Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
protocols::mainchain_potential::GenerateMainchainPotentialOptions Class Reference

Options container for the generator for mainchain potentials. More...

#include <GenerateMainchainPotentialOptions.hh>

Inheritance diagram for protocols::mainchain_potential::GenerateMainchainPotentialOptions:
Inheritance graph
[legend]

Public Member Functions

 GenerateMainchainPotentialOptions (bool const initialize_from_globals=false)
 Default constructor. More...
 
 GenerateMainchainPotentialOptions (GenerateMainchainPotentialOptions const &)=default
 Copy constructor. Set to default. More...
 
 ~GenerateMainchainPotentialOptions () override
 Destructor. More...
 
GenerateMainchainPotentialOptionsOP clone () const
 Clone function: create a copy of this object, and return an owning pointer to the copy. More...
 
void set_residue_name (std::string const &name_in)
 Set the name of the residue type for which we'll be generating a mainchain potential. More...
 
void set_make_pre_proline_potential (bool const setting)
 Set whether we're generating a pre-proline potential. More...
 
void set_dimensions (utility::vector1< int > const &dimensions_in)
 Set the vector of number of points in each dimension for the mainchain potential that we're generating. More...
 
void set_mainchain_torsions_covered (utility::vector1< int > const &mainchain_torsions_in)
 Set which mainchain torsions are covered. More...
 
void set_scorefxn_filename (std::string const &filename_in)
 Set name of the scorefunction that we'll use. An empty string indicates that the default should be used. More...
 
void set_kbt (core::Real const &kbt_in)
 Set the Boltzmann temperature. More...
 
void set_do_minimization (bool const setting)
 Set whether we're minimizing each rotamer. More...
 
void set_minimization_type (std::string const &type_in)
 Set the minimization type. More...
 
void set_minimization_threshold (core::Real const &threshold_in)
 Set the minimization threshold. More...
 
void set_output_filename (std::string const &filename_in)
 Set the mainchain potential filename to write. More...
 
void set_write_potentials_for_individual_scoreterms (bool const setting)
 Set whether we are writing mainchain potentials for individual scoreterms. More...
 
void set_symmetrize_output (bool const setting)
 Set whether the output should be made symmetric. More...
 
std::string const & residue_name () const
 Get the name of the residue type for which we'll be generating a mainchain potential. More...
 
bool make_pre_proline_potential () const
 Get whether we're generating a pre-proline potential. More...
 
utility::vector1< core::Size >
const & 
dimensions () const
 Access the vector of the number of points in each dimension for a given residue type. (Const-access)/. More...
 
utility::vector1< core::Size >
const & 
mainchain_torsions_covered () const
 Get which mainchain torsions are covered. More...
 
std::string const & get_scorefxn_filename () const
 Name of the scorefunction that we'll use. An empty string indicates that the default should be used. More...
 
core::Real const & kbt () const
 Get the Boltzmann temperature. More...
 
bool do_minimization () const
 Get whether we're minimizing each rotamer. More...
 
std::string const & minimization_type () const
 Get the minimization type. More...
 
core::Real const & minimization_threshold () const
 Get the minimization threshold. More...
 
std::string const & output_filename () const
 Get the mainchain potential filename to write. More...
 
bool write_potentials_for_individual_scoreterms () const
 Are we writing mainchain potentials for individual scoreterms? More...
 
bool symmetrize_output () const
 Should the output be made symmetric? More...
 

Static Public Member Functions

static void register_options ()
 Static function used to register releavnt options. More...
 

Private Member Functions

void do_initialization_from_globals ()
 Initialize this object from the global options system. More...
 

Private Attributes

std::string residue_name_
 Name of the residue type for which we'll be generating a mainchain potential. More...
 
std::string scorefxn_filename_
 Name of the scorefunction that we'll use. More...
 
bool make_pre_proline_potential_
 If true, then we generate a potential for a position before a proline, sarcosine, or other N-substituted building block (e.g. a peptoid). If false, then the next residue's nitrogen is unsubstituted. More...
 
utility::vector1< core::Sizedimensions_
 The number of points in each dimension for a given residue type. More...
 
utility::vector1< core::Sizemainchain_torsions_covered_
 Which mainchain torsions are covered? More...
 
core::Real kbt_
 The Boltzmann temperature for average energy calculation. More...
 
bool do_minimization_
 Should each rotamer be minimized? Default true. More...
 
std::string minimization_type_
 Minimization flavour to use to approximate the Hessian matrix. Defaults to dfpmin (which is really lbfgs). More...
 
core::Real minimization_threshold_
 The minimization threshold at which minimization trajectories are aborted. Defaults to 1.0E-7. More...
 
std::string output_filename_
 The mainchain potential filename to write. More...
 
bool write_potentials_for_individual_scoreterms_
 Are we writing mainchain potentials for individual scoreterms? More...
 
bool symmetrize_output_
 Should the output be made symmetric? False by default. More...
 

Friends

class ::GenerateMainchainPotentialTests
 

Detailed Description

Options container for the generator for mainchain potentials.

Constructor & Destructor Documentation

protocols::mainchain_potential::GenerateMainchainPotentialOptions::GenerateMainchainPotentialOptions ( bool const  initialize_from_globals = false)

Default constructor.

"True" indicates that we should initialize from the global options system. "False" by default, meaning that all options are set to default values.

protocols::mainchain_potential::GenerateMainchainPotentialOptions::GenerateMainchainPotentialOptions ( GenerateMainchainPotentialOptions const &  )
default

Copy constructor. Set to default.

protocols::mainchain_potential::GenerateMainchainPotentialOptions::~GenerateMainchainPotentialOptions ( )
override

Destructor.

Member Function Documentation

GenerateMainchainPotentialOptionsOP protocols::mainchain_potential::GenerateMainchainPotentialOptions::clone ( ) const

Clone function: create a copy of this object, and return an owning pointer to the copy.

utility::vector1< core::Size > const& protocols::mainchain_potential::GenerateMainchainPotentialOptions::dimensions ( ) const
inline

Access the vector of the number of points in each dimension for a given residue type. (Const-access)/.

The length of this vector must match the number of mainchain dihedral DoFs for which we're generating a mainchain potential.

References dimensions_.

void protocols::mainchain_potential::GenerateMainchainPotentialOptions::do_initialization_from_globals ( )
private
bool protocols::mainchain_potential::GenerateMainchainPotentialOptions::do_minimization ( ) const
inline

Get whether we're minimizing each rotamer.

References do_minimization_.

std::string const& protocols::mainchain_potential::GenerateMainchainPotentialOptions::get_scorefxn_filename ( ) const
inline

Name of the scorefunction that we'll use. An empty string indicates that the default should be used.

References scorefxn_filename_.

core::Real const& protocols::mainchain_potential::GenerateMainchainPotentialOptions::kbt ( ) const
inline

Get the Boltzmann temperature.

References kbt_.

utility::vector1< core::Size > const& protocols::mainchain_potential::GenerateMainchainPotentialOptions::mainchain_torsions_covered ( ) const
inline

Get which mainchain torsions are covered.

If this is an empty vector, it indicates that all mainchain torsions are covered.

References mainchain_torsions_covered_.

bool protocols::mainchain_potential::GenerateMainchainPotentialOptions::make_pre_proline_potential ( ) const
inline

Get whether we're generating a pre-proline potential.

If true, then we generate a potential for a position before a proline, sarcosine, or other N-substituted building block (e.g. a peptoid). If false, then the next residue's nitrogen is unsubstituted.

Note
Determines the patch applied to the C-terminus.

References make_pre_proline_potential_.

core::Real const& protocols::mainchain_potential::GenerateMainchainPotentialOptions::minimization_threshold ( ) const
inline

Get the minimization threshold.

References minimization_threshold_.

std::string const& protocols::mainchain_potential::GenerateMainchainPotentialOptions::minimization_type ( ) const
inline

Get the minimization type.

References minimization_type_.

std::string const& protocols::mainchain_potential::GenerateMainchainPotentialOptions::output_filename ( ) const
inline

Get the mainchain potential filename to write.

References output_filename_.

Referenced by do_initialization_from_globals().

void protocols::mainchain_potential::GenerateMainchainPotentialOptions::register_options ( )
static

Static function used to register releavnt options.

std::string const& protocols::mainchain_potential::GenerateMainchainPotentialOptions::residue_name ( ) const
inline

Get the name of the residue type for which we'll be generating a mainchain potential.

References residue_name_.

void protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_dimensions ( utility::vector1< int > const &  dimensions_in)

Set the vector of number of points in each dimension for the mainchain potential that we're generating.

This takes a vector of ints, not Sizes, because that's what comes from the global options system.

References dimensions_.

Referenced by do_initialization_from_globals().

void protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_do_minimization ( bool const  setting)

Set whether we're minimizing each rotamer.

References do_minimization_.

Referenced by do_initialization_from_globals().

void protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_kbt ( core::Real const &  kbt_in)

Set the Boltzmann temperature.

References kbt_.

void protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_mainchain_torsions_covered ( utility::vector1< int > const &  mainchain_torsions_in)

Set which mainchain torsions are covered.

If this is an empty vector, it indicates that all mainchain torsions are covered. This takes a vector of ints, not Sizes, because that's what comes from the global options sytem.

Note
Pass this an empty vector to set the default (all mainchain torsions for the residue type.)

References mainchain_torsions_covered_.

Referenced by do_initialization_from_globals().

void protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_make_pre_proline_potential ( bool const  setting)

Set whether we're generating a pre-proline potential.

If true, then we generate a potential for a position before a proline, sarcosine, or other N-substituted building block (e.g. a peptoid). If false, then the next residue's nitrogen is unsubstituted.

Note
Determines the patch applied to the C-terminus.

References make_pre_proline_potential_.

void protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_minimization_threshold ( core::Real const &  threshold_in)

Set the minimization threshold.

References minimization_threshold_.

Referenced by do_initialization_from_globals().

void protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_minimization_type ( std::string const &  type_in)

Set the minimization type.

References minimization_type_.

Referenced by do_initialization_from_globals().

void protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_output_filename ( std::string const &  filename_in)

Set the mainchain potential filename to write.

References output_filename_, and protocols::TR().

Referenced by do_initialization_from_globals().

void protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_residue_name ( std::string const &  name_in)

Set the name of the residue type for which we'll be generating a mainchain potential.

References residue_name_.

void protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_scorefxn_filename ( std::string const &  filename_in)

Set name of the scorefunction that we'll use. An empty string indicates that the default should be used.

References scorefxn_filename_.

Referenced by do_initialization_from_globals().

void protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_symmetrize_output ( bool const  setting)

Set whether the output should be made symmetric.

References symmetrize_output_, and protocols::TR().

Referenced by do_initialization_from_globals().

void protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_write_potentials_for_individual_scoreterms ( bool const  setting)

Set whether we are writing mainchain potentials for individual scoreterms.

References protocols::TR(), and write_potentials_for_individual_scoreterms_.

Referenced by do_initialization_from_globals().

bool protocols::mainchain_potential::GenerateMainchainPotentialOptions::symmetrize_output ( ) const
inline

Should the output be made symmetric?

References symmetrize_output_.

bool protocols::mainchain_potential::GenerateMainchainPotentialOptions::write_potentials_for_individual_scoreterms ( ) const
inline

Are we writing mainchain potentials for individual scoreterms?

Default false.

References write_potentials_for_individual_scoreterms_.

Friends And Related Function Documentation

friend class ::GenerateMainchainPotentialTests
friend

Member Data Documentation

utility::vector1< core::Size > protocols::mainchain_potential::GenerateMainchainPotentialOptions::dimensions_
private

The number of points in each dimension for a given residue type.

The length of this vector must match the number of mainchain dihedral DoFs for which we're generating a mainchain potential.

Referenced by dimensions(), and set_dimensions().

bool protocols::mainchain_potential::GenerateMainchainPotentialOptions::do_minimization_
private

Should each rotamer be minimized? Default true.

Referenced by do_minimization(), and set_do_minimization().

core::Real protocols::mainchain_potential::GenerateMainchainPotentialOptions::kbt_
private

The Boltzmann temperature for average energy calculation.

Defaults to 0.63 kcal/mol. I'm not sure whether this is right for the mm_std scorefunction, though.

Referenced by kbt(), and set_kbt().

utility::vector1< core::Size > protocols::mainchain_potential::GenerateMainchainPotentialOptions::mainchain_torsions_covered_
private

Which mainchain torsions are covered?

If this is an empty vector, it indicates that all mainchain torsions are covered.

Referenced by do_initialization_from_globals(), mainchain_torsions_covered(), and set_mainchain_torsions_covered().

bool protocols::mainchain_potential::GenerateMainchainPotentialOptions::make_pre_proline_potential_
private

If true, then we generate a potential for a position before a proline, sarcosine, or other N-substituted building block (e.g. a peptoid). If false, then the next residue's nitrogen is unsubstituted.

Determines the patch applied to the C-terminus.

Referenced by do_initialization_from_globals(), make_pre_proline_potential(), and set_make_pre_proline_potential().

core::Real protocols::mainchain_potential::GenerateMainchainPotentialOptions::minimization_threshold_
private

The minimization threshold at which minimization trajectories are aborted. Defaults to 1.0E-7.

Referenced by minimization_threshold(), and set_minimization_threshold().

std::string protocols::mainchain_potential::GenerateMainchainPotentialOptions::minimization_type_
private

Minimization flavour to use to approximate the Hessian matrix. Defaults to dfpmin (which is really lbfgs).

Referenced by minimization_type(), and set_minimization_type().

std::string protocols::mainchain_potential::GenerateMainchainPotentialOptions::output_filename_
private

The mainchain potential filename to write.

Referenced by output_filename(), and set_output_filename().

std::string protocols::mainchain_potential::GenerateMainchainPotentialOptions::residue_name_
private

Name of the residue type for which we'll be generating a mainchain potential.

Referenced by do_initialization_from_globals(), residue_name(), and set_residue_name().

std::string protocols::mainchain_potential::GenerateMainchainPotentialOptions::scorefxn_filename_
private

Name of the scorefunction that we'll use.

If an empty string (no user-specified scorefunction), then the GenerateMainchainPotential class has a default that it uses.

Referenced by get_scorefxn_filename(), and set_scorefxn_filename().

bool protocols::mainchain_potential::GenerateMainchainPotentialOptions::symmetrize_output_
private

Should the output be made symmetric? False by default.

Referenced by set_symmetrize_output(), and symmetrize_output().

bool protocols::mainchain_potential::GenerateMainchainPotentialOptions::write_potentials_for_individual_scoreterms_
private

Are we writing mainchain potentials for individual scoreterms?

Default false.

Referenced by set_write_potentials_for_individual_scoreterms(), and write_potentials_for_individual_scoreterms().


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