class for fitting a length of secondary structure keeping the same dihedrals More...

#include <SecStructMinimizeMultiFunc.hh>

Inheritance diagram for protocols::ncbb::SecStructMinimizeMultiFunc:

Public Member Functions
	~SecStructMinimizeMultiFunc () override
	Destructor. More...

	SecStructMinimizeMultiFunc (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn_in, core::optimization::MinimizerMap &min_map, std::string const alpha_beta_pattern, std::string const dihedral_pattern)
	Constructor. More...

core::Real	operator() (core::optimization::Multivec const &vars) const override
	Calculate function value (rms squared) More...

void	dfunc (core::optimization::Multivec const &vars, core::optimization::Multivec &dE_dvars) const override
	Calculate function value derivatives. More...

core::optimization::Multivec	dofs_to_vars (core::optimization::Multivec const &dofs) const
	give short set of torsions from full dofs More...

core::optimization::Multivec	vars_to_dofs (core::optimization::Multivec const &vars) const
	give full dofs from short set of torsions More...

void	dump (core::optimization::Multivec const &vars, core::optimization::Multivec const &vars2) const override
	Error state reached – derivative does not match gradient. More...

Public Member Functions inherited from core::optimization::Multifunc
	~Multifunc () override=default
	Destructor. More...

virtual bool	abort_min (Multivec const &) const
	Christophe added the following to allow premature end of minimization If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN! More...

Private Member Functions
void	get_dofs_for_pose0 ()

void	get_dofs_map ()

core::Real	dofs_for_pose0 (core::Size const i_dof) const

core::optimization::Multivec	dEddofs_to_dEdvars (core::optimization::Multivec const &dEdtors) const

void	setup_minimization_graph (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, core::optimization::MinimizerMap const &min_map) const

bool	uniq_refers_to_beta (char const uniq) const

Private Attributes
std::map< core::Size, utility::vector1< core::Size > >	map_BB_to_DOF_

std::map< core::Size, core::Size >	map_DOF_to_BB_

core::pose::Pose &	pose_

core::scoring::ScoreFunction &	scorefxn_

core::optimization::MinimizerMap &	min_map_

core::pose::Pose &	pose0_

core::optimization::Multivec	dofs_for_pose0_

std::string	alpha_beta_pattern_

std::string	dihedral_pattern_
	The pattern at which dihedrals are applied. More...

std::map< core::Size, utility::vector1 < core::id::TorsionID > >	vars_index_to_torsion_id_

core::Size	nvar_

Additional Inherited Members
Public Types inherited from core::optimization::Multifunc
typedef utility::VirtualBase	parent

Protected Member Functions inherited from core::optimization::Multifunc
	Multifunc ()
	Default constructor. More...

	Multifunc (Multifunc const &)
	Copy constructor. More...

Multifunc &	operator= (Multifunc const &)
	Copy assignment. More...

Detailed Description

class for fitting a length of secondary structure keeping the same dihedrals

Constructor & Destructor Documentation

protocols::ncbb::SecStructMinimizeMultiFunc::~SecStructMinimizeMultiFunc ( )

overridedefault

Destructor.

protocols::ncbb::SecStructMinimizeMultiFunc::SecStructMinimizeMultiFunc	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction &	scorefxn_in,
		core::optimization::MinimizerMap &	min_map,
		std::string const	alpha_beta_pattern,
		std::string const	dihedral_pattern
	)

Constructor.

References alpha_beta_pattern_, core::id::BB, protocols::ncbb::count_uniq_char(), dihedral_pattern_, get_dofs_for_pose0(), get_dofs_map(), min_map_, nvar_, pose_, scorefxn_, setup_minimization_graph(), protocols::TR(), uniq_refers_to_beta(), and vars_index_to_torsion_id_.

Member Function Documentation

Multivec protocols::ncbb::SecStructMinimizeMultiFunc::dEddofs_to_dEdvars ( core::optimization::Multivec const & dEdtors ) const

private

References map_BB_to_DOF_, and nvar_.

Referenced by dfunc().

void protocols::ncbb::SecStructMinimizeMultiFunc::dfunc	(	core::optimization::Multivec const &	vars,
		core::optimization::Multivec &	dE_dvars
	)		const

overridevirtual

Calculate function value derivatives.

Implements core::optimization::Multifunc.

References core::optimization::atom_tree_dfunc(), dEddofs_to_dEdvars(), min_map_, pose_, scorefxn_, protocols::TR(), and vars_to_dofs().

core::Real protocols::ncbb::SecStructMinimizeMultiFunc::dofs_for_pose0 ( core::Size const i_dof ) const

inlineprivate

References dofs_for_pose0_.

Multivec protocols::ncbb::SecStructMinimizeMultiFunc::dofs_to_vars ( core::optimization::Multivec const & dofs ) const

give short set of torsions from full dofs

References map_BB_to_DOF_, and nvar_.

void protocols::ncbb::SecStructMinimizeMultiFunc::dump	(	core::optimization::Multivec const &	vars,
		core::optimization::Multivec const &	vars2
	)		const

overridevirtual

Error state reached – derivative does not match gradient.

Useful debugging code that can be re-enabled by changing the boolean variables at the top of this function.

Reimplemented from core::optimization::Multifunc.

void protocols::ncbb::SecStructMinimizeMultiFunc::get_dofs_for_pose0 ( )

private

References core::optimization::MinimizerMap::copy_dofs_from_pose(), core::optimization::MinimizerMap::dof_nodes(), dofs_for_pose0_, min_map_, and pose0_.

Referenced by SecStructMinimizeMultiFunc().

void protocols::ncbb::SecStructMinimizeMultiFunc::get_dofs_map ( )

private

References core::optimization::MinimizerMap::dof_nodes(), map_BB_to_DOF_, map_DOF_to_BB_, min_map_, nvar_, protocols::TR(), and vars_index_to_torsion_id_.

Referenced by SecStructMinimizeMultiFunc().

Real protocols::ncbb::SecStructMinimizeMultiFunc::operator() ( core::optimization::Multivec const & vars ) const

overridevirtual

Calculate function value (rms squared)

Implements core::optimization::Multifunc.

References core::optimization::MinimizerMap::copy_dofs_to_pose(), min_map_, pose_, scorefxn_, protocols::TR(), and vars_to_dofs().

void protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		core::optimization::MinimizerMap const &	min_map
	)		const