Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::generalized_kinematic_closure::GeneralizedKIC Class Reference

#include <GeneralizedKIC.hh>

Public Member Functions

 GeneralizedKIC ()
 Creator for GeneralizedKIC mover. More...
 
virtual ~GeneralizedKIC ()
 Destructor for GeneralizedKIC mover. More...
 
virtual protocols::moves::MoverOP clone () const
 Clone operator to create a pointer to a fresh GeneralizedKIC object that copies this one. More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 Fresh_instance operator to create a pointer to a fresh GeneralizedKIC object that does NOT copy this one. More...
 
virtual void apply (core::pose::Pose &pose)
 Actually apply the mover to the pose. More...
 
virtual std::string get_name () const
 Returns the name of this mover ("GeneralizedKIC"). More...
 
virtual void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &)
 parse XML (specifically in the context of the parser/Rosetta_scripting scheme) More...
 
void add_loop_residue (core::Size const residue_index)
 Add a residue (by index in the pose) to the list of residues making up the loop to be closed. This function checks that the index is within the range of indices in the pose, and that there is a geometric connection between this residue and the previous one in the list. More...
 
void set_mover_effect_on_bonded_geometry (core::Size const effect)
 Function to set the effect of this mover on parts of the pose that are covalently attached to the loop to be closed, but which aren't part of it. Settings are: 0 – Moves the loop only; can pull apart covalent bonds to anything outside of the loop that isn't an anchor point. 1 – Moves the loop and anything downstream of the loop in the foldtree. Can still pull apart connections to non-child geometry. More...
 
core::Size get_mover_effect_on_bonded_geometry ()
 Function to get the effect of this mover on parts of the pose that are covalently attached to the loop to be closed, but which aren't part of it. Return values are: 0 – Moves the loop only; can pull apart covalent bonds to anything outside of the loop that isn't an anchor point. 1 – Moves the loop and anything downstream of the loop in the foldtree. Can still pull apart connections to non-child geometry. More...
 
void set_build_ideal_geometry (bool const buildideal)
 Set whether or not this mover builds ideal geometry for the loop, or uses the existing geometry, imperfect bond lengths/angles and all. More...
 
void set_pivot_atoms (core::Size const rsd1, std::string const &at1, core::Size const rsd2, std::string const &at2, core::Size const rsd3, std::string const &at3)
 Function to set the pivot atoms for kinematic closure: More...
 
bool get_build_ideal_geometry ()
 Get whether or not this mover builds ideal geometry for the loop, or uses the existing geometry, imperfect bond lengths/angles and all. More...
 
bool last_run_successful ()
 Returns whether or not the last call to apply() sucessfully closed the loop. Defaults to false if apply() hasn't yet been called. More...
 
void close_bond (core::Size const rsd1, std::string const &at1, core::Size const rsd2, std::string const &at2, core::Size const rsd1_before, std::string const &at1_before, core::Size const rsd2_after, std::string const &at2_after, core::Real const &bondlength, core::Real const &bondangle1, core::Real const &bondangle2, core::Real const &torsion, bool const randomize_this_torsion, bool const randomize_flanking_torsions)
 Tells GeneralizedKIC to close a bond, setting bond length, bond angle, and bond torsion values. This actually just adds appropriate set_dihedral, set_bondangle, and set_bondlength perturbers to the perturber list. Note that subsequent perturbers OR the closure itself can overwrite the bond length, bond angle, or torsion angles set here. More...
 
void set_selector_type (selector::selector_type const &stype)
 Set the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters). More...
 
void set_selector_type (std::string const &stypename)
 Set the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters). This sets the selector by name. More...
 
void set_selector_scorefunction (core::scoring::ScoreFunctionOP sfxn)
 Set the selector's scorefunction. More...
 
void set_selector_kbt (core::Real const &kbt)
 Set the selector's Boltzmann temperature value. More...
 
selector::selector_type get_selector_type () const
 Get the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters). More...
 
std::string get_selector_type_name () const
 Get the name of the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters). More...
 
void add_perturber ()
 Add a new perturber to the list of perturbers. More...
 
void add_perturber (perturber::perturber_effect const &effect)
 Add a new perturber to the list of perturbers, setting the effect. More...
 
void add_perturber (std::string const &effectname)
 Add a new perturber to the list of perturbers, setting the effect by effect name string. More...
 
void set_perturber_effect (core::Size const perturber_index, perturber::perturber_effect const &effect)
 Set a perturber's effect. More...
 
void add_value_to_perturber_value_list (core::Size const perturber_index, core::Real const &val)
 Add a value to the list of values that a perturber takes. More...
 
void add_value_to_perturber_value_list (core::Real const &val)
 Add a value to the list of values that a perturber takes. This operates on the last perturber in the perturber list. More...
 
void add_residue_to_perturber_residue_list (core::Size const perturber_index, core::Size const residue_index)
 Add a residue to the list of residues that a perturber takes. Note that residue_index is based on indices of the ORIGINAL POSE, not the loop in isolation. More...
 
void add_residue_to_perturber_residue_list (core::Size const residue_index)
 Add a residue to the list of residues that a perturber takes. Note that residue_index is based on indices of the ORIGINAL POSE, not the loop in isolation. This version acts on the last perturber added. More...
 
void add_atomset_to_perturber_atomset_list (core::Size const perturber_index, utility::vector1< core::id::NamedAtomID > const &atomset)
 Add a set of AtomIDs to the list of sets of AtomIDs that a perturber takes. More...
 
void add_atomset_to_perturber_atomset_list (utility::vector1< core::id::NamedAtomID > const &atomset)
 Add a set of AtomIDs to the list of sets of AtomIDs that a perturber takes. This operates on the last perturber in the perturber list. More...
 
void add_filter ()
 Add a new filter to the list of filters. More...
 
void add_filter (filter::filter_type const &filtertype)
 Add a new filter to the list of filters, setting the filter type. More...
 
void add_filter (std::string const &filtertypename)
 Add a new filter to the list of filters, setting the filter type by name. More...
 
void add_filter_parameter (core::Size const filter_index, std::string const &param_name, core::Real const &value)
 Add a real-valued parameter to a filter's parameter list. More...
 
void add_filter_parameter (core::Size const filter_index, std::string const &param_name, core::Size const value)
 Add an integer-valued parameter to a filter's parameter list. More...
 
void add_filter_parameter (core::Size const filter_index, std::string const &param_name, bool const value)
 Add a Boolean-valued parameter to a filter's parameter list. More...
 
void add_filter_parameter (core::Size const filter_index, std::string const &param_name, std::string const &value)
 Add a string-valued parameter to a filter's parameter list. More...
 
void add_filter_parameter (std::string const &param_name, core::Real const &value)
 Add a real-valued parameter to the last filter's parameter list. More...
 
void add_filter_parameter (std::string const &param_name, core::Size const value)
 Add an integer-valued parameter to the last filter's parameter list. More...
 
void add_filter_parameter (std::string const &param_name, bool const value)
 Add a Boolean-valued parameter to the last filter's parameter list. More...
 
void add_filter_parameter (std::string const &param_name, std::string const &value)
 Add a string-valued parameter to the last filter's parameter list. More...
 
void set_closure_attempts (core::Size const attempts)
 Set the number of closure attempts. More...
 
core::Size get_closure_attempts () const
 Returns the number of closure attempts. More...
 
void set_ntries_before_giving_up (core::Size const ntries)
 Sets number of tries before giving up. More...
 
core::Size get_ntries_before_giving_up () const
 Gets number of tries before giving up. More...
 
bool n_closure_attempts_is_a_maximum () const
 Returns whether the number of closure attempts is a maximum number of attempts. More...
 
void set_n_closure_attempts_is_a_maximum (bool const is_max)
 Sets whether the number of closure attempts is a maximum number of attempts. More...
 
- 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
 
void set_type (std::string const &setting)
 
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)
 
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
 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Private Member Functions

void get_path (core::Size const first_atom, core::Size const second_atom, core::conformation::Residue const &rsd, utility::vector1< core::Size > &path_indices)
 Gets a path through atoms in the residue from one connection atom to another within a residue. More...
 
core::Size get_connection (core::Size const res_with_connection, core::Size const other_res, core::pose::Pose const &pose)
 Function to get the FIRST connection in res_with_connection that connects it to other_res: More...
 
bool has_geometric_connection (core::Size const residue1, core::Size const residue2, core::pose::Pose const &pose)
 Function that returns true if two residues in a pose have a direct geometric connection, and false otherwise. More...
 
void infer_anchor_connIDs (core::pose::Pose const &pose)
 As the list of residues in the loop to be closed is updated, we need to figure out how that loop is connected to the geometry outside of the loop (i.e. what's considred the connection to stationary geometry). This function loops through all connIDs on the terminal residues of the loop to be closed and picks the first one that links to geometry not in the loop as the anchor connnection. TODO: Add a manual override to specifiy that a different connection is the anchor. More...
 
void addloweranchor (core::pose::Pose &perturbedloop_pose, core::pose::Pose const &pose)
 Find the residue that is the anchor of the lower end of the loop that we're about to close and add it to the loop pose by a jump. More...
 
void addloopgeometry (core::pose::Pose &perturbedloop_pose, core::pose::Pose const &pose, bool const build_ideal, core::Size const effect_on_bonded_geom, utility::vector1< std::pair< core::Size, core::Size > > &residue_map)
 Add the loop geometry from the starting pose to the temporary pose used for kinematic closure. This will also add the downstream geometry if effect_on_bonded_geom==1. Finally, this will build ideal geometry if build_ideal==true. More...
 
void addupperanchor (core::pose::Pose &perturbedloop_pose, core::pose::Pose const &pose)
 Find the residue that is the anchor of the upper end of the loop that we're about to close and add it to the loop pose by a bond. More...
 
bool doKIC (core::pose::Pose &pose, core::pose::Pose const &original_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)
 Do the actual kinematic closure. More...
 
void generate_atomlist (core::pose::Pose const &pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)
 Generate the list of atomIDs for the chain that will be closed by kinematic closure. More...
 
void generate_bridgeobjects_data_from_atomlist (utility::vector1< utility::vector1< core::Real > > &atoms, utility::vector1< core::Real > &dt, utility::vector1< core::Real > &da, utility::vector1< core::Real > &db, utility::vector1< core::Size > &order)
 Generate the numeric::kinematic_closure::bridgeObjects data from the atomlist_ object. More...
 
core::Size get_perturbedloop_rsd (core::Size const original_pose_rsd, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)
 Given a residue_map vector of pairs, where each pair is < residue_index_in_perturbedloop_pose, residue_index_in_original_pose >, and a residue index in the original pose, return the corresponding residue index in the perturbed loop pose. More...
 
void pick_pivots (core::pose::Pose const &original_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< core::Size > &pivots)
 Pick the pivots for kinematic closure. More...
 
void apply_perturbations (core::pose::Pose const &loop_pose, core::pose::Pose const &original_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< core::Real > &torsions, utility::vector1< core::Real > &bondangles, utility::vector1< core::Real > &bondlengths) const
 Apply the list of perturbers (everything in perturberlist_) to alter the desired torsion, desired angle, and desired bond length lists prior to calling bridgeObjects. More...
 
void filter_solutions (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< utility::vector1< core::Real > > &torsions, utility::vector1< utility::vector1< core::Real > > &bondangles, utility::vector1< utility::vector1< core::Real > > &bondlengths, int &nsol) const
 Apply filters to the list of solutions, and proceed to eliminate any and all that fail to pass filters. More...
 
void select_solution (core::pose::Pose &pose, core::pose::Pose const &original_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &torsions, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &bondangles, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &bondlengths, utility::vector1< core::Size > const &nsol_for_attempt, core::Size const total_solutions) const
 Applies the selector to choose a solution and set a loop pose. More...
 
void prune_extra_atoms (utility::vector1< core::Size > &pivots)
 Trims extra atoms from the start and end of the atom list, if the first and last pivots are not the fifth and fifth-last atoms, respectively. More...
 

