Rosetta Protocols  2014.35
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
protocols::ligand_docking::LigandBaseProtocol Class Reference

Shared functionality for protocols that dock ligands. More...

#include <LigandBaseProtocol.hh>

Public Member Functions

 LigandBaseProtocol ()
virtual ~LigandBaseProtocol ()
core::scoring::ScoreFunctionOP get_scorefxn ()
core::scoring::ScoreFunctionCOP get_scorefxn () const
virtual void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
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::func::FuncOP restr_func) const
void reorder_foldtree_around_mobile_regions (core::pose::Pose &pose, core::Size const &jump_id, utility::vector1< bool > const &mobile_bb, core::Size const &lig_id) const
 reorders a fold tree such that movement in the mobile regions will More...
void get_non_bb_clashing_rotamers (core::pose::Pose const &pose, core::Size seqpos, core::scoring::ScoreFunctionCOP scofx, utility::vector1< core::conformation::ResidueCOP > &accepted_rotamers) const
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
virtual ~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)
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
virtual void parse_my_tag (TagCOP tag, basic::datacache::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
 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...
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...

Protected Member Functions

core::scoring::ScoreFunctionOP make_tweaked_scorefxn (std::string const &weights_tag, bool estat_exclude_protein, bool estat_upweight, bool hbonds_downweight)
core::Vector choose_desired_centroid (core::pose::Pose const &pose, core::Size jump_id, utility::vector1< core::Vector >)
void move_ligand_to_desired_centroid (core::pose::Pose &pose, core::Size jump_id, utility::vector1< core::Vector > start_from_pts)
void move_ligand_to_desired_centroid (core::pose::Pose &pose, core::Size jump_id, core::Vector desired_centroid)
core::kinematics::MoveMapOP make_movemap (core::pose::Pose const &pose, core::Size jump_id, core::Real sc_padding, bool include_all_rsds, bool include_backbone, bool include_ligands, bool include_water) const
core::pack::task::PackerTaskOP make_packer_task (core::pose::Pose const &pose, ObjexxFCL::FArray1D_bool const &allow_repack, bool ligand_protonation) const
 Shared machinery for the next two. More...
core::pack::task::PackerTaskOP make_packer_task (core::pose::Pose const &pose, int jump_id, core::Real sc_padding, bool include_all_rsds, bool ligand_protonation) const
 Receptor (interface?) plus ligand. More...
core::pack::task::PackerTaskOP