def merge(hklout="fast_dp.mtz", aimless_log="aimless.log"):
"""Merge the reflections from XDS_ASCII.HKL with Aimless to get
statistics - this will use pointless for the reflection file format
mashing."""
run_job("pointless",
["-c", "xdsin", "XDS_ASCII.HKL", "hklout", "xds_sorted.mtz"])
log = run_job(
"aimless",
["hklin", "xds_sorted.mtz", "hklout", hklout, "xmlout", "aimless.xml"],
[
"bins 20",
"run 1 all",
"scales constant",
"anomalous on",
"cycles 0",
"output unmerged",
"sdcorrection norefine full 1 0 0",
],
)
with open(aimless_log, "w") as fout:
for record in log:
fout.write(record)
# check for errors
for record in log:
if "!!!! No data !!!!" in record:
raise RuntimeError("aimless complains no data")
return parse_aimless_log(log)
def scale(unit_cell, xds_inp, space_group_number, resolution_high=0.0):
"""Perform the scaling with the spacegroup and unit cell calculated
from pointless and correct. N.B. this scaling is done by CORRECT."""
assert unit_cell
assert xds_inp
assert space_group_number
with open("CORRECT.INP", "w") as fout:
for k in sorted(xds_inp):
if "SEGMENT" in k:
continue
v = xds_inp[k]
if isinstance(v, list):
for _v in v:
fout.write("%s=%s\n" % (k, _v))
else:
fout.write("%s=%s\n" % (k, v))
fout.write("SPACE_GROUP_NUMBER=%d\n" % space_group_number)
fout.write("UNIT_CELL_CONSTANTS=%f %f %f %f %f %f\n" %
tuple(unit_cell))
fout.write("JOB=CORRECT\n")
fout.write("REFINE(CORRECT)=CELL AXIS ORIENTATION POSITION BEAM\n")
fout.write("INCLUDE_RESOLUTION_RANGE= 100 %f\n" % resolution_high)
fout.write("%s\n" % segment_text(xds_inp))
shutil.copyfile("CORRECT.INP", "XDS.INP")
run_job("xds_par")
# once again should check on the general happiness of everything...
for step in ["CORRECT"]:
lastrecord = open("%s.LP" % step).readlines()[-1]
if "!!! ERROR !!!" in lastrecord:
raise RuntimeError(
"error in %s: %s" %
(step, lastrecord.replace("!!! ERROR !!!", "").strip()))
# and get the postrefined cell constants from GXPARM.XDS - but continue
# to work for the old format too...
with open("GXPARM.XDS", "r") as fh:
gxparm = fh.readlines()
if gxparm and "XPARM.XDS" in gxparm[0]:
# new format
space_group = spacegroup_number_to_name(int(gxparm[3].split()[0]))
unit_cell = tuple(map(float, gxparm[3].split()[1:]))
else:
# old format:
space_group = spacegroup_number_to_name(int(gxparm[7].split()[0]))
unit_cell = tuple(map(float, gxparm[7].split()[1:]))
# FIXME also get the postrefined mosaic spread out...
# and the total number of good reflections
nref = 0
for record in open("CORRECT.LP", "r"):
if "NUMBER OF ACCEPTED OBSERVATIONS" in record:
nref = int(record.split()[-1])
refined_beam = read_xparm_get_refined_beam("GXPARM.XDS")
# hack in xdsstat (but don't cry if it fails)
xdsstat_output = run_job("xdsstat", [], ["XDS_ASCII.HKL"])
with open("xdsstat.log", "w") as fh:
fh.write("".join(xdsstat_output))
return unit_cell, space_group, nref, refined_beam
def autoindex(xds_inp, input_cell=None):
"""Perform the autoindexing, using metatdata, get a list of possible
lattices and record / return the triclinic cell constants (get these from
XPARM.XDS)."""
assert xds_inp
xds_inp = add_spot_range(xds_inp)
with open("AUTOINDEX.INP", "w") as fout:
for k in sorted(xds_inp):
if "SEGMENT" in k:
continue
v = xds_inp[k]
if isinstance(v, list):
for _v in v:
fout.write("%s=%s\n" % (k, _v))
else:
fout.write("%s=%s\n" % (k, v))
fout.write("%s\n" % segment_text(xds_inp))
if input_cell:
fout.write("SPACE_GROUP_NUMBER=1\n")
fout.write("UNIT_CELL_CONSTANTS=%f %f %f %f %f %f\n" %
tuple(input_cell))
fout.write("JOB=XYCORR INIT COLSPOT IDXREF\n")
fout.write("REFINE(IDXREF)=CELL AXIS ORIENTATION POSITION BEAM\n")
fout.write("MAXIMUM_ERROR_OF_SPOT_POSITION= 2.0\n")
fout.write("MINIMUM_FRACTION_OF_INDEXED_SPOTS= 0.5\n")
shutil.copyfile("AUTOINDEX.INP", "XDS.INP")
log = run_job("xds_par")
with open("autoindex.log", "w") as fout:
fout.write("".join(log))
# sequentially check for errors... XYCORR INIT COLSPOT IDXREF
for step in ["XYCORR", "INIT", "COLSPOT", "IDXREF"]:
lastrecord = open("%s.LP" % step).readlines()[-1]
if "!!! ERROR !!!" in lastrecord:
raise RuntimeError(
"error in %s: %s" %
(step, lastrecord.replace("!!! ERROR !!!", "").strip()))
results = read_xds_idxref_lp("IDXREF.LP")
# FIXME if input cell was given, verify that this is an allowed
# permutation. If it was not, raise a RuntimeError. This remains to be
# fixed
write("All autoindexing results:")
write("%3s %6s %6s %6s %6s %6s %6s" %
("Lattice", "a", "b", "c", "alpha", "beta", "gamma"))
for r in sorted((r for r in results if isinstance(r, int)), reverse=True):
cell = results[r][1]
write("%7s %6.2f %6.2f %6.2f %6.2f %6.2f %6.2f" % (
spacegroup_to_lattice(r),
cell[0],
cell[1],
cell[2],
cell[3],
cell[4],
cell[5],
))
# should probably print this for debugging
try:
return results[1][1]
except Exception:
raise RuntimeError("getting P1 cell for autoindex")
def integrate(xds_inp, p1_unit_cell, resolution_low, n_jobs, n_processors):
"""Peform the integration with a triclinic basis."""
assert xds_inp
assert p1_unit_cell
with open("INTEGRATE.INP", "w") as fout:
for k in sorted(xds_inp):
if "SEGMENT" in k:
continue
v = xds_inp[k]
if isinstance(v, list):
for _v in v:
fout.write("%s=%s\n" % (k, _v))
else:
fout.write("%s=%s\n" % (k, v))
fout.write("REFINE(INTEGRATE)= POSITION BEAM ORIENTATION CELL\n")
fout.write("JOB=DEFPIX INTEGRATE\n")
fout.write("%s\n" % segment_text(xds_inp))
if n_processors:
fout.write("MAXIMUM_NUMBER_OF_PROCESSORS=%d\n" % n_processors)
if n_jobs:
fout.write("MAXIMUM_NUMBER_OF_JOBS=%d\n" % n_jobs)
fout.write("INCLUDE_RESOLUTION_RANGE= %f 0.0\n" % resolution_low)
shutil.copyfile("INTEGRATE.INP", "XDS.INP")
run_job("xds_par")
# FIXME need to check that all was hunky-dory in here!
for step in ["DEFPIX", "INTEGRATE"]:
if not os.path.exists("%s.LP" % step):
continue
lastrecord = open("%s.LP" % step).readlines()[-1]
if "!!! ERROR !!!" in lastrecord:
raise RuntimeError("error in %s: %s" %
(step, lastrecord.replace("!!! ERROR !!!",
"").strip().lower()))
if not os.path.exists("INTEGRATE.LP"):
step = "INTEGRATE"
for record in open("LP_01.tmp").readlines():
if "!!! ERROR !!! AUTOMATIC DETERMINATION OF SPOT SIZE " in record:
raise RuntimeError("error in %s: %s" %
(step, record.replace("!!! ERROR !!!",
"").strip().lower()))
elif "!!! ERROR !!! CANNOT OPEN OR READ FILE LP_01.tmp" in record:
raise RuntimeError("integration error: cluster error")
# check for some specific errors
for step in ["INTEGRATE"]:
for record in open("%s.LP" % step).readlines():
if "!!! ERROR !!! AUTOMATIC DETERMINATION OF SPOT SIZE " in record:
raise RuntimeError("error in %s: %s" %
(step, record.replace("!!! ERROR !!!",
"").strip().lower()))
elif "!!! ERROR !!! CANNOT OPEN OR READ FILE LP_01.tmp" in record:
raise RuntimeError("integration error: cluster error")
# if all was ok, look in the working directory for files named
# forkintegrate_job.o341858 &c. and remove them. - N.B. this is site
# specific!
for f in os.listdir(os.getcwd()):
if "forkintegrate_job." in f[:18]:
try:
os.remove(f)
except Exception:
pass
# get the mosaic spread ranges
mosaics = []
for record in open("INTEGRATE.LP"):
if "CRYSTAL MOSAICITY (DEGREES)" in record:
mosaics.append(float(record.split()[-1]))
mosaic = sum(mosaics) / len(mosaics)
return min(mosaics), mosaic, max(mosaics)