices)):
if i != 0:
bmf.read(struct_len*(atom_indices[i]-atom_indices[i-1] - 1))
else:
bmf.read(struct_len*(atom_indices[0]))
data = bmf.read(struct_len)
s = unpack(struct_fmt,data)[0]
appenddens(s)
# check that resulting list of same length as atom_indices
if len(density) != len(atom_indices):
print 'Error in processing of density map using atom-tagged map'
sys.exit()
else:
print 'Unknown map type --> terminating script'
sys.exit()
logfile.close()
bmf.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 maptype in ('atom_map'):
if max(density) == rho.density['max']:
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:{}'.format(max(density),rho.density['max'])
sys.exit()
# if each voxel value is an atom number, then want to convert to integer
if maptype in ('atom_map'):
density_final = [int(dens)/100 for dens in density]
elif maptype in ('density_map'):
density_final = density
else:
print 'Unknown map type --> terminating script'
sys.exit()
rho.vxls_val = density_final
if maptype in ('atom_map'):
return rho,atom_indices
else:
return rho
