def get_map_data_and_symmetry(crystal_symmetry=None,
map_data=None,
map_coeffs=None,
map_file=None,
map_coeffs_file=None,
map_coeffs_labels=None,
out=sys.stdout):
if map_file:
from cctbx.maptbx.segment_and_split_map import get_map_object
map_data,space_group,unit_cell,crystal_symmetry,origin_frac,acc,\
original_crystal_symmetry,original_unit_cell_grid=\
get_map_object(file_name=map_file,out=out)
map_data = map_data.as_double()
if not map_data:
if not map_coeffs:
map_coeffs = get_map_coeffs(map_coeffs_file=map_coeffs_file,
map_coeffs_labels=map_coeffs_labels)
if not map_coeffs:
raise Sorry("Need map_coeffs_file")
fft_map = map_coeffs.fft_map(resolution_factor=0.25)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
if map_coeffs and not crystal_symmetry:
crystal_symmetry = map_coeffs.crystal_symmetry()
assert crystal_symmetry is not None
return map_data, map_coeffs, crystal_symmetry
def get_map(params=None, out=sys.stdout):
if params.input_files.map_file:
from cctbx.maptbx.segment_and_split_map import get_map_object
map_data, space_group, unit_cell, crystal_symmetry, origin_frac = get_map_object(
file_name=params.input_files.map_file, out=out)
map_data = map_data.as_double()
elif params.input_files.map_coeffs_file:
map_coeffs = get_map_coeffs_from_file(
map_coeffs_file=params.input_files.map_coeffs_file,
map_coeffs_labels=params.input_files.map_coeffs_labels)
if not map_coeffs:
raise Sorry("Could not get map coeffs from %s with labels %s" %
(params.input_files.map_coeffs_file,
params.input_files.map_coeffs_labels))
print >> out, "Map coefficients read from %s with labels %s" % (
params.input_files.map_coeffs_file,
str(params.input_files.map_coeffs_labels))
crystal_symmetry = map_coeffs.crystal_symmetry()
from cctbx.maptbx.segment_and_split_map import get_map_from_map_coeffs
map_data = get_map_from_map_coeffs(map_coeffs=map_coeffs,
crystal_symmetry=crystal_symmetry)
if not params.crystal_info.resolution:
params.crystal_info.resolution = map_coeffs.d_min()
print >> out, "Resolution from map_coeffs is %7.2f A" % (
params.crystal_info.resolution)
else:
raise Sorry("Need ccp4 map or map_coeffs")
if params.crystal_info.resolution is None:
raise Sorry("Need resolution if map is supplied")
return map_data, crystal_symmetry
def get_map(params=None,out=sys.stdout):
if params.input_files.map_file:
from cctbx.maptbx.segment_and_split_map import get_map_object
map_data,space_group,unit_cell,crystal_symmetry,origin_frac=get_map_object(
file_name=params.input_files.map_file,out=out)
map_data=map_data.as_double()
elif params.input_files.map_coeffs_file:
map_coeffs=get_map_coeffs_from_file(
map_coeffs_file=params.input_files.map_coeffs_file,
map_coeffs_labels=params.input_files.map_coeffs_labels)
if not map_coeffs:
raise Sorry("Could not get map coeffs from %s with labels %s" %(
params.input_files.map_coeffs_file,params.input_files.map_coeffs_labels))
print >>out,"Map coefficients read from %s with labels %s" %(
params.input_files.map_coeffs_file,
str(params.input_files.map_coeffs_labels))
crystal_symmetry=map_coeffs.crystal_symmetry()
from cctbx.maptbx.segment_and_split_map import get_map_from_map_coeffs
map_data=get_map_from_map_coeffs(
map_coeffs=map_coeffs,crystal_symmetry=crystal_symmetry)
if not params.crystal_info.resolution:
params.crystal_info.resolution=map_coeffs.d_min()
print >>out,"Resolution from map_coeffs is %7.2f A" %(
params.crystal_info.resolution)
else:
raise Sorry("Need ccp4 map or map_coeffs")
if params.crystal_info.resolution is None:
raise Sorry("Need resolution if map is supplied")
return map_data,crystal_symmetry
def get_map_and_model(params=None,
map_data=None,
crystal_symmetry=None,
pdb_inp=None,
ncs_obj=None,
half_map_data_list=None,
map_coords_inside_cell=True,
get_map_labels=None,
out=sys.stdout):
acc=None # accessor used to shift map back to original location if desired
origin_frac=(0,0,0)
map_labels=None
if map_data and crystal_symmetry:
original_crystal_symmetry=crystal_symmetry
original_unit_cell_grid=None
acc=map_data.accessor()
shift_needed = not \
(map_data.focus_size_1d() > 0 and map_data.nd() == 3 and
map_data.is_0_based())
if(shift_needed):
origin_shift=(
map_data.origin()[0]/map_data.all()[0],
map_data.origin()[1]/map_data.all()[1],
map_data.origin()[2]/map_data.all()[2])
origin_frac=origin_shift # NOTE: fraction of NEW cell
map_data = map_data.shift_origin()
else:
origin_frac=(0.,0.,0.)
