def read_from_mtz(mtzin="", colin="F,SIGF"):
"""Reads reflection and sigmas, returns a HKL_data_F_sigF_float object
Parameters:
mtzin -- a string path to an MTZ file containing measured reflections
colin -- configurable column name, defaults to F,SIGF, could also be DANO,SIGDANO
callback -- a function that takes care of log string and xml flushing
Returns:
a plain text log string, an XML etree and a clipper.HKL_data_F_sigf object"""
log_string = "\n >> clipper_tools: io.structure_factors.read_from_mtz"
log_string += "\n mtzin: %s" % mtzin
xml_root = etree.Element('input_file')
xml_root.attrib['name'] = mtzin
xml_root.attrib['type'] = 'mini MTZ'
hkl_data = clipper.HKL_data_F_sigF_float()
hkl_info = clipper.HKL_info()
if mtzin is not "":
mtzfilein = clipper.CCP4MTZfile()
mtzfilein.open_read(mtzin)
mtzfilein.import_hkl_info(hkl_info, True)
mtzfilein.import_hkl_data(hkl_data, "*/*/[" + colin + "]")
else:
return log_string, xml_root, hkl_data, hkl_info
print(dir(hkl_data))
log_string += "\n << read_from_mtz has finished\n"
xml_root.attrib['ok'] = 'yes'
return log_string, xml_root, hkl_info, hkl_data
def __init__(self, mtz_in_path=None):
self.mtz = clipper.CCP4MTZfile()
self.hkl_info = clipper.HKL_info()
self.mtz_in_path = mtz_in_path
if self.mtz_in_path is not None:
assert os.path.exists(self.mtz_in_path)
self.spacegroup = None
self.cell = None
self.column_data = {}
def write_to_mtz(dataout=None, mtzout=''):
log_string = '\n >> clipper_tools: io.map_coefficients.write_to_mtz'
log_string += '\n mtzout: %s' % mtzout
xml_root = etree.Element('output_file')
xml_root.attrib['name'] = mtzout
xml_root.attrib['type'] = 'mini MTZ'
if dataout is not None and mtzout is not '':
mtzfileout = clipper.CCP4MTZfile()
mtzfileout.open_write(mtzout)
mtzfileout.export_hkl_info(dataout.hkl_info())
mtzfileout.export_hkl_data(dataout, '*/*/[F, PHI]')
mtzfileout.close_write()
xml_root.attrib['ok'] = 'yes'
else:
xml_root.attrib['ok'] = 'no'
log_string += '\n << write_to_mtz has finished\n'
return log_string, xml_root
def write_to_mtz(dataout=None, mtzout=""):
log_string = "\n >> clipper_tools: io.map_coefficients.write_to_mtz"
log_string += "\n mtzout: %s" % mtzout
xml_root = etree.Element('output_file')
xml_root.attrib['name'] = mtzout
xml_root.attrib['type'] = 'mini MTZ'
if dataout is not None and mtzout is not "":
mtzfileout = clipper.CCP4MTZfile()
mtzfileout.open_write(mtzout)
mtzfileout.export_hkl_info(dataout.hkl_info())
mtzfileout.export_hkl_data(dataout, "*/*/[F, PHI]")
mtzfileout.close_write()
xml_root.attrib['ok'] = "yes"
else:
xml_root.attrib['ok'] = "no"
log_string += "\n << write_to_mtz has finished\n"
return log_string, xml_root
def prepare_map(mapin='', resol=8.0, callback=_callbacks.interactive_flush):
"""Reads EM map, sets origin to 0, pads cell and computes finely-sampled structure factors
Parameters:
