def parse_pointless_output_for_symm(output):
lines = output.splitlines()
ret = {}
best_symm, best_cell = None, None
read_flag = False
for l in lines:
if l.startswith("Best Solution:"):
group_type = l.split()[2]
assert group_type in ("point", "space") # How can we support Laue?
best_symm = l[l.index("group")+6:].strip()
read_flag = True
elif read_flag and "Reindex operator:" in l:
tmp = l.split(":")[1]
tmp = tmp[tmp.index("[")+1:tmp.index("]")]
ret["reindex_op"] = sgtbx.change_of_basis_op(tmp)
elif read_flag and "Laue group probability:" in l:
ret["laue_prob"] = util.safe_float(l.split(":")[1])
elif read_flag and "Unit cell:" in l:
r = re_cell.search(l)
if r:
best_cell = map(float, r.groups())
if None not in (best_symm, best_cell):
ret["symm"] = crystal.symmetry(unit_cell=best_cell, space_group_symbol=best_symm,
assert_is_compatible_unit_cell=False)
return ret
def parse(self, lpin):
self.by_frame = {}
self.by_framediff = {}
reading = ""
for l in open(lpin):
if "Frame #refs #misfits Iobs sigma Iobs/sigma Peak Corr Rmeas #rmeas #unique" in l:
reading = "by_frame"
elif reading == "by_frame":
if "For inline graphs use a Java browser" in l:
reading = ""
continue
if len(l) < 94: continue
# frame, nrefs, nmisfits, iobs, sigma, ios, peak, corr, rmeas, nrmeas, nuniq, (dummy)
sp = l[:6], l[6:13], l[13:18], l[18:28], l[28:38], l[38:48], l[
48:58], l[58:68], l[68:78], l[78:85], l[85:92]
self.by_frame.setdefault("frame", []).append(int(sp[0]))
self.by_frame.setdefault("nrefs", []).append(int(sp[1]))
self.by_frame.setdefault("nmisfits", []).append(int(sp[2]))
self.by_frame.setdefault("iobs", []).append(safe_float(sp[3]))
self.by_frame.setdefault("sigma", []).append(safe_float(sp[4]))
self.by_frame.setdefault("ios", []).append(safe_float(sp[5]))
self.by_frame.setdefault("peak", []).append(safe_float(sp[6]))
self.by_frame.setdefault("corr", []).append(safe_float(sp[7]))
self.by_frame.setdefault("rmeas", []).append(safe_float(sp[8]))
self.by_frame.setdefault("nrmeas", []).append(int(sp[9]))
self.by_frame.setdefault("nuniq", []).append(int(sp[10]))
elif "Framediff #refs R_d n-notfriedel Rd-notfriedel n-friedel Rd-friedel" in l:
reading = "by_framediff"
elif reading == "by_framediff":
if "For inline graphs use a Java browser" in l:
reading = ""
continue
if len(l) < 71: continue
# Framediff #refs R_d n-notfriedel Rd-notfriedel n-friedel Rd-friedel, (dummy)
sp = l[:6], l[6:14], l[14:24], l[24:32], l[32:42], l[42:50], l[
50:60]
self.by_framediff.setdefault("framediff",
[]).append(int(sp[0]))
self.by_framediff.setdefault("nrefs", []).append(int(sp[1]))
self.by_framediff.setdefault("rd", []).append(float(sp[2]))
def parse(self, lpin):
self.by_frame = {}
self.by_framediff = {}
reading = ""
for l in open(lpin):
if "Frame #refs #misfits Iobs sigma Iobs/sigma Peak Corr Rmeas #rmeas #unique" in l:
reading = "by_frame"
elif reading == "by_frame":
if "For inline graphs use a Java browser" in l:
reading = ""
continue
if len(l) < 94: continue
# frame, nrefs, nmisfits, iobs, sigma, ios, peak, corr, rmeas, nrmeas, nuniq, (dummy)
sp = l[:6], l[6:13], l[13:18], l[18:28], l[28:38], l[38:48], l[48:58], l[58:68], l[68:78], l[78:85], l[85:92]
self.by_frame.setdefault("frame", []).append(int(sp[0]))
self.by_frame.setdefault("nrefs", []).append(int(sp[1]))
self.by_frame.setdefault("nmisfits", []).append(int(sp[2]))
self.by_frame.setdefault("iobs", []).append(safe_float(sp[3]))
self.by_frame.setdefault("sigma", []).append(safe_float(sp[4]))
self.by_frame.setdefault("ios", []).append(safe_float(sp[5]))
self.by_frame.setdefault("peak", []).append(safe_float(sp[6]))
self.by_frame.setdefault("corr", []).append(safe_float(sp[7]))
self.by_frame.setdefault("rmeas", []).append(safe_float(sp[8]))
self.by_frame.setdefault("nrmeas", []).append(int(sp[9]))
self.by_frame.setdefault("nuniq", []).append(int(sp[10]))
elif "Framediff #refs R_d n-notfriedel Rd-notfriedel n-friedel Rd-friedel" in l:
reading = "by_framediff"
elif reading == "by_framediff":
if "For inline graphs use a Java browser" in l:
reading = ""
continue
if len(l) < 71: continue
# Framediff #refs R_d n-notfriedel Rd-notfriedel n-friedel Rd-friedel, (dummy)
sp = l[:6], l[6:14], l[14:24], l[24:32], l[32:42], l[42:50], l[50:60]
self.by_framediff.setdefault("framediff", []).append(int(sp[0]))
self.by_framediff.setdefault("nrefs", []).append(int(sp[1]))
self.by_framediff.setdefault("rd", []).append(float(sp[2]))
def parse(self, lpin):
reading = ""
self.table = {}
self.error_table = {}
self.space_group = None
self.unit_cell = map(lambda x: float("nan"), xrange(6))
self.unit_cell_esd = map(lambda x: float("nan"), xrange(6))
self.a_b_ISa = map(lambda x: float("nan"), xrange(3))
self.snippets = {}
lines = open(lpin).readlines()
for i, l in enumerate(lines):
if l.startswith(" FRIEDEL'S_LAW="):
self.anomalous_flag = "FALSE" in l
# ************ SELECTED SPACE GROUP AND UNIT CELL FOR THIS DATA SET ************
elif "SELECTED SPACE GROUP AND UNIT CELL FOR THIS DATA SET" in l:
reading = "selected_symmetry"
elif reading == "selected_symmetry":
# Info before refinement
if "SPACE_GROUP_NUMBER=" in l:
self.space_group = sgtbx.space_group_info(int(l[l.index("=")+1:])).group()
elif "UNIT_CELL_CONSTANTS=" in l:
# Will be overridden if refined
tmp = l[l.index("=")+1:]
self.unit_cell = map(float, (tmp[0:9],tmp[9:18],tmp[18:27],tmp[27:35],tmp[35:43],tmp[43:51]))
if "********" in l:
reading = ""
# ******************************************************************************
# REFINEMENT OF DIFFRACTION PARAMETERS USING ALL IMAGES
# ******************************************************************************
elif l.startswith(" UNIT CELL PARAMETERS"):
cell_params = map(float, (l[21:32], l[32:42], l[42:52], l[52:60], l[60:68], l[68:76]))
self.unit_cell = cell_params
elif l.startswith(" E.S.D. OF CELL PARAMETERS"):
esd_params = map(float, (l[26:35], l[35:43], l[43:51], l[51:59], l[59:67], l[67:75]))
self.unit_cell_esd = esd_params
elif l.startswith(" SPACE GROUP NUMBER"):
self.space_group = sgtbx.space_group_info(int(l[20:])).group()
# ******************************************************************************
# CORRECTION PARAMETERS FOR THE STANDARD ERROR OF REFLECTION INTENSITIES
# ******************************************************************************
elif "a b ISa" in l:
reading = "ISa"
self.snippets["ISa"] = l
elif reading == "ISa":
a, b, ISa = map(float, l.split())
reading = ""
self.a_b_ISa = a, b, ISa
self.snippets["ISa"] += l
# ******************************************************************************
# STANDARD ERROR OF REFLECTION INTENSITIES AS FUNCTION OF RESOLUTION
# FOR DATA SET XDS_ASCII.HKL
# ******************************************************************************
elif "RESOLUTION RANGE I/Sigma Chi^2 R-FACTOR R-FACTOR NUMBER ACCEPTED REJECTED" in l:
reading = "error_table"
elif reading == "error_table":
if l.startswith(" ***"):
reading = ""
continue
if len(l.split()) < 3: continue
sp = errortable_split(l)
# Note that the last line is about overall data
self.error_table.setdefault("dmax", []).append(float(sp[0]))
self.error_table.setdefault("dmin", []).append(float(sp[1]))
self.error_table.setdefault("ios", []).append(safe_float(sp[2]))
self.error_table.setdefault("chisq", []).append(safe_float(sp[3]))
self.error_table.setdefault("r_merge", []).append(safe_float(sp[4]))
self.error_table.setdefault("number", []).append(int(sp[6]))
self.error_table.setdefault("nacc", []).append(int(sp[7]))
self.error_table.setdefault("nrej", []).append(int(sp[8]))
#if "SUMMARY OF DATA SET STATISTICS FOR IMAGE":
# ******************************************************************************
# STATISTICS OF SAVED DATA SET "XDS_ASCII.HKL" (DATA_RANGE= x x)
# FILE TYPE: XDS_ASCII MERGE=FALSE FRIEDEL'S_LAW=x
# ******************************************************************************
elif 'STATISTICS OF SAVED DATA SET "XDS_ASCII.HKL"' in l:
reading = "stats_all"
continue
elif "SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION" in l:
self.snippets["table1"] = l
if reading == "stats_all":
key = "all"
self.table[key] = {}
for ll in lines[i+1:i+4]: self.snippets["table1"] += ll
for ll in lines[i+4:i+4+10]:
self.snippets["table1"] += ll
sp = table_split(ll)
assert len(sp) == 14
self.table[key].setdefault("dmin", []).append(float(sp[0]) if sp[0]!="total" else None)
self.table[key].setdefault("redundancy", []).append(float(sp[1])/float(sp[2]) if float(sp[2]) > 0 else 0)
self.table[key].setdefault("cmpl", []).append(float(sp[4][:-1]))
self.table[key].setdefault("r_merge", []).append(float(sp[5][:-1]))
self.table[key].setdefault("i_over_sigma", []).append(float(sp[8]))
self.table[key].setdefault("r_meas", []).append(safe_float(sp[9][:-1]))
self.table[key].setdefault("cc_half", []).append(float(sp[10].replace("*","")))
self.table[key].setdefault("cc_ano", []).append(float(sp[11].replace("*","")))
self.table[key].setdefault("sig_ano", []).append(float(sp[12]))
if sp[0]=="total": # in case less than 9 shells
break
def parse(self, lpin):
reading = ""
self.table = {}
self.error_table = {}
self.space_group, self.unit_cell, self.unit_cell_esd = None, None, None
self.a_b_ISa = [float("nan"), float("nan"),float("nan")]
self.snippets = {}
lines = open(lpin).readlines()
for i, l in enumerate(lines):
if l.startswith(" FRIEDEL'S_LAW="):
self.anomalous_flag = "FALSE" in l
# ************ SELECTED SPACE GROUP AND UNIT CELL FOR THIS DATA SET ************
elif "SELECTED SPACE GROUP AND UNIT CELL FOR THIS DATA SET" in l:
reading = "selected_symmetry"
elif reading == "selected_symmetry":
# Info before refinement
if "SPACE_GROUP_NUMBER=" in l:
self.space_group = sgtbx.space_group_info(int(l[l.index("=")+1:])).group()
elif "UNIT_CELL_CONSTANTS=" in l:
# Will be overridden if refined
tmp = l[l.index("=")+1:]
self.unit_cell = map(float, (tmp[0:9],tmp[9:18],tmp[18:27],tmp[27:35],tmp[35:43],tmp[43:51]))
if "********" in l:
reading = ""
# ******************************************************************************
# REFINEMENT OF DIFFRACTION PARAMETERS USING ALL IMAGES
# ******************************************************************************
elif l.startswith(" UNIT CELL PARAMETERS"):
cell_params = map(float, (l[21:32], l[32:42], l[42:52], l[52:60], l[60:68], l[68:76]))
self.unit_cell = cell_params
elif l.startswith(" E.S.D. OF CELL PARAMETERS"):
esd_params = map(float, (l[26:35], l[35:43], l[43:51], l[51:59], l[59:67], l[67:75]))
self.unit_cell_esd = esd_params
elif l.startswith(" SPACE GROUP NUMBER"):
self.space_group = sgtbx.space_group_info(int(l[20:])).group()
# ******************************************************************************
# CORRECTION PARAMETERS FOR THE STANDARD ERROR OF REFLECTION INTENSITIES
# ******************************************************************************
elif "a b ISa" in l:
reading = "ISa"
self.snippets["ISa"] = l
elif reading == "ISa":
a, b, ISa = map(float, l.split())
reading = ""
self.a_b_ISa = a, b, ISa
self.snippets["ISa"] += l
# ******************************************************************************
# STANDARD ERROR OF REFLECTION INTENSITIES AS FUNCTION OF RESOLUTION
# FOR DATA SET XDS_ASCII.HKL
# ******************************************************************************
elif "RESOLUTION RANGE I/Sigma Chi^2 R-FACTOR R-FACTOR NUMBER ACCEPTED REJECTED" in l:
reading = "error_table"
elif reading == "error_table":
if l.startswith(" ***"):
reading = ""
continue
if len(l.split()) < 3: continue
sp = errortable_split(l)
# Note that the last line is about overall data
self.error_table.setdefault("dmax", []).append(float(sp[0]))
self.error_table.setdefault("dmin", []).append(float(sp[1]))
self.error_table.setdefault("ios", []).append(safe_float(sp[2]))
self.error_table.setdefault("chisq", []).append(safe_float(sp[3]))
self.error_table.setdefault("r_merge", []).append(safe_float(sp[4]))
self.error_table.setdefault("number", []).append(int(sp[6]))
self.error_table.setdefault("nacc", []).append(int(sp[7]))
self.error_table.setdefault("nrej", []).append(int(sp[8]))
#if "SUMMARY OF DATA SET STATISTICS FOR IMAGE":
# ******************************************************************************
# STATISTICS OF SAVED DATA SET "XDS_ASCII.HKL" (DATA_RANGE= x x)
# FILE TYPE: XDS_ASCII MERGE=FALSE FRIEDEL'S_LAW=x
# ******************************************************************************
elif 'STATISTICS OF SAVED DATA SET "XDS_ASCII.HKL"' in l:
reading = "stats_all"
continue
elif "SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION" in l:
self.snippets["table1"] = l
if reading == "stats_all":
key = "all"
self.table[key] = {}
for ll in lines[i+1:i+4]: self.snippets["table1"] += ll
for ll in lines[i+4:i+4+10]:
self.snippets["table1"] += ll
sp = table_split(ll)
assert len(sp) == 14
self.table[key].setdefault("dmin", []).append(float(sp[0]) if sp[0]!="total" else None)
self.table[key].setdefault("redundancy", []).append(float(sp[1])/float(sp[2]) if float(sp[2]) > 0 else 0)
self.table[key].setdefault("cmpl", []).append(float(sp[4][:-1]))
self.table[key].setdefault("r_merge", []).append(float(sp[5][:-1]))
self.table[key].setdefault("i_over_sigma", []).append(float(sp[8]))
self.table[key].setdefault("r_meas", []).append(safe_float(sp[9][:-1]))
self.table[key].setdefault("cc_half", []).append(float(sp[10].replace("*","")))
self.table[key].setdefault("cc_ano", []).append(float(sp[11].replace("*","")))
self.table[key].setdefault("sig_ano", []).append(float(sp[12]))
