class that holds all the parameters for one specific constraint More...

#include <EnzConstraintParameters.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::EnzConstraintParameters:

Public Member Functions
void	set_mcfi (toolbox::match_enzdes_util::MatchConstraintFileInfoCOP mcfi)

	EnzConstraintParameters ()

void	init (core::Size cst_block, core::chemical::ResidueTypeSetCOP src_restype_set, EnzConstraintIOCAP src_enz_io)

void	init ()

	EnzConstraintParameters (EnzConstraintParameters const &other)
	copy constructor More...

	~EnzConstraintParameters () override

EnzConstraintParametersCOP	get_self_ptr () const
	self pointers More...

EnzConstraintParametersOP	get_self_ptr ()

EnzConstraintParametersCAP	get_self_weak_ptr () const

void	show_definitions () const

void	generate_pose_specific_data (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx) const

bool	is_empty () const

bool	is_covalent () const

bool	missing_in_pose (core::pose::Pose const &pose) const

core::Size	cst_block () const
	function that takes all rotamers for the ResidueType(s) of the residue that's missing in the pose and places them according to the geometry specified in the mcfi More...

void	set_cst_block (core::Size cst_block)

bool	update_pdb_remarks (core::pose::Pose &pose) const
	updates the pdb remarks according to what is in the EnzCstTemplateRes member data. returns false in case any error occured More...

EnzConstraintIOCAP	enz_io () const

EnzCstTemplateResOP	nonconst_resA ()

EnzCstTemplateResOP	nonconst_resB ()

EnzCstTemplateResCOP	resA () const

EnzCstTemplateResCOP	resB () const

EnzCstTemplateResCOP	get_missing_template_res (core::pose::Pose const &pose) const

EnzCstTemplateResCOP	get_missing_template_other_res (core::pose::Pose const &pose) const

std::set< std::string >	allowed_res_name3_at_position (core::pose::Pose const &pose, core::Size seqpos) const
	all residue names specified in the cstfile returns an empty set if the constraints don't apply to the specifed position More...

void	set_external_position_for_resA (core::Size pos)

void	set_external_position_for_resB (core::Size pos)

void	remove_covalent_connections_from_pose (core::pose::Pose &pose) const

void	remap_resid (core::id::SequenceMapping const &smap)

Static Public Member Functions
static core::scoring::func::FuncOP	convert_GeomSampleInfo_to_FuncOP (toolbox::match_enzdes_util::GeomSampleInfoCOP gsi, core::Real &ideal_val)

Private Member Functions
void	generate_active_pose_constraints (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx) const
	process the information in template residues and the func op pointers to add More...

void	make_constraint_covalent (core::pose::Pose &pose, core::Size resA_pos, core::Size resB_pos, core::Size resA_At, core::Size resB_At) const

void	make_constraint_covalent_helper (core::pose::Pose &pose, EnzCstTemplateResOP template_res, core::Size res_pos, core::Size Atpos, core::Real itorsion, core::Real iangle, core::Real idis, std::string &res_varname) const
	helper function so stuff doesn't need to be written twice More...

core::Size	determine_best_constraint (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scofx, utility::vector1< core::scoring::constraints::ConstraintCOP > candidate_csts) const
	function to determine the lowest scoring constraint in a vector of input constraints More...

Detailed Description

class that holds all the parameters for one specific constraint

Constructor & Destructor Documentation

◆ EnzConstraintParameters() [1/2]

protocols::toolbox::match_enzdes_util::EnzConstraintParameters::EnzConstraintParameters ( )

◆ EnzConstraintParameters() [2/2]

protocols::toolbox::match_enzdes_util::EnzConstraintParameters::EnzConstraintParameters ( EnzConstraintParameters const & other )

copy constructor

WARNING: currently this probably doesn't copy the functions or active pose constraints

References enz_io_.

◆ ~EnzConstraintParameters()

protocols::toolbox::match_enzdes_util::EnzConstraintParameters::~EnzConstraintParameters ( )

overridedefault

Member Function Documentation

◆ allowed_res_name3_at_position()

std::set< std::string > protocols::toolbox::match_enzdes_util::EnzConstraintParameters::allowed_res_name3_at_position	(	core::pose::Pose const &	pose,
		core::Size	seqpos
	)		const

all residue names specified in the cstfile returns an empty set if the constraints don't apply to the specifed position

References cst_block_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), resA_, and resB_.

◆ convert_GeomSampleInfo_to_FuncOP()

core::scoring::func::FuncOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::convert_GeomSampleInfo_to_FuncOP	(	toolbox::match_enzdes_util::GeomSampleInfoCOP	gsi,
		core::Real &	ideal_val
	)

static

References protocols::toolbox::match_enzdes_util::tr().

Referenced by set_mcfi().

◆ cst_block()

core::Size protocols::toolbox::match_enzdes_util::EnzConstraintParameters::cst_block ( ) const

inline

function that takes all rotamers for the ResidueType(s) of the residue that's missing in the pose and places them according to the geometry specified in the mcfi

References cst_block_.

Referenced by init(), set_cst_block(), and update_pdb_remarks().

◆ determine_best_constraint()

core::Size protocols::toolbox::match_enzdes_util::EnzConstraintParameters::determine_best_constraint	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunctionCOP	scofx,
		utility::vector1< core::scoring::constraints::ConstraintCOP >	candidate_csts
	)		const

private

function to determine the lowest scoring constraint in a vector of input constraints

there might be a slightly faster and slightly more complicated way to implement this,

but since this function will only be called once per input pose (if it is called at all),

it probably doesn't matter.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::pose::Pose::energies(), core::scoring::ScoreFunction::set_weight(), and core::scoring::Energies::total_energies().

Referenced by generate_active_pose_constraints().

◆ enz_io()

EnzConstraintIOCAP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::enz_io ( ) const

inline

References enz_io_.

◆ generate_active_pose_constraints()

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::generate_active_pose_constraints	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP	scofx
	)		const

private

process the information in template residues and the func op pointers to add

to the constraint set in the right format

References angleA_, angleB_, core::conformation::Residue::atom_name(), cst_block_, determine_best_constraint(), disAB_, empty_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), is_covalent_, make_constraint_covalent(), remove_covalent_connections_from_pose(), core::pose::Pose::residue(), torsionA_, torsionAB_, torsionB_, and protocols::toolbox::match_enzdes_util::tr().

Referenced by generate_pose_specific_data().

◆ generate_pose_specific_data()

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::generate_pose_specific_data	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP	scofx
	)		const

References generate_active_pose_constraints(), resA_, and resB_.

◆ get_missing_template_other_res()

EnzCstTemplateResCOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::get_missing_template_other_res ( core::pose::Pose const & pose ) const

References cst_block_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), resA_, and resB_.

◆ get_missing_template_res()

EnzCstTemplateResCOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::get_missing_template_res ( core::pose::Pose const & pose ) const

References cst_block_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), resA_, and resB_.

◆ get_self_ptr() [1/2]

EnzConstraintParametersOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::get_self_ptr ( )

inline

◆ get_self_ptr() [2/2]

EnzConstraintParametersCOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::get_self_ptr ( ) const

inline

self pointers

◆ get_self_weak_ptr()

EnzConstraintParametersCAP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::get_self_weak_ptr ( ) const

inline

Referenced by init(), and set_mcfi().

◆ init() [1/2]

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::init ( void )

References get_self_weak_ptr(), resA_, resB_, and restype_set_.

Referenced by init().

◆ init() [2/2]

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::init	(	core::Size	cst_block,
		core::chemical::ResidueTypeSetCOP	src_restype_set,
		EnzConstraintIOCAP	src_enz_io
	)

References angleA_, angleB_, cst_block(), cst_block_, disAB_, empty_, enz_io_, init(), is_covalent_, resA_, resB_, restype_set_, torsionA_, torsionAB_, and torsionB_.

◆ is_covalent()

bool protocols::toolbox::match_enzdes_util::EnzConstraintParameters::is_covalent ( ) const

inline

References is_covalent_.

◆ is_empty()

bool protocols::toolbox::match_enzdes_util::EnzConstraintParameters::is_empty ( ) const

inline

References empty_.

◆ make_constraint_covalent()

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent	(	core::pose::Pose &	pose,
		core::Size	resA_pos,
		core::Size	resB_pos,
		core::Size	resA_At,
		core::Size	resB_At
	)		const

private

◆ make_constraint_covalent_helper()

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper	(	core::pose::Pose &	pose,
		EnzCstTemplateResOP	template_res,
		core::Size	res_pos,
		core::Size	Atpos,
		core::Real	itorsion,
		core::Real	iangle,
		core::Real	idis,
		std::string &	res_varname
	)		const

private

helper function so stuff doesn't need to be written twice

References core::conformation::Residue::atom_name(), core::chemical::ResidueTypeBase::get_disulfide_atom_name(), core::pose::get_restype_for_pose(), core::chemical::ResidueType::is_disulfide_bonded(), core::chemical::ResidueType::is_metal(), core::chemical::ResidueTypeBase::mode(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::chemical::residue_type_all_patches_name(), core::chemical::residue_type_base_name(), and core::chemical::orbitals::strip_whitespace().

Referenced by make_constraint_covalent().

◆ missing_in_pose()

bool protocols::toolbox::match_enzdes_util::EnzConstraintParameters::missing_in_pose ( core::pose::Pose const & pose ) const

References cst_block_, and protocols::toolbox::match_enzdes_util::get_enzdes_observer().

◆ nonconst_resA()

EnzCstTemplateResOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::nonconst_resA ( )

References resA_.

◆ nonconst_resB()

EnzCstTemplateResOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::nonconst_resB ( )

References resB_.

◆ remap_resid()

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::remap_resid ( core::id::SequenceMapping const & smap )

References resA_, and resB_.

◆ remove_covalent_connections_from_pose()

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::remove_covalent_connections_from_pose ( core::pose::Pose & pose ) const

References cst_block_, and protocols::toolbox::match_enzdes_util::get_enzdes_observer().

Referenced by generate_active_pose_constraints().

◆ resA()

EnzCstTemplateResCOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::resA ( ) const

References resA_.

Referenced by update_pdb_remarks().

◆ resB()

EnzCstTemplateResCOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::resB ( ) const

References resB_.

Referenced by update_pdb_remarks().

◆ set_cst_block()

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::set_cst_block ( core::Size cst_block )

inline

References cst_block(), and cst_block_.

◆ set_external_position_for_resA()

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::set_external_position_for_resA ( core::Size pos )

References resA_.

◆ set_external_position_for_resB()

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::set_external_position_for_resB ( core::Size pos )

References resB_.

◆ set_mcfi()

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::set_mcfi ( toolbox::match_enzdes_util::MatchConstraintFileInfoCOP mcfi )

◆ show_definitions()

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::show_definitions ( ) const

References resA_, resB_, and protocols::toolbox::match_enzdes_util::tr().

◆ update_pdb_remarks()

bool protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks ( core::pose::Pose & pose ) const

updates the pdb remarks according to what is in the EnzCstTemplateRes member data. returns false in case any error occured

References protocols::toolbox::match_enzdes_util::assemble_remark_line(), core::pose::PDBInfo::chain(), cst_block(), cst_block_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::conformation::Residue::is_ligand(), core::conformation::Residue::name3(), core::pose::PDBInfo::number(), core::pose::Pose::pdb_info(), resA(), resB(), core::pose::Pose::residue(), protocols::toolbox::match_enzdes_util::split_up_remark_line(), and protocols::toolbox::match_enzdes_util::tr().

Member Data Documentation

◆ angleA_

core::scoring::func::FuncOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::angleA_

private

Referenced by generate_active_pose_constraints(), init(), and set_mcfi().

◆ angleB_

core::scoring::func::FuncOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::angleB_

private

Referenced by generate_active_pose_constraints(), init(), and set_mcfi().

◆ cst_block_

core::Size protocols::toolbox::match_enzdes_util::EnzConstraintParameters::cst_block_

private

Referenced by allowed_res_name3_at_position(), cst_block(), generate_active_pose_constraints(), get_missing_template_other_res(), get_missing_template_res(), init(), make_constraint_covalent(), missing_in_pose(), remove_covalent_connections_from_pose(), set_cst_block(), and update_pdb_remarks().

◆ disAB_

core::scoring::func::FuncOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::disAB_

private

Referenced by generate_active_pose_constraints(), init(), and set_mcfi().

◆ empty_

bool protocols::toolbox::match_enzdes_util::EnzConstraintParameters::empty_

mutableprivate

Referenced by generate_active_pose_constraints(), init(), and is_empty().

◆ enz_io_

EnzConstraintIOCAP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::enz_io_

private

Referenced by enz_io(), EnzConstraintParameters(), and init().

◆ is_covalent_

bool protocols::toolbox::match_enzdes_util::EnzConstraintParameters::is_covalent_

private

Referenced by generate_active_pose_constraints(), init(), is_covalent(), and set_mcfi().

◆ mcfi_

toolbox::match_enzdes_util::MatchConstraintFileInfoCOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::mcfi_

private

Referenced by set_mcfi().

◆ nangleA_

core::Real protocols::toolbox::match_enzdes_util::EnzConstraintParameters::nangleA_

private

Referenced by make_constraint_covalent(), and set_mcfi().

◆ nangleB_

core::Real protocols::toolbox::match_enzdes_util::EnzConstraintParameters::nangleB_

private

Referenced by make_constraint_covalent(), and set_mcfi().

◆ ndisAB_

core::Real protocols::toolbox::match_enzdes_util::EnzConstraintParameters::ndisAB_

private

Referenced by set_mcfi().

◆ ntorsionA_

core::Real protocols::toolbox::match_enzdes_util::EnzConstraintParameters::ntorsionA_

private

Referenced by make_constraint_covalent(), and set_mcfi().

◆ ntorsionAB_

core::Real protocols::toolbox::match_enzdes_util::EnzConstraintParameters::ntorsionAB_

private

Referenced by set_mcfi().

◆ ntorsionB_

core::Real protocols::toolbox::match_enzdes_util::EnzConstraintParameters::ntorsionB_

private

Referenced by make_constraint_covalent(), and set_mcfi().

◆ resA_

EnzCstTemplateResOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::resA_

private

Referenced by allowed_res_name3_at_position(), generate_pose_specific_data(), get_missing_template_other_res(), get_missing_template_res(), init(), make_constraint_covalent(), nonconst_resA(), remap_resid(), resA(), set_external_position_for_resA(), set_mcfi(), and show_definitions().

◆ resB_

EnzCstTemplateResOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::resB_

private

Referenced by allowed_res_name3_at_position(), generate_pose_specific_data(), get_missing_template_other_res(), get_missing_template_res(), init(), make_constraint_covalent(), nonconst_resB(), remap_resid(), resB(), set_external_position_for_resB(), set_mcfi(), and show_definitions().

◆ restype_set_

core::chemical::ResidueTypeSetCOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::restype_set_

private

Referenced by init(), and make_constraint_covalent().

◆ torsionA_

core::scoring::func::FuncOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::torsionA_

private

Referenced by generate_active_pose_constraints(), init(), and set_mcfi().

◆ torsionAB_

core::scoring::func::FuncOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::torsionAB_

private

Referenced by generate_active_pose_constraints(), init(), and set_mcfi().

◆ torsionB_

core::scoring::func::FuncOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::torsionB_

private

Referenced by generate_active_pose_constraints(), init(), and set_mcfi().

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

src/protocols/toolbox/match_enzdes_util/EnzConstraintParameters.hh
src/protocols/toolbox/match_enzdes_util/EnzConstraintParameters.cc

Private Attributes
EnzCstTemplateResOP	resA_

EnzCstTemplateResOP	resB_

toolbox::match_enzdes_util::MatchConstraintFileInfoCOP	mcfi_

core::scoring::func::FuncOP	disAB_

core::scoring::func::FuncOP	angleA_

core::scoring::func::FuncOP	angleB_

core::scoring::func::FuncOP	torsionA_

core::scoring::func::FuncOP	torsionB_

core::scoring::func::FuncOP	torsionAB_

core::Real	ndisAB_

core::Real	nangleA_

core::Real	nangleB_

core::Real	ntorsionA_

core::Real	ntorsionB_

core::Real	ntorsionAB_

bool	is_covalent_

bool	empty_

core::chemical::ResidueTypeSetCOP	restype_set_

EnzConstraintIOCAP	enz_io_

core::Size	cst_block_

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ EnzConstraintParameters() [1/2]

◆ EnzConstraintParameters() [2/2]

◆ ~EnzConstraintParameters()

Member Function Documentation

◆ allowed_res_name3_at_position()

◆ convert_GeomSampleInfo_to_FuncOP()

◆ cst_block()

◆ determine_best_constraint()

◆ enz_io()

◆ generate_active_pose_constraints()

◆ generate_pose_specific_data()

◆ get_missing_template_other_res()

◆ get_missing_template_res()

◆ get_self_ptr() [1/2]

◆ get_self_ptr() [2/2]

◆ get_self_weak_ptr()

◆ init() [1/2]

◆ init() [2/2]

◆ is_covalent()

◆ is_empty()

◆ make_constraint_covalent()

◆ make_constraint_covalent_helper()

◆ missing_in_pose()

◆ nonconst_resA()

◆ nonconst_resB()

◆ remap_resid()

◆ remove_covalent_connections_from_pose()

◆ resA()

◆ resB()

◆ set_cst_block()

◆ set_external_position_for_resA()

◆ set_external_position_for_resB()

◆ set_mcfi()

◆ show_definitions()

◆ update_pdb_remarks()

Member Data Documentation

◆ angleA_

◆ angleB_

◆ cst_block_

◆ disAB_

◆ empty_

◆ enz_io_

◆ is_covalent_

◆ mcfi_

◆ nangleA_

◆ nangleB_

◆ ndisAB_

◆ ntorsionA_

◆ ntorsionAB_

◆ ntorsionB_

◆ resA_

◆ resB_

◆ restype_set_

◆ torsionA_

◆ torsionAB_

◆ torsionB_