Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
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::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
 

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

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_.

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

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 
)
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().

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().

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

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

References cst_pairs_.

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

References cst_pairs_.

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

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

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
EnzConstraintIOCOP protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_self_ptr ( ) const
inline
EnzConstraintIOOP protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_self_ptr ( )
inline
EnzConstraintIOCAP protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_self_weak_ptr ( ) const
inline
EnzConstraintIOAP protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_self_weak_ptr ( )
inline
void protocols::toolbox::match_enzdes_util::EnzConstraintIO::initialize_with_mcfi_list ( utility::vector1< MatchConstraintFileInfoListOP mcfi_list_vec)
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().

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

References mcfi_lists_.

utility::vector1< core::Size > protocols::toolbox::match_enzdes_util::EnzConstraintIO::ordered_constrained_positions ( core::pose::Pose const &  pose) const
void protocols::toolbox::match_enzdes_util::EnzConstraintIO::process_pdb_header ( core::pose::Pose pose,
bool  accept_missing_blocks 
)
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().

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_.

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

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_.

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

References cst_pairs_.

Member Data Documentation

utility::vector1< EnzConstraintParametersOP > protocols::toolbox::match_enzdes_util::EnzConstraintIO::cst_pairs_
protected
utility::vector1< toolbox::match_enzdes_util::MatchConstraintFileInfoListOP > protocols::toolbox::match_enzdes_util::EnzConstraintIO::mcfi_lists_
private
core::chemical::ResidueTypeSetCOP protocols::toolbox::match_enzdes_util::EnzConstraintIO::restype_set_
private
utility::vector1< std::pair< core::Size, core::Size> > protocols::toolbox::match_enzdes_util::EnzConstraintIO::target_downstream_res_
private

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