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protocols::ligand_docking::LigandDockProtocol Class Reference

#include <LigandDockProtocol.hh>

Inheritance diagram for protocols::ligand_docking::LigandDockProtocol:
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Collaboration diagram for protocols::ligand_docking::LigandDockProtocol:
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Public Member Functions

 LigandDockProtocol ()
 
 LigandDockProtocol (std::string const protocol, bool const minimize_ligand, bool const minimize_backbone, bool const tether_ligand, bool const mutate_same_name3, core::Real const ligand_chi_stddev_deg, core::Real const protein_CA_stddev_Ang, core::Real const ligand_tether_stddev_Ang_=-1, core::Size const ligand_shear_moves=0)
 
virtual ~LigandDockProtocol ()
 
void add_start_from (core::Real x, core::Real y, core::Real z)
 
virtual void apply (core::pose::Pose &pose)
 Creates a new hierarchy of Movers for each Pose passed in. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void append_ligand_docking_scores (core::pose::Pose const &before, core::pose::Pose const &after, core::scoring::ScoreFunctionCOP scorefxn, std::map< std::string, core::Real > &scores, protocols::toolbox::match_enzdes_util::EnzConstraintIOCOP constraint_io=NULL) const
 Scores to be output that aren't normal scorefunction terms. More...
 
- 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
 

Private Member Functions

 LigandDockProtocol (LigandDockProtocol const &that)
 
void classic_protocol (core::pose::Pose &pose, int jump_id, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo, core::Size num_cycles, core::Size repack_every_Nth) const
 
void shear_min_protocol (core::pose::Pose &pose, int jump_id, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo, core::Size num_cycles) const
 
void optimize_orientation3 (core::pose::Pose &pose, int jump_id, core::Size lig_id)
 Repeatedly randomize ligand orientation in a given location to find where some ligand rotamer has minimal clashes with the backbone. More...
 
void random_conformer (core::pose::Pose &pose) const
 Replace current ligand(s) with conformers picked randomly from the library. More...
 
protocols::moves::MoverOP make_dockmcm_mover (core::pose::Pose const &pose, int jump_id, protocols::moves::MoverOP repack_mover, protocols::moves::MoverOP rigbod_mover, core::kinematics::MoveMapOP movemap, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo) const
 Build Mover for Monte Carlo Minimization protocol. More...
 
void restrain_ligand_chis (core::pose::Pose &pose)
 

Private Attributes

std::string protocol_
 
bool minimize_ligand_
 
bool minimize_backbone_
 
bool tether_ligand_
 
bool ligand_protonation_
 
core::Real ligand_chi_stddev_deg_
 
core::Real protein_CA_stddev_Ang_
 
core::Real ligand_tether_stddev_Ang_
 
core::Size ligand_shear_moves_
 
bool minimize_all_rsds_
 
bool repack_all_rsds_
 
bool rottrials_all_rsds_
 
bool minimize_water_
 
utility::vector1< core::Vectorstart_from_pts_
 
utility::vector1
< protocols::ligand_docking::ResidueTorsionRestraintsOP
ligand_torsion_restraints_
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 
- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
 
- 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 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::ligand_docking::LigandDockProtocol::LigandDockProtocol ( )
protocols::ligand_docking::LigandDockProtocol::LigandDockProtocol ( std::string const  protocol,
bool const  minimize_ligand,
bool const  minimize_backbone,
bool const  tether_ligand,
bool const  mutate_same_name3,
core::Real const  ligand_chi_stddev_deg,
core::Real const  protein_CA_stddev_Ang,
core::Real const  ligand_tether_stddev_Ang_ = -1,
core::Size const  ligand_shear_moves = 0 
)
protocols::ligand_docking::LigandDockProtocol::~LigandDockProtocol ( )
virtual
protocols::ligand_docking::LigandDockProtocol::LigandDockProtocol ( LigandDockProtocol const &  that)
private

Member Function Documentation

void protocols::ligand_docking::LigandDockProtocol::add_start_from ( core::Real  x,
core::Real  y,
core::Real  z 
)

References start_from_pts_.

void protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores ( core::pose::Pose const &  before,
core::pose::Pose const &  after,
core::scoring::ScoreFunctionCOP  scorefxn,
std::map< std::string, core::Real > &  scores,
protocols::toolbox::match_enzdes_util::EnzConstraintIOCOP  constraint_io = NULL 
) const
void protocols::ligand_docking::LigandDockProtocol::apply ( core::pose::Pose pose)
virtual

Creates a new hierarchy of Movers for each Pose passed in.

Some Movers (e.g. repack) require knowledge of the Pose to create, and are only valid for that Pose and other conformations of it (i.e. poses with the same number of residues, jumps, etc). In general, we expect each Pose coming in here to be from a different PDB file. The cost of creating these objects anew should be minimal compared to the processing work they do.

Reimplemented from protocols::ligand_docking::LigandBaseProtocol.

Reimplemented in protocols::ligand_docking::LigandDockMain.

References protocols::docking::FaDockingSlideIntoContact::apply(), protocols::ligand_docking::LigandBaseProtocol::bb_interface_cutoff_, classic_protocol(), core::pose::Pose::fold_tree(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_jump_id(), protocols::ligand_docking::LigandBaseProtocol::hard_scorefxn_, ligand_tether_stddev_Ang_, ligand_torsion_restraints_, core::pack::dunbrack::load_unboundrot(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), minimize_all_rsds_, minimize_backbone_, minimize_ligand_, minimize_water_, protocols::ligand_docking::LigandBaseProtocol::move_ligand_to_desired_centroid(), optimize_orientation3(), protein_CA_stddev_Ang_, protocol_, random_conformer(), core::pose::Pose::remove_constraint(), restrain_ligand_chis(), protocols::ligand_docking::LigandBaseProtocol::restrain_ligand_nbr_atom(), protocols::ligand_docking::LigandBaseProtocol::sc_interface_padding_, protocols::ligand_docking::LigandBaseProtocol::scorefxn_, protocols::ligand_docking::LigandBaseProtocol::setup_bbmin_foldtree(), shear_min_protocol(), protocols::ligand_docking::LigandBaseProtocol::soft_scorefxn_, start_from_pts_, tether_ligand_, and protocols::ligand_docking::LigandBaseProtocol::use_soft_rep_.

Referenced by protocols::ligand_docking::LigandDockMain::apply().

void protocols::ligand_docking::LigandDockProtocol::classic_protocol ( core::pose::Pose pose,
int  jump_id,
core::scoring::ScoreFunctionOP  scorefxn,
protocols::moves::MonteCarloOP  monteCarlo,
core::Size  num_cycles,
core::Size  repack_every_Nth 
) const
private
std::string protocols::ligand_docking::LigandDockProtocol::get_name ( ) const
virtual

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

Reimplemented from protocols::ligand_docking::LigandBaseProtocol.

Reimplemented in protocols::ligand_docking::LigandDockMain.

protocols::moves::MoverOP protocols::ligand_docking::LigandDockProtocol::make_dockmcm_mover ( core::pose::Pose const &  pose,
int  jump_id,
protocols::moves::MoverOP  repack_mover,
protocols::moves::MoverOP  rigbod_mover,
core::kinematics::MoveMapOP  movemap,
core::scoring::ScoreFunctionOP  scorefxn,
protocols::moves::MonteCarloOP  monteCarlo 
) const
private

Build Mover for Monte Carlo Minimization protocol.

References protocols::moves::no_stats.

void protocols::ligand_docking::LigandDockProtocol::optimize_orientation3 ( core::pose::Pose pose,
int  jump_id,
core::Size  lig_id 
)
private
void protocols::ligand_docking::LigandDockProtocol::random_conformer ( core::pose::Pose pose) const
private

Replace current ligand(s) with conformers picked randomly from the library.

References core::conformation::Residue::is_polymer(), ligand_torsion_restraints_, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::ligand_docking::LigandDockProtocol::restrain_ligand_chis ( core::pose::Pose pose)
private
void protocols::ligand_docking::LigandDockProtocol::shear_min_protocol ( core::pose::Pose pose,
int  jump_id,
core::scoring::ScoreFunctionOP  scorefxn,
protocols::moves::MonteCarloOP  monteCarlo,
core::Size  num_cycles 
) const
private

Member Data Documentation

core::Real protocols::ligand_docking::LigandDockProtocol::ligand_chi_stddev_deg_
private
bool protocols::ligand_docking::LigandDockProtocol::ligand_protonation_
private
core::Size protocols::ligand_docking::LigandDockProtocol::ligand_shear_moves_
private
core::Real protocols::ligand_docking::LigandDockProtocol::ligand_tether_stddev_Ang_
private

Referenced by apply(), and LigandDockProtocol().

utility::vector1< protocols::ligand_docking::ResidueTorsionRestraintsOP > protocols::ligand_docking::LigandDockProtocol::ligand_torsion_restraints_
private
bool protocols::ligand_docking::LigandDockProtocol::minimize_all_rsds_
private
bool protocols::ligand_docking::LigandDockProtocol::minimize_backbone_
private

Referenced by apply(), and LigandDockProtocol().

bool protocols::ligand_docking::LigandDockProtocol::minimize_ligand_
private
bool protocols::ligand_docking::LigandDockProtocol::minimize_water_
private
core::Real protocols::ligand_docking::LigandDockProtocol::protein_CA_stddev_Ang_
private

Referenced by apply(), and LigandDockProtocol().

std::string protocols::ligand_docking::LigandDockProtocol::protocol_
private

Referenced by apply(), and LigandDockProtocol().

bool protocols::ligand_docking::LigandDockProtocol::repack_all_rsds_
private
bool protocols::ligand_docking::LigandDockProtocol::rottrials_all_rsds_
private
utility::vector1< core::Vector > protocols::ligand_docking::LigandDockProtocol::start_from_pts_
private
bool protocols::ligand_docking::LigandDockProtocol::tether_ligand_
private

Referenced by apply(), and LigandDockProtocol().


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