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

 
Modules
       
cctbx.adp_restraints
smtbx.refinement.constraints
cctbx.crystal
cctbx.array_family.flex
cctbx.geometry_restraints
smtbx.refinement.least_squares
libtbx
scitbx
cctbx.sgtbx
smtbx
smtbx.refinement.restraints.adp_restraints
cctbx.xray

 
Classes
       
__builtin__.object
crystal_symmetry_builder
crystal_structure_builder
restrained_crystal_structure_builder
electron_density_peak
reflection_data_source_builder
twinning_builder

 
class crystal_structure_builder(crystal_symmetry_builder)
    
Method resolution order:
crystal_structure_builder
crystal_symmetry_builder
__builtin__.object

Methods defined here:
__init__(self, set_grad_flags=True, min_distance_sym_equiv=0.5)
add_electron_density_peak(self, site, height)
add_residue(self, residue_number, residue_class)
add_scatterer(self, scatterer, is_refined, occupancy_includes_symmetry_factor, conformer_index=None, sym_excl_index=None, residue_number=None, residue_class=None)
If the parameter set_grad_flags passed to the constructor was True,
the scatterer.flags.grad_xxx() will be set to True
if the corresponding variables have been found to be refined
by the parser using this builder.
make_structure(self)

Methods inherited from crystal_symmetry_builder:
make_crystal_symmetry(self, unit_cell, space_group)
set_unit_cell_parameter_sigmas(self, s)

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

 
class crystal_symmetry_builder(__builtin__.object)
     Methods defined here:
make_crystal_symmetry(self, unit_cell, space_group)
set_unit_cell_parameter_sigmas(self, s)

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

 
class electron_density_peak(__builtin__.object)
     Methods defined here:
__init__(self, site, height)

Data descriptors defined here:
height
site

 
class reflection_data_source_builder(__builtin__.object)
    A builder which is passed the information about the reflections
corresponding to the parsed
 
Attributes:
 
  - reflection_file_format: a string to identify the format, compatible with
            iotbx.reflection_file_reader.any_reflection_file
  - data_change_of_basis_op: the instance of sgtbx.change_of_basis_op that
                        shall be applied to the Miller indices to match
                        the parsed model
  - data_scale: the scale of the data and their standard deviations
 
  Methods defined here:
create_shelx_reflection_data_source(self, format, indices_transform=None, change_of_basis_op=None, data_scale=1)
format is one of 3, 4, 5, etc.
data_scale scales the data and their standard deviations

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

 
class restrained_crystal_structure_builder(crystal_structure_builder)
    
Method resolution order:
restrained_crystal_structure_builder
crystal_structure_builder
crystal_symmetry_builder
__builtin__.object

Methods defined here:
__init__(self, *args, **kwds)
add_proxy(self, restraint_type, *args, **kwds)
process_restraint(self, restraint_type, *args, **kwds)
proxies(self)

Data descriptors defined here:
restraints_manager

Data and other attributes defined here:
adp_restraint_types = {'adp_similarity': <class 'smtbx.refinement.restraints.adp_restraints.adp_similarity_restraints'>, 'adp_u_eq_similarity': <class 'smtbx.refinement.restraints.adp_restraints.adp_u_eq_similarity_restraints'>, 'adp_volume_similarity': <class 'smtbx.refinement.restraints.adp_restraints.adp_volume_similarity_restraints'>, 'fixed_u_eq_adp': <class 'smtbx.refinement.restraints.adp_restraints.fixed_u_eq_adp_restraints'>, 'isotropic_adp': <class 'smtbx.refinement.restraints.adp_restraints.isotropic_adp_restraints'>, 'rigid_bond': <class 'smtbx.refinement.restraints.adp_restraints.rigid_bond_restraints'>}
adp_restraint_types_requiring_connectivity_only = {'adp_similarity': <class 'smtbx.refinement.restraints.adp_restraints.adp_similarity_restraints'>, 'rigid_bond': <class 'smtbx.refinement.restraints.adp_restraints.rigid_bond_restraints'>}
geometry_restraint_types = {'angle': <class 'cctbx_geometry_restraints_ext.angle_proxy'>, 'bond': <class 'cctbx_geometry_restraints_ext.bond_simple_proxy'>, 'bond_similarity': <class 'cctbx_geometry_restraints_ext.bond_similarity_proxy'>, 'chirality': <class 'cctbx_geometry_restraints_ext.chirality_proxy'>, 'dihedral': <class 'cctbx_geometry_restraints_ext.dihedral_proxy'>, 'planarity': <class 'cctbx_geometry_restraints_ext.planarity_proxy'>}

Methods inherited from crystal_structure_builder:
add_electron_density_peak(self, site, height)
add_residue(self, residue_number, residue_class)
add_scatterer(self, scatterer, is_refined, occupancy_includes_symmetry_factor, conformer_index=None, sym_excl_index=None, residue_number=None, residue_class=None)
If the parameter set_grad_flags passed to the constructor was True,
the scatterer.flags.grad_xxx() will be set to True
if the corresponding variables have been found to be refined
by the parser using this builder.
make_structure(self)

Methods inherited from crystal_symmetry_builder:
make_crystal_symmetry(self, unit_cell, space_group)
set_unit_cell_parameter_sigmas(self, s)

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

 
class twinning_builder(__builtin__.object)
    Construct twin components
They come as a tuple of instances of xray.twin_component.
If R is the twin law, the i-th component corresponds to the domain
where Miller indices are to be transformed by R^(i+1). The domain
with untransformed Miller indices is omitted as its fraction is just
1 minus the sum of the listed fractions.
As a result, the 0th component holds the twin law.
 
  Methods defined here:
make_merohedral_twinning(self, twin_law, fractions)
make_non_merohedral_twinning_with_transformed_hkl(self, fractions)

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:
non_merohedral_twin_components_with_transformed_hkl = ()
twin_components = ()

 
Functions
       
mixin_builder_class(mixin_name, *mixed_builders)
This function will make on-the-fly a builder class with the given
name, that inherits from the given builders

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