mmtbx.scaling
index
/net/chevy/raid1/nat/src/cctbx_project/mmtbx/scaling/__init__.py

Base module for Xtriage and related scaling functionality; this imports the
Boost.Python extensions into the local namespace, and provides core functions
for displaying the results of Xtriage.

 
Package Contents
       
absence_likelihood
absences
absolute_scaling
basic_analyses
data_statistics
fa_estimation
fest
make_param
massage_twin_detwin_data
matthews
outlier_plots
outlier_rejection
pair_analyses
pre_scale
random_omit
relative_scaling
relative_wilson
remove_outliers
rip_scale
sad_scale
sigmaa_estimation
sir_scale
siras_scale
ta_alpha_beta_calc
thorough_outlier_test
tst_outlier
tst_scaling
tst_sigmaa
tst_xtriage_massage_data
tst_xtriage_twin_analyses
twin_analyses
twin_analyses_new
twmad_scale
xtriage

 
Classes
       
__builtin__.object
xtriage_analysis
libtbx.slots_getstate_setstate(__builtin__.object)
data_analysis
xtriage_output
printed_output

 
class data_analysis(libtbx.slots_getstate_setstate)
    
Method resolution order:
data_analysis
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
show(self, out=<open file '<stdout>', mode 'w'>, prefix='')

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

Methods inherited from libtbx.slots_getstate_setstate:
__getstate__(self)
__setstate__(self, state)

 
class printed_output(xtriage_output)
    Output class for displaying raw text with minimal formatting.
 
 
Method resolution order:
printed_output
xtriage_output
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__init__(self, out)
newline(self)
show_header(self, text)
show_lines(self, text)
show_paragraph_header(self, text)
show_plot(self, table)
show_plots_row(self, tables)
show_preformatted_text(self, text)
show_sub_header(self, title)
show_table(self, table, indent=0, plot_button=None)
show_text(self, text)
show_text_columns(self, rows, indent=0)
warn(self, text)
write(self, text)

Data descriptors defined here:
out

Methods inherited from xtriage_output:
flush(self)
Support for generic filehandle methods.
show(self, text)

Data descriptors inherited from xtriage_output:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

Data and other attributes inherited from xtriage_output:
gui_output = False

Methods inherited from libtbx.slots_getstate_setstate:
__getstate__(self)
__setstate__(self, state)

 
class xtriage_analysis(__builtin__.object)
    Base class for analyses performed by Xtriage.  This does not impose any
restrictions on content or functionality, but simply provides a show()
method suitable for either filehandle-like objects or objects derived from
the xtriage_output class.  Child classes should implement _show_impl.
 
  Methods defined here:
show(self, out=None)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class xtriage_output(libtbx.slots_getstate_setstate)
    Base class for generic output wrappers.
 
 
Method resolution order:
xtriage_output
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
flush(self)
Support for generic filehandle methods.
newline(self)
Print a newline and nothing else.
show(self, text)
show_header(self, title)
Start a new section with the specified title.
show_lines(self, text)
Show partially formatted text, preserving paragraph breaks.
show_paragraph_header(self, text)
Show a header/title for a paragraph or small block of text.
show_plot(self, table)
Display a plot, if supported by the given output class.
show_plots_row(self, tables)
Display a series of plots in a single row.  Only used for the Phenix GUI.
show_preformatted_text(self, text)
Show text with spaces and line breaks preserved; in some contexts this
will be done using a monospaced font.
show_sub_header(self, title)
Start a sub-section with the specified title.
show_table(self, table, indent=0, plot_button=None)
Display a formatted table.
show_text(self, text)
Show unformatted text.
show_text_columns(self, rows, indent=0)
Display a set of left-justified text columns.  The number of columns is
arbitrary but this will usually be key:value pairs.
warn(self, text)
Display a warning message.
write(self, text)
Support for generic filehandle methods.

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

Data and other attributes defined here:
gui_output = False

Methods inherited from libtbx.slots_getstate_setstate:
__getstate__(self)
__setstate__(self, state)

 
Functions
       
StringIO(...)
StringIO([s]) -- Return a StringIO-like stream for reading or writing
gamma_prot(...)
gamma_prot( (float)arg1) -> float :
 
    C++ signature :
        double gamma_prot(double)
get_d_star_sq_high_limit(...)
get_d_star_sq_high_limit() -> float :
 
    C++ signature :
        double get_d_star_sq_high_limit()
get_d_star_sq_low_limit(...)
get_d_star_sq_low_limit() -> float :
 
    C++ signature :
        double get_d_star_sq_low_limit()
get_gamma_prot(...)
get_gamma_prot( (object)arg1) -> double :
 
    C++ signature :
        scitbx::af::shared<double> get_gamma_prot(scitbx::af::const_ref<double, scitbx::af::trivial_accessor>)
get_sigma_prot_sq(...)
get_sigma_prot_sq( (object)arg1, (float)arg2) -> double :
 
    C++ signature :
        scitbx::af::shared<double> get_sigma_prot_sq(scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,double)
kernel_normalisation(...)
kernel_normalisation( (object)d_star_sq_hkl, (object)I_hkl, (object)epsilon, (object)d_star_sq_array, (float)kernel_width) -> double :
 
    C++ signature :
        scitbx::af::shared<double> kernel_normalisation(scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,double)
ml_normalise(...)
ml_normalise( (object)d_star_sq, (object)f_obs, (object)epsilon, (object)sigma_sq, (object)gamma_prot, (bool)centric, (float)p_scale, (float)p_B_wilson [, (bool)wiggle=True]) -> double :
 
    C++ signature :
        scitbx::af::shared<double> ml_normalise(scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<bool, scitbx::af::trivial_accessor>,double,double [,bool=True])
ml_normalise_aniso(...)
ml_normalise_aniso( (miller_index)hkl, (object)f_obs, (float)p_scale, (unit_cell)unit_cell, (object)u_star [, (bool)volume_correction_rwgk=False]) -> double :
 
    C++ signature :
        scitbx::af::shared<double> ml_normalise_aniso(scitbx::af::const_ref<cctbx::miller::index<int>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,double,cctbx::uctbx::unit_cell,scitbx::sym_mat3<double> [,bool=False])
sigma_prot_sq(...)
sigma_prot_sq( (float)arg1, (float)arg2) -> float :
 
    C++ signature :
        double sigma_prot_sq(double,double)
wilson_get_aniso_scale(...)
wilson_get_aniso_scale( (object)arg1, (float)arg2, (float)arg3, (object)arg4) -> float :
 
    C++ signature :
        double wilson_get_aniso_scale(cctbx::miller::index<int>,double,double,scitbx::sym_mat3<double>)
wilson_single_nll(...)
wilson_single_nll( (float)d_star_sq, (float)f_obs, (float)sigma_f_obs, (float)epsilon, (float)sigma_sq, (float)gamma_prot, (bool)centric, (float)p_scale, (float)p_B_wilson [, (bool)transform=True]) -> float :
 
    C++ signature :
        double wilson_single_nll(double,double,double,double,double,double,bool,double,double [,bool=True])
wilson_single_nll_aniso(...)
wilson_single_nll_aniso( (object)arg1, (float)arg2, (float)arg3, (float)arg4, (float)arg5, (float)arg6, (bool)arg7, (float)arg8, (unit_cell)arg9, (object)arg10) -> float :
 
    C++ signature :
        double wilson_single_nll_aniso(cctbx::miller::index<int>,double,double,double,double,double,bool,double,cctbx::uctbx::unit_cell,scitbx::sym_mat3<double>)
wilson_single_nll_aniso_gradient(...)
wilson_single_nll_aniso_gradient( (object)arg1, (float)arg2, (float)arg3, (float)arg4, (float)arg5, (float)arg6, (bool)arg7, (float)arg8, (unit_cell)arg9, (object)arg10) -> double :
 
    C++ signature :
        scitbx::af::shared<double> wilson_single_nll_aniso_gradient(cctbx::miller::index<int>,double,double,double,double,double,bool,double,cctbx::uctbx::unit_cell,scitbx::sym_mat3<double>)
wilson_single_nll_gradient(...)
wilson_single_nll_gradient( (float)d_star_sq, (float)f_obs, (float)sigma_f_obs, (float)epsilon, (float)sigma_sq, (float)gamma_prot, (bool)centric, (float)p_scale, (float)p_B_wilson) -> tuple :
 
    C++ signature :
        scitbx::af::tiny<double, 2ul> wilson_single_nll_gradient(double,double,double,double,double,double,bool,double,double)
wilson_total_nll(...)
wilson_total_nll( (object)d_star_sq, (object)f_obs, (object)sigma_f_obs, (object)epsilon, (object)sigma_sq, (object)gamma_prot, (bool)centric, (float)p_scale, (float)p_B_wilson [, (bool)transform=True]) -> float :
 
    C++ signature :
        double wilson_total_nll(scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<bool, scitbx::af::trivial_accessor>,double,double [,bool=True])
wilson_total_nll_aniso(...)
wilson_total_nll_aniso( (miller_index)arg1, (object)arg2, (object)arg3, (object)arg4, (object)arg5, (object)arg6, (bool)arg7, (float)arg8, (unit_cell)arg9, (object)arg10) -> float :
 
    C++ signature :
        double wilson_total_nll_aniso(scitbx::af::const_ref<cctbx::miller::index<int>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<bool, scitbx::af::trivial_accessor>,double,cctbx::uctbx::unit_cell,scitbx::sym_mat3<double>)
wilson_total_nll_aniso_gradient(...)
wilson_total_nll_aniso_gradient( (miller_index)arg1, (object)arg2, (object)arg3, (object)arg4, (object)arg5, (object)arg6, (bool)arg7, (float)arg8, (unit_cell)arg9, (object)arg10) -> double :
 
    C++ signature :
        scitbx::af::shared<double> wilson_total_nll_aniso_gradient(scitbx::af::const_ref<cctbx::miller::index<int>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<bool, scitbx::af::trivial_accessor>,double,cctbx::uctbx::unit_cell,scitbx::sym_mat3<double>)
wilson_total_nll_aniso_gradient_orbit(...)
wilson_total_nll_aniso_gradient_orbit( (miller_index)arg1, (object)arg2, (object)arg3, (object)arg4, (object)arg5, (object)arg6, (bool)arg7, (float)arg8, (unit_cell)arg9, (space_group)arg10, (object)arg11) -> double :
 
    C++ signature :
        scitbx::af::shared<double> wilson_total_nll_aniso_gradient_orbit(scitbx::af::const_ref<cctbx::miller::index<int>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<bool, scitbx::af::trivial_accessor>,double,cctbx::uctbx::unit_cell,cctbx::sgtbx::space_group,scitbx::sym_mat3<double>)
wilson_total_nll_gradient(...)
wilson_total_nll_gradient( (object)d_star_sq, (object)f_obs, (object)sigma_f_obs, (object)epsilon, (object)sigma_sq, (object)gamma_prot, (bool)centric, (float)p_scale, (float)p_B_wilson) -> tuple :
 
    C++ signature :
        scitbx::af::tiny<double, 2ul> wilson_total_nll_gradient(scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<bool, scitbx::af::trivial_accessor>,double,double)

 
Data
        division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)