Private Attributes

utility::vector1< core::Sizeloopresidues_
 The list of residues (as inidices of the original pose) making up the loop to be closed. More...
 
core::Size effect_on_bonded_geometry_
 The effect of the GeneralizedKIC mover on geometry that is covalently bound to the loop to be closed, but which is not part of that loop segment. 0 means that the mover will only move the loop, possibly tearing apart covalent bonds to other parts of the pose. 1 means that the mover will move the loop along with anything that is downstream in the FoldTree. More...
 
core::Size lower_anchor_connID_
 The lower end of the loop to be closed is presumably connected to geometry that is not moved by this mover. However, the connection could be through backbone or sidechain. The mover needs to know the connection ID on the lower end of the loop to the anchor geometry. Note: This will be set to 0 if the only connection that this residue can form is to the loop. More...
 
core::Size upper_anchor_connID_
 The upper end of the loop to be closed is presumably connected to geometry that is not moved by this mover. However, the connection could be through backbone or sidechain. The mover needs to know the connection ID on the upper end of the loop to the anchor geometry. Note: This will be set to 0 if the only connection that this residue can form is to the loop. More...
 
bool build_ideal_geometry_
 Should the mover build ideal geometry for the loop to be closed? Default true. More...
 
bool last_run_successful_
 Was the last apply() successful in generating a new kinematically-closed structure? More...
 
utility::vector1< std::pair
< core::id::AtomID,
numeric::xyzVector< core::Real > > > 
atomlist_
 List of the atoms in the segment to be closed, and their x,y,z coordinates. Note that the atomIDs refer to residue indices that correspond to the temporary pose created by the apply() function, not to the indices in the original pose. More...
 
core::Size pivot_1_rsd_
 Pivot residue 1 (index based on original pose). More...
 
std::string pivot_1_atmname_
 Pivot atom 1 name. More...
 
core::Size pivot_2_rsd_
 Pivot residue 2 (index based on original pose). More...
 
std::string pivot_2_atmname_
 Pivot atom 2 name. More...
 
core::Size pivot_3_rsd_
 Pivot residue 3 (index based on original pose). More...
 
std::string pivot_3_atmname_
 Pivot atom 3 name. More...
 
perturber::GeneralizedKICperturberOPs perturberlist_
 List of GeneralizedKICperturbers to apply prior to kinematic closure. More...
 
filter::GeneralizedKICfilterOPs filterlist_
 List of GeneralizedKICfilters to apply to eliminate bad solutions. More...
 
selector::GeneralizedKICselectorOP selector_
 The selection algorithm to use to pick a solution from the set of solutions passing the filters. More...
 
core::Size n_closure_attempts_
 The number of closure attempts to carry out. More...
 
bool n_closure_attempts_is_a_maximum_
 Should n_closure_attempts_ be the number attempted, or a maximum number of attempts? If false, n_closure_attempts_ attempts are made, and then a solution is chosen. If true, attempts are made until a solution is found OR n_closure_attempts_ is reached. More...
 
protocols::filters::ContingentFilterOP rosettascripts_filter_
 Owning pointer for the RosettaScripts ContingentFilter associated with this mover, if there is one. More...
 
bool rosettascripts_filter_exists_
 Bool determining whether there exists a RosettaScripts ContingentFilter associated with this mover. More...
 
core::Size ntries_before_giving_up_
 The number of tries to make before giving up if no solution has been found yet. More...
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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 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...
 

Constructor & Destructor Documentation

protocols::generalized_kinematic_closure::GeneralizedKIC::GeneralizedKIC ( )

Creator for GeneralizedKIC mover.

Referenced by clone(), and fresh_instance().

protocols::generalized_kinematic_closure::GeneralizedKIC::~GeneralizedKIC ( )
virtual

Destructor for GeneralizedKIC mover.

Member Function Documentation

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_atomset_to_perturber_atomset_list ( core::Size const  perturber_index,
utility::vector1< core::id::NamedAtomID > const &  atomset 
)

Add a set of AtomIDs to the list of sets of AtomIDs that a perturber takes.

References perturberlist_, and runtime_assert_string_msg.

Referenced by add_atomset_to_perturber_atomset_list(), close_bond(), and parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_atomset_to_perturber_atomset_list ( utility::vector1< core::id::NamedAtomID > const &  atomset)

Add a set of AtomIDs to the list of sets of AtomIDs that a perturber takes. This operates on the last perturber in the perturber list.

References add_atomset_to_perturber_atomset_list(), perturberlist_, and runtime_assert_string_msg.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter ( )

Add a new filter to the list of filters.

References filterlist_.

Referenced by add_filter(), and parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter ( filter::filter_type const &  filtertype)

Add a new filter to the list of filters, setting the filter type.

References add_filter(), and filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter ( std::string const &  filtertypename)

Add a new filter to the list of filters, setting the filter type by name.

See src/protocols/generalized_kinematic_closure/filter/GeneralizedKICfilter.cc for the list of filter type names.

References add_filter(), and filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter ( core::Size const  filter_index,
std::string const &  param_name,
core::Real const &  value 
)

Add a real-valued parameter to a filter's parameter list.

References filterlist_.

Referenced by add_filter_parameter(), and parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter ( core::Size const  filter_index,
std::string const &  param_name,
core::Size const  value 
)

Add an integer-valued parameter to a filter's parameter list.

References filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter ( core::Size const  filter_index,
std::string const &  param_name,
bool const  value 
)

Add a Boolean-valued parameter to a filter's parameter list.

References filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter ( core::Size const  filter_index,
std::string const &  param_name,
std::string const &  value 
)

Add a string-valued parameter to a filter's parameter list.

References filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter ( std::string const &  param_name,
core::Real const &  value 
)

Add a real-valued parameter to the last filter's parameter list.

References add_filter_parameter(), and filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter ( std::string const &  param_name,
core::Size const  value 
)

Add an integer-valued parameter to the last filter's parameter list.

References add_filter_parameter(), and filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter ( std::string const &  param_name,
bool const  value 
)

Add a Boolean-valued parameter to the last filter's parameter list.

References add_filter_parameter(), and filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter ( std::string const &  param_name,
std::string const &  value 
)

Add a string-valued parameter to the last filter's parameter list.

References add_filter_parameter(), and filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_loop_residue ( core::Size const  residue_index)

Add a residue (by index in the pose) to the list of residues making up the loop to be closed. This function checks that the index is within the range of indices in the pose, and that there is a geometric connection between this residue and the previous one in the list.

References loopresidues_, and protocols::generalized_kinematic_closure::TR.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_perturber ( )

Add a new perturber to the list of perturbers.

References perturberlist_.

Referenced by add_perturber(), close_bond(), and parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_perturber ( perturber::perturber_effect const &  effect)

Add a new perturber to the list of perturbers, setting the effect.

References add_perturber(), and perturberlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_perturber ( std::string const &  effectname)

Add a new perturber to the list of perturbers, setting the effect by effect name string.

References add_perturber(), and perturberlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_residue_to_perturber_residue_list ( core::Size const  perturber_index,
core::Size const  residue_index 
)

Add a residue to the list of residues that a perturber takes. Note that residue_index is based on indices of the ORIGINAL POSE, not the loop in isolation.

References perturberlist_, and runtime_assert_string_msg.

Referenced by add_residue_to_perturber_residue_list(), and parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_residue_to_perturber_residue_list ( core::Size const  residue_index)

Add a residue to the list of residues that a perturber takes. Note that residue_index is based on indices of the ORIGINAL POSE, not the loop in isolation. This version acts on the last perturber added.

References add_residue_to_perturber_residue_list(), perturberlist_, and runtime_assert_string_msg.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_value_to_perturber_value_list ( core::Size const  perturber_index,
core::Real const &  val 
)

Add a value to the list of values that a perturber takes.

References perturberlist_, and runtime_assert_string_msg.

Referenced by add_value_to_perturber_value_list(), close_bond(), and parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_value_to_perturber_value_list ( core::Real const &  val)

Add a value to the list of values that a perturber takes. This operates on the last perturber in the perturber list.

References add_value_to_perturber_value_list(), perturberlist_, and runtime_assert_string_msg.

void protocols::generalized_kinematic_closure::GeneralizedKIC::addloopgeometry ( core::pose::Pose perturbedloop_pose,
core::pose::Pose const &  pose,
bool const  build_ideal,
core::Size const  effect_on_bonded_geom,
utility::vector1< std::pair< core::Size, core::Size > > &  residue_map 
)
private

Add the loop geometry from the starting pose to the temporary pose used for kinematic closure. This will also add the downstream geometry if effect_on_bonded_geom==1. Finally, this will build ideal geometry if build_ideal==true.

References core::pose::Pose::append_residue_by_bond(), core::conformation::Residue::clone(), loopresidues_, lower_anchor_connID_, core::pose::Pose::n_residue(), core::conformation::Residue::n_residue_connections(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), and utility_exit_with_message.

Referenced by apply().

void protocols::generalized_kinematic_closure::GeneralizedKIC::addloweranchor ( core::pose::Pose perturbedloop_pose,
core::pose::Pose const &  pose 
)
private

Find the residue that is the anchor of the lower end of the loop that we're about to close and add it to the loop pose by a jump.

References core::pose::Pose::append_residue_by_jump(), core::pose::Pose::clear(), core::conformation::Residue::clone(), loopresidues_, lower_anchor_connID_, core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), and utility_exit_with_message.

Referenced by apply().

void protocols::generalized_kinematic_closure::GeneralizedKIC::addupperanchor ( core::pose::Pose perturbedloop_pose,
core::pose::Pose const &  pose 
)
private
void protocols::generalized_kinematic_closure::GeneralizedKIC::apply ( core::pose::Pose pose)
virtual
void protocols::generalized_kinematic_closure::GeneralizedKIC::apply_perturbations ( core::pose::Pose const &  loop_pose,
core::pose::Pose const &  original_pose,
utility::vector1< std::pair< core::Size, core::Size > > const &  residue_map,
utility::vector1< core::Real > &  torsions,
utility::vector1< core::Real > &  bondangles,
utility::vector1< core::Real > &  bondlengths 
) const
private

Apply the list of perturbers (everything in perturberlist_) to alter the desired torsion, desired angle, and desired bond length lists prior to calling bridgeObjects.

Apply the list of perturbers (everything in perturberlist_) to alter the desired torsion, desired angle, and desired bond length lists prior to calling bridgeObjects. Note that later perturbers might overwrite earlier perturbers' effects.

Detailed:
Parameters
[in]loop_pose– A pose consisting of just the loop to be closed.
[in]original_pose– A pose consisting of the full, original structure.
[in]residue_map– The mapping of (residue in loop_pose, residue in original_pose).
[in,out]torsions– The desired torsion angles, potentially altered or overwritten by the perturbers.
[in,out]bondangles– The desired bond angles, potentially altered or overwritten by the perturbers.
[in,out]bondlenghts– The desired bond lengths, potentially altered or overwritten by the perturbers.

