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protocols::enzdes::SecondaryMatchProtocol Class Reference

#include <SecondaryMatchProtocol.hh>

Inheritance diagram for protocols::enzdes::SecondaryMatchProtocol:
Inheritance graph
Collaboration diagram for protocols::enzdes::SecondaryMatchProtocol:
Collaboration graph

Public Member Functions

 SecondaryMatchProtocol ()
 ~SecondaryMatchProtocol ()
void apply (core::pose::Pose &start_pose)
virtual std::string get_name () const
 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< Sizecatalytic_res (core::pose::Pose const &pose) const
std::set< Size > const & design_targets (core::pose::Pose const &pose) 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 ()
virtual ~LigandBaseProtocol ()
core::scoring::ScoreFunctionOP get_scorefxn ()
core::scoring::ScoreFunctionCOP get_scorefxn () const
core::Size get_ligand_jump_id (core::pose::Pose const &pose) const
core::Size get_ligand_id (core::pose::Pose const &pose) const
 Return the residue sequence number for our ligand. More...
core::Size get_ligand_id (core::pose::Pose const &pose, core::Size jump_id) const
 Return the residue sequence number for our ligand. More...
void restrain_protein_Calphas (core::pose::Pose &pose, utility::vector1< bool > const &is_restrained, core::scoring::constraints::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 ~Mover ()
virtual MoverSP create ()
virtual void apply (core::io::serialization::PipeMap &pmap)
virtual void parse_state (SerializableState const &state)
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void save_state (SerializableState &state)
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 Mover (Mover const &other)
Moveroperator= (Mover const &other)
 assignment operator More...
virtual core::Real last_proposal_density_ratio ()
std::string const & type () const
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...
void set_current_tag (std::string const &new_tag)
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 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...
void type (const std::string &type_in)
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string get_type () const
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...
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 reinitialize_for_each_job () const
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const

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
< core::conformation::ResidueOP > > 
< core::conformation::ResidueCOP,
< core::conformation::ResidueCOP,
core::Size > > 
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_
< toolbox::match_enzdes_util::EnzConstraintParametersCOP

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
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 ()
- 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_

Constructor & Destructor Documentation

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

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 
void protocols::enzdes::SecondaryMatchProtocol::apply ( core::pose::Pose start_pose)
void protocols::enzdes::SecondaryMatchProtocol::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

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)
bool protocols::enzdes::SecondaryMatchProtocol::generate_and_dump_pose_found_residues_combinations ( core::pose::PoseCOP  ref_poseCOP)
std::string protocols::enzdes::SecondaryMatchProtocol::get_name ( ) const

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_, and found_res_compatibility_determined_.

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 

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)

References trial_positions_.

Member Data Documentation

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

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