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

 
Modules
       
smtbx.refinement.constraints
smtbx.refinement.least_squares
smtbx

 
Classes
       
__builtin__.object
weighting_scheme_builder
iotbx.builders.crystal_structure_builder(iotbx.builders.crystal_symmetry_builder)
constrained_crystal_structure_builder
weighted_constrained_restrained_crystal_structure_builder(constrained_crystal_structure_builder, iotbx.builders.restrained_crystal_structure_builder, weighting_scheme_builder)

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

Methods defined here:
__init__(self, *args, **kwds)
add_occupancy_pair_affine_constraint(self, scatterer_indices, linear_form)
Add a constraint on the occupancies of a pair of scatterers that is
affine, i.e. linear_form shall be ((a0, a1), b) and then
   a0*occ0 + a1*occ1 = b
where (occ0, occ1) are the occupancies of the scatterers whose indices
are given in `scatterer_indices`.
add_u_iso_proportional_to_pivot_u_eq(self, u_iso_scatterer_index, u_eq_scatterer_index, multiplier)
end_geometrical_constraint(self)
make_geometrical_constraint_type(self, constraint_name)
start_geometrical_constraint(self, type_, bond_length, rotating, stretching, pivot_relative_pos)

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

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

 
class weighted_constrained_restrained_crystal_structure_builder(constrained_crystal_structure_builder, iotbx.builders.restrained_crystal_structure_builder, weighting_scheme_builder)
    
Method resolution order:
weighted_constrained_restrained_crystal_structure_builder
constrained_crystal_structure_builder
iotbx.builders.restrained_crystal_structure_builder
iotbx.builders.crystal_structure_builder
iotbx.builders.crystal_symmetry_builder
weighting_scheme_builder
__builtin__.object

Methods inherited from constrained_crystal_structure_builder:
__init__(self, *args, **kwds)
add_occupancy_pair_affine_constraint(self, scatterer_indices, linear_form)
Add a constraint on the occupancies of a pair of scatterers that is
affine, i.e. linear_form shall be ((a0, a1), b) and then
   a0*occ0 + a1*occ1 = b
where (occ0, occ1) are the occupancies of the scatterers whose indices
are given in `scatterer_indices`.
add_u_iso_proportional_to_pivot_u_eq(self, u_iso_scatterer_index, u_eq_scatterer_index, multiplier)
end_geometrical_constraint(self)
make_geometrical_constraint_type(self, constraint_name)
start_geometrical_constraint(self, type_, bond_length, rotating, stretching, pivot_relative_pos)

Methods inherited from iotbx.builders.restrained_crystal_structure_builder:
add_proxy(self, restraint_type, *args, **kwds)
process_restraint(self, restraint_type, *args, **kwds)
proxies(self)

Data descriptors inherited from iotbx.builders.restrained_crystal_structure_builder:
restraints_manager

Data and other attributes inherited from iotbx.builders.restrained_crystal_structure_builder:
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 iotbx.builders.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 iotbx.builders.crystal_symmetry_builder:
make_crystal_symmetry(self, unit_cell, space_group)
set_unit_cell_parameter_sigmas(self, s)

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

Methods inherited from weighting_scheme_builder:
make_shelx_weighting_scheme(self, a, b, c=0, d=0, e=0, f=0.3333333333333333)

 
class weighting_scheme_builder(__builtin__.object)
     Methods defined here:
make_shelx_weighting_scheme(self, a, b, c=0, d=0, e=0, f=0.3333333333333333)

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

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