#include <RemodelEnzdesCstModule.hh>

Inheritance diagram for protocols::forge::remodel::RemodelEnzdesCstModule:

Public Member Functions
	RemodelEnzdesCstModule (protocols::forge::remodel::RemodelData external_data)

	~RemodelEnzdesCstModule () override

void	apply (core::pose::Pose &pose)

void	blueprint_cst_definition (core::pose::Pose &pose)

void	enable_constraint_scoreterms (core::scoring::ScoreFunctionOP scorefxn)

void	use_backbone_only_blocks ()

void	use_all_blocks ()

Public Member Functions inherited from protocols::toolbox::match_enzdes_util::EnzConstraintIO
	EnzConstraintIO (core::chemical::ResidueTypeSetCOP src_restype_set)
	@ brief constructor for EnzConstraintIO class, builds up function types More...

	~EnzConstraintIO () override

EnzConstraintIOCOP	get_self_ptr () const
	self pointers More...

EnzConstraintIOOP	get_self_ptr ()

EnzConstraintIOCAP	get_self_weak_ptr () const

EnzConstraintIOAP	get_self_weak_ptr ()

void	read_enzyme_cstfile (std::string fname)
	reads the enzyme cstfile and for each block of residue residue constraints, creates a new More...

void	initialize_with_mcfi_list (utility::vector1< MatchConstraintFileInfoListOP > mcfi_list_vec)

toolbox::match_enzdes_util::MatchConstraintFileInfoListCOP	mcfi_list (core::Size block) const

core::Size	num_mcfi_lists () const

void	add_constraints_to_pose (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx, bool accept_blocks_missing_header)

void	add_constraints_to_pose_for_block_without_clearing_and_header_processing (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx, core::Size cst_block) const
	BE CAREFUL when using this function, it generates constraints. More...

void	add_pregenerated_constraints_to_pose (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx) const
	convenience function that will add constraints to the pose if they have More...

void	remove_constraints_from_pose (core::pose::Pose &pose, bool const keep_covalent, bool const fail_on_constraints_missing) const

void	remove_constraints_from_pose_for_block (core::pose::Pose &pose, core::Size cst_block, bool const fail_on_constraints_missing) const

void	remove_position_from_template_res_for_block (core::pose::Pose &pose, core::Size pos, core::Size cst_block) const

void	remove_position_from_template_res (core::pose::Pose &pose, core::Size pos) const

void	process_pdb_header (core::pose::Pose &pose, bool accept_missing_blocks)
	reads the residue numbers that the constraints will be applied to. More...

bool	contains_position (core::pose::Pose const &pose, core::Size const seqpos) const
	are constraints specified for this position? More...

bool	is_backbone_only_cst (core::pose::Pose const &pose, core::Size const seqpos) const
	are the constraints specified at this position mediated through backbone interactions only? More...

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

utility::vector1< std::string >	allowed_res_name3_at_position (core::pose::Pose const &pose, core::Size const seqpos) const

void	show_cst_definitions () const

void	remap_resid (core::id::SequenceMapping const &smap)
	changing the constrained residues if the sequence length changes More...

void	set_position_for_missing_res_in_parameter_block (core::pose::Pose &pose, core::Size cst_block, core::Size respos) const

void	clear_active_pose_constraints_for_block (core::pose::Pose &pose, core::Size cst_block) const

void	set_external_position_for_resA_in_parameter_block (core::Size cst_block, core::Size respos)

void	set_external_position_for_resB_in_parameter_block (core::Size cst_block, core::Size respos)

EnzConstraintParametersCOP	enz_cst_params (core::Size block) const

utility::vector1 < EnzConstraintParametersCOP >	enz_cst_params_missing_in_pose (core::pose::Pose const &pose) const

utility::vector1< core::Size >	ordered_constrained_positions (core::pose::Pose const &pose) const

core::Size	mcfi_lists_size () const

core::Size	enz_cst_params_size ()

utility::vector1< std::pair < core::Size, core::Size > > const &	target_downstream_res () const

Private Attributes
protocols::forge::remodel::RemodelData	remodel_data_

core::Size	cstblocksize_

core::scoring::ScoreFunctionOP	scorefxn_

bool	backbone_only_

Additional Inherited Members
Protected Attributes inherited from protocols::toolbox::match_enzdes_util::EnzConstraintIO
utility::vector1 < EnzConstraintParametersOP >	cst_pairs_

Constructor & Destructor Documentation

protocols::forge::remodel::RemodelEnzdesCstModule::RemodelEnzdesCstModule ( protocols::forge::remodel::RemodelData external_data )

References core::scoring::get_score_function(), remodel_data_, and scorefxn_.

protocols::forge::remodel::RemodelEnzdesCstModule::~RemodelEnzdesCstModule ( )

overridedefault

Member Function Documentation

void protocols::forge::remodel::RemodelEnzdesCstModule::apply ( core::pose::Pose & pose )

References protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_constraints_to_pose_for_block_without_clearing_and_header_processing(), protocols::forge::remodel::RemodelDesignMover::apply(), backbone_only_, blueprint_cst_definition(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::cst_pairs_, cstblocksize_, enable_constraint_scoreterms(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_self_ptr(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::mcfi_list(), remodel_data_, scorefxn_, protocols::forge::remodel::RemodelDesignMover::set_state(), protocols::forge::remodel::TR(), and protocols::forge::remodel::RemodelWorkingSet::workingSetGen().

void protocols::forge::remodel::RemodelEnzdesCstModule::blueprint_cst_definition ( core::pose::Pose & pose )

References protocols::forge::remodel::RemodelData::blueprint, protocols::toolbox::match_enzdes_util::EnzConstraintIO::cst_pairs_, cstblocksize_, core::sequence::end, core::chemical::ResidueTypeBase::name3(), remodel_data_, core::pose::Pose::residue_type(), and protocols::forge::remodel::TR().

Referenced by apply().

void protocols::forge::remodel::RemodelEnzdesCstModule::enable_constraint_scoreterms ( core::scoring::ScoreFunctionOP scorefxn )

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::scoring::res_type_constraint, and protocols::forge::remodel::TR().

Referenced by apply().

void protocols::forge::remodel::RemodelEnzdesCstModule::use_all_blocks ( )

References backbone_only_.

void protocols::forge::remodel::RemodelEnzdesCstModule::use_backbone_only_blocks ( )

References backbone_only_.

Member Data Documentation

bool protocols::forge::remodel::RemodelEnzdesCstModule::backbone_only_

private

Referenced by apply(), use_all_blocks(), and use_backbone_only_blocks().

core::Size protocols::forge::remodel::RemodelEnzdesCstModule::cstblocksize_

private

Referenced by apply(), and blueprint_cst_definition().

protocols::forge::remodel::RemodelData protocols::forge::remodel::RemodelEnzdesCstModule::remodel_data_

private

Referenced by apply(), blueprint_cst_definition(), and RemodelEnzdesCstModule().

core::scoring::ScoreFunctionOP protocols::forge::remodel::RemodelEnzdesCstModule::scorefxn_

private

Referenced by apply(), and RemodelEnzdesCstModule().

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

src/protocols/forge/remodel/RemodelEnzdesCstModule.hh
src/protocols/forge/remodel/RemodelEnzdesCstModule.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation