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protocols::enzdes::SecondaryMatchProtocol Class Reference

#include <SecondaryMatchProtocol.hh>

Inheritance diagram for protocols::enzdes::SecondaryMatchProtocol:
Inheritance graph
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Public Member Functions

 SecondaryMatchProtocol ()
 
 ~SecondaryMatchProtocol () override
 
void apply (core::pose::Pose &start_pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
core::Size residues_compatible (core::conformation::ResidueCOP res1, core::conformation::ResidueCOP res2) const
 lookup function to determine whether to residues are compatible More...
 
bool do_matching (core::pose::Pose &start_pose)
 
void set_trial_positions (utility::vector1< core::Size > const &trial_pos)
 
- Public Member Functions inherited from protocols::enzdes::EnzdesBaseProtocol
 EnzdesBaseProtocol ()
 
utility::vector1< core::Sizecatalytic_res (core::pose::Pose const &pose) const
 
std::set< core::Size > const & design_targets (core::pose::Pose const &pose) const
 
utility::vector1< core::Sizerb_min_jumps () const
 
void rb_min_jumps (utility::vector1< core::Size > const )
 
bool is_catalytic_position (core::pose::Pose const &pose, core::Size const seqpos) const
 
core::chemical::ResidueTypeSetCAP restype_set () const
 
void generate_explicit_ligand_rotamer_poses (core::pose::Pose const &orig_pose, utility::vector1< core::pose::PoseOP > &ligrot_poses, core::scoring::ScoreFunctionCOP scofx)
 
core::scoring::ScoreFunctionCOP reduced_scorefxn () const
 
core::scoring::ScoreFunctionOP reduced_scorefxn ()
 
core::Real design_targets_score (core::pose::Pose const &pose) const
 
virtual void remap_resid (core::pose::Pose const &pose, core::id::SequenceMapping const &smap)
 
void remove_enzdes_constraints (core::pose::Pose &pose, bool keep_covalent) const
 
void add_pregenerated_enzdes_constraints (core::pose::Pose &pose) const
 
void cst_minimize (core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool cst_opt=false) const
 
core::pack::task::PackerTaskOP create_enzdes_pack_task (core::pose::Pose &pose, bool design=true)
 
void setup_sequence_recovery_cache (core::pose::Pose &pose, core::pack::task::PackerTask const &task) const
 
void set_all_jumps_minimizable (bool const &setting)
 
void set_minimize_options (bool const &min_sc, bool const &min_bb, bool const &min_rb, bool const &min_lig, bool backrub=false)
 
void set_fix_cataa (bool const &setting)
 
core::kinematics::MoveMapOP create_enzdes_movemap (core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool min_all_jumps=false) const
 
void enzdes_pack (core::pose::Pose &pose, core::pack::task::PackerTaskCOP, core::scoring::ScoreFunctionCOP scorefxn, core::Size cycles, bool minimize_after_packing, bool pack_unconstrained, bool favor_native) const
 
void set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
 
void setup_bbmin_ft_and_csts (core::pose::Pose &pose, utility::vector1< bool > allow_move_bb, core::Size jump_id) const
 
- Public Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
 LigandBaseProtocol ()
 
 ~LigandBaseProtocol () override
 
LigandBaseProtocolOP shared_from_this ()
 
core::scoring::ScoreFunctionOP get_scorefxn ()
 
core::scoring::ScoreFunctionCOP get_scorefxn () const
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void restrain_protein_Calphas (core::pose::Pose &pose, utility::vector1< bool > const &is_restrained, core::scoring::func::FuncOP restr_func) const
 
void reorder_foldtree_around_mobile_regions (core::pose::Pose &pose, core::Size const &jump_id, utility::vector1< bool > const &mobile_bb, core::Size const &lig_id) const
 reorders a fold tree such that movement in the mobile regions will More...
 
void get_non_bb_clashing_rotamers (core::pose::Pose const &pose, core::Size seqpos, core::scoring::ScoreFunctionCOP scofx, utility::vector1< core::conformation::ResidueCOP > &accepted_rotamers) const
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Protected Member Functions

void add_enz_cst_interaction_to_pose (core::pose::Pose &pose, toolbox::match_enzdes_util::EnzConstraintParametersCOP params, toolbox::match_enzdes_util::EnzCstTemplateResCOP missing_template, toolbox::match_enzdes_util::EnzCstTemplateResCOP present_template, toolbox::match_enzdes_util::EnzConstraintIOCOP cstio)
 
void find_all_allowed_positions (core::pose::Pose const &pose)
 
bool generate_and_dump_pose_found_residues_combinations (core::pose::PoseCOP ref_poseCOP)
 
bool restype_possible_at_position (core::pose::Pose const &pose, core::chemical::ResidueTypeCOP restype, core::conformation::ResidueCOP target_residue, core::Size const trial_pos)
 rough check whether the two residues in question are close to each other More...
 
void determine_found_residues_compatibility (core::pose::PoseCOP ref_poseCOP)
 this function does clash checks between all residues that were found, and saves the information in a map More...
 
- Protected Member Functions inherited from protocols::enzdes::EnzdesBaseProtocol
void setup_enzdes_constraints (core::pose::Pose &pose, bool allow_missing_remark_blocks) const
 
void enable_constraint_scoreterms ()
 
void disable_constraint_scoreterms ()
 function to disable constraint scoring terms: : this will leave eventual covalent connections set up by EnzConstraintIO untouched. More...
 
bool exchange_ligands_in_pose (core::pose::Pose &pose, bool check_bb_clashes, core::scoring::ScoreFunctionCOP scofx)
 
- Protected Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
core::scoring::ScoreFunctionOP make_tweaked_scorefxn (std::string const &weights_tag, bool estat_exclude_protein, bool estat_upweight, bool hbonds_downweight)
 
core::Vector choose_desired_centroid (core::pose::Pose const &pose, core::Size jump_id, utility::vector1< core::Vector >)
 
void move_ligand_to_desired_centroid (core::pose::Pose &pose, core::Size jump_id, utility::vector1< core::Vector > start_from_pts)
 
void move_ligand_to_desired_centroid (core::pose::Pose &pose, core::Size jump_id, core::Vector desired_centroid)
 
core::kinematics::MoveMapOP make_movemap (core::pose::Pose const &pose, core::Size jump_id, core::Real sc_padding, bool include_all_rsds, bool include_backbone, bool include_ligands, bool include_water) const
 
core::pack::task::PackerTaskOP make_packer_task (core::pose::Pose const &pose, ObjexxFCL::FArray1D_bool const &allow_repack, bool ligand_protonation) const
 Shared machinery for the next two. More...
 
core::pack::task::PackerTaskOP make_packer_task (core::pose::Pose const &pose, int jump_id, core::Real sc_padding, bool include_all_rsds, bool ligand_protonation) const
 Receptor (interface?) plus ligand. More...
 
core::pack::task::PackerTaskOP make_packer_task_ligand_only (core::pose::Pose const &pose, int jump_id, bool ligand_protonation) const
 Just ligand, not the receptor. More...
 
void find_interface_rsds (core::pose::Pose const &pose, int jump_id, core::Real padding, ObjexxFCL::FArray1D_bool &is_interface) const
 
void find_interface_backbone (core::pose::Pose const &pose, int jump_id, core::Real cutoff_dist, utility::vector1< bool > &is_interface, utility::vector1< bool > &is_around_interface) const
 
core::scoring::constraints::ConstraintOP restrain_ligand_nbr_atom (core::pose::Pose &pose, core::Size lig_id, core::Real stddev_Angstroms) const
 
void setup_bbmin_foldtree (core::pose::Pose &pose, core::Size const &jump_id, core::Real cutoff_dist, core::Real stddev_Angstroms)
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Private Attributes

utility::vector1
< utility::vector1
< core::conformation::ResidueOP > > 
found_resis_
 
std::map
< core::conformation::ResidueCOP,
std::map
< core::conformation::ResidueCOP,
core::Size > > 
found_res_compatibility_
 
bool found_res_compatibility_determined_
 
utility::vector1< core::Sizetrial_positions_
 
core::scoring::ScoreFunctionOP reduced_scofx_
 
core::Size cut1_
 
core::Size cut2_
 
core::Size cut3_
 
core::Size cut4_
 
utility::vector1
< toolbox::match_enzdes_util::EnzConstraintParametersCOP
match_params_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 
- Static Public Member Functions inherited from protocols::enzdes::EnzdesBaseProtocol
static void register_options ()
 
- Static Public Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
static core::Size get_ligand_jump_id (core::pose::Pose const &pose)
 
static core::Size get_ligand_id (core::pose::Pose const &pose)
 Return the residue sequence number for our ligand. More...
 
static core::Size get_ligand_id (core::pose::Pose const &pose, core::Size jump_id)
 Return the residue sequence number for our ligand. More...
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 
- Protected Attributes inherited from protocols::enzdes::EnzdesBaseProtocol
core::scoring::ScoreFunctionOP reduced_sfxn_
 
std::set< core::Sizedesign_targets_
 
bool include_all_design_targets_in_design_interface_
 
- Protected Attributes inherited from protocols::ligand_docking::LigandBaseProtocol
bool use_soft_rep_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::scoring::ScoreFunctionOP hard_scorefxn_
 
core::scoring::ScoreFunctionOP soft_scorefxn_
 
core::Real sc_interface_padding_
 
core::Real bb_interface_cutoff_
 
core::pack::rotamer_set::UnboundRotamersOperationOP unboundrot_
 

Constructor & Destructor Documentation

protocols::enzdes::SecondaryMatchProtocol::SecondaryMatchProtocol ( )
protocols::enzdes::SecondaryMatchProtocol::~SecondaryMatchProtocol ( )
overridedefault

Member Function Documentation

void protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose ( core::pose::Pose pose,
toolbox::match_enzdes_util::EnzConstraintParametersCOP  params,
toolbox::match_enzdes_util::EnzCstTemplateResCOP  missing_template,
toolbox::match_enzdes_util::EnzCstTemplateResCOP  present_template,
toolbox::match_enzdes_util::EnzConstraintIOCOP  cstio 
)
protected
void protocols::enzdes::SecondaryMatchProtocol::apply ( core::pose::Pose )
overridevirtual
void protocols::enzdes::SecondaryMatchProtocol::determine_found_residues_compatibility ( core::pose::PoseCOP  ref_poseCOP)
protected

this function does clash checks between all residues that were found, and saves the information in a map

References found_res_compatibility_, found_res_compatibility_determined_, found_resis_, core::scoring::pair, and reduced_scofx_.

Referenced by generate_and_dump_pose_found_residues_combinations().

bool protocols::enzdes::SecondaryMatchProtocol::do_matching ( core::pose::Pose start_pose)
void protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions ( core::pose::Pose const &  pose)
protected
bool protocols::enzdes::SecondaryMatchProtocol::generate_and_dump_pose_found_residues_combinations ( core::pose::PoseCOP  ref_poseCOP)
protected
std::string protocols::enzdes::SecondaryMatchProtocol::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Reimplemented from protocols::enzdes::EnzdesBaseProtocol.

core::Size protocols::enzdes::SecondaryMatchProtocol::residues_compatible ( core::conformation::ResidueCOP  res1,
core::conformation::ResidueCOP  res2 
) const

lookup function to determine whether to residues are compatible

References found_res_compatibility_, found_res_compatibility_determined_, and core::id::to_string().

bool protocols::enzdes::SecondaryMatchProtocol::restype_possible_at_position ( core::pose::Pose const &  pose,
core::chemical::ResidueTypeCOP  restype,
core::conformation::ResidueCOP  target_residue,
core::Size const  trial_pos 
)
protected

rough check whether the two residues in question are close to each other

References core::pose::Pose::residue(), protocols::enzdes::tr(), and core::conformation::Residue::xyz().

Referenced by add_enz_cst_interaction_to_pose().

void protocols::enzdes::SecondaryMatchProtocol::set_trial_positions ( utility::vector1< core::Size > const &  trial_pos)
inline

References trial_positions_.

Member Data Documentation

core::Size protocols::enzdes::SecondaryMatchProtocol::cut1_
private
core::Size protocols::enzdes::SecondaryMatchProtocol::cut2_
private
core::Size protocols::enzdes::SecondaryMatchProtocol::cut3_
private
core::Size protocols::enzdes::SecondaryMatchProtocol::cut4_
private
std::map< core::conformation::ResidueCOP, std::map< core::conformation::ResidueCOP, core::Size > > protocols::enzdes::SecondaryMatchProtocol::found_res_compatibility_
private
bool protocols::enzdes::SecondaryMatchProtocol::found_res_compatibility_determined_
private
utility::vector1< utility::vector1< core::conformation::ResidueOP > > protocols::enzdes::SecondaryMatchProtocol::found_resis_
private
utility::vector1< toolbox::match_enzdes_util::EnzConstraintParametersCOP > protocols::enzdes::SecondaryMatchProtocol::match_params_
private
core::scoring::ScoreFunctionOP protocols::enzdes::SecondaryMatchProtocol::reduced_scofx_
private
utility::vector1< core::Size > protocols::enzdes::SecondaryMatchProtocol::trial_positions_
private

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