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

 
Package Contents
       
analyze_peptides
cbetadev
clashscore
convert_lists
datasets
ensembles
experimental
graphics
ligands
model_properties
molprobity (package)
ramalyze
regression (package)
restraints
rna_validate
rotalyze
sequence
utils
waters

 
Classes
       
__builtin__.object
dummy_validation
libtbx.slots_getstate_setstate(__builtin__.object)
atom_base
atom(atom_base, entity)
atom_info
entity
atoms
residue
validation

 
class atom(atom_base, entity)
    Base class for validation results for a single atom.  This is distinct from
the atom_info class above, which is used to track individual atoms within
a multi-atom validation result.
 
 
Method resolution order:
atom
atom_base
entity
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
is_single_residue_object(self)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)
altloc
atom_selection
b_iso
chain_id
element
icode
name
occupancy
outlier
resname
resseq
score
segid
symop
xyz

Methods inherited from atom_base:
__cmp__(self, other)
__eq__(self, other)
__init__(self, **kwds)
atom_group_id_str(self)
id_str(self, ignore_altloc=False)
residue_group_id_str(self)

Data and other attributes inherited from atom_base:
__atom_attr__ = ['name', 'element', 'xyz', 'symop', 'occupancy', 'b_iso']
__atom_slots__ = ['chain_id', 'resseq', 'icode', 'resname', 'altloc', 'segid', 'name', 'element', 'xyz', 'symop', 'occupancy', 'b_iso']

Methods inherited from entity:
__hash__(self)
__str__(self)
as_kinemage(self)
Returns a kinemage string for displaying an outlier.
as_list(self)
Optional; returns old format used by some tools in mmtbx.validation.
as_selection_string(self)
Returns PDB atom selection string for the atom(s) involved.
as_string(self, prefix='')
as_table_row_molprobity(self)
Returns a list of formatted table cells for display by MolProbity.
as_table_row_phenix(self)
Returns a list of formatted table cells for display by Phenix.
format_old(self)
format_score(self, replace_none_with='None')
is_outlier(self)
zoom_info(self)
Returns data needed to zoom/recenter the graphics programs from the Phenix
GUI.

Static methods inherited from entity:
header()
Format for header in result listings.

Data and other attributes inherited from entity:
molprobity_table_labels = []
score_format = '%s'

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

 
class atom_base(libtbx.slots_getstate_setstate)
    Container for metadata for a single atom, in the context of validation
results involving multiple atoms.  Intended to be used as-is inside various
atoms classes.
 
 
Method resolution order:
atom_base
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__cmp__(self, other)
__eq__(self, other)
__init__(self, **kwds)
atom_group_id_str(self)
id_str(self, ignore_altloc=False)
residue_group_id_str(self)

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:
__atom_attr__ = ['name', 'element', 'xyz', 'symop', 'occupancy', 'b_iso']
__atom_slots__ = ['chain_id', 'resseq', 'icode', 'resname', 'altloc', 'segid', 'name', 'element', 'xyz', 'symop', 'occupancy', 'b_iso']

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

 
class atom_info(atom_base)
    Container for metadata for a single atom, in the context of validation
results involving multiple atoms.  Intended to be used as-is inside various
atoms classes.
 
 
Method resolution order:
atom_info
atom_base
libtbx.slots_getstate_setstate
__builtin__.object

Data descriptors defined here:
altloc
b_iso
chain_id
element
icode
name
occupancy
resname
resseq
segid
symop
xyz

Methods inherited from atom_base:
__cmp__(self, other)
__eq__(self, other)
__init__(self, **kwds)
atom_group_id_str(self)
id_str(self, ignore_altloc=False)
residue_group_id_str(self)

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

Data and other attributes inherited from atom_base:
__atom_attr__ = ['name', 'element', 'xyz', 'symop', 'occupancy', 'b_iso']
__atom_slots__ = ['chain_id', 'resseq', 'icode', 'resname', 'altloc', 'segid', 'name', 'element', 'xyz', 'symop', 'occupancy', 'b_iso']

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

 
class atoms(entity)
    Base class for validation results involving a specific set of atoms, such
as covalent geometry restraints, clashes, etc.
 
 
Method resolution order:
atoms
entity
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__eq__(self, other)
get_altloc(self)
is_in_chain(self, chain_id)
is_single_residue_object(self)
n_atoms(self)
sites_cart(self)

Data descriptors defined here:
atom_selection
atoms_info
outlier
score
xyz

Data and other attributes defined here:
__atoms_attr__ = ['atoms_info']

Methods inherited from entity:
__cmp__(self, other)
__hash__(self)
__init__(self, **kwds)
__str__(self)
as_kinemage(self)
Returns a kinemage string for displaying an outlier.
as_list(self)
Optional; returns old format used by some tools in mmtbx.validation.
as_selection_string(self)
Returns PDB atom selection string for the atom(s) involved.
as_string(self, prefix='')
as_table_row_molprobity(self)
Returns a list of formatted table cells for display by MolProbity.
as_table_row_phenix(self)
Returns a list of formatted table cells for display by Phenix.
format_old(self)
format_score(self, replace_none_with='None')
id_str(self, ignore_altloc=None)
Returns a formatted (probably fixed-width) string describing the molecular
entity being validation, independent of the analysis type.
is_outlier(self)
zoom_info(self)
Returns data needed to zoom/recenter the graphics programs from the Phenix
GUI.

Static methods inherited from entity:
header()
Format for header in result listings.

Data and other attributes inherited from entity:
molprobity_table_labels = []
score_format = '%s'

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

 
class dummy_validation(__builtin__.object)
    Placeholder for cases where values may be undefined because of molecule type
(e.g. all-RNA structures) but we want to substitute None automatically.
 
  Methods defined here:
__getattr__(self, name)
__nonzero__(self)

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

 
class entity(libtbx.slots_getstate_setstate)
    Base class for all validation results.  This includes a boolean outlier flag,
the information used to zoom in the Phenix GUI (optional, but strongly
recommended), and some kind of numerical score (also optional, but strongly
recommended - although some analyses may require multiple distinct scores).
 
 
Method resolution order:
entity
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__cmp__(self, other)
__eq__(self, other)
Compare two validation results to determine whether they correspond to the
same molecular entity and analysis type.  This is intended to be used for
analysis of a structure before-and-after refinement (etc.).
__hash__(self)
__init__(self, **kwds)
__str__(self)
as_kinemage(self)
Returns a kinemage string for displaying an outlier.
as_list(self)
Optional; returns old format used by some tools in mmtbx.validation.
as_selection_string(self)
Returns PDB atom selection string for the atom(s) involved.
as_string(self, prefix='')
as_table_row_molprobity(self)
Returns a list of formatted table cells for display by MolProbity.
as_table_row_phenix(self)
Returns a list of formatted table cells for display by Phenix.
format_old(self)
format_score(self, replace_none_with='None')
id_str(self, ignore_altloc=None)
Returns a formatted (probably fixed-width) string describing the molecular
entity being validation, independent of the analysis type.
is_outlier(self)
is_single_residue_object(self)
zoom_info(self)
Returns data needed to zoom/recenter the graphics programs from the Phenix
GUI.

Static methods defined here:
header()
Format for header in result listings.

Data descriptors defined here:
atom_selection
outlier
score
xyz

Data and other attributes defined here:
molprobity_table_labels = []
score_format = '%s'

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

 
class residue(entity)
    Base class for validation information about a single residue, which depending
on context could mean either any one of the residue_group, atom_group, or
residue objects from the PDB hierarchy.
 
 
Method resolution order:
residue
entity
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__eq__(self, other)
assert_all_attributes_defined(self)
atom_group_id_str(self)
atom_selection_string(self)
id_str(self, ignore_altloc=False)
is_same_residue(self, other, ignore_altloc=False)
# XXX probably needs to be flexible about altloc...
is_same_residue_group(self, other)
is_single_residue_object(self)
residue_group_id_str(self)
residue_id(self, ignore_altloc=False)
resseq_as_int(self)
set_coordinates_from_hierarchy(self, pdb_hierarchy, atom_selection_cache=None)
simple_id(self)

Data descriptors defined here:
altloc
atom_selection
chain_id
icode
occupancy
outlier
resid
resname
resseq
score
segid
xyz

Methods inherited from entity:
__cmp__(self, other)
__hash__(self)
__init__(self, **kwds)
__str__(self)
as_kinemage(self)
Returns a kinemage string for displaying an outlier.
as_list(self)
Optional; returns old format used by some tools in mmtbx.validation.
as_selection_string(self)
Returns PDB atom selection string for the atom(s) involved.
as_string(self, prefix='')
as_table_row_molprobity(self)
Returns a list of formatted table cells for display by MolProbity.
as_table_row_phenix(self)
Returns a list of formatted table cells for display by Phenix.
format_old(self)
format_score(self, replace_none_with='None')
is_outlier(self)
zoom_info(self)
Returns data needed to zoom/recenter the graphics programs from the Phenix
GUI.

Static methods inherited from entity:
header()
Format for header in result listings.

Data and other attributes inherited from entity:
molprobity_table_labels = []
score_format = '%s'

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

 
class validation(libtbx.slots_getstate_setstate)
    Container for a set of results from a single analysis (rotamers, clashes,
etc.).  This is responsible for the console display of these results and
associated statistics.  Individual modules will subclass this and override
the unimplemented methods.
 
 
Method resolution order:
validation
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__init__(self)
as_coot_data(self)
Return results in a format suitable for unpickling in Coot.
as_gui_table_data(self, outliers_only=True, include_zoom=False)
Format results for display in the Phenix GUI.
as_kinemage(self)
coot_todo(self)
find_atom_group(self, other=None, atom_group_id_str=None)
Attempt to locate a result corresponding to a given atom_group object.
find_residue(self, other=None, residue_id_str=None)
get_outliers_count_and_fraction(self)
get_outliers_goal(self)
get_result_class(self)
iter_results(self, outliers_only=True)
outlier_selection(self)
Return a flex.size_t object containing the i_seqs of atoms flagged as
outliers (either individually or as part of an atom_group).  This needs
to be implemented in the underlying classes unless they include a
pre-built _outlier_i_seqs attribute.
show(self, out=<open file '<stdout>', mode 'w'>, prefix=' ', outliers_only=True, verbose=True)
show_old_output(self, out=<open file '<stdout>', mode 'w'>, verbose=False)
For backwards compatibility with output formats of older utilities
(phenix.ramalyze et al.).
show_summary(self, out=<open file '<stdout>', mode 'w'>, prefix='')

Data descriptors defined here:
n_outliers
n_total
percent_outliers
results

Data and other attributes defined here:
gui_formats = []
gui_list_headers = []
output_header = None
program_description = None

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

 
Functions
       
get_atoms_info(pdb_atoms, iselection, use_segids_in_place_of_chainids=False)

 
Data
        __residue_attr__ = ['chain_id', 'resseq', 'icode', 'resname', 'altloc', 'segid']
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
molprobity_cmdline_phil_str = "\n model = None\n .type = path\n .help =... True\n .type = bool\n .help = '''Verbose'''\n"