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

#include <EnzConstraintIO.hh>

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Public Member Functions

 EnzConstraintIO (core::chemical::ResidueTypeSetCAP src_restype_set)
 @ brief constructor for EnzConstraintIO class, builds up function types More...
 
virtual ~EnzConstraintIO ()
 
void read_enzyme_cstfile (std::string fname)
 reads the enzyme cstfile and for each block of residue residue constraints, creates a new More...
 
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
 

Static Public Member Functions

static EnzConstraintIO * get_instance ()
 

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::ResidueTypeSetCAP restype_set_
 

Static Private Attributes

static EnzConstraintIOOP generic_instance_ = NULL
 

Detailed Description

Definition at line 73 of file EnzConstraintIO.hh.

Constructor & Destructor Documentation

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

@ brief constructor for EnzConstraintIO class, builds up function types

Definition at line 77 of file EnzConstraintIO.cc.

References cst_pairs_, mcfi_lists_, and restype_set_.

Referenced by get_instance().

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

Definition at line 84 of file EnzConstraintIO.cc.

Member Function Documentation

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

Definition at line 400 of file EnzConstraintIO.cc.

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

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

Definition at line 435 of file EnzConstraintIO.cc.

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().

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.)

Definition at line 535 of file EnzConstraintIO.cc.

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().

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

Definition at line 648 of file EnzConstraintIO.cc.

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

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

Definition at line 720 of file EnzConstraintIO.cc.

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

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?

Definition at line 592 of file EnzConstraintIO.cc.

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

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

Definition at line 912 of file EnzConstraintIO.cc.

References mcfi_lists_, and target_downstream_res_.

Referenced by read_enzyme_cstfile().

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

Definition at line 836 of file EnzConstraintIO.cc.

References cst_pairs_.

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

Definition at line 843 of file EnzConstraintIO.cc.

References cst_pairs_.

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

Definition at line 237 of file EnzConstraintIO.hh.

References cst_pairs_.

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

Definition at line 371 of file EnzConstraintIO.cc.

References cst_pairs_, and 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

Definition at line 383 of file EnzConstraintIO.cc.

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().

EnzConstraintIO * protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_instance ( )
static

Definition at line 87 of file EnzConstraintIO.cc.

References EnzConstraintIO(), core::chemical::FA_STANDARD, generic_instance_, and core::chemical::ChemicalManager::get_instance().

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?

Definition at line 607 of file EnzConstraintIO.cc.

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

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

Definition at line 192 of file EnzConstraintIO.cc.

References mcfi_lists_.

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

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

Definition at line 906 of file EnzConstraintIO.cc.

References mcfi_lists_.

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

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

Definition at line 91 of file EnzConstraintIO.hh.

References mcfi_lists_.

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

Definition at line 860 of file EnzConstraintIO.cc.

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

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.

Definition at line 204 of file EnzConstraintIO.cc.

References cst_pairs_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), mcfi_lists_, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::toolbox::match_enzdes_util::split_up_remark_line(), and core::pose::Pose::total_residue().

Referenced by add_constraints_to_pose().

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

Definition at line 106 of file EnzConstraintIO.cc.

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

Referenced by protocols::forge::remodel::RemodelEnzdesCstModule::RemodelEnzdesCstModule().

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

changing the constrained residues if the sequence length changes

Definition at line 698 of file EnzConstraintIO.cc.

References cst_pairs_.

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

Definition at line 459 of file EnzConstraintIO.cc.

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

Referenced by add_constraints_to_pose().

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

Definition at line 478 of file EnzConstraintIO.cc.

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

Referenced by remove_constraints_from_pose().

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

Definition at line 521 of file EnzConstraintIO.cc.

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

Definition at line 512 of file EnzConstraintIO.cc.

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

Referenced by remove_position_from_template_res().

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

Definition at line 730 of file EnzConstraintIO.cc.

References cst_pairs_.

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

Definition at line 740 of file EnzConstraintIO.cc.

References cst_pairs_.

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

Definition at line 707 of file EnzConstraintIO.cc.

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

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

Definition at line 686 of file EnzConstraintIO.cc.

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

Referenced by add_constraints_to_pose().

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

Definition at line 240 of file EnzConstraintIO.hh.

References target_downstream_res_.

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

Definition at line 634 of file EnzConstraintIO.cc.

References cst_pairs_.

Member Data Documentation

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

Definition at line 245 of file EnzConstraintIO.hh.

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(), 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().

EnzConstraintIOOP protocols::toolbox::match_enzdes_util::EnzConstraintIO::generic_instance_ = NULL
staticprivate

Definition at line 282 of file EnzConstraintIO.hh.

Referenced by get_instance().

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

Definition at line 271 of file EnzConstraintIO.hh.

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

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

Definition at line 276 of file EnzConstraintIO.hh.

Referenced by EnzConstraintIO(), and read_enzyme_cstfile().

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

Definition at line 274 of file EnzConstraintIO.hh.

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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