iotbx.table_one
index
/net/chevy/raid1/nat/src/cctbx_project/iotbx/table_one.py

WARNING: IN DEVELOPMENT AND INCOMPLETE.
 
Tools for formatting the standard "Table 1" in MX papers.  Relies on other
methods (phenix.refine, phenix.model_vs_data, phenix.merging_statistics, etc.)
to extract statistics for display.

 
Modules
       
re
libtbx.str_utils

 
Classes
       
libtbx.slots_getstate_setstate(__builtin__.object)
column
table

 
class column(libtbx.slots_getstate_setstate)
    Statistics for a single structure, including optional high-resolution
shell.  Any combination of standard attributes is permitted as keyword
arguments to the constructor.  (Note that the high-resolution shell is
itself another instance of this class, with fewer keywords specified.)
 
 
Method resolution order:
column
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__init__(self, **kwds)
__repr__(self)
add_outer_shell(self, **kwds)
format_stat(self, name)

Data descriptors defined here:
adp_mean
adp_mean_lig
adp_mean_mm
adp_mean_wat
angle_rmsd
anomalous_flag
bond_rmsd
cc_free
cc_one_half
cc_star
cc_work
clashscore
completeness
d_max_min
i_over_sigma
label
multiplicity
n_atoms
n_free
n_ligand_atoms
n_macro_atoms
n_nuc
n_refl
n_refl_all
n_refl_refine
n_residues
n_waters
outer_shell
r_free
r_meas
r_sym
r_work
rama_allowed
rama_favored
rama_outliers
rota_outliers
space_group
unit_cell
wavelength
wilson_b

Data and other attributes defined here:
kw = ('adp_mean_wat', ' solvent', '%.2f', None)

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

 
class table(libtbx.slots_getstate_setstate)
    Combined table of statistics for one or more structures published together.
 
 
Method resolution order:
table
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__init__(self, text_field_separation=4, count_anomalous_pairs_separately=False)
add_column(self, col)
format_as_csv(self)
format_as_rtf(self)
format_as_txt(self)
save_csv(self, file_name)
save_rtf(self, file_name)
save_txt(self, file_name)

Data descriptors defined here:
columns
count_anomalous_pairs_separately
text_field_separation

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

 
Functions
       
format_d_max_min(d_max_min)
Format a resolution range (e.g. '30 - 2.56')
format_value(fs, value)
# XXX is this superfluous?
resize_column(cell_values, alignment='right')

 
Data
        angstrom = '\xc3\x85'
cif_tag = None
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
fs = '%.2f'
keyword_formats = {'adp_mean': '%.2f', 'adp_mean_lig': '%.2f', 'adp_mean_mm': '%.2f', 'adp_mean_wat': '%.2f', 'angle_rmsd': '%.2f', 'bond_rmsd': '%.3f', 'cc_free': '%.3f', 'cc_one_half': '%.3g', 'cc_star': '%.3g', 'cc_work': '%.3f', ...}
keywords = [('wavelength', 'Wavelength', '%.4g', None), ('d_max_min', 'Resolution range', '%.3g - %.3g', None), ('space_group', 'Space group', '%s', None), ('unit_cell', 'Unit cell', '%g %g %g %g %g %g', None), ('n_refl_all', 'Total reflections', '%d', '_reflns.pdbx_number_measured_all'), ('n_refl', 'Unique reflections', '%d', '_reflns.number_obs'), ('multiplicity', 'Multiplicity', '%.1f', '_reflns.pdbx_redundancy'), ('completeness', 'Completeness (%)', '%.2f', '_reflns.percent_possible_obs'), ('i_over_sigma', 'Mean I/sigma(I)', '%.2f', '_reflns.pdbx_netI_over_sigmaI'), ('wilson_b', 'Wilson B-factor', '%.2f', '_reflns.B_iso_Wilson_estimate'), ('r_sym', 'R-merge', '%.4g', '_reflns.pdbx_Rmerge_I_obs'), ('r_meas', 'R-meas', '%.4g', '_reflns.pdbx_Rrim_I_obs'), ('cc_one_half', 'CC1/2', '%.3g', '_reflns.phenix_cc_1/2'), ('cc_star', 'CC*', '%.3g', '_reflns.phenix_cc_star'), ('n_refl_refine', 'Reflections used in refinement', '%d', None), ('n_free', 'Reflections used for R-free', '%d', '_refine.ls_number_reflns_R_free'), ('r_work', 'R-work', '%.4f', '_refine.ls_R_factor_R_work'), ('r_free', 'R-free', '%.4f', '_refine.ls_R_factor_R_free'), ('cc_work', 'CC(work)', '%.3f', None), ('cc_free', 'CC(free)', '%.3f', None), ...]
kw = 'adp_mean_wat'
label = ' solvent'
optional_if_none = set(['adp_mean_lig', 'adp_mean_wat', 'cc_free', 'cc_star', 'cc_work', 'n_ligand_atoms', ...])