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protocols::toolbox::match_enzdes_util::EnzConstraintIO Class Reference

#include <EnzConstraintIO.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::EnzConstraintIO:
Inheritance graph
[legend]

Public Member Functions

 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
 

Protected Attributes

utility::vector1< EnzConstraintParametersOP > cst_pairs_
 

Private Member Functions

void generate_pose_specific_data (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx) const
 prepares the class for reading in data from a pose/pdb More...
 
void generate_pose_specific_data_for_block (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx, core::Size cst_block) const
 
void determine_target_downstream_res ()
 

Private Attributes

utility::vector1< toolbox::match_enzdes_util::MatchConstraintFileInfoListOP > mcfi_lists_
 
utility::vector1< std::pair< core::Size, core::Size > > target_downstream_res_
 
core::chemical::ResidueTypeSetCOP restype_set_
 

Constructor & Destructor Documentation

◆ EnzConstraintIO()

protocols::toolbox::match_enzdes_util::EnzConstraintIO::EnzConstraintIO ( core::chemical::ResidueTypeSetCOP  src_restype_set)

@ brief constructor for EnzConstraintIO class, builds up function types

References cst_pairs_, mcfi_lists_, and restype_set_.

◆ ~EnzConstraintIO()

protocols::toolbox::match_enzdes_util::EnzConstraintIO::~EnzConstraintIO ( )
overridedefault

Member Function Documentation

◆ add_constraints_to_pose()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_constraints_to_pose ( core::pose::Pose &  pose,
core::scoring::ScoreFunctionCOP  scofx,
bool  accept_blocks_missing_header 
)

References add_constraints_to_pose_for_block_without_clearing_and_header_processing(), cst_pairs_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), get_self_ptr(), process_pdb_header(), remove_constraints_from_pose(), show_cst_definitions(), and protocols::toolbox::match_enzdes_util::tr().

◆ add_constraints_to_pose_for_block_without_clearing_and_header_processing()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::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.

without clearing the internal data structures and reading in

the information in the pdb REMARKs

if you're unsure use the above one

References core::pose::Pose::add_constraints(), generate_pose_specific_data_for_block(), and protocols::toolbox::match_enzdes_util::get_enzdes_observer().

Referenced by add_constraints_to_pose(), add_pregenerated_constraints_to_pose(), and protocols::forge::remodel::RemodelEnzdesCstModule::apply().

◆ add_pregenerated_constraints_to_pose()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::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

been previously generated. BE CAREFUL when using this function, it relies on the

pose having the same residue types at the same constrained positions as in the pose

that was originally used to generate the constraints. If in doubt, it's safer to

regenerate the constraints before adding (i.e. use the above add_constraints_to_pose

function.)

References core::pose::Pose::add_constraint(), add_constraints_to_pose_for_block_without_clearing_and_header_processing(), core::pose::Pose::constraint_set(), cst_pairs_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), and protocols::toolbox::match_enzdes_util::tr().

◆ allowed_res_name3_at_position()

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

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

◆ clear_active_pose_constraints_for_block()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::clear_active_pose_constraints_for_block ( core::pose::Pose &  pose,
core::Size  cst_block 
) const

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

◆ contains_position()

bool protocols::toolbox::match_enzdes_util::EnzConstraintIO::contains_position ( core::pose::Pose const &  pose,
core::Size const  seqpos 
) const

are constraints specified for this position?

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

◆ determine_target_downstream_res()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::determine_target_downstream_res ( )
private

References mcfi_lists_, and target_downstream_res_.

Referenced by initialize_with_mcfi_list(), and read_enzyme_cstfile().

◆ enz_cst_params()

EnzConstraintParametersCOP protocols::toolbox::match_enzdes_util::EnzConstraintIO::enz_cst_params ( core::Size  block) const

References cst_pairs_.

◆ enz_cst_params_missing_in_pose()

utility::vector1< EnzConstraintParametersCOP > protocols::toolbox::match_enzdes_util::EnzConstraintIO::enz_cst_params_missing_in_pose ( core::pose::Pose const &  pose) const

References cst_pairs_.

◆ enz_cst_params_size()

core::Size protocols::toolbox::match_enzdes_util::EnzConstraintIO::enz_cst_params_size ( )
inline

References cst_pairs_.

◆ generate_pose_specific_data()

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

prepares the class for reading in data from a pose/pdb

References cst_pairs_, and generate_pose_specific_data_for_block().

◆ generate_pose_specific_data_for_block()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::generate_pose_specific_data_for_block ( core::pose::Pose &  pose,
core::scoring::ScoreFunctionCOP  scofx,
core::Size  cst_block 
) const
private

References cst_pairs_, and protocols::toolbox::match_enzdes_util::tr().

Referenced by add_constraints_to_pose_for_block_without_clearing_and_header_processing(), and generate_pose_specific_data().

◆ get_self_ptr() [1/2]

EnzConstraintIOOP protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_self_ptr ( )
inline

◆ get_self_ptr() [2/2]

EnzConstraintIOCOP protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_self_ptr ( ) const
inline

self pointers

Referenced by add_constraints_to_pose(), and protocols::forge::remodel::RemodelEnzdesCstModule::apply().

◆ get_self_weak_ptr() [1/2]

EnzConstraintIOAP protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_self_weak_ptr ( )
inline

◆ get_self_weak_ptr() [2/2]

EnzConstraintIOCAP protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_self_weak_ptr ( ) const
inline

Referenced by initialize_with_mcfi_list(), and read_enzyme_cstfile().

◆ initialize_with_mcfi_list()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::initialize_with_mcfi_list ( utility::vector1< MatchConstraintFileInfoListOP >  mcfi_list_vec)

References cst_pairs_, determine_target_downstream_res(), get_self_weak_ptr(), mcfi_list(), mcfi_lists_, and restype_set_.

◆ is_backbone_only_cst()

bool protocols::toolbox::match_enzdes_util::EnzConstraintIO::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?

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

◆ mcfi_list()

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

References mcfi_lists_.

Referenced by protocols::forge::remodel::RemodelEnzdesCstModule::apply(), protocols::match::Matcher::initialize_from_file(), and initialize_with_mcfi_list().

◆ mcfi_lists_size()

core::Size protocols::toolbox::match_enzdes_util::EnzConstraintIO::mcfi_lists_size ( ) const

References mcfi_lists_.

Referenced by protocols::match::Matcher::initialize_from_file().

◆ num_mcfi_lists()

core::Size protocols::toolbox::match_enzdes_util::EnzConstraintIO::num_mcfi_lists ( ) const
inline

References mcfi_lists_.

◆ ordered_constrained_positions()

utility::vector1< core::Size > protocols::toolbox::match_enzdes_util::EnzConstraintIO::ordered_constrained_positions ( core::pose::Pose const &  pose) const

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

◆ process_pdb_header()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::process_pdb_header ( core::pose::Pose &  pose,
bool  accept_missing_blocks 
)

reads the residue numbers that the constraints will be applied to.

References cst_pairs_, core::pose::PDBPoseMap::find(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), mcfi_lists_, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::toolbox::match_enzdes_util::split_up_remark_line(), core::id::to_string(), and protocols::toolbox::match_enzdes_util::tr().

Referenced by add_constraints_to_pose().

◆ read_enzyme_cstfile()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::read_enzyme_cstfile ( std::string  fname)

reads the enzyme cstfile and for each block of residue residue constraints, creates a new

instance of EnzConstraintParameters

References cst_pairs_, determine_target_downstream_res(), get_self_weak_ptr(), mcfi_lists_, restype_set_, and protocols::toolbox::match_enzdes_util::tr().

◆ remap_resid()

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

changing the constrained residues if the sequence length changes

References cst_pairs_.

◆ remove_constraints_from_pose()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_constraints_from_pose ( core::pose::Pose &  pose,
bool const  keep_covalent,
bool const  fail_on_constraints_missing 
) const

References cst_pairs_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), and remove_constraints_from_pose_for_block().

Referenced by add_constraints_to_pose().

◆ remove_constraints_from_pose_for_block()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_constraints_from_pose_for_block ( core::pose::Pose &  pose,
core::Size  cst_block,
bool const  fail_on_constraints_missing 
) const

References cst_pairs_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), and core::pose::Pose::remove_constraints().

Referenced by remove_constraints_from_pose().

◆ remove_position_from_template_res()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_position_from_template_res ( core::pose::Pose &  pose,
core::Size  pos 
) const

References cst_pairs_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), and remove_position_from_template_res_for_block().

◆ remove_position_from_template_res_for_block()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_position_from_template_res_for_block ( core::pose::Pose &  pose,
core::Size  pos,
core::Size  cst_block 
) const

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

Referenced by remove_position_from_template_res().

◆ set_external_position_for_resA_in_parameter_block()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::set_external_position_for_resA_in_parameter_block ( core::Size  cst_block,
core::Size  respos 
)

References cst_pairs_.

◆ set_external_position_for_resB_in_parameter_block()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::set_external_position_for_resB_in_parameter_block ( core::Size  cst_block,
core::Size  respos 
)

References cst_pairs_.

◆ set_position_for_missing_res_in_parameter_block()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::set_position_for_missing_res_in_parameter_block ( core::pose::Pose &  pose,
core::Size  cst_block,
core::Size  respos 
) const

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

◆ show_cst_definitions()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::show_cst_definitions ( ) const

References cst_pairs_, and protocols::toolbox::match_enzdes_util::tr().

Referenced by add_constraints_to_pose().

◆ target_downstream_res()

utility::vector1< std::pair< core::Size, core::Size> > const& protocols::toolbox::match_enzdes_util::EnzConstraintIO::target_downstream_res ( ) const
inline

References target_downstream_res_.

◆ update_pdb_remarks_for_backbone_params()

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::update_pdb_remarks_for_backbone_params ( core::pose::Pose &  pose) const

References cst_pairs_.

Member Data Documentation

◆ cst_pairs_

utility::vector1< EnzConstraintParametersOP > protocols::toolbox::match_enzdes_util::EnzConstraintIO::cst_pairs_
protected

Referenced by add_constraints_to_pose(), add_pregenerated_constraints_to_pose(), allowed_res_name3_at_position(), protocols::forge::remodel::RemodelEnzdesCstModule::apply(), protocols::forge::remodel::RemodelEnzdesCstModule::blueprint_cst_definition(), clear_active_pose_constraints_for_block(), enz_cst_params(), enz_cst_params_missing_in_pose(), enz_cst_params_size(), EnzConstraintIO(), generate_pose_specific_data(), generate_pose_specific_data_for_block(), initialize_with_mcfi_list(), is_backbone_only_cst(), process_pdb_header(), read_enzyme_cstfile(), remap_resid(), remove_constraints_from_pose(), remove_constraints_from_pose_for_block(), remove_position_from_template_res(), set_external_position_for_resA_in_parameter_block(), set_external_position_for_resB_in_parameter_block(), set_position_for_missing_res_in_parameter_block(), show_cst_definitions(), and update_pdb_remarks_for_backbone_params().

◆ mcfi_lists_

utility::vector1< toolbox::match_enzdes_util::MatchConstraintFileInfoListOP > protocols::toolbox::match_enzdes_util::EnzConstraintIO::mcfi_lists_
private

Referenced by determine_target_downstream_res(), EnzConstraintIO(), initialize_with_mcfi_list(), mcfi_list(), mcfi_lists_size(), num_mcfi_lists(), process_pdb_header(), and read_enzyme_cstfile().

◆ restype_set_

core::chemical::ResidueTypeSetCOP protocols::toolbox::match_enzdes_util::EnzConstraintIO::restype_set_
private

Referenced by EnzConstraintIO(), initialize_with_mcfi_list(), and read_enzyme_cstfile().

◆ target_downstream_res_

utility::vector1< std::pair< core::Size, core::Size> > protocols::toolbox::match_enzdes_util::EnzConstraintIO::target_downstream_res_
private

Referenced by determine_target_downstream_res(), and target_downstream_res().

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