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protocols::forge::remodel::RemodelEnzdesCstModule Class Reference

#include <RemodelEnzdesCstModule.hh>

Inheritance diagram for protocols::forge::remodel::RemodelEnzdesCstModule:
Inheritance graph
[legend]

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

Member Function Documentation

void protocols::forge::remodel::RemodelEnzdesCstModule::apply ( core::pose::Pose pose)
void protocols::forge::remodel::RemodelEnzdesCstModule::blueprint_cst_definition ( core::pose::Pose pose)
void protocols::forge::remodel::RemodelEnzdesCstModule::enable_constraint_scoreterms ( core::scoring::ScoreFunctionOP  scorefxn)
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
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
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: