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protocols::helical_bundle::BundleParametrizationCalculator Class Reference

BundleParametrizationCalculator class, used for parametric helical bundle backbone generation. More...

#include <BundleParametrizationCalculator.hh>

Inheritance diagram for protocols::helical_bundle::BundleParametrizationCalculator:
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Public Types

typedef
core::conformation::parametric::ParameterizationCalculatorProperties 
ParameterizationCalculatorProperties
 

Public Member Functions

 BundleParametrizationCalculator (bool const use_degrees=false)
 constructors More...
 
 BundleParametrizationCalculator (bool const use_degrees, protocols::helical_bundle::parameters::BundleParametersCOP params_in)
 Params constructor. More...
 
 BundleParametrizationCalculator (BundleParametrizationCalculator const &src)
 Copy constructor. More...
 
 ~BundleParametrizationCalculator () override
 Destructor. More...
 
core::conformation::parametric::ParametrizationCalculatorOP clone () const override
 Copy this object ( allocate actual memory for it ) More...
 
void init_from_file (std::string const &filename)
 Read a Crick params file and initialize this calculator. More...
 
void copy_unset_params_from_globals (BundleParametrizationCalculatorCOP global_calculator)
 Copy the parameter values for parameters that have not been set from the global parameters. More...
 
bool copy_params_from_previous_helices_makebundlehelix_style (core::pose::Pose const &prev_helices_pose)
 Copy the parameter values for parameters that copy values from previous helices, from the previous helices. More...
 
bool build_helix (core::pose::Pose &pose) const
 Attempts to build a helix based on the current Crick parameters. More...
 
bool build_helix (core::pose::Pose &pose, core::Size const helix_start, core::Size const helix_end) const
 Attempts to build a helix based on the current Crick parameters. More...
 
void set_use_degrees (bool const setting)
 Set whether this calculator uses degrees or radians for the user-set angles. More...
 
bool use_degrees () const
 Get whether this calculator expects input in degrees or radians for user-set angles. More...
 
void set_perturbation_type_globally (std::string const &perturbation_type_in)
 Set the perturbation type for all parameters. More...
 
core::Size repeats_per_turn () const
 Get the number of repeats needed to go one full turn. More...
 
core::Size residues_per_repeat () const
 The number of residues per repeating unit. More...
 
core::Size residues_per_turn () const
 The number of residues needed for one full turn. More...
 
- Public Member Functions inherited from core::conformation::parametric::ParametrizationCalculator
 ParametrizationCalculator ()
 Constructor. More...
 
 ParametrizationCalculator (ParametersOP parameters)
 Constructor with input Parameters object. More...
 
 ParametrizationCalculator (ParametrizationCalculator const &src)
 Copy constructor. More...
 
 ~ParametrizationCalculator () override=0
 Pure virtual destructor means don't instantiate this base class!. More...
 
ParametrizationCalculatorCOP get_self_ptr () const
 self pointers More...
 
ParametrizationCalculatorOP get_self_ptr ()
 
ParametrizationCalculatorCAP get_self_weak_ptr () const
 
ParametrizationCalculatorAP get_self_weak_ptr ()
 
ParametersCOP parameters_cop () const
 Get a const-owning pointer to the Parameters object. More...
 
ParameterOP parameter (core::Size const index)
 Access a parameter. More...
 
ParameterCOP parameter_cop (core::Size const index) const
 Access a parameter. More...
 
RealValuedParameterOP real_parameter (core::Size const index)
 Accesses a real-valued parameter. More...
 
RealVectorValuedParameterOP realvector_parameter (core::Size const index)
 Accesses a realvector-valued parameter. More...
 
SizeValuedParameterOP size_parameter (core::Size const index)
 Accesses a size-valued parameter. More...
 
SizeVectorValuedParameterOP sizevector_parameter (core::Size const index)
 Accesses a sizevector-valued parameter. More...
 
BooleanValuedParameterOP boolean_parameter (core::Size const index)
 Accesses a boolean-valued parameter. More...
 
RealValuedParameterCOP real_parameter_cop (core::Size const index) const
 Accesses a real-valued parameter (const-access). More...
 
RealVectorValuedParameterCOP realvector_parameter_cop (core::Size const index) const
 Accesses a realvector-valued parameter (const-access). More...
 
SizeValuedParameterCOP size_parameter_cop (core::Size const index) const
 Accesses a size-valued parameter (const-access). More...
 
SizeVectorValuedParameterCOP sizevector_parameter_cop (core::Size const index) const
 Accesses a sizevector-valued parameter (const-access). More...
 
BooleanValuedParameterCOP boolean_parameter_cop (core::Size const index) const
 Accesses a boolean-valued parameter (const-access). More...
 

Static Public Member Functions

static bool copy_params_from_previous_helices_perturbbundle_style (parameters::BundleParametersSetCOP paramset, core::Size const copy_from_helix_index, BPC_Parameters const parameter_type, core::conformation::parametric::RealValuedParameterOP parameter_to_copy_to, protocols::helical_bundle::parameters::BundleParametersCOP current_helix_params)
 Copy the parameter values for parameters that copy values from previous helices, from the previous helices. More...
 
static
core::conformation::parametric::ParameterType 
parameter_type_from_enum (BPC_Parameters param_enum)
 Get the parameter type from the BPC_Parameters enum. More...
 
static std::string const & parameter_description_from_enum (BPC_Parameters param_enum)
 Given a BPC_Parameters enum, get a short lay-language description (used for annotating output) of the parameter. More...
 
static std::string const & short_parameter_description_from_enum (BPC_Parameters param_type)
 Get the short parameter name from the BPC_Parameters enum. More...
 
static std::string const & parameter_units_from_enum (BPC_Parameters param_type)
 Get the parameter units from the BPC_Parameters enum. More...
 
static
ParameterizationCalculatorProperties
const & 
parameter_properties_from_enum (BPC_Parameters param_enum)
 Given a BPC_Parameters enum, get whether this parameter is one that the user can set, whether it can be sampled, whether it can be perturbed, and whether it's global for a ParametersSet (helical bundle). More...
 
static std::string const & parameter_name_from_enum (BPC_Parameters param_type)
 Get the parameter name from the BPC_Parameters enum. More...
 
static BPC_Parameters parameter_enum_from_name (std::string const &name)
 Get the BPC_Parameters enum from the parameter name. More...
 

Private Member Functions

void set_use_degrees_for_parameters ()
 Update whether certain parameters expect their inputs in degrees. More...
 

Private Attributes

bool use_degrees_
 

Additional Inherited Members

- Protected Member Functions inherited from core::conformation::parametric::ParametrizationCalculator
void add_parameter (std::string const &parameter_name, ParameterType type, std::string const &description, std::string const &short_description, std::string const &units, ParameterizationCalculatorProperties const &properties)
 Add a parameter to this calculator, automatically determining the type. More...
 
void add_real_parameter (std::string const &parameter_name, ParameterType type, std::string const &description, std::string const &short_description, std::string const &units, ParameterizationCalculatorProperties const &properties)
 Add a real-valued parameter to this calculator. More...
 
void add_realvector_parameter (std::string const &parameter_name, ParameterType type, std::string const &description, std::string const &short_description, std::string const &units, ParameterizationCalculatorProperties const &properties)
 Add a vector-valued parameter to this calculator. More...
 
void add_size_parameter (std::string const &parameter_name, ParameterType type, std::string const &description, std::string const &short_description, std::string const &units, ParameterizationCalculatorProperties const &properties)
 Add a core::Size-valued parameter to this calculator. More...
 
void add_sizevector_parameter (std::string const &parameter_name, ParameterType type, std::string const &description, std::string const &short_description, std::string const &units, ParameterizationCalculatorProperties const &properties)
 Add a integer vector-valued parameter to this calculator. More...
 
void add_boolean_parameter (std::string const &parameter_name, ParameterType type, std::string const &description, std::string const &short_description, std::string const &units, ParameterizationCalculatorProperties const &properties)
 Add a Boolean-valued parameter to this calculator. More...
 
void add_custom_parameter (std::string const &parameter_name, ParameterType const type, std::string const &description, std::string const &short_description, std::string const &units, ParameterizationCalculatorProperties const &properties, ParameterOP parameter_in)
 Add a custom parameter. More...
 

Detailed Description

BundleParametrizationCalculator class, used for parametric helical bundle backbone generation.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::helical_bundle::BundleParametrizationCalculator::BundleParametrizationCalculator ( bool const  use_degrees = false)
protocols::helical_bundle::BundleParametrizationCalculator::BundleParametrizationCalculator ( bool const  use_degrees,
protocols::helical_bundle::parameters::BundleParametersCOP  params_in 
)

Params constructor.

protocols::helical_bundle::BundleParametrizationCalculator::BundleParametrizationCalculator ( BundleParametrizationCalculator const &  src)

Copy constructor.

Deep-copies the stored parameters.

Deep-copies the stored parameters (by calling the copy constructor of the base class).

protocols::helical_bundle::BundleParametrizationCalculator::~BundleParametrizationCalculator ( )
override

Destructor.

Member Function Documentation

bool protocols::helical_bundle::BundleParametrizationCalculator::build_helix ( core::pose::Pose pose) const

Attempts to build a helix based on the current Crick parameters.

Returns true for FAILURE and false for SUCCESS. The object "pose" is replaced with a new helix if this operation succeeds.

References core::pose::Pose::total_residue().

Referenced by protocols::helical_bundle::PerturbBundleHelix::apply().

bool protocols::helical_bundle::BundleParametrizationCalculator::build_helix ( core::pose::Pose pose,
core::Size const  helix_start,
core::Size const  helix_end 
) const

Attempts to build a helix based on the current Crick parameters.

Returns true for FAILURE and false for SUCCESS. The object "pose" is replaced with a new helix if this operation succeeds.

Note
This version takes parameters for the start and end of the helix.

References protocols::helical_bundle::align_mainchain_atoms_of_residue_range(), core::conformation::parametric::ParametrizationCalculator::boolean_parameter_cop(), protocols::helical_bundle::BPC_atoms_per_residue, protocols::helical_bundle::BPC_delta_omega0, protocols::helical_bundle::BPC_delta_omega1, protocols::helical_bundle::BPC_delta_omega1_peratom, protocols::helical_bundle::BPC_delta_t, protocols::helical_bundle::BPC_delta_z1_peratom, protocols::helical_bundle::BPC_epsilon, protocols::helical_bundle::BPC_invert_helix, protocols::helical_bundle::BPC_omega0, protocols::helical_bundle::BPC_omega1, protocols::helical_bundle::BPC_r0, protocols::helical_bundle::BPC_r1_peratom, protocols::helical_bundle::BPC_repeating_unit_offset, protocols::helical_bundle::BPC_residues_per_repeat, protocols::helical_bundle::BPC_set_bondangles, protocols::helical_bundle::BPC_set_bondlengths, protocols::helical_bundle::BPC_set_dihedrals, protocols::helical_bundle::BPC_z0_offset, protocols::helical_bundle::BPC_z1, protocols::helical_bundle::BPC_z1_offset, protocols::helical_bundle::copy_helix_bondangles(), protocols::helical_bundle::copy_helix_bondlengths(), protocols::helical_bundle::copy_helix_dihedrals(), protocols::helical_bundle::generate_atom_positions(), protocols::helical_bundle::place_atom_positions(), core::conformation::parametric::ParametrizationCalculator::real_parameter_cop(), core::conformation::parametric::ParametrizationCalculator::realvector_parameter_cop(), core::conformation::parametric::ParametrizationCalculator::size_parameter_cop(), core::conformation::parametric::ParametrizationCalculator::sizevector_parameter_cop(), core::pose::Pose::total_residue(), and protocols::helical_bundle::TR().

core::conformation::parametric::ParametrizationCalculatorOP protocols::helical_bundle::BundleParametrizationCalculator::clone ( ) const
overridevirtual

Copy this object ( allocate actual memory for it )

Implements core::conformation::parametric::ParametrizationCalculator.

bool protocols::helical_bundle::BundleParametrizationCalculator::copy_params_from_previous_helices_makebundlehelix_style ( core::pose::Pose const &  prev_helices_pose)

Copy the parameter values for parameters that copy values from previous helices, from the previous helices.

This function should be called before build_helix().

Note
This function assumes that the input pose consists only of previous helices, and stores N ParametersSet objects for N helices, each with 1 Parameters object contained.
Returns
Returns true for failure, false for success.

This function should be called before build_helix().

Returns
Returns true for failure, false for success.

References protocols::helical_bundle::BPC_end_of_list, core::pose::Pose::conformation(), core::conformation::Conformation::n_parameters_sets(), core::conformation::parametric::ParametrizationCalculator::parameter(), core::conformation::parametric::ParametrizationCalculator::parameters_cop(), and core::conformation::Conformation::parameters_set().

bool protocols::helical_bundle::BundleParametrizationCalculator::copy_params_from_previous_helices_perturbbundle_style ( parameters::BundleParametersSetCOP  paramset,
core::Size const  copy_from_helix_index,
BPC_Parameters const  parameter_type,
core::conformation::parametric::RealValuedParameterOP  parameter_to_copy_to,
protocols::helical_bundle::parameters::BundleParametersCOP  current_helix_params 
)
static

Copy the parameter values for parameters that copy values from previous helices, from the previous helices.

This function should be called before build_helix().

Note
This function assumes that the input pose is the whole shebang passed to the PerturbBundle mover. Unlike copy_params_from_previous_helices_makebundlehelix_style(), this functon does not modify the BundleParametrizationCalculator. Instead it copies the parameter value for the given parameter from the indicated previous helix to the indicated parameter object.
Returns
Returns true for failure, false for success.

Referenced by protocols::helical_bundle::PerturbBundle::perturb_values().

void protocols::helical_bundle::BundleParametrizationCalculator::copy_unset_params_from_globals ( BundleParametrizationCalculatorCOP  global_calculator)

Copy the parameter values for parameters that have not been set from the global parameters.

This function should be called before build_helix().

References protocols::helical_bundle::BPC_end_of_list, core::conformation::parametric::ParametrizationCalculator::parameter(), and core::conformation::parametric::ParametrizationCalculator::parameters_cop().

void protocols::helical_bundle::BundleParametrizationCalculator::init_from_file ( std::string const &  filename)
std::string const & protocols::helical_bundle::BundleParametrizationCalculator::parameter_description_from_enum ( BPC_Parameters  param_enum)
static

Given a BPC_Parameters enum, get a short lay-language description (used for annotating output) of the parameter.

Returns "INVALID!!!" if invalid.

Referenced by BundleParametrizationCalculator().

BPC_Parameters protocols::helical_bundle::BundleParametrizationCalculator::parameter_enum_from_name ( std::string const &  name)
static

Get the BPC_Parameters enum from the parameter name.

Returns BPC_unknown_parameter if this can't be parsed.

References protocols::helical_bundle::BPC_end_of_list, protocols::helical_bundle::BPC_unknown_parameter, and parameter_name_from_enum().

std::string const & protocols::helical_bundle::BundleParametrizationCalculator::parameter_name_from_enum ( BPC_Parameters  param_type)
static
core::conformation::parametric::ParameterizationCalculatorProperties const & protocols::helical_bundle::BundleParametrizationCalculator::parameter_properties_from_enum ( BPC_Parameters  param_enum)
static

Given a BPC_Parameters enum, get whether this parameter is one that the user can set, whether it can be sampled, whether it can be perturbed, and whether it's global for a ParametersSet (helical bundle).

Referenced by BundleParametrizationCalculator().

core::conformation::parametric::ParameterType protocols::helical_bundle::BundleParametrizationCalculator::parameter_type_from_enum ( BPC_Parameters  param_enum)
static

Get the parameter type from the BPC_Parameters enum.

Returns PT_invalid_type if invalid.

References protocols::helical_bundle::BPC_atoms_per_residue, protocols::helical_bundle::BPC_delta_omega0, protocols::helical_bundle::BPC_delta_omega1, protocols::helical_bundle::BPC_delta_omega1_peratom, protocols::helical_bundle::BPC_delta_t, protocols::helical_bundle::BPC_delta_z1_peratom, protocols::helical_bundle::BPC_epsilon, protocols::helical_bundle::BPC_invert_helix, protocols::helical_bundle::BPC_omega0, protocols::helical_bundle::BPC_omega1, protocols::helical_bundle::BPC_r0, protocols::helical_bundle::BPC_r1_peratom, protocols::helical_bundle::BPC_repeating_unit_offset, protocols::helical_bundle::BPC_residues_per_repeat, protocols::helical_bundle::BPC_set_bondangles, protocols::helical_bundle::BPC_set_bondlengths, protocols::helical_bundle::BPC_set_dihedrals, protocols::helical_bundle::BPC_unknown_parameter, protocols::helical_bundle::BPC_z0_offset, protocols::helical_bundle::BPC_z1, protocols::helical_bundle::BPC_z1_offset, core::conformation::parametric::PT_angle, core::conformation::parametric::PT_angle_vector, core::conformation::parametric::PT_boolean, core::conformation::parametric::PT_generic_natural_number, core::conformation::parametric::PT_generic_natural_number_vector, core::conformation::parametric::PT_generic_nonnegative_valued_real, core::conformation::parametric::PT_generic_nonnegative_valued_real_vector, core::conformation::parametric::PT_generic_real, core::conformation::parametric::PT_generic_real_vector, core::conformation::parametric::PT_generic_whole_number, and core::conformation::parametric::PT_invalid_type.

Referenced by BundleParametrizationCalculator().

std::string const & protocols::helical_bundle::BundleParametrizationCalculator::parameter_units_from_enum ( BPC_Parameters  param_type)
static

Get the parameter units from the BPC_Parameters enum.

Given a BPC_Parameters enum, units for the parameter.

Referenced by BundleParametrizationCalculator().

core::Size protocols::helical_bundle::BundleParametrizationCalculator::repeats_per_turn ( ) const

Get the number of repeats needed to go one full turn.

This is rounded UP. So for an alpha helix, with about 3.6 repeating units (residues) per turn, this function returns 4.

References protocols::helical_bundle::BPC_omega1, and core::conformation::parametric::ParametrizationCalculator::real_parameter_cop().

Referenced by residues_per_turn().

core::Size protocols::helical_bundle::BundleParametrizationCalculator::residues_per_repeat ( ) const
core::Size protocols::helical_bundle::BundleParametrizationCalculator::residues_per_turn ( ) const

The number of residues needed for one full turn.

This is repeats_per_turn() * residues_per_repeat().

References repeats_per_turn(), and residues_per_repeat().

void protocols::helical_bundle::BundleParametrizationCalculator::set_perturbation_type_globally ( std::string const &  perturbation_type_in)
void protocols::helical_bundle::BundleParametrizationCalculator::set_use_degrees ( bool const  setting)

Set whether this calculator uses degrees or radians for the user-set angles.

Defaults to radians (false).

References set_use_degrees_for_parameters(), and use_degrees_.

void protocols::helical_bundle::BundleParametrizationCalculator::set_use_degrees_for_parameters ( )
private
std::string const & protocols::helical_bundle::BundleParametrizationCalculator::short_parameter_description_from_enum ( BPC_Parameters  param_enum)
static

Get the short parameter name from the BPC_Parameters enum.

Given a BPC_Parameters enum, get a one- or two-word lay-language description (used for annotating output) of the parameter.

Returns "INVALID!!!" if invalid.

Referenced by BundleParametrizationCalculator().

bool protocols::helical_bundle::BundleParametrizationCalculator::use_degrees ( ) const
inline

Get whether this calculator expects input in degrees or radians for user-set angles.

References use_degrees_.

Member Data Documentation

bool protocols::helical_bundle::BundleParametrizationCalculator::use_degrees_
private

The documentation for this class was generated from the following files: