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

#include <GenerateMainchainPotentialOptions.hh>

Inheritance diagram for protocols::mainchain_potential::GenerateMainchainPotentialOptions:

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::Size >	dimensions_
	The number of points in each dimension for a given residue type. More...

utility::vector1< core::Size >	mainchain_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

Initialize this object from the global options system.

References mainchain_torsions_covered_, make_pre_proline_potential_, output_filename(), residue_name_, set_dimensions(), set_do_minimization(), set_mainchain_torsions_covered(), set_minimization_threshold(), set_minimization_type(), set_output_filename(), set_scorefxn_filename(), set_symmetrize_output(), set_write_potentials_for_individual_scoreterms(), and protocols::TR().

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:

src/protocols/mainchain_potential/GenerateMainchainPotentialOptions.hh
src/protocols/mainchain_potential/GenerateMainchainPotentialOptions.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation