def xds2mtz(xds_file, dir_name, hklout=None, run_xtriage=False, run_ctruncate=False, dmin=None, dmax=None, force_anomalous=False):
if hklout is None:
hklout = os.path.splitext(os.path.basename(xds_file))[0] + ".mtz"
# if output file already exists, exit.
if os.path.isfile(os.path.join(dir_name, hklout)):
raise Exception(os.path.join(dir_name, hklout), "already exists.")
# read header
header = {}
for l in open(xds_file):
if l.startswith("!END_OF_HEADER"):
break
headers = re_xds_kwd.findall(l[l.index("!")+1:])
for k, v in headers:
if k == "FRIEDEL'S_LAW":
header["FRIEDEL'S_LAW"] = v.strip()
if k == "SPACE_GROUP_NUMBER":
header["SPACE_GROUP_NUMBER"] = v.strip()
if k == "X-RAY_WAVELENGTH":
header["X-RAY_WAVELENGTH"] = v.strip() # XXX could be wrong if XSCALE result
if force_anomalous:
header["FRIEDEL'S_LAW"] = "FALSE"
# make output directory
if not os.path.isdir(dir_name):
os.makedirs(dir_name)
logout = open(os.path.join(dir_name, "xds2mtz.log"), "w")
print >>logout, "xds2mtz.py running in %s" % os.getcwd()
print >>logout, "output directory: %s" % dir_name
print >>logout, "original file: %s" % xds_file
print "Header information read from", xds_file
for k in header:
print k, "=", header[k]
print
##
# convert to MTZ
print >>logout, "FRIEDEL'S_LAW= %s" % header["FRIEDEL'S_LAW"]
print >>logout, ""
logout.flush()
if header["FRIEDEL'S_LAW"] == "TRUE":
print xds_file, "is not anomalous dataset."
print
xds2mtz_normal(xds_file,
mtzout=os.path.join(dir_name, hklout),
sg=header["SPACE_GROUP_NUMBER"],
wavelen=header.get("X-RAY_WAVELENGTH","0"),
logout=logout,
use_ctruncate=run_ctruncate,
dmin=dmin, dmax=dmax)
if run_xtriage:
print "Running xtriage.."
run_xtriage_in_module_if_possible(args=[hklout], wdir=dir_name)
else:
print xds_file, "is anomalous dataset."
print
xds2mtz_anom(xds_file,
mtzout=os.path.join(dir_name, hklout),
sg=header["SPACE_GROUP_NUMBER"],
wavelen=header.get("X-RAY_WAVELENGTH","0"),
logout=logout,
use_ctruncate=run_ctruncate,
dmin=dmin, dmax=dmax)
if run_xtriage:
print "Running xtriage.."
run_xtriage_in_module_if_possible(args=[hklout, 'input.xray_data.obs_labels="I(+),SIGI(+),I(-),SIGI(-)"'],
wdir=dir_name)
def read_header(self):
re_item = re.compile("!ITEM_([^=]+)=([0-9]+)")
colindex = {} # {"H":1, "K":2, "L":3, ...}
nitemfound = 0
flag_data_start = False
num_hkl = 0
headers = []
for line in open(self._filein):
if flag_data_start:
if line.startswith("!END_OF_DATA"):
break
num_hkl += 1
continue
if line.startswith('!END_OF_HEADER'):
flag_data_start = True
continue
if line.startswith("! ISET="):
pars = dict(re_xds_kwd.findall(line))
iset = int(pars["ISET"])
if iset not in self.input_files: self.input_files[iset] = [None, None]
if "INPUT_FILE" in pars:
self.input_files[iset][0] = pars["INPUT_FILE"]
elif "X-RAY_WAVELENGTH" in pars:
tmp = pars["X-RAY_WAVELENGTH"]
if " (" in tmp: tmp = tmp[:tmp.index(" (")]
self.input_files[iset][1] = tmp
else:
headers.extend(re_xds_kwd.findall(line[line.index("!")+1:]))
self.nx, self.ny, self.anomalous, self.zmin, self.zmax = (None,)*5
for key, val in headers:
if key == "NUMBER_OF_ITEMS_IN_EACH_DATA_RECORD":
nitem = int(val.strip())
print >>self._log, 'number of items according to header is', nitem
elif key == "UNIT_CELL_CONSTANTS":
a, b, c, al, be, ga = map(lambda x:float(x), val.strip().split())
elif key == "UNIT_CELL_A-AXIS":
self.a_axis = tuple(map(float, val.split()))
elif key == "UNIT_CELL_B-AXIS":
self.b_axis = tuple(map(float, val.split()))
elif key == "UNIT_CELL_C-AXIS":
self.c_axis = tuple(map(float, val.split()))
elif key.startswith("ITEM_"):
item, ind = key[len("ITEM_"):], int(val)
colindex[item] = ind - 1
nitemfound += 1
elif key == "NX":
self.nx = int(val)
elif key == "NY":
self.ny = int(val)
elif key == "QX":
self.qx = float(val)
elif key == "QY":
self.qy = float(val)
elif key == "ORGX":
self.orgx = float(val)
elif key == "ORGY":
self.orgy = float(val)
elif key == "DATA_RANGE":
self.zmin, self.zmax = map(lambda x:int(x), val.strip().split())
elif key == "SPACE_GROUP_NUMBER":
ispgrp = int(val.strip())
elif key == "FRIEDEL'S_LAW":
assert val.strip() in ("TRUE", "FALSE")
self.anomalous = val.strip() == "FALSE"
elif key == "DETECTOR_DISTANCE":
self.distance = float(val)
elif key == "X-RAY_WAVELENGTH":
self.wavelength = float(val.split()[0])
elif key == "INCIDENT_BEAM_DIRECTION":
self.incident_axis = tuple(map(float, val.split()))
elif key == "ROTATION_AXIS":
self.rotation_axis = tuple(map(float, val.split()))
elif key == "VARIANCE_MODEL":
self.variance_model = tuple(map(float, val.split()))
assert nitem == len(colindex)
self._colindex = colindex
self._num_hkl = num_hkl
self.symm = crystal.symmetry(unit_cell=(a, b, c, al, be, ga),
space_group=ispgrp)
self.symm.show_summary(self._log)
print >>self._log, 'data_range=', self.zmin, self.zmax
def xds2mtz(xds_file,
dir_name,
hklout=None,
run_xtriage=False,
run_ctruncate=False,
dmin=None,
dmax=None,
force_anomalous=False,
with_multiplicity=False,
space_group=None,
flag_source=None,
add_flag=False):
if hklout is None:
hklout = os.path.splitext(os.path.basename(xds_file))[0] + ".mtz"
# if output file already exists, exit.
if os.path.isfile(os.path.join(dir_name, hklout)):
raise Exception(os.path.join(dir_name, hklout), "already exists.")
# read header
header = {}
for l in open(xds_file):
if l.startswith("!END_OF_HEADER"):
break
headers = re_xds_kwd.findall(l[l.index("!") + 1:])
for k, v in headers:
if k == "FRIEDEL'S_LAW":
header["FRIEDEL'S_LAW"] = v.strip()
if k == "SPACE_GROUP_NUMBER":
header["SPACE_GROUP_NUMBER"] = v.strip()
if k == "X-RAY_WAVELENGTH":
header["X-RAY_WAVELENGTH"] = v.strip(
) # XXX could be wrong if XSCALE result
anom_flag = header["FRIEDEL'S_LAW"] == "FALSE"
if force_anomalous: anom_flag = True
sginfo_org = sgtbx.space_group_info(header["SPACE_GROUP_NUMBER"])
if space_group:
sginfo = sgtbx.space_group_info(space_group)
else:
sginfo = sginfo_org
# make output directory
if not os.path.isdir(dir_name):
os.makedirs(dir_name)
print "Header information read from", xds_file
for k in header:
print k, "=", header[k]
print
logout = open(os.path.join(dir_name, "xds2mtz.log"), "w")
print >> logout, "xds2mtz.py running in %s" % os.getcwd()
print >> logout, "output directory: %s" % dir_name
print >> logout, "original file: %s" % xds_file
print >> logout, "flag_source: %s" % flag_source
print >> logout, "space group: %s (SPACE_GROUP_NUMBER=%s; requested space_group=%s)" % (
sginfo, header.get("SPACE_GROUP_NUMBER", ""), space_group)
if sginfo_org.group().build_derived_reflection_intensity_group(
False) != sginfo.group().build_derived_reflection_intensity_group(
False):
print >> logout, " WARNING!! specified space group is incompatible with original file (%s)." % sginfo_org
print >> logout, "anomalous: %s (FRIEDEL'S_LAW=%s force_anomalous=%s)" % (
anom_flag, header["FRIEDEL'S_LAW"], force_anomalous)
print >> logout, ""
logout.flush()
##
# convert to MTZ
xds2mtz_work(xds_file,
mtzout=os.path.join(dir_name, hklout),
sg=str(sginfo).replace(" ", ""),
wavelen=header.get("X-RAY_WAVELENGTH", "0"),
logout=logout,
anom_flag=anom_flag,
use_ctruncate=run_ctruncate,
dmin=dmin,
dmax=dmax)
if run_xtriage:
print "Running xtriage.."
args = [hklout]
if anom_flag:
args.append(
'input.xray_data.obs_labels="I(+),SIGI(+),I(-),SIGI(-)"')
run_xtriage_in_module_if_possible(args=args, wdir=dir_name)
if with_multiplicity:
add_multi(xds_file,
os.path.join(dir_name, hklout),
dmin=dmin,
dmax=dmax,
force_anomalous=anom_flag)
if flag_source is not None:
copy_test_flag(os.path.join(dir_name, hklout),
flag_source,
log_out=logout)
elif add_flag:
add_test_flag(os.path.join(dir_name, hklout), log_out=logout)
def read_header(self):
re_item = re.compile("!ITEM_([^=]+)=([0-9]+)")
colindex = {} # {"H":1, "K":2, "L":3, ...}
nitemfound = 0
flag_data_start = False
num_hkl = 0
headers = []
for line in open(self._filein):
if flag_data_start:
if line.startswith("!END_OF_DATA"):
break
num_hkl += 1
continue
if line.startswith('!END_OF_HEADER'):
flag_data_start = True
continue
if line.startswith("!Generated by dials"):
self.by_dials = True
continue
if line.startswith("! ISET="):
pars = dict(re_xds_kwd.findall(line))
iset = int(pars["ISET"])
if iset not in self.input_files:
self.input_files[iset] = [None, None, None]
if "INPUT_FILE" in pars:
self.input_files[iset][0] = pars["INPUT_FILE"]
elif "X-RAY_WAVELENGTH" in pars:
tmp = pars["X-RAY_WAVELENGTH"]
if " (" in tmp: tmp = tmp[:tmp.index(" (")]
self.input_files[iset][1] = tmp
elif "UNIT_CELL_CONSTANTS" in pars:
tmp = pars["UNIT_CELL_CONSTANTS"]
self.input_files[iset][2] = tmp
else:
headers.extend(re_xds_kwd.findall(line[line.index("!") + 1:]))
self.nx, self.ny, self.anomalous, self.zmin, self.zmax = (None, ) * 5
for key, val in headers:
if key == "NUMBER_OF_ITEMS_IN_EACH_DATA_RECORD":
nitem = int(val.strip())
print >> self._log, 'number of items according to header is', nitem
elif key == "UNIT_CELL_CONSTANTS":
a, b, c, al, be, ga = map(lambda x: float(x),
val.strip().split())
elif key == "UNIT_CELL_A-AXIS":
self.a_axis = tuple(map(float, val.split()))
elif key == "UNIT_CELL_B-AXIS":
self.b_axis = tuple(map(float, val.split()))
elif key == "UNIT_CELL_C-AXIS":
self.c_axis = tuple(map(float, val.split()))
elif key.startswith("ITEM_"):
item, ind = key[len("ITEM_"):], int(val)
colindex[item] = ind - 1
nitemfound += 1
elif key == "NX":
self.nx = int(val)
elif key == "NY":
self.ny = int(val)
elif key == "QX":
self.qx = float(val)
elif key == "QY":
self.qy = float(val)
elif key == "ORGX":
self.orgx = float(val)
elif key == "ORGY":
self.orgy = float(val)
elif key == "DATA_RANGE":
self.zmin, self.zmax = map(lambda x: int(x),
val.strip().split())
elif key == "SPACE_GROUP_NUMBER":
ispgrp = int(val.strip())
elif key == "FRIEDEL'S_LAW":
assert val.strip() in ("TRUE", "FALSE")
self.anomalous = val.strip() == "FALSE"
elif key == "DETECTOR_DISTANCE":
self.distance = float(val)
elif key == "X-RAY_WAVELENGTH":
self.wavelength = float(val.split()[0])
elif key == "INCIDENT_BEAM_DIRECTION":
self.incident_axis = tuple(map(float, val.split()))
elif key == "ROTATION_AXIS":
self.rotation_axis = tuple(map(float, val.split()))
elif key == "OSCILLATION_RANGE":
self.osc_range = float(val.split()[0])
elif key == "VARIANCE_MODEL":
self.variance_model = tuple(map(float, val.split()))
assert nitem == len(colindex)
self._colindex = colindex
self._num_hkl = num_hkl
self.symm = crystal.symmetry(unit_cell=(a, b, c, al, be, ga),
space_group=ispgrp)
self.symm.show_summary(self._log)
print >> self._log, 'data_range=', self.zmin, self.zmax
def xds2mtz(xds_file,
dir_name,
hklout=None,
run_xtriage=False,
run_ctruncate=False,
dmin=None,
dmax=None,
force_anomalous=False,
with_multiplicity=False,
sgnum=None):
if hklout is None:
hklout = os.path.splitext(os.path.basename(xds_file))[0] + ".mtz"
# if output file already exists, exit.
if os.path.isfile(os.path.join(dir_name, hklout)):
raise Exception(os.path.join(dir_name, hklout), "already exists.")
# read header
header = {}
for l in open(xds_file):
if l.startswith("!END_OF_HEADER"):
break
headers = re_xds_kwd.findall(l[l.index("!") + 1:])
for k, v in headers:
if k == "FRIEDEL'S_LAW":
header["FRIEDEL'S_LAW"] = v.strip()
if k == "SPACE_GROUP_NUMBER":
header["SPACE_GROUP_NUMBER"] = v.strip()
if k == "X-RAY_WAVELENGTH":
header["X-RAY_WAVELENGTH"] = v.strip(
) # XXX could be wrong if XSCALE result
if force_anomalous:
header["FRIEDEL'S_LAW"] = "FALSE"
if sgnum is not None:
header["SPACE_GROUP_NUMBER"] = str(sgnum)
# make output directory
if not os.path.isdir(dir_name):
os.makedirs(dir_name)
logout = open(os.path.join(dir_name, "xds2mtz.log"), "w")
print >> logout, "xds2mtz.py running in %s" % os.getcwd()
print >> logout, "output directory: %s" % dir_name
print >> logout, "original file: %s" % xds_file
print "Header information read from", xds_file
for k in header:
print k, "=", header[k]
print
##
# convert to MTZ
print >> logout, "FRIEDEL'S_LAW= %s" % header["FRIEDEL'S_LAW"]
print >> logout, ""
logout.flush()
if header["FRIEDEL'S_LAW"] == "TRUE":
print xds_file, "is not anomalous dataset."
print
xds2mtz_normal(xds_file,
mtzout=os.path.join(dir_name, hklout),
sg=header["SPACE_GROUP_NUMBER"],
wavelen=header.get("X-RAY_WAVELENGTH", "0"),
logout=logout,
use_ctruncate=run_ctruncate,
dmin=dmin,
dmax=dmax)
if run_xtriage:
print "Running xtriage.."
run_xtriage_in_module_if_possible(args=[hklout], wdir=dir_name)
if with_multiplicity:
add_multi(xds_file,
os.path.join(dir_name, hklout),
dmin=dmin,
dmax=dmax,
force_anomalous=False)
else:
print xds_file, "is anomalous dataset."
print
xds2mtz_anom(xds_file,
mtzout=os.path.join(dir_name, hklout),
sg=header["SPACE_GROUP_NUMBER"],
wavelen=header.get("X-RAY_WAVELENGTH", "0"),
logout=logout,
use_ctruncate=run_ctruncate,
dmin=dmin,
dmax=dmax)
if run_xtriage:
print "Running xtriage.."
run_xtriage_in_module_if_possible(args=[
hklout,
'input.xray_data.obs_labels="I(+),SIGI(+),I(-),SIGI(-)"'
],
wdir=dir_name)
if with_multiplicity:
add_multi(xds_file,
os.path.join(dir_name, hklout),
dmin=dmin,
dmax=dmax,
force_anomalous=True)