elif params.input_files.map_file:
print >>out,"\nReading map from %s\n" %( params.input_files.map_file)
from cctbx.maptbx.segment_and_split_map import get_map_object
map_data,space_group,unit_cell,crystal_symmetry,origin_frac,acc,\
original_crystal_symmetry,original_unit_cell_grid,map_labels=\
get_map_object(file_name=params.input_files.map_file,
must_allow_sharpening=(not params.control.ignore_map_limitations),
get_map_labels=True,out=out)
map_data=map_data.as_double()
if origin_frac != (0,0,0) and acc is None:
print >>out,"\nWARNING: Unable to place output map at position of "+\
"input map though input map has non-zero origin at %s\n" %(
str(origin_frac))
elif params.input_files.map_coeffs_file:
map_coeffs=get_map_coeffs_from_file(
map_coeffs_file=params.input_files.map_coeffs_file,
map_coeffs_labels=params.input_files.map_coeffs_labels)
if not map_coeffs:
raise Sorry("Could not get map coeffs from %s with labels %s" %(
params.input_files.map_coeffs_file,params.input_files.map_coeffs_labels))
print >>out,"Map coefficients read from %s with labels %s" %(
params.input_files.map_coeffs_file,
str(params.input_files.map_coeffs_labels))
crystal_symmetry=map_coeffs.crystal_symmetry()
from cctbx.maptbx.segment_and_split_map import get_map_from_map_coeffs
map_data=get_map_from_map_coeffs(
map_coeffs=map_coeffs,crystal_symmetry=crystal_symmetry)
acc=map_data.accessor()
original_crystal_symmetry=crystal_symmetry
original_unit_cell_grid=None
if not params.crystal_info.resolution:
params.crystal_info.resolution=map_coeffs.d_min()
print >>out,"Resolution from map_coeffs is %7.2f A" %(
params.crystal_info.resolution)
else:
raise Sorry("Need ccp4 map or map_coeffs")
if params.input_files.half_map_file:
if len(params.input_files.half_map_file) != 2:
raise Sorry("Please supply zero or two half_map files")
half_map_data_list=[]
from cctbx.maptbx.segment_and_split_map import get_map_object
for file_name in params.input_files.half_map_file:
print >>out,"\nReading half-map from %s\n" %(file_name)
half_map_data,half_map_space_group,half_map_unit_cell,\
half_map_crystal_symmetry,half_map_origin_frac,half_map_acc,\
half_map_original_crystal_symmetry,half_map_original_unit_cell_grid=\
get_map_object(file_name=file_name,out=out)
half_map_data=half_map_data.as_double()
assert half_map_crystal_symmetry.is_similar_symmetry(crystal_symmetry)
half_map_data_list.append(half_map_data)
if params.crystal_info.resolution is None:
raise Sorry("Need resolution if map is supplied")
if params.crystal_info.resolution >= 10:
print >>out,"\n** WARNING: auto_sharpen is designed for maps at a "+\
"resolution of about 4.5 A\nor better. Sharpening may be"+\
"poor at %7.0f A" %(params.crystal_info.resolution)
if params.input_files.pdb_file and not pdb_inp: # get model
model_file=params.input_files.pdb_file
if not os.path.isfile(model_file):
raise Sorry("Missing the model file: %s" %(model_file))
pdb_inp=iotbx.pdb.input(file_name=model_file)
if pdb_inp: # XXX added 2019-05-05
if origin_frac != (0,0,0):
print >>out,"Shifting model by %s" %(str(origin_frac))
from cctbx.maptbx.segment_and_split_map import \
apply_shift_to_pdb_hierarchy
origin_shift=crystal_symmetry.unit_cell().orthogonalize(
(-origin_frac[0],-origin_frac[1],-origin_frac[2]))
pdb_inp=apply_shift_to_pdb_hierarchy(
origin_shift=origin_shift,
crystal_symmetry=crystal_symmetry,
pdb_hierarchy=pdb_inp.construct_hierarchy(),
out=out).as_pdb_input()
if map_coords_inside_cell:
# put inside (0,1)
pdb_inp=map_inside_cell(pdb_inp,crystal_symmetry=crystal_symmetry)
if params.input_files.ncs_file and not ncs_obj: # NCS
from cctbx.maptbx.segment_and_split_map import get_ncs
ncs_obj,dummy_tracking_data=get_ncs(params,out=out)
if origin_frac != (0,0,0):
origin_shift=crystal_symmetry.unit_cell().orthogonalize(
(-origin_frac[0],-origin_frac[1],-origin_frac[2]))
print >>out,"Shifting NCS by (%7.2f,%7.2f,%7.2f) " %((origin_shift))
from scitbx.math import matrix
ncs_obj=ncs_obj.coordinate_offset(
coordinate_offset=matrix.col(origin_shift))
if get_map_labels:
return pdb_inp,map_data,half_map_data_list,ncs_obj,crystal_symmetry,acc,\
original_crystal_symmetry,original_unit_cell_grid,map_labels
else:
return pdb_inp,map_data,half_map_data_list,ncs_obj,crystal_symmetry,acc,\
original_crystal_symmetry,original_unit_cell_grid
def get_map_and_model(params=None,
map_data=None,
crystal_symmetry=None,
pdb_inp=None,
ncs_obj=None,
half_map_data_list=None,
out=sys.stdout):
acc = None # accessor used to shift map back to original location if desired
origin_frac = (0, 0, 0)
acc = None
if map_data and crystal_symmetry:
pass # we are set
elif params.input_files.map_file:
print >> out, "\nReading map from %s\n" % (params.input_files.map_file)
from cctbx.maptbx.segment_and_split_map import get_map_object
map_data,space_group,unit_cell,crystal_symmetry,origin_frac,acc=\
get_map_object(file_name=params.input_files.map_file,out=out)
map_data = map_data.as_double()
if origin_frac != (0, 0, 0) and acc is None:
print >>out,"\nWARNING: Unable to place output map at position of "+\
"input map though input map has non-zero origin at %s\n" %(
str(origin_frac))
elif params.input_files.map_coeffs_file:
map_coeffs = get_map_coeffs_from_file(
map_coeffs_file=params.input_files.map_coeffs_file,
map_coeffs_labels=params.input_files.map_coeffs_labels)
if not map_coeffs:
raise Sorry("Could not get map coeffs from %s with labels %s" %
(params.input_files.map_coeffs_file,
params.input_files.map_coeffs_labels))
print >> out, "Map coefficients read from %s with labels %s" % (
params.input_files.map_coeffs_file,
str(params.input_files.map_coeffs_labels))
crystal_symmetry = map_coeffs.crystal_symmetry()
from cctbx.maptbx.segment_and_split_map import get_map_from_map_coeffs
map_data = get_map_from_map_coeffs(map_coeffs=map_coeffs,
crystal_symmetry=crystal_symmetry)
acc = map_data.accessor()
if not params.crystal_info.resolution:
params.crystal_info.resolution = map_coeffs.d_min()
print >> out, "Resolution from map_coeffs is %7.2f A" % (
params.crystal_info.resolution)
else:
raise Sorry("Need ccp4 map or map_coeffs")
if params.input_files.half_map_file:
if len(params.input_files.half_map_file) != 2:
raise Sorry("Please supply zero or two half_map files")
half_map_data_list = []
from cctbx.maptbx.segment_and_split_map import get_map_object
for file_name in params.input_files.half_map_file:
print >> out, "\nReading half-map from %s\n" % (file_name)
half_map_data,half_map_space_group,half_map_unit_cell,\
half_map_crystal_symmetry,half_map_origin_frac,half_map_acc=\
get_map_object(file_name=file_name,out=out)
half_map_data = half_map_data.as_double()
assert half_map_crystal_symmetry.is_similar_symmetry(
crystal_symmetry)
half_map_data_list.append(half_map_data)
if params.crystal_info.resolution is None:
raise Sorry("Need resolution if map is supplied")
if params.input_files.pdb_file and not pdb_inp: # get model
model_file = params.input_files.pdb_file
if not os.path.isfile(model_file):
raise Sorry("Missing the model file: %s" % (model_file))
pdb_inp = iotbx.pdb.input(file_name=model_file)
if origin_frac != (0, 0, 0):
print >> out, "Shifting model by %s" % (str(origin_frac))
from cctbx.maptbx.segment_and_split_map import \
apply_shift_to_pdb_hierarchy
origin_shift = crystal_symmetry.unit_cell().orthogonalize(
(-origin_frac[0], -origin_frac[1], -origin_frac[2]))
pdb_inp = apply_shift_to_pdb_hierarchy(
origin_shift=origin_shift,
crystal_symmetry=crystal_symmetry,
pdb_hierarchy=pdb_inp.construct_hierarchy(),
out=out).as_pdb_input()
if params.input_files.ncs_file and not ncs_obj: # NCS
from cctbx.maptbx.segment_and_split_map import get_ncs
ncs_obj, dummy_tracking_data = get_ncs(params, out=out)
if origin_frac != (0, 0, 0):
origin_shift = crystal_symmetry.unit_cell().orthogonalize(
(-origin_frac[0], -origin_frac[1], -origin_frac[2]))
print >> out, "Shifting NCS by (%7.2f,%7.2f,%7.2f) " % (
(origin_shift))
from scitbx.math import matrix
ncs_obj = ncs_obj.coordinate_offset(
coordinate_offset=matrix.col(origin_shift))
return pdb_inp, map_data, half_map_data_list, ncs_obj, crystal_symmetry, acc