def __init__(self,
fmodel,
map_type_str,
fo_scale,
fc_scale,
use_shelx_weight,
shelx_weight_parameter,
map_calculation_helper=None):
self.mch = map_calculation_helper
self.mnm = mmtbx.map_names(map_name_string = map_type_str)
self.fmodel = fmodel
self.fc_scale = fc_scale
self.fo_scale = fo_scale
self.f_obs = None
self.f_model = None
self.use_shelx_weight = use_shelx_weight
self.shelx_weight_parameter = shelx_weight_parameter
if(not self.mnm.ml_map):
self.f_obs = self.fmodel.f_obs().data()*fo_scale
else:
if(self.mch is None): self.mch = self.fmodel.map_calculation_helper()
if(self.fmodel.hl_coeffs() is None):
self.f_obs = self.mch.f_obs.data()*fo_scale*self.mch.fom
else:
cp = fmodel.combine_phases(map_calculation_helper = self.mch)
self.f_obs = self.mch.f_obs.data()*fo_scale*cp.f_obs_phase_and_fom_source()
def check_expected_error(s):
cntr = 0
try:
r = mmtbx.map_names(map_name_string=s)
except Sorry, e:
assert str(e).count("Wrong map type requested: %s" % s) == 1
cntr += 1
def __init__(self,
fmodel,
map_type_str,
acentrics_scale = 2.0,
centrics_scale = 1.0):
"""
Compute x and y for x*Fobs-y*Fmodel given map type string
"""
self.fmodel = fmodel
mnm = mmtbx.map_names(map_name_string = map_type_str)
# R.Read, SIGMAA: 2mFo-DFc (acentrics) & mFo (centrics)
centric_flags = self.fmodel.f_obs().centric_flags().data()
acentric_flags = ~centric_flags
if(mnm.k != 0):
self.fo_scale = flex.double(self.fmodel.f_obs().size(), 1.0)
else: self.fo_scale = flex.double(self.fmodel.f_obs().size(), 0.0)
if(mnm.n != 0):
self.fc_scale = flex.double(self.fmodel.f_obs().size(), 1.0)
else: self.fc_scale = flex.double(self.fmodel.f_obs().size(), 0.0)
abs_kn = abs(mnm.k*mnm.n)
if(mnm.k != abs(mnm.n) and abs_kn > 1.e-6):
self.fo_scale.set_selected(acentric_flags, mnm.k)
self.fo_scale.set_selected( centric_flags, max(mnm.k-centrics_scale,0.))
self.fc_scale.set_selected(acentric_flags, mnm.n)
self.fc_scale.set_selected( centric_flags, max(mnm.n-centrics_scale,0.))
elif(mnm.k == abs(mnm.n) and abs_kn > 1.e-6):
fo_scale_k = self.fo_scale*mnm.k
self.fc_scale_n = self.fc_scale*mnm.n
self.fo_scale.set_selected(acentric_flags, fo_scale_k*acentrics_scale)
self.fo_scale.set_selected( centric_flags, fo_scale_k)
self.fc_scale.set_selected(acentric_flags, self.fc_scale_n*acentrics_scale)
self.fc_scale.set_selected( centric_flags, self.fc_scale_n)
else:
self.fo_scale *= mnm.k
self.fc_scale *= mnm.n
def validate_map_params(params):
from mmtbx import map_names
labels = []
for map_coeffs in params.map_coefficients:
if (map_coeffs.map_type is not None):
try:
decode_map = map_names(map_coeffs.map_type)
except RuntimeError as e:
raise Sorry(str(e))
f = map_coeffs.mtz_label_amplitudes
phi = map_coeffs.mtz_label_phases
if (f in labels) or (phi in labels):
raise Sorry((
"The map coefficients with MTZ labels %s,%s duplicates at"
+
" least one previously defined label. You may output multiple sets "
+
"of coefficients with the same map type, but the column labels must "
+ "be unique.") % (f, phi))
elif (None in [f, phi]):
raise Sorry(
"Please specify both MTZ column labels for map_type '%s'."
% map_coeffs.map_type)
labels.extend([f, phi])
if (hasattr(params, "map")):
for map in params.map:
if (map.grid_resolution_factor > 0.5):
# XXX can't we enforce this in phil?
raise Sorry(
"The grid resolution factor for CCP4 and X-PLOR maps " +
"must be 0.5 or less.")
return True
def __init__(self,
fmodel,
map_type_str,
fo_scale,
fc_scale,
use_shelx_weight,
shelx_weight_parameter,
map_calculation_helper=None):
self.mch = map_calculation_helper
self.mnm = mmtbx.map_names(map_name_string = map_type_str)
self.fmodel = fmodel
self.fc_scale = fc_scale
self.fo_scale = fo_scale
self.f_obs = None
self.f_model = None
self.use_shelx_weight = use_shelx_weight
self.shelx_weight_parameter = shelx_weight_parameter
if(not self.mnm.ml_map):
self.f_obs = self.fmodel.f_obs().data()*fo_scale
else:
if(self.mch is None): self.mch = self.fmodel.map_calculation_helper()
if(self.fmodel.hl_coeffs() is None):
self.f_obs = self.mch.f_obs.data()*fo_scale*self.mch.fom
else:
cp = fmodel.combine_phases(map_calculation_helper = self.mch)
self.f_obs = self.mch.f_obs.data()*fo_scale*cp.f_obs_phase_and_fom_source()
def __init__(self,
fmodel,
map_type_str,
acentrics_scale = 2.0,
centrics_scale = 1.0):
"""
Compute x and y for x*Fobs-y*Fmodel given map type string
"""
self.fmodel = fmodel
mnm = mmtbx.map_names(map_name_string = map_type_str)
# R.Read, SIGMAA: 2mFo-DFc (acentrics) & mFo (centrics)
centric_flags = self.fmodel.f_obs().centric_flags().data()
acentric_flags = ~centric_flags
if(mnm.k != 0):
self.fo_scale = flex.double(self.fmodel.f_obs().size(), 1.0)
else: self.fo_scale = flex.double(self.fmodel.f_obs().size(), 0.0)
if(mnm.n != 0):
self.fc_scale = flex.double(self.fmodel.f_obs().size(), 1.0)
else: self.fc_scale = flex.double(self.fmodel.f_obs().size(), 0.0)
abs_kn = abs(mnm.k*mnm.n)
if(mnm.k != abs(mnm.n) and abs_kn > 1.e-6):
self.fo_scale.set_selected(acentric_flags, mnm.k)
self.fo_scale.set_selected( centric_flags, max(mnm.k-centrics_scale,0.))
self.fc_scale.set_selected(acentric_flags, mnm.n)
self.fc_scale.set_selected( centric_flags, max(mnm.n-centrics_scale,0.))
elif(mnm.k == abs(mnm.n) and abs_kn > 1.e-6):
fo_scale_k = self.fo_scale*mnm.k
self.fc_scale_n = self.fc_scale*mnm.n
self.fo_scale.set_selected(acentric_flags, fo_scale_k*acentrics_scale)
self.fo_scale.set_selected( centric_flags, fo_scale_k)
self.fc_scale.set_selected(acentric_flags, self.fc_scale_n*acentrics_scale)
self.fc_scale.set_selected( centric_flags, self.fc_scale_n)
else:
self.fo_scale *= mnm.k
self.fc_scale *= mnm.n
def map_coefficients_from_fmodel(
params,
fmodel = None,
map_calculation_server = None,
post_processing_callback=None,
pdb_hierarchy=None):
assert [fmodel, map_calculation_server].count(None) == 1
from mmtbx import map_tools
import mmtbx
from cctbx import miller
mnm = mmtbx.map_names(map_name_string = params.map_type)
if(mnm.k==0 and abs(mnm.n)==1):
# FIXME Fcalc maps require that fmodel is not None!
if (fmodel is None) :
fmodel = map_calculation_server.fmodel
return compute_f_calc(fmodel, params)
if(fmodel is not None and
fmodel.is_twin_fmodel_manager() and
mnm.phaser_sad_llg):
return None
if(fmodel is not None):
e_map_obj = fmodel.electron_density_map()
xrs = fmodel.xray_structure
else:
e_map_obj = map_calculation_server
xrs = map_calculation_server.fmodel.xray_structure
coeffs = None
coeffs = e_map_obj.map_coefficients(
map_type = params.map_type,
acentrics_scale = params.acentrics_scale,
centrics_pre_scale = params.centrics_pre_scale,
fill_missing = params.fill_missing_f_obs,
isotropize = params.isotropize,
exclude_free_r_reflections=params.exclude_free_r_reflections,
ncs_average=getattr(params, "ncs_average", False),
post_processing_callback=post_processing_callback,
pdb_hierarchy=pdb_hierarchy,
merge_anomalous=True)
if (coeffs is None) : return None
if(params.sharpening):
from mmtbx import map_tools
coeffs, b_sharp = map_tools.sharp_map(
sites_frac = xrs.sites_frac(),
map_coeffs = coeffs,
b_sharp = params.sharpening_b_factor)
# XXX need to figure out why this happens
if (coeffs is None) :
raise RuntimeError(("Map coefficient generation failed (map_type=%s, "
"sharpening=%s, isotropize=%s, anomalous=%s.") %
(params.map_type, params.sharpening, params.isotropize,
fmodel.f_obs().anomalous_flag()))
if(coeffs.anomalous_flag()) :
coeffs = coeffs.average_bijvoet_mates()
return coeffs
def validate_map_params(params):
from mmtbx import map_names
labels = []
for map_coeffs in params.map_coefficients:
if (map_coeffs.map_type is not None):
try:
decode_map = map_names(map_coeffs.map_type)
except RuntimeError, e:
raise Sorry(str(e))
f = map_coeffs.mtz_label_amplitudes
phi = map_coeffs.mtz_label_phases
if (f in labels) or (phi in labels):
raise Sorry((
"The map coefficients with MTZ labels %s,%s duplicates at"
+
" least one previously defined label. You may output multiple sets "
+
"of coefficients with the same map type, but the column labels must "
+ "be unique.") % (f, phi))
elif (None in [f, phi]):
raise Sorry(
"Please specify both MTZ column labels for map_type '%s'."
% map_coeffs.map_type)
labels.extend([f, phi])
def map_coefficients(self,
map_type,
acentrics_scale = 2.0,
centrics_pre_scale = 1.0,
exclude_free_r_reflections=False,
fill_missing=False,
fill_missing_method="f_model",
isotropize=True,
sharp=False,
pdb_hierarchy=None, # XXX required for map_type=llg
merge_anomalous=None,
use_shelx_weight=False,
shelx_weight_parameter=1.5):
map_name_manager = mmtbx.map_names(map_name_string = map_type)
# Special case #1: anomalous map
if(map_name_manager.anomalous):
if(self.anom_diff is not None):
# Formula from page 141 in "The Bijvoet-Difference Fourier Synthesis",
# Jeffrey Roach, METHODS IN ENZYMOLOGY, VOL. 374
return miller.array(miller_set = self.anom_diff,
data = self.anom_diff.data()/(2j))
else: return None
# Special case #2: anomalous residual map
elif (map_name_manager.anomalous_residual):
if (self.anom_diff is not None):
return anomalous_residual_map_coefficients(
fmodel=self.fmodel,
exclude_free_r_reflections=exclude_free_r_reflections)
else : return None
# Special case #3: Phaser SAD LLG map
elif (map_name_manager.phaser_sad_llg):
if (pdb_hierarchy is None):
raise RuntimeError("pdb_hierarchy must not be None when a Phaser SAD "+
"LLG map is requested.")
if (self.anom_diff is not None):
return get_phaser_sad_llg_map_coefficients(
fmodel=self.fmodel,
pdb_hierarchy=pdb_hierarchy)
else :
return None
# Special case #4: Fcalc map
mnm = mmtbx.map_names(map_name_string = map_type)
if(mnm.k==0 and abs(mnm.n)==1):
if(fill_missing):
return self.fmodel.xray_structure.structure_factors(
d_min = self.fmodel.f_obs().d_min()).f_calc()
else:
return self.fmodel.f_obs().structure_factors_from_scatterers(
xray_structure = self.fmodel.xray_structure).f_calc()
#
if(self.mch is None):
self.mch = self.fmodel.map_calculation_helper()
ffs = fo_fc_scales(
fmodel = self.fmodel,
map_type_str = map_type,
acentrics_scale = acentrics_scale,
centrics_scale = centrics_pre_scale)
fo_scale, fc_scale = ffs.fo_scale, ffs.fc_scale
coeffs = combine(
fmodel = self.fmodel,
map_type_str = map_type,
fo_scale = fo_scale,
fc_scale = fc_scale,
map_calculation_helper = self.mch,
use_shelx_weight = use_shelx_weight,
shelx_weight_parameter = shelx_weight_parameter).map_coefficients()
r_free_flags = None
# XXX the default scale array (used for the isotropize option) needs to be
# calculated and processed now to avoid array size errors
scale_default = 1. / (self.fmodel.k_isotropic()*self.fmodel.k_anisotropic())
scale_array = coeffs.customized_copy(data=scale_default)
if (exclude_free_r_reflections):
if (coeffs.anomalous_flag()):
coeffs = coeffs.average_bijvoet_mates()
r_free_flags = self.fmodel.r_free_flags()
if (r_free_flags.anomalous_flag()):
r_free_flags = r_free_flags.average_bijvoet_mates()
scale_array = scale_array.average_bijvoet_mates()
coeffs = coeffs.select(~r_free_flags.data())
scale_array = scale_array.select(~r_free_flags.data())
scale=None
if(isotropize):
if(scale is None):
if (scale_array.anomalous_flag()) and (not coeffs.anomalous_flag()):
scale_array = scale_array.average_bijvoet_mates()
scale = scale_array.data()
coeffs = coeffs.customized_copy(data = coeffs.data()*scale)
if(fill_missing):
if(coeffs.anomalous_flag()):
coeffs = coeffs.average_bijvoet_mates()
coeffs = fill_missing_f_obs(
coeffs = coeffs,
fmodel = self.fmodel,
method = fill_missing_method)
if(sharp):
ss = 1./flex.pow2(coeffs.d_spacings().data()) / 4.
from cctbx import adptbx
b = flex.mean(self.fmodel.xray_structure.extract_u_iso_or_u_equiv() *
adptbx.u_as_b(1))/2
k_sharp = 1./flex.exp(-ss * b)
coeffs = coeffs.customized_copy(data = coeffs.data()*k_sharp)
if (merge_anomalous) and (coeffs.anomalous_flag()):
return coeffs.average_bijvoet_mates()
return coeffs
def exercise():
r = mmtbx.map_names(map_name_string = "anom")
assert r.format() == "anomalous_difference", r.format()
r = mmtbx.map_names(map_name_string = "anomalous")
assert r.format() == "anomalous_difference", r.format()
r = mmtbx.map_names(map_name_string = " Anomal-diff ")
assert r.format() == "anomalous_difference", r.format()
r = mmtbx.map_names(map_name_string = "LLG")
assert r.format() == "phaser_sad_llg"
r = mmtbx.map_names(map_name_string = " SAD")
assert r.format() == "phaser_sad_llg"
#
r = mmtbx.map_names(map_name_string = "3.mFo-2DFc ")
assert r.format() == "3mFobs-2DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "mFo-DFc ")
assert r.format() == "mFobs-DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "mFo-1.DFc ")
assert r.format() == "mFobs-DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "+3.mFo+2DFc ")
assert r.format() == "3mFobs+2DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "-3.mFo+2DFc")
assert r.format() == "-3mFobs+2DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "-2DFc+3.mFo")
assert r.format() == "3mFobs-2DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "- 2 D F c + 3 . m F o ")
assert r.format() == "3mFobs-2DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "- D F ca lc 2.0 + m F oBS 3 .0")
assert r.format() == "3mFobs-2DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "-2DFc-3.mFo")
assert r.format() == "-3mFobs-2DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "+2DFc+3.mFo")
assert r.format() == "3mFobs+2DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "-3.mF_OBS-2D_F_cAlC")
assert r.format() == "-3mFobs-2DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "+3.mF_o+2 . D F_MODEL")
assert r.format() == "3mFobs+2DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "0.75mFobs-1.37DFmodel")
assert r.format() == "0.75mFobs-1.37DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "0.99999mFobs-1.00001DFmodel")
assert r.format() == "0.99999mFobs-1.00001DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "0mFobs-0DFmodel")
assert r.format() == "0mFobs-0DFmodel", r.format()
#
r = mmtbx.map_names(map_name_string = "3.Fo-2Fc ")
assert r.format() == "3Fobs-2Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "Fo-Fc ")
assert r.format() == "Fobs-Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "Fo-1.Fc ")
assert r.format() == "Fobs-Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "+3.Fo+2Fc ")
assert r.format() == "3Fobs+2Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "-3.Fo+2Fc")
assert r.format() == "-3Fobs+2Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "-2Fc+3.Fo")
assert r.format() == "3Fobs-2Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "- 2 F c + 3 . F o ")
assert r.format() == "3Fobs-2Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "- F ca lc 2.0 + F oBS 3 .0")
assert r.format() == "3Fobs-2Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "-2Fc-3.Fo")
assert r.format() == "-3Fobs-2Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "+2Fc+3.Fo")
assert r.format() == "3Fobs+2Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "-3.F_OBS-2_F_cAlC")
assert r.format() == "-3Fobs-2Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "+3.F_o+2 . F_MODEL")
assert r.format() == "3Fobs+2Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "0.75Fobs-1.37Fmodel")
assert r.format() == "0.75Fobs-1.37Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "0.99999Fobs-1.00001Fmodel")
assert r.format() == "0.99999Fobs-1.00001Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "0Fobs-0Fmodel")
assert r.format() == "0Fobs-0Fmodel", r.format()
#
r = mmtbx.map_names(map_name_string = "fc")
assert r.format() == "0Fobs+Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "FMODEL")
assert r.format() == "0Fobs+Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "dfc")
assert r.format() == "0mFobs+DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "dFMODEL")
assert r.format() == "0mFobs+DFmodel", r.format()
#
r = mmtbx.map_names(map_name_string = "fo")
assert r.format() == "Fobs-0Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "FoBS")
assert r.format() == "Fobs-0Fmodel", r.format()
r = mmtbx.map_names(map_name_string = "mfo")
assert r.format() == "mFobs-0DFmodel", r.format()
r = mmtbx.map_names(map_name_string = "MFOBS")
assert r.format() == "mFobs-0DFmodel", r.format()
#
r = mmtbx.map_names(map_name_string = "3.mFo-2DFc__filled")
assert r.format() == "3mFobs-2DFmodel_filled", r.format()
r = mmtbx.map_names(map_name_string = "3.Fo-2Fc+filled")
assert r.format() == "3Fobs-2Fmodel_filled", r.format()
#
def check_expected_error(s):
cntr = 0
try: r = mmtbx.map_names(map_name_string = s)
except Sorry, e:
assert str(e).count("Wrong map type requested: %s"%s)==1
cntr += 1
assert cntr == 1
def check_expected_error(s):
cntr = 0
try: r = mmtbx.map_names(map_name_string = s)
except Sorry, e:
assert str(e).count("Wrong map type requested: %s"%s)==1
cntr += 1
def exercise():
r = mmtbx.map_names(map_name_string="anom")
assert r.format() == "anomalous_difference", r.format()
r = mmtbx.map_names(map_name_string="anomalous")
assert r.format() == "anomalous_difference", r.format()
r = mmtbx.map_names(map_name_string=" Anomal-diff ")
assert r.format() == "anomalous_difference", r.format()
r = mmtbx.map_names(map_name_string="LLG")
assert r.format() == "phaser_sad_llg"
r = mmtbx.map_names(map_name_string=" SAD")
assert r.format() == "phaser_sad_llg"
#
r = mmtbx.map_names(map_name_string="3.mFo-2DFc ")
assert r.format() == "3mFobs-2DFmodel", r.format()
r = mmtbx.map_names(map_name_string="mFo-DFc ")
assert r.format() == "mFobs-DFmodel", r.format()
r = mmtbx.map_names(map_name_string="mFo-1.DFc ")
assert r.format() == "mFobs-DFmodel", r.format()
r = mmtbx.map_names(map_name_string="+3.mFo+2DFc ")
assert r.format() == "3mFobs+2DFmodel", r.format()
r = mmtbx.map_names(map_name_string="-3.mFo+2DFc")
assert r.format() == "-3mFobs+2DFmodel", r.format()
r = mmtbx.map_names(map_name_string="-2DFc+3.mFo")
assert r.format() == "3mFobs-2DFmodel", r.format()
r = mmtbx.map_names(map_name_string="- 2 D F c + 3 . m F o ")
assert r.format() == "3mFobs-2DFmodel", r.format()
r = mmtbx.map_names(map_name_string="- D F ca lc 2.0 + m F oBS 3 .0")
assert r.format() == "3mFobs-2DFmodel", r.format()
r = mmtbx.map_names(map_name_string="-2DFc-3.mFo")
assert r.format() == "-3mFobs-2DFmodel", r.format()
r = mmtbx.map_names(map_name_string="+2DFc+3.mFo")
assert r.format() == "3mFobs+2DFmodel", r.format()
r = mmtbx.map_names(map_name_string="-3.mF_OBS-2D_F_cAlC")
assert r.format() == "-3mFobs-2DFmodel", r.format()
r = mmtbx.map_names(map_name_string="+3.mF_o+2 . D F_MODEL")
assert r.format() == "3mFobs+2DFmodel", r.format()
r = mmtbx.map_names(map_name_string="0.75mFobs-1.37DFmodel")
assert r.format() == "0.75mFobs-1.37DFmodel", r.format()
r = mmtbx.map_names(map_name_string="0.99999mFobs-1.00001DFmodel")
assert r.format() == "0.99999mFobs-1.00001DFmodel", r.format()
r = mmtbx.map_names(map_name_string="0mFobs-0DFmodel")
assert r.format() == "0mFobs-0DFmodel", r.format()
#
r = mmtbx.map_names(map_name_string="3.Fo-2Fc ")
assert r.format() == "3Fobs-2Fmodel", r.format()
r = mmtbx.map_names(map_name_string="Fo-Fc ")
assert r.format() == "Fobs-Fmodel", r.format()
r = mmtbx.map_names(map_name_string="Fo-1.Fc ")
assert r.format() == "Fobs-Fmodel", r.format()
r = mmtbx.map_names(map_name_string="+3.Fo+2Fc ")
assert r.format() == "3Fobs+2Fmodel", r.format()
r = mmtbx.map_names(map_name_string="-3.Fo+2Fc")
assert r.format() == "-3Fobs+2Fmodel", r.format()
r = mmtbx.map_names(map_name_string="-2Fc+3.Fo")
assert r.format() == "3Fobs-2Fmodel", r.format()
r = mmtbx.map_names(map_name_string="- 2 F c + 3 . F o ")
assert r.format() == "3Fobs-2Fmodel", r.format()
r = mmtbx.map_names(map_name_string="- F ca lc 2.0 + F oBS 3 .0")
assert r.format() == "3Fobs-2Fmodel", r.format()
r = mmtbx.map_names(map_name_string="-2Fc-3.Fo")
assert r.format() == "-3Fobs-2Fmodel", r.format()
r = mmtbx.map_names(map_name_string="+2Fc+3.Fo")
assert r.format() == "3Fobs+2Fmodel", r.format()
r = mmtbx.map_names(map_name_string="-3.F_OBS-2_F_cAlC")
assert r.format() == "-3Fobs-2Fmodel", r.format()
r = mmtbx.map_names(map_name_string="+3.F_o+2 . F_MODEL")
assert r.format() == "3Fobs+2Fmodel", r.format()
r = mmtbx.map_names(map_name_string="0.75Fobs-1.37Fmodel")
assert r.format() == "0.75Fobs-1.37Fmodel", r.format()
r = mmtbx.map_names(map_name_string="0.99999Fobs-1.00001Fmodel")
assert r.format() == "0.99999Fobs-1.00001Fmodel", r.format()
r = mmtbx.map_names(map_name_string="0Fobs-0Fmodel")
assert r.format() == "0Fobs-0Fmodel", r.format()
#
r = mmtbx.map_names(map_name_string="fc")
assert r.format() == "0Fobs+Fmodel", r.format()
r = mmtbx.map_names(map_name_string="FMODEL")
assert r.format() == "0Fobs+Fmodel", r.format()
r = mmtbx.map_names(map_name_string="dfc")
assert r.format() == "0mFobs+DFmodel", r.format()
r = mmtbx.map_names(map_name_string="dFMODEL")
assert r.format() == "0mFobs+DFmodel", r.format()
#
r = mmtbx.map_names(map_name_string="fo")
assert r.format() == "Fobs-0Fmodel", r.format()
r = mmtbx.map_names(map_name_string="FoBS")
assert r.format() == "Fobs-0Fmodel", r.format()
r = mmtbx.map_names(map_name_string="mfo")
assert r.format() == "mFobs-0DFmodel", r.format()
r = mmtbx.map_names(map_name_string="MFOBS")
assert r.format() == "mFobs-0DFmodel", r.format()
#
r = mmtbx.map_names(map_name_string="3.mFo-2DFc__filled")
assert r.format() == "3mFobs-2DFmodel_filled", r.format()
r = mmtbx.map_names(map_name_string="3.Fo-2Fc+filled")
assert r.format() == "3Fobs-2Fmodel_filled", r.format()
#
def check_expected_error(s):
cntr = 0
try:
r = mmtbx.map_names(map_name_string=s)
except Sorry, e:
assert str(e).count("Wrong map type requested: %s" % s) == 1
cntr += 1
assert cntr == 1
def map_coefficients(self,
map_type,
acentrics_scale = 2.0,
centrics_pre_scale = 1.0,
exclude_free_r_reflections=False,
fill_missing=False,
fill_missing_method="f_model",
ncs_average=False,
isotropize=True,
sharp=False,
post_processing_callback=None,
pdb_hierarchy=None, # XXX required for map_type=llg
merge_anomalous=None,
use_shelx_weight=False,
shelx_weight_parameter=1.5) :
map_name_manager = mmtbx.map_names(map_name_string = map_type)
# Special case #1: anomalous map
if(map_name_manager.anomalous):
if(self.anom_diff is not None):
# Formula from page 141 in "The Bijvoet-Difference Fourier Synthesis",
# Jeffrey Roach, METHODS IN ENZYMOLOGY, VOL. 374
return miller.array(miller_set = self.anom_diff,
data = self.anom_diff.data()/(2j))
else: return None
# Special case #2: anomalous residual map
elif (map_name_manager.anomalous_residual) :
if (self.anom_diff is not None) :
return anomalous_residual_map_coefficients(
fmodel=self.fmodel,
exclude_free_r_reflections=exclude_free_r_reflections)
else : return None
# Special case #3: Phaser SAD LLG map
elif (map_name_manager.phaser_sad_llg) :
if (pdb_hierarchy is None) :
raise RuntimeError("pdb_hierarchy must not be None when a Phaser SAD "+
"LLG map is requested.")
if (self.anom_diff is not None) :
return get_phaser_sad_llg_map_coefficients(
fmodel=self.fmodel,
pdb_hierarchy=pdb_hierarchy)
else :
return None
# Special case #4: Fcalc map
mnm = mmtbx.map_names(map_name_string = map_type)
if(mnm.k==0 and abs(mnm.n)==1):
if(fill_missing):
return self.fmodel.xray_structure.structure_factors(
d_min = self.fmodel.f_obs().d_min()).f_calc()
else:
return self.fmodel.f_obs().structure_factors_from_scatterers(
xray_structure = self.fmodel.xray_structure).f_calc()
#
if(self.mch is None):
self.mch = self.fmodel.map_calculation_helper()
ffs = fo_fc_scales(
fmodel = self.fmodel,
map_type_str = map_type,
acentrics_scale = acentrics_scale,
centrics_scale = centrics_pre_scale)
fo_scale, fc_scale = ffs.fo_scale, ffs.fc_scale
coeffs = combine(
fmodel = self.fmodel,
map_type_str = map_type,
fo_scale = fo_scale,
fc_scale = fc_scale,
map_calculation_helper = self.mch,
use_shelx_weight = use_shelx_weight,
shelx_weight_parameter = shelx_weight_parameter).map_coefficients()
r_free_flags = None
# XXX the default scale array (used for the isotropize option) needs to be
# calculated and processed now to avoid array size errors
scale_default = 1. / (self.fmodel.k_isotropic()*self.fmodel.k_anisotropic())
scale_array = coeffs.customized_copy(data=scale_default)
if (exclude_free_r_reflections) :
if (coeffs.anomalous_flag()) :
coeffs = coeffs.average_bijvoet_mates()
r_free_flags = self.fmodel.r_free_flags()
if (r_free_flags.anomalous_flag()) :
r_free_flags = r_free_flags.average_bijvoet_mates()
scale_array = scale_array.average_bijvoet_mates()
coeffs = coeffs.select(~r_free_flags.data())
scale_array = scale_array.select(~r_free_flags.data())
scale=None
if (ncs_average) and (post_processing_callback is not None) :
# XXX NCS averaging done here
assert hasattr(post_processing_callback, "__call__")
coeffs = post_processing_callback(
map_coeffs=coeffs,
fmodel=self.fmodel,
map_type=map_type)
if(isotropize):
if(scale is None):
if (scale_array.anomalous_flag()) and (not coeffs.anomalous_flag()) :
scale_array = scale_array.average_bijvoet_mates()
scale = scale_array.data()
coeffs = coeffs.customized_copy(data = coeffs.data()*scale)
if(fill_missing):
if(coeffs.anomalous_flag()):
coeffs = coeffs.average_bijvoet_mates()
coeffs = fill_missing_f_obs(
coeffs = coeffs,
fmodel = self.fmodel,
method = fill_missing_method)
if(sharp):
ss = 1./flex.pow2(coeffs.d_spacings().data()) / 4.
from cctbx import adptbx
b = flex.mean(self.fmodel.xray_structure.extract_u_iso_or_u_equiv() *
adptbx.u_as_b(1))/2
k_sharp = 1./flex.exp(-ss * b)
coeffs = coeffs.customized_copy(data = coeffs.data()*k_sharp)
if (merge_anomalous) and (coeffs.anomalous_flag()) :
return coeffs.average_bijvoet_mates()
return coeffs