Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::ligand_docking::LigandDockProtocol Class Reference

#include <LigandDockProtocol.hh>

Inheritance diagram for protocols::ligand_docking::LigandDockProtocol:
Inheritance graph

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)
 ~LigandDockProtocol () override
LigandDockProtocolOP shared_from_this ()
void add_start_from (core::Real x, core::Real y, core::Real z)
void apply (core::pose::Pose &pose) override
 Creates a new hierarchy of Movers for each Pose passed in. More...
std::string get_name () const override
 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=nullptr) const
 Scores to be output that aren't normal scorefunction terms. More...
- Public Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
 LigandBaseProtocol ()
 ~LigandBaseProtocol () override
LigandBaseProtocolOP shared_from_this ()
core::scoring::ScoreFunctionOP get_scorefxn ()
core::scoring::ScoreFunctionCOP get_scorefxn () const
void restrain_protein_Calphas (core::pose::Pose &pose, utility::vector1< bool > const &is_restrained, core::scoring::func::FuncOP restr_func)
void reorder_foldtree_around_mobile_regions (core::pose::Pose &pose, core::Size const &jump_id, utility::vector1< bool > const &mobile_bb, core::Size const &lig_id) const
 reorders a fold tree such that movement in the mobile regions will More...
void get_non_bb_clashing_rotamers (core::pose::Pose const &pose, core::Size seqpos, core::scoring::ScoreFunctionCOP scofx, utility::vector1< core::conformation::ResidueCOP > &accepted_rotamers) const
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
virtual MoverOP create ()
MoverCOP get_self_ptr () const
MoverOP get_self_ptr ()
MoverCAP get_self_weak_ptr () const
MoverAP get_self_weak_ptr ()
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
void set_type (std::string const &setting)
 Set the 'type' string. More...
std::string get_type () const
void type (const std::string &type_in)
 Set the 'type' string. More...
std::string const & type () const
 Get the set 'type' string. More...
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
PoseCOP get_input_pose () const
PoseCOP get_native_pose () const
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void set_current_tag (std::string const &new_tag)
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
virtual core::Real last_proposal_density_ratio ()
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
virtual Stringsinfo ()
 non-const accessor More...
virtual Strings const & info () const
 const accessor More...
virtual void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions

 LigandDockProtocol (LigandDockProtocol const &)=delete
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::ResidueTorsionRestraintsOPligand_torsion_restraints_

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
typedef core::pose::Pose Pose
typedef core::pose::PoseCOP PoseCOP
typedef std::list< std::string > Strings
- Static Public Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
static core::Size get_ligand_jump_id (core::pose::Pose const &pose)
static core::Size get_ligand_id (core::pose::Pose const &pose)
 Return the residue sequence number for our ligand. More...
static core::Size get_ligand_id (core::pose::Pose const &pose, core::Size jump_id)
 Return the residue sequence number for our ligand. More...
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
static void register_options ()
 Overload this static method if you access options within the mover. More...
- Protected 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)
core::pack::rotamer_set::UnboundRotamersOperationOP unboundrot ()
 Nonconst access to the unboundrot_ object. More...
core::scoring::ScoreFunctionOP scorefxn ()
 Access the scorefunction. More...
void set_scorefxn (core::scoring::ScoreFunctionCOP const &sfxn_in)
 Set the scorefunction (cloning the input). More...
core::scoring::ScoreFunctionOP hard_scorefxn ()
 Access the hard scorefunction. More...
core::scoring::ScoreFunctionOP soft_scorefxn ()
 Access the soft scorefunction. More...
core::Real sc_interface_padding () const
 Access the sc_interface_padding. More...
core::Real bb_interface_cutoff () const
 Access the bb_interface_cutoff. More...
void set_sc_interface_padding (core::Real const setting)
 Set the sc_interface_padding. More...
void set_bb_interface_cutoff (core::Real const setting)
 Set the bb_interface_cutoff. More...
bool use_soft_rep () const
 Are we using soft repulsion? 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

◆ LigandDockProtocol() [1/3]

protocols::ligand_docking::LigandDockProtocol::LigandDockProtocol ( )

◆ LigandDockProtocol() [2/3]

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 

◆ ~LigandDockProtocol()

protocols::ligand_docking::LigandDockProtocol::~LigandDockProtocol ( )

◆ LigandDockProtocol() [3/3]

protocols::ligand_docking::LigandDockProtocol::LigandDockProtocol ( LigandDockProtocol const &  )

Member Function Documentation

◆ add_start_from()

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

References start_from_pts_.

◆ append_ligand_docking_scores()

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 = nullptr 
) const

◆ apply()

void protocols::ligand_docking::LigandDockProtocol::apply ( core::pose::Pose pose)

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.

References protocols::docking::FaDockingSlideIntoContact::apply(), protocols::ligand_docking::LigandBaseProtocol::bb_interface_cutoff(), classic_protocol(), core::chemical::FA_STANDARD, 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(), protocols::loops::read_loop_fragments(), protocols::antibody::design::relax, 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::set_scorefxn(), protocols::ligand_docking::LigandBaseProtocol::setup_bbmin_foldtree(), shear_min_protocol(), protocols::ligand_docking::LigandBaseProtocol::soft_scorefxn(), start_from_pts_, core::util::switch_to_residue_type_set(), tether_ligand_, protocols::ligand_docking::TR(), and protocols::ligand_docking::LigandBaseProtocol::use_soft_rep().

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

◆ classic_protocol()

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

◆ get_name()

std::string protocols::ligand_docking::LigandDockProtocol::get_name ( ) const

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

Reimplemented from protocols::ligand_docking::LigandBaseProtocol.

◆ make_dockmcm_mover()

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

Build Mover for Monte Carlo Minimization protocol.

References protocols::moves::no_stats, and protocols::ligand_docking::LigandBaseProtocol::scorefxn().

◆ optimize_orientation3()

void protocols::ligand_docking::LigandDockProtocol::optimize_orientation3 ( core::pose::Pose pose,
int  jump_id,
core::Size  lig_id 

◆ random_conformer()

void protocols::ligand_docking::LigandDockProtocol::random_conformer ( core::pose::Pose pose) const

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::size().

Referenced by apply().

◆ restrain_ligand_chis()

void protocols::ligand_docking::LigandDockProtocol::restrain_ligand_chis ( core::pose::Pose pose)

◆ shared_from_this()

LigandDockProtocolOP protocols::ligand_docking::LigandDockProtocol::shared_from_this ( )

◆ shear_min_protocol()

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

Member Data Documentation

◆ ligand_chi_stddev_deg_

core::Real protocols::ligand_docking::LigandDockProtocol::ligand_chi_stddev_deg_

◆ ligand_protonation_

bool protocols::ligand_docking::LigandDockProtocol::ligand_protonation_

◆ ligand_shear_moves_

core::Size protocols::ligand_docking::LigandDockProtocol::ligand_shear_moves_

◆ ligand_tether_stddev_Ang_

core::Real protocols::ligand_docking::LigandDockProtocol::ligand_tether_stddev_Ang_

Referenced by apply(), and LigandDockProtocol().

◆ ligand_torsion_restraints_

utility::vector1< protocols::ligand_docking::ResidueTorsionRestraintsOP > protocols::ligand_docking::LigandDockProtocol::ligand_torsion_restraints_

◆ minimize_all_rsds_

bool protocols::ligand_docking::LigandDockProtocol::minimize_all_rsds_

◆ minimize_backbone_

bool protocols::ligand_docking::LigandDockProtocol::minimize_backbone_

Referenced by apply(), and LigandDockProtocol().

◆ minimize_ligand_

bool protocols::ligand_docking::LigandDockProtocol::minimize_ligand_

◆ minimize_water_

bool protocols::ligand_docking::LigandDockProtocol::minimize_water_

◆ protein_CA_stddev_Ang_

core::Real protocols::ligand_docking::LigandDockProtocol::protein_CA_stddev_Ang_

Referenced by apply(), and LigandDockProtocol().

◆ protocol_

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

Referenced by apply(), and LigandDockProtocol().

◆ repack_all_rsds_

bool protocols::ligand_docking::LigandDockProtocol::repack_all_rsds_

◆ rottrials_all_rsds_

bool protocols::ligand_docking::LigandDockProtocol::rottrials_all_rsds_

◆ start_from_pts_

utility::vector1< core::Vector > protocols::ligand_docking::LigandDockProtocol::start_from_pts_

◆ tether_ligand_

bool protocols::ligand_docking::LigandDockProtocol::tether_ligand_

Referenced by apply(), and LigandDockProtocol().

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