mapin -- a string path to a map that will be read into a clipper.NXmap_float object
resol -- estimated resolution (float)
callback -- a function that takes care of log string and xml flushing
Returns:
a plain text log string, an XML etree and a clipper.HKL_data_F_phi_float object"""
def determine_extent(numpy_in, tolerance):
"""Reads numpy array, determines the extent of the electron density
Parameters:
numpy_in -- a numpy array containing grid points
tolerance -- number of points in a plane with value greater than 1 sigma
Returns:
a vector of grid indices: (min_u, max_u, min_v, max_v, min_w, max_w)"""
log_string = ''
min = clipper.Coord_orth()
max = clipper.Coord_orth()
map_mean = numpy.mean(map_numpy)
map_std = numpy.std(map_numpy)
mask = map_numpy > map_mean + map_std
sum_u = sum(sum(mask))
sum_w = sum(sum(numpy.transpose(mask)))
sum_v = sum(numpy.transpose(sum(mask)))
log_string += '\n >> dumping 1D summaries of the map\'s content:\n\n >> U:\n %s\n' % sum_u
log_string += '\n >> V:\n %s\n' % sum_v
log_string += '\n >> W:\n %s\n' % sum_w
point_list = []
for idx_u, val_u in enumerate(sum_u):
if val_u > tolerance:
point_list.append(idx_u)
min_u = point_list[0]
max_u = point_list[-1]
log_string += '\n >> First meaningful U: %i ; Last meaningful U: %i' % (
min_u, max_u)
point_list = []
for idx_v, val_v in enumerate(sum_v):
if val_v > tolerance:
point_list.append(idx_v)
min_v = point_list[0]
max_v = point_list[-1]
log_string += '\n >> First meaningful V: %i ; Last meaningful V: %i' % (
min_v, max_v)
point_list = []
for idx_w, val_w in enumerate(sum_w):
if val_w > tolerance:
point_list.append(idx_w)
min_w = point_list[0]
max_w = point_list[-1]
log_string += '\n >> First meaningful W: %i ; Last meaningful W: %i\n' % (
min_w, max_w)
extent = [min_u, max_u, min_v, max_v, min_w, max_w]
return extent, log_string
################# end determine_extent ################
############### main function ################
# create log string so console-based apps get some feedback
log_string = '\n >> clipper_tools: mr_from_em.prepare_map'
log_string += '\n mapin: %s' % mapin
log_string += '\n resol: %s' % resol
# create XML tree, to be merged in a global structured results file
xml_root = etree.Element('structure_factors')
xml_root.attrib['mapin'] = mapin
xml_root.attrib['resol'] = str(resol)
callback(log_string, xml_root)
phaser_params = {}
nxmap = clipper.NXmap_double()
xmap = clipper.Xmap_double()
map_file = clipper.CCP4MAPfile()
sg = clipper.Spacegroup.p1()
resol *= 0.9
resolution = clipper.Resolution(resol)
# nothing in, nothing out
if mapin == '':
return log_string, xml_root, None
# read the cryoEM map into nxmap, get map data irrespective of origin
map_file.open_read(mapin)
map_file.import_nxmap_double(nxmap)
map_file.close_read()
log_string += '\n >> file %s has been read as nxmap' % mapin
callback(log_string, xml_root)
# read the cryoEM map into xmap to get cell dimensions, etc.
map_file.open_read(mapin)
map_file.import_xmap_double(xmap)
map_file.close_read()
log_string += '\n >> file %s has been read as xmap' % mapin
callback(log_string, xml_root)
log_string += '\n >> cell parameters: %s' % xmap.cell().format()
log_string += '\n original translation: %s' % nxmap.operator_orth_grid(
).trn()
# put map content in a numpy data structure
map_numpy = numpy.zeros(
(nxmap.grid().nu(), nxmap.grid().nv(), nxmap.grid().nw()),
dtype='double')
log_string += '\n >> exporting a numpy array of %i x %i x %i grid points' \
% (nxmap.grid().nu(), nxmap.grid().nv(), nxmap.grid().nw())
callback(log_string, xml_root)
data_points = nxmap.export_numpy(map_numpy)
log_string += '\n >> %i data points have been exported' % data_points
callback(log_string, xml_root)
map_mean = numpy.mean(map_numpy)
map_stdv = numpy.std(map_numpy)
log_string += '\n >> map mean (stdev): %.4f (%.4f)' % (map_mean, map_stdv)
# compute the extent
extent, temp_log = determine_extent(map_numpy, 30)
log_string += temp_log
extent_list = [
extent[1] - extent[0], extent[3] - extent[2], extent[5] - extent[4]
]
max_extent = max(extent_list)
# create padded xmap and import numpy array
origin_trans = clipper.vec3_double(
extent[0] + ((extent[1] - extent[0]) / 2),
extent[2] + ((extent[3] - extent[2]) / 2),
extent[4] + ((extent[5] - extent[4]) / 2))
large_a = (xmap.cell().a() *
(max_extent + xmap.grid_asu().nu())) / xmap.grid_asu().nu()
large_b = (xmap.cell().b() *
(max_extent + xmap.grid_asu().nv())) / xmap.grid_asu().nv()
large_c = (xmap.cell().c() *
(max_extent + xmap.grid_asu().nw())) / xmap.grid_asu().nw()
cell_desc = clipper.Cell_descr(large_a, large_b, large_c, \
xmap.cell().alpha(), xmap.cell().beta(), xmap.cell().gamma())
large_p1_cell = clipper.Cell(cell_desc)
large_grid_sampling = clipper.Grid_sampling(
max_extent + xmap.grid_asu().nu(), max_extent + xmap.grid_asu().nv(),
max_extent + xmap.grid_asu().nw())
large_xmap = clipper.Xmap_double(sg, large_p1_cell, large_grid_sampling)
log_string += '\n >> new grid: nu=%i nv=%i nw=%i' % (large_xmap.grid_asu(
).nu(), large_xmap.grid_asu().nv(), large_xmap.grid_asu().nw())
log_string += '\n >> putting map into a large p1 cell...'
log_string += '\n >> new cell parameters: %s' % large_p1_cell.format()
callback(log_string, xml_root)
large_xmap.import_numpy(map_numpy)
# dump map to disk
map_file = clipper.CCP4MAPfile()
map_file.open_write('mapout_padded.mrc')
map_file.export_xmap_double(large_xmap)
map_file.close_write()
log_string += '\n >> map file mapout_padded.mrc written to disk'
callback(log_string, xml_root)
# import it back to nxmap so we can trivially shift the origin
map_file.open_read('mapout_padded.mrc')
map_file.import_nxmap_double(nxmap)
map_file.close_read()
log_string += '\n >> file mapout_padded.mrc has been read back as nxmap'
callback(log_string, xml_root)
# now shift the origin
rtop_zero = clipper.RTop_double(nxmap.operator_orth_grid().rot(),
origin_trans)
log_string += '\n >> moving origin...'
log_string += '\n original translation: %s new origin: %s' % (
nxmap.operator_orth_grid().trn(), rtop_zero.trn())
callback(log_string, xml_root)
nxmap_zero = clipper.NXmap_double(nxmap.grid(), rtop_zero)
nxmap_zero.import_numpy(map_numpy)
# dump map to disk
map_file.open_write('mapout_padded_zero.mrc')
map_file.export_nxmap_double(nxmap_zero)
map_file.close_write()
log_string += '\n >> map file mapout_padded_zero.mrc written to disk'
callback(log_string, xml_root)
# read it back to an xmap so we can fft-it
new_xmap = clipper.Xmap_double()
map_file.open_read('mapout_padded_zero.mrc')
map_file.import_xmap_double(new_xmap)
map_file.close_read()
log_string += '\n >> map file mapout_padded_zero.mrc read back as xmap'
callback(log_string, xml_root)
# create HKL_info using user-supplied resolution parameter
hkl_info = clipper.HKL_info(sg, large_p1_cell, resolution, True)
# fft the map
f_phi = clipper.HKL_data_F_phi_float(hkl_info, large_p1_cell)
log_string += '\n >> now computing map coefficients to %0.1f A resolution...' % resol
callback(log_string, xml_root)
new_xmap.fft_to(f_phi)
log_string += '\n >> writing map coefficients to MTZ file mapout_padded_zero.mtz'
callback(log_string, xml_root)
# setup an MTZ file so we can export our map coefficients
mtzout = clipper.CCP4MTZfile()
mtzout.open_write('mapout_padded_zero.mtz')
mtzout.export_hkl_info(f_phi.hkl_info())
mtzout.export_hkl_data(f_phi, '*/*/[F, PHI]')
mtzout.close_write()
log_string += '\n >> all done'
callback(log_string, xml_root)
return log_string, xml_root, f_phi, phaser_params
arg += 1
limit_e = float(sys.argv[arg])
elif ( sys.argv[arg] == "-e-weight" ):
arg += 1
weight_e = float(sys.argv[arg])
elif ( sys.argv[arg] == "-anomalous" ):
adiff = True;
elif ( sys.argv[arg] == "-origin-removal" ):
oremv = True;
if len(sys.argv) <= 1:
print "Usage: cpatterson\n\t-mtzin <filename>\n\t-mapout <filename>\n\t-colin-fo <colpath>\n\t-colin-fano <colpath>\n\t-colin-fdiff <colpath>\n\t-resolution <reso>\n\t-grid <nu>,<nv>,<nw>\n\t-e-limit <limit>\n\t-e-weight <weight>\n\t-anomalous\n\t-origin-removal\nCalculate Patterson from Fobs or Fano.\nFor E-Patterson <weight> = 1, for F-Patterson <weight> = 0, and other values.\n<limit> can reject reflections or differences by E-value.\n";
sys.exit(1);
# make data objects
mtzin = clipper.CCP4MTZfile()
cxtl =clipper.MTZcrystal()
hkls = clipper.HKL_info()
hklp = clipper.HKL_info()
# typedef clipper::HKL_data_base::HKL_reference_index HRI; ??
mtzin.set_column_label_mode( clipper.CCP4MTZfile.Legacy );
# open file
mtzin.open_read( ipfile );
spgr = mtzin.spacegroup();
print spgr.symbol_hm()
cell = mtzin.cell();
print cell.a(),cell.b(),cell.c(),cell.alpha(),cell.beta(),cell.gamma()
if ( ipcolf != "NONE" ):
def smartSplitMTZ(inputFilePath=None,
inputColumnPath=None,
objectPath=None,
intoDirectory=None):
if inputFilePath is None:
raise Exception("smartSplitMTZ Exception:",
"Must provide an input file")
if not os.path.isfile(inputFilePath):
raise Exception("smartSplitMTZ Exception:",
"inputFile must exist" + str(inputFilePath))
if inputColumnPath is None:
raise Exception(
"smartSplitMTZ Exception:",
"Must provide an input columnPath e.g. '/*/*/[F,SIGFP]'")
if objectPath is not None and intoDirectory is not None:
raise Exception(
"smartSplitMTZ Exception:",
"Provide either full output path for file, or name of directory where file should be placed"
)
if objectPath is None and intoDirectory is None:
raise Exception(
"smartSplitMTZ Exception:",
"Provide either full output path for file, or name of directory where file should be placed"
)
mtz_file = clipper.CCP4MTZfile()
hkl_info = clipper.HKL_info()
mtz_file.open_read(inputFilePath)
mtz_file.import_hkl_info(hkl_info)
xtal = clipper.MTZcrystal()
mtz_file.import_crystal(xtal, inputColumnPath)
dataset = clipper.MTZdataset()
mtz_file.import_dataset(dataset, inputColumnPath)
providedColumnPaths = mtz_file.column_paths()
selectedColumnLabelsExp = re.compile(
r"^/(?P<XtalName>[A-Za-z0-9_. -+\*,]+)/(?P<DatasetName>[A-Za-z0-9_. -+\*,]+)/\[(?P<Columns>[A-Za-z0-9_. -+\*,]+)\]"
)
columnsMatch = selectedColumnLabelsExp.search(inputColumnPath)
selectedColumnLabelExp = re.compile(
r"^/(?P<XtalName>[A-Za-z0-9_. -+\*,]+)/(?P<DatasetName>[A-Za-z0-9_. -+\*,]+)/(?P<Column>[A-Za-z0-9_. -+\*,]+)"
)
columnMatch = selectedColumnLabelExp.search(inputColumnPath)
if columnsMatch is not None:
selectedColumnPaths = [
"/{}/{}/{}".format(columnsMatch.group("XtalName"),
columnsMatch.group("DatasetName"), column)
for column in columnsMatch.group("Columns").split(",")
]
elif columnMatch is not None:
selectedColumnPaths = [
"/{}/{}/{}".format(columnMatch.group("XtalName"),
columnMatch.group("DatasetName"),
columnMatch.group("Column"))
]
typeSignature = ""
for selectedColumnPath in selectedColumnPaths:
selectedColumnMatch = selectedColumnLabelExp.search(selectedColumnPath)
for providedColumnPath in providedColumnPaths:
#Generating clipper String and then calling str to deal with
#Known unpredictable bug in clipper-python
try:
columnName, columnType = str(
clipper.String(providedColumnPath)).split(" ")
except NotImplementedError as err:
columnName, columnType = str(providedColumnPath).split(" ")
parsedColumnMatch = selectedColumnLabelExp.search(columnName)
if ((selectedColumnMatch.group("XtalName") == "*"
or selectedColumnMatch.group("XtalName")
== parsedColumnMatch.group("XtalName"))
and (selectedColumnMatch.group("DatasetName") == "*"
or selectedColumnMatch.group("DatasetName")
== parsedColumnMatch.group("DatasetName"))
and selectedColumnMatch.group("Column")
== parsedColumnMatch.group("Column")):
typeSignature += columnType
break
if typeSignature == "FQ":
extractedData = clipper.HKL_data_F_sigF_float(hkl_info)
cls = CCP4XtalData.CObsDataFile
contentType = 4
if typeSignature == "JQ":
extractedData = clipper.HKL_data_I_sigI_float(hkl_info)
cls = CCP4XtalData.CObsDataFile
contentType = 3
if typeSignature == "GLGL" or typeSignature == "FQFQ":
extractedData = clipper.HKL_data_F_sigF_ano_float(hkl_info)
cls = CCP4XtalData.CObsDataFile
contentType = 2
if typeSignature == "KMKM" or typeSignature == "JQJQ":
extractedData = clipper.HKL_data_I_sigI_ano_float(hkl_info)
cls = CCP4XtalData.CObsDataFile
contentType = 1
elif typeSignature == "AAAA":
extractedData = clipper.HKL_data_ABCD_float(hkl_info)
cls = CCP4XtalData.CPhsDataFile
contentType = 1
elif typeSignature == "PW":
extractedData = clipper.HKL_data_Phi_fom_float(hkl_info)
cls = CCP4XtalData.CPhsDataFile
contentType = 2
elif typeSignature == "I":
extractedData = clipper.HKL_data_Flag(hkl_info)
cls = CCP4XtalData.CFreeRDataFile
contentType = 1
outputColumnPath = "[{}]".format(','.join(
getattr(cls, "CONTENT_SIGNATURE_LIST")[contentType - 1]))
mtz_file.import_hkl_data(extractedData, inputColumnPath)
mtz_file.close_read()
if intoDirectory is not None:
firstGuess = os.path.join(
intoDirectory,
typeSignature + '_ColumnsFrom_' + os.path.split(inputFilePath)[1])
objectPath = availableNameBasedOn(firstGuess)
mtzout = clipper.CCP4MTZfile()
mtzout.open_write(objectPath)
mtzout.export_hkl_info(hkl_info)
outputColumnPath = "/{}/{}/{}".format(str(xtal.crystal_name()),
str(dataset.dataset_name()),
outputColumnPath)
mtzout.export_crystal(xtal, outputColumnPath)
mtzout.export_dataset(dataset, outputColumnPath)
mtzout.export_hkl_data(extractedData, outputColumnPath)
mtzout.close_write()
return objectPath