def run_cycles(self, xds_ascii_files):
self.all_data_root = os.path.dirname(os.path.commonprefix(xds_ascii_files))
self.removed_files = []
self.removed_reason = {}
print >>self.out, "********************* START FUNCTION ***********************"
if self.reference_file:
self.run_cycle([self.reference_file,]+xds_ascii_files)
else:
self.run_cycle(xds_ascii_files)
if self.res_params.estimate:
#self.cut_resolution(self.get_last_cycle_number())
for run_i in xrange(1, self.get_last_cycle_number()+1):
try: self.estimate_resolution(run_i)
except: print >>self.out, traceback.format_exc() # Don't want to stop the program.
for wd in glob.glob(os.path.join(self.workdir_org, "run_*")):
if os.path.exists(os.path.join(wd, "ccp4")): continue
xscale_hkl = os.path.abspath(os.path.join(wd, "xscale.hkl"))
sg = None # Use user-specified one. Otherwise follow pointless.
try:
sg = XDS_ASCII(xscale_hkl, read_data=False).symm.space_group()
laue_symm_str = str(sg.build_derived_reflection_intensity_group(False).info())
worker = Pointless()
result = worker.run_for_symm(xdsin=xscale_hkl,
logout=os.path.join(wd, "pointless.log"),
choose_laue=laue_symm_str,
xdsin_to_p1=True)
if "symm" in result:
print >>self.out, "Pointless suggestion (forcing %s symmetry):" % laue_symm_str
result["symm"].show_summary(self.out, " ")
sg = str(result["symm"].space_group_info())
else:
print >>self.out, "Pointless failed."
except:
# Don't want to stop the program.
print >>self.out, traceback.format_exc()
if self.space_group is not None:
sg = str(self.space_group.info())
try:
xds2mtz.xds2mtz(xds_file=xscale_hkl,
dir_name=os.path.join(wd, "ccp4"),
run_xtriage=True, run_ctruncate=True,
with_multiplicity=True,
space_group=sg,
flag_source=self.ref_mtz)
except:
# Don't want to stop the program.
print >>self.out, traceback.format_exc()
return self.removed_files, self.removed_reason
def run_cycles(self, xds_ascii_files):
self.all_data_root = os.path.dirname(os.path.commonprefix(xds_ascii_files))
self.removed_files = []
self.removed_reason = {}
print >>self.out, "********************* START FUNCTION ***********************"
if self.reference_file:
self.run_cycle([self.reference_file,]+xds_ascii_files)
else:
self.run_cycle(xds_ascii_files)
for i in xrange(1, self.get_last_cycle_number()+1):
wd = os.path.join(self.workdir_org, "run_%.2d"%i)
xds2mtz.xds2mtz(xds_file=os.path.abspath(os.path.join(wd, "xscale.hkl")),
dir_name=os.path.join(wd, "ccp4"),
run_xtriage=True, run_ctruncate=True)
return self.removed_files, self.removed_reason
def run(params):
xdsinp = "XDS.INP"
workdir = os.getcwd()
params.wfac1.sort()
params.minpk.sort()
digit_wfac1 = str(get_digit(params.wfac1))
digit_minpk = str(get_digit(params.minpk))
backup_needed = files.generated_by_CORRECT + ("XDS.INP", )
bk_prefix = make_backup(backup_needed)
try:
for wfac1 in params.wfac1:
for minpk in params.minpk:
work_name = ("CORRECT_wfac1_%." + digit_wfac1 + "f_minpk_%." +
digit_minpk + "f") % (wfac1, minpk)
modify_xdsinp(xdsinp,
inp_params=[
("JOB", "CORRECT"),
("WFAC1", wfac1),
("MINPK", minpk),
])
call("xds")
# make .mtz file
xds2mtz.xds2mtz(os.path.abspath("XDS_ASCII.HKL"),
dir_name=os.path.join(workdir,
"ccp4_" + work_name),
run_ctruncate=True,
run_xtriage=True)
if params.mtz_free is not None:
copy_testflag(mtzfree=params.mtz_free,
mtzin=os.path.join(workdir,
"ccp4_" + work_name,
"XDS_ASCII.mtz"))
make_backup(backup_needed, work_name + "_")
finally:
# 6. Revert XDS.INP, etc.
revert_files(backup_needed, bk_prefix)
def run(params):
xdsinp = "XDS.INP"
workdir = os.getcwd()
params.wfac1.sort()
params.minpk.sort()
digit_wfac1 = str(get_digit(params.wfac1))
digit_minpk = str(get_digit(params.minpk))
backup_needed = files.generated_by_CORRECT + ("XDS.INP",)
bk_prefix = make_backup(backup_needed)
try:
for wfac1 in params.wfac1:
for minpk in params.minpk:
work_name = ("CORRECT_wfac1_%." + digit_wfac1 + "f_minpk_%." + digit_minpk + "f") % (wfac1, minpk)
modify_xdsinp(xdsinp, inp_params=[("JOB", "CORRECT"), ("WFAC1", wfac1), ("MINPK", minpk)])
call("xds")
# make .mtz file
xds2mtz.xds2mtz(
os.path.abspath("XDS_ASCII.HKL"),
dir_name=os.path.join(workdir, "ccp4_" + work_name),
run_ctruncate=True,
run_xtriage=True,
)
if params.mtz_free is not None:
copy_testflag(
mtzfree=params.mtz_free, mtzin=os.path.join(workdir, "ccp4_" + work_name, "XDS_ASCII.mtz")
)
make_backup(backup_needed, work_name + "_")
finally:
# 6. Revert XDS.INP, etc.
revert_files(backup_needed, bk_prefix)
# 1. Backup XDS.INP, etc. (Make copies; not renaming)
bk_prefix = make_backup(backup_needed)
try:
# CORRECT with a
modify_xdsinp(xdsinp, inp_params=[("JOB","CORRECT"),
("CORRECTIONS", None),
("NBATCH", None),
("MINIMUM_I/SIGMA", None),
("WFAC1", None)
])
call("xds", stdout=open("CORRECT_a_xds.log", "w"))
# make xds_CORRECT.mtz
xds2mtz.xds2mtz(os.path.abspath("XDS_ASCII.HKL"), dir_name=os.path.join(workdir, "xdsconv_CORRECT"),
hklout="xds_CORRECT.mtz")
# make CORRECT_a_forscale.mtz
call("pointless -copy xdsin XDS_ASCII.HKL hklout %s/CORRECT_a_forscale.mtz" % workdir)
make_backup(backup_needed, "CORRECT_a_")
# CORRECT with b
#modify_xdsinp(xdsinp, mode="b")
modify_xdsinp(xdsinp, inp_params=[("JOB","CORRECT"),
("CORRECTIONS", ""),
("NBATCH", "1"),
("MINIMUM_I/SIGMA", "50"),
("WFAC1", "2")
])
call("xds", stdout=open("CORRECT_b_xds.log", "w"))
def run(params):
xdsinp = "XDS.INP"
workdir = os.getcwd()
# concerning DELPHI=
if len(params.delphi) == 0:
params.delphi = [get_delphi_defined(xdsinp)]
params.delphi.sort()
digit_delphi = str(get_digit(params.delphi))
# concerning REFINE(INTEGRATE)=
if params.all_refine_combinations:
refine_params = make_all_refine_combinations()
else:
refine_params = get_refine_defined(xdsinp)
backup_needed = files.generated_by_INTEGRATE + ("XDS.INP",)
if params.run_correct:
backup_needed += files.generated_by_CORRECT
bk_prefix = None
try:
for rp in refine_params:
rp_str = "refine_none" if len(rp) == 0 else "refine_" + "+".join(rp)
for delphi in params.delphi:
delphi_str = ("delphi_%."+digit_delphi+"f") % delphi
bk_prefix = make_backup(backup_needed) # Backup existing XDS.INP and others
work_name = "INTEGRATE_%s_%s" % (rp_str, delphi_str)
inp_params = [("JOB","INTEGRATE"),
("DELPHI", delphi),
("REFINE(INTEGRATE)", " ".join(rp))
]
if params.run_correct:
inp_params[0] = ("JOB","INTEGRATE CORRECT")
modify_xdsinp(xdsinp, inp_params=inp_params)
call("xds_par", stdout=sys.stdout)
# Move files into a new directory.
os.mkdir(work_name)
for f in backup_needed:
shutil.move(f, work_name)
if params.run_correct:
# make .mtz file
try:
call("xdsstat", stdin="\n", stdout=open(os.path.join(work_name, "XDSSTAT.LP"),"w"), wdir=work_name)
xds2mtz.xds2mtz(os.path.abspath(os.path.join(work_name, "XDS_ASCII.HKL")),
dir_name=os.path.join(workdir, work_name, "ccp4"),
run_ctruncate=False, run_xtriage=True
)
if params.mtz_free is not None:
copy_testflag(mtzfree=params.mtz_free,
mtzin=os.path.join(workdir, work_name, "ccp4", "XDS_ASCII.mtz"))
except:
print traceback.format_exc()
print "Ignoring xds2mtz error.."
print
revert_files(backup_needed, bk_prefix) # Revert XDS.INP and others
finally:
# 6. Revert XDS.INP, etc.
revert_files(backup_needed, bk_prefix)
# 1. Backup XDS.INP, etc. (Make copies; not renaming)
bk_prefix = make_backup(backup_needed)
try:
# CORRECT with a
modify_xdsinp(xdsinp,
inp_params=[("JOB", "CORRECT"), ("CORRECTIONS", None),
("NBATCH", None), ("MINIMUM_I/SIGMA", None),
("WFAC1", None)])
call("xds", stdout=open("CORRECT_a_xds.log", "w"))
# make xds_CORRECT.mtz
xds2mtz.xds2mtz(os.path.abspath("XDS_ASCII.HKL"),
dir_name=os.path.join(workdir, "xdsconv_CORRECT"),
hklout="xds_CORRECT.mtz")
# make CORRECT_a_forscale.mtz
call(
"pointless -copy xdsin XDS_ASCII.HKL hklout %s/CORRECT_a_forscale.mtz"
% workdir)
make_backup(backup_needed, "CORRECT_a_")
# CORRECT with b
#modify_xdsinp(xdsinp, mode="b")
modify_xdsinp(xdsinp,
inp_params=[("JOB", "CORRECT"), ("CORRECTIONS", ""),
("NBATCH", "1"), ("MINIMUM_I/SIGMA", "50"),
("WFAC1", "2")])