References atomlist_, perturberlist_, and protocols::generalized_kinematic_closure::TR.

Referenced by doKIC().

protocols::moves::MoverOP protocols::generalized_kinematic_closure::GeneralizedKIC::clone ( ) const
virtual

Clone operator to create a pointer to a fresh GeneralizedKIC object that copies this one.

Reimplemented from protocols::moves::Mover.

References GeneralizedKIC().

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::close_bond ( core::Size const  rsd1,
std::string const &  at1,
core::Size const  rsd2,
std::string const &  at2,
core::Size const  rsd1_before,
std::string const &  at1_before,
core::Size const  rsd2_after,
std::string const &  at2_after,
core::Real const &  bondlength,
core::Real const &  bondangle1,
core::Real const &  bondangle2,
core::Real const &  torsion,
bool const  randomize_this_torsion,
bool const  randomize_flanking_torsions 
)

Tells GeneralizedKIC to close a bond, setting bond length, bond angle, and bond torsion values. This actually just adds appropriate set_dihedral, set_bondangle, and set_bondlength perturbers to the perturber list. Note that subsequent perturbers OR the closure itself can overwrite the bond length, bond angle, or torsion angles set here.

Detailed:
Parameters
[in]rsd1– The index of the first atom's residue (indexed based on residue indices in the original pose).
[in]at1– The name of the first atom defining the bond to be closed.
[in]rsd2– The index of the second atom's residue (indexed based on residue indices in the original pose).
[in]at1– The name of the second atom defining the bond to be closed.
[in]bondlength– The length of the bond between the two atoms.
[in]bondangle1– The bond angle defined by (atom preceding at1 in the chain to be closed), (atm1), (atm2).
[in]bondangle1– The bond angle defined by (atm1), (atm2), (atom following at2 in the chain to be closed).
[in]torsion– The torsion angle defined by (atom preceding at1 in the chain to be closed), (atm1), (atm2), (atom following at2 in the chain to be closed).

References add_atomset_to_perturber_atomset_list(), add_perturber(), add_value_to_perturber_value_list(), protocols::RG, and numeric::random::RandomGenerator::uniform().

Referenced by parse_my_tag().

bool protocols::generalized_kinematic_closure::GeneralizedKIC::doKIC ( core::pose::Pose pose,
core::pose::Pose const &  original_pose,
utility::vector1< std::pair< core::Size, core::Size > > const &  residue_map 
)
private

Do the actual kinematic closure.

Inputs are pose (the loop to be closed), original_pose (the reference pose, unchanged by operation), and residue_map (the mapping of residues from pose to original_pose). Output is pose (the loop to be closed, in a new, closed conformation if successful) and a boolean value indicating success or failure.

References apply_perturbations(), atomlist_, bridgeObjects(), filter_solutions(), generate_atomlist(), generate_bridgeobjects_data_from_atomlist(), get_ntries_before_giving_up(), n_closure_attempts_, n_closure_attempts_is_a_maximum(), protocols::forge::methods::order(), pick_pivots(), select_solution(), and protocols::generalized_kinematic_closure::TR.

Referenced by apply().

void protocols::generalized_kinematic_closure::GeneralizedKIC::filter_solutions ( core::pose::Pose const &  original_pose,
core::pose::Pose const &  loop_pose,
utility::vector1< std::pair< core::Size, core::Size > > const &  residue_map,
utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &  atomlist,
utility::vector1< utility::vector1< core::Real > > &  torsions,
utility::vector1< utility::vector1< core::Real > > &  bondangles,
utility::vector1< utility::vector1< core::Real > > &  bondlengths,
int nsol 
) const
private

Apply filters to the list of solutions, and proceed to eliminate any and all that fail to pass filters.

This removes entries from the torsions, bondangles, and bondlengths lists, and decrements nsol (the number of solutions) appropriately.

Parameters
[in]original_pose– A pose consisting of the full, original structure.
[in]loop_pose– A pose consisting of just the loop to be closed.
[in]residue_map– The mapping of (residue in loop_pose, residue in original_pose).
[in]atomlist– The list of atomIDs in the chain that was closed, plus their xyz coordinates from the original pose.
[in,out]torsions– The torsion angles returned by bridgeObjects, as a matrix of [solution #][torsion index]. Columns can be deleted by filters.
[in,out]bondangles– The bond angles returned by bridgeObjects, as a matrix of [solution #][bondangle index]. Columns can be deleted by filters.
[in,out]bondlenghts– The bond lengths returned by bridgeObjects, as a matrix of [solution #][bondlength index]. Columns can be deleted by filters.
[in,out]nsol– The number of solutions, which can be decremented as filters delete solutions. Note that this must be an int, not a core::Size.

This removes entries from the torsions, bondangles, and bondlengths lists, and decrements nsol (the number of solutions) appropriately.

Parameters
[in,out]torsions– The torsion angles returned by bridgeObjects, as a matrix of [solution #][torsion index]. Columns can be deleted by filters.
[in,out]bondangles– The bond angles returned by bridgeObjects, as a matrix of [solution #][bondangle index]. Columns can be deleted by filters.
[in,out]bondlenghts– The bond lengths returned by bridgeObjects, as a matrix of [solution #][bondlength index]. Columns can be deleted by filters.
[in,out]nsol– The number of solutions, which can be decremented as filters delete solutions. Note that this must be an int, not a core::Size.

References apply(), filterlist_, and protocols::generalized_kinematic_closure::TR.

Referenced by doKIC().

protocols::moves::MoverOP protocols::generalized_kinematic_closure::GeneralizedKIC::fresh_instance ( ) const
virtual

Fresh_instance operator to create a pointer to a fresh GeneralizedKIC object that does NOT copy this one.

Reimplemented from protocols::moves::Mover.

References GeneralizedKIC().

void protocols::generalized_kinematic_closure::GeneralizedKIC::generate_atomlist ( core::pose::Pose const &  pose,
utility::vector1< std::pair< core::Size, core::Size > > const &  residue_map 
)
private
void protocols::generalized_kinematic_closure::GeneralizedKIC::generate_bridgeobjects_data_from_atomlist ( utility::vector1< utility::vector1< core::Real > > &  atoms,
utility::vector1< core::Real > &  dt,
utility::vector1< core::Real > &  da,
utility::vector1< core::Real > &  db,
utility::vector1< core::Size > &  order 
)
private

Generate the numeric::kinematic_closure::bridgeObjects data from the atomlist_ object.

References atomlist_, chainTORS(), and protocols::kinmatch::xyz().

Referenced by doKIC().

bool protocols::generalized_kinematic_closure::GeneralizedKIC::get_build_ideal_geometry ( )
inline

Get whether or not this mover builds ideal geometry for the loop, or uses the existing geometry, imperfect bond lengths/angles and all.

References build_ideal_geometry_.

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::get_closure_attempts ( ) const
inline

Returns the number of closure attempts.

Perturbation, closure, and filtering is carried out for every closure attempt. Successful closures from ALL attempts are then selected from by selectors.

References n_closure_attempts_.

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::get_connection ( core::Size const  res_with_connection,
core::Size const  other_res,
core::pose::Pose const &  pose 
)
private

Function to get the FIRST connection in res_with_connection that connects it to other_res:

References core::conformation::Residue::connections_to_residue(), core::pose::Pose::n_residue(), nres, core::pose::Pose::residue(), and runtime_assert_string_msg.

Referenced by generate_atomlist().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::get_mover_effect_on_bonded_geometry ( )
inline

Function to get the effect of this mover on parts of the pose that are covalently attached to the loop to be closed, but which aren't part of it. Return values are: 0 – Moves the loop only; can pull apart covalent bonds to anything outside of the loop that isn't an anchor point. 1 – Moves the loop and anything downstream of the loop in the foldtree. Can still pull apart connections to non-child geometry.

References effect_on_bonded_geometry_.

std::string protocols::generalized_kinematic_closure::GeneralizedKIC::get_name ( ) const
virtual

Returns the name of this mover ("GeneralizedKIC").

Implements protocols::moves::Mover.

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::get_ntries_before_giving_up ( ) const
inline

Gets number of tries before giving up.

The algorithm tries n_closure_attempts_ times if and only if at least one solution is found in the first ntries_before_giving_up_ attempts.

References ntries_before_giving_up_.

Referenced by doKIC().

void protocols::generalized_kinematic_closure::GeneralizedKIC::get_path ( core::Size const  first_atom,
core::Size const  second_atom,
core::conformation::Residue const &  rsd,
utility::vector1< core::Size > &  path_indices 
)
private

Gets a path through atoms in the residue from one connection atom to another within a residue.

get_path

This is not necessarily the shortest path, geometrically, but hopefully it will do for our purposes. (I didn't want to reimplement Dijkstra's algorithm, since that would tax my programming abilities and would result in unnecessarily slow performance.) This algorithm works by stepping back (child->parent) from the higher-index atom until (a) it finds the lower-index atom, or (b) it reaches the root. If it reaches the root, it then starts at the lower-index atom and traces back until it reaches an atom already in the path. The chosen path is therefore the path from one atom, to the nearest common ancestor, to the other atom.

Parameters
[in]first_atom– The index of the first atom in the path.
[in]second_atom– The index of the first atom in the path.
[in]rsd– The residue object (const instance).
[out]path_indices– The list of indices of the atoms found in the path.
Author
Vikram K. Mulligan

References core::chemical::ResidueType::atom_base(), core::conformation::Residue::natoms(), runtime_assert_string_msg, and core::conformation::Residue::type().

Referenced by generate_atomlist().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::get_perturbedloop_rsd ( core::Size const  original_pose_rsd,
utility::vector1< std::pair< core::Size, core::Size > > const &  residue_map 
)
private

Given a residue_map vector of pairs, where each pair is < residue_index_in_perturbedloop_pose, residue_index_in_original_pose >, and a residue index in the original pose, return the corresponding residue index in the perturbed loop pose.

References utility_exit_with_message.

selector::selector_type protocols::generalized_kinematic_closure::GeneralizedKIC::get_selector_type ( ) const
inline

Get the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters).

References selector_.

std::string protocols::generalized_kinematic_closure::GeneralizedKIC::get_selector_type_name ( ) const
inline

Get the name of the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters).

References selector_.

bool protocols::generalized_kinematic_closure::GeneralizedKIC::has_geometric_connection ( core::Size const  residue1,
core::Size const  residue2,
core::pose::Pose const &  pose 
)
private

Function that returns true if two residues in a pose have a direct geometric connection, and false otherwise.

References core::conformation::Residue::is_bonded(), and core::pose::Pose::residue().

void protocols::generalized_kinematic_closure::GeneralizedKIC::infer_anchor_connIDs ( core::pose::Pose const &  pose)
private

As the list of residues in the loop to be closed is updated, we need to figure out how that loop is connected to the geometry outside of the loop (i.e. what's considred the connection to stationary geometry). This function loops through all connIDs on the terminal residues of the loop to be closed and picks the first one that links to geometry not in the loop as the anchor connnection. TODO: Add a manual override to specifiy that a different connection is the anchor.

References core::conformation::Residue::connection_incomplete(), protocols::generalized_kinematic_closure::is_in_list(), loopresidues_, lower_anchor_connID_, core::conformation::Residue::n_residue_connections(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), and upper_anchor_connID_.

Referenced by apply().

bool protocols::generalized_kinematic_closure::GeneralizedKIC::last_run_successful ( )
inline

Returns whether or not the last call to apply() sucessfully closed the loop. Defaults to false if apply() hasn't yet been called.

References last_run_successful_.

bool protocols::generalized_kinematic_closure::GeneralizedKIC::n_closure_attempts_is_a_maximum ( ) const
inline

Returns whether the number of closure attempts is a maximum number of attempts.

If true, attempts are made until a solution is found OR n_closure_attempts_ is reached. If false, n_closure_attempts_ attempts are made, and then a solution is chosen from among the successful solutions (if any).

References n_closure_attempts_is_a_maximum_.

Referenced by doKIC().

void protocols::generalized_kinematic_closure::GeneralizedKIC::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &   
)
virtual
void protocols::generalized_kinematic_closure::GeneralizedKIC::pick_pivots ( core::pose::Pose const &  original_pose,
utility::vector1< std::pair< core::Size, core::Size > > const &  residue_map,
utility::vector1< core::Size > &  pivots 
)
private
void protocols::generalized_kinematic_closure::GeneralizedKIC::prune_extra_atoms ( utility::vector1< core::Size > &  pivots)
private

Trims extra atoms from the start and end of the atom list, if the first and last pivots are not the fifth and fifth-last atoms, respectively.

References atomlist_, and runtime_assert_string_msg.

Referenced by pick_pivots().

void protocols::generalized_kinematic_closure::GeneralizedKIC::select_solution ( core::pose::Pose pose,
core::pose::Pose const &  original_pose,
utility::vector1< std::pair< core::Size, core::Size > > const &  residue_map,
utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &  atomlist,
utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &  torsions,
utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &  bondangles,
utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &  bondlengths,
utility::vector1< core::Size > const &  nsol_for_attempt,
core::Size const  total_solutions 
) const
private

Applies the selector to choose a solution and set a loop pose.

Parameters
[in,out]pose– The loop to be closed. This function puts it into its new, closed conformation.
[in]original_pose– The original pose. Can be used for reference by selectors.
[in]residue_map– Mapping of (loop residue, original pose residue).
[in]atomlist– The list of (AtomID, original XYZ coordinates of atoms) representing the chain that was closed.
[in]torsions– Matrix of [closure attempt #][solution #][torsion #] with torsion values for each torsion angle in the chain. A selector will pick one solution.
[in]bondangles– Matrix of [closure attempt #][solution #][angle #] with bond angle values for each bond angle in the chain. A selector will pick one solution.
[in]bondlengths– Matrix of [closure attempt #][solution #][bondlength #] with bond length for each bond in the chain. A selector will pick one solution.
[in]nsol_for_attempt– List of the number of solutions for each attempt.
[in]total_solutions– Total number of solutions found.

References selector_.

Referenced by doKIC().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_build_ideal_geometry ( bool const  buildideal)
inline

Set whether or not this mover builds ideal geometry for the loop, or uses the existing geometry, imperfect bond lengths/angles and all.

References build_ideal_geometry_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_closure_attempts ( core::Size const  attempts)

Set the number of closure attempts.

Perturbation, closure, and filtering is carried out for every closure attempt. Successful closures from ALL attempts are then selected from by selectors.

References n_closure_attempts_, and protocols::generalized_kinematic_closure::TR.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_mover_effect_on_bonded_geometry ( core::Size const  effect)

Function to set the effect of this mover on parts of the pose that are covalently attached to the loop to be closed, but which aren't part of it. Settings are: 0 – Moves the loop only; can pull apart covalent bonds to anything outside of the loop that isn't an anchor point. 1 – Moves the loop and anything downstream of the loop in the foldtree. Can still pull apart connections to non-child geometry.

References effect_on_bonded_geometry_, and utility_exit_with_message.

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_n_closure_attempts_is_a_maximum ( bool const  is_max)
inline

Sets whether the number of closure attempts is a maximum number of attempts.

If true, attempts are made until a solution is found OR n_closure_attempts_ is reached. If false, n_closure_attempts_ attempts are made, and then a solution is chosen from among the successful solutions (if any).

References n_closure_attempts_is_a_maximum_.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_ntries_before_giving_up ( core::Size const  ntries)

Sets number of tries before giving up.

If this is set to 0, then no such check is made. The algorithm tries n_closure_attempts_ times if and only if at least one solution is found in the first ntries_before_giving_up_ attempts.

References ntries_before_giving_up_, and protocols::generalized_kinematic_closure::TR.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_effect ( core::Size const  perturber_index,
perturber::perturber_effect const &  effect 
)

Set a perturber's effect.

Detailed:
Parameters
[in]perturber_index– The index in the list of perturbers already added.
[in]effect– The perturber effect type, based on the perturber::perturber_effect enum (e.g. set_dihedral, randomize_backbone, etc.).

References perturberlist_, and runtime_assert_string_msg.

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_pivot_atoms ( core::Size const  rsd1,
std::string const &  at1,
core::Size const  rsd2,
std::string const &  at2,
core::Size const  rsd3,
std::string const &  at3 
)

Function to set the pivot atoms for kinematic closure:

References pivot_1_atmname_, pivot_1_rsd_, pivot_2_atmname_, pivot_2_rsd_, pivot_3_atmname_, and pivot_3_rsd_.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_selector_kbt ( core::Real const &  kbt)

Set the selector's Boltzmann temperature value.

References selector_.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_selector_scorefunction ( core::scoring::ScoreFunctionOP  sfxn)

Set the selector's scorefunction.

References selector_.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_selector_type ( selector::selector_type const &  stype)

Set the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters).

References selector_.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_selector_type ( std::string const &  stypename)

Set the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters). This sets the selector by name.

References selector_.

Member Data Documentation

utility::vector1< std::pair < core::id::AtomID, numeric::xyzVector<core::Real> > > protocols::generalized_kinematic_closure::GeneralizedKIC::atomlist_
private

List of the atoms in the segment to be closed, and their x,y,z coordinates. Note that the atomIDs refer to residue indices that correspond to the temporary pose created by the apply() function, not to the indices in the original pose.

Referenced by apply_perturbations(), doKIC(), generate_atomlist(), generate_bridgeobjects_data_from_atomlist(), pick_pivots(), and prune_extra_atoms().

bool protocols::generalized_kinematic_closure::GeneralizedKIC::build_ideal_geometry_
private

Should the mover build ideal geometry for the loop to be closed? Default true.

Referenced by apply(), get_build_ideal_geometry(), and set_build_ideal_geometry().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::effect_on_bonded_geometry_
private

The effect of the GeneralizedKIC mover on geometry that is covalently bound to the loop to be closed, but which is not part of that loop segment. 0 means that the mover will only move the loop, possibly tearing apart covalent bonds to other parts of the pose. 1 means that the mover will move the loop along with anything that is downstream in the FoldTree.

Referenced by apply(), get_mover_effect_on_bonded_geometry(), and set_mover_effect_on_bonded_geometry().

filter::GeneralizedKICfilterOPs protocols::generalized_kinematic_closure::GeneralizedKIC::filterlist_
private

List of GeneralizedKICfilters to apply to eliminate bad solutions.

Referenced by add_filter(), add_filter_parameter(), and filter_solutions().

bool protocols::generalized_kinematic_closure::GeneralizedKIC::last_run_successful_
private

Was the last apply() successful in generating a new kinematically-closed structure?

Referenced by apply(), and last_run_successful().

utility::vector1< core::Size > protocols::generalized_kinematic_closure::GeneralizedKIC::loopresidues_
private

The list of residues (as inidices of the original pose) making up the loop to be closed.

Referenced by add_loop_residue(), addloopgeometry(), addloweranchor(), addupperanchor(), apply(), and infer_anchor_connIDs().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::lower_anchor_connID_
private

The lower end of the loop to be closed is presumably connected to geometry that is not moved by this mover. However, the connection could be through backbone or sidechain. The mover needs to know the connection ID on the lower end of the loop to the anchor geometry. Note: This will be set to 0 if the only connection that this residue can form is to the loop.

Referenced by addloopgeometry(), addloweranchor(), and infer_anchor_connIDs().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::n_closure_attempts_
private

The number of closure attempts to carry out.

Perturbation, closure, and filtering is carried out for every closure attempt. Successful closures from ALL attempts are then selected from by selectors. Zero means no limit.

Referenced by doKIC(), get_closure_attempts(), and set_closure_attempts().

bool protocols::generalized_kinematic_closure::GeneralizedKIC::n_closure_attempts_is_a_maximum_
private

Should n_closure_attempts_ be the number attempted, or a maximum number of attempts? If false, n_closure_attempts_ attempts are made, and then a solution is chosen. If true, attempts are made until a solution is found OR n_closure_attempts_ is reached.

Referenced by n_closure_attempts_is_a_maximum(), and set_n_closure_attempts_is_a_maximum().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::ntries_before_giving_up_
private

The number of tries to make before giving up if no solution has been found yet.

If this is set to 0, then no such check is made. The algorithm tries n_closure_attempts_ times if and only if at least one solution is found in the first ntries_before_giving_up_ attempts.

Referenced by get_ntries_before_giving_up(), and set_ntries_before_giving_up().

perturber::GeneralizedKICperturberOPs protocols::generalized_kinematic_closure::GeneralizedKIC::perturberlist_
private
std::string protocols::generalized_kinematic_closure::GeneralizedKIC::pivot_1_atmname_
private

Pivot atom 1 name.

Referenced by pick_pivots(), and set_pivot_atoms().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::pivot_1_rsd_
private

Pivot residue 1 (index based on original pose).

Referenced by pick_pivots(), and set_pivot_atoms().

std::string protocols::generalized_kinematic_closure::GeneralizedKIC::pivot_2_atmname_
private

Pivot atom 2 name.

Referenced by pick_pivots(), and set_pivot_atoms().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::pivot_2_rsd_
private

Pivot residue 2 (index based on original pose).

Referenced by pick_pivots(), and set_pivot_atoms().

std::string protocols::generalized_kinematic_closure::GeneralizedKIC::pivot_3_atmname_
private

Pivot atom 3 name.

Referenced by pick_pivots(), and set_pivot_atoms().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::pivot_3_rsd_
private

Pivot residue 3 (index based on original pose).

Referenced by pick_pivots(), and set_pivot_atoms().

protocols::filters::ContingentFilterOP protocols::generalized_kinematic_closure::GeneralizedKIC::rosettascripts_filter_
private

Owning pointer for the RosettaScripts ContingentFilter associated with this mover, if there is one.

Referenced by apply(), and parse_my_tag().

bool protocols::generalized_kinematic_closure::GeneralizedKIC::rosettascripts_filter_exists_
private

Bool determining whether there exists a RosettaScripts ContingentFilter associated with this mover.

Referenced by apply(), and parse_my_tag().

selector::GeneralizedKICselectorOP protocols::generalized_kinematic_closure::GeneralizedKIC::selector_
private

The selection algorithm to use to pick a solution from the set of solutions passing the filters.

Referenced by get_selector_type(), get_selector_type_name(), select_solution(), set_selector_kbt(), set_selector_scorefunction(), and set_selector_type().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::upper_anchor_connID_
private

The upper end of the loop to be closed is presumably connected to geometry that is not moved by this mover. However, the connection could be through backbone or sidechain. The mover needs to know the connection ID on the upper end of the loop to the anchor geometry. Note: This will be set to 0 if the only connection that this residue can form is to the loop.

Referenced by addupperanchor(), and infer_anchor_connIDs().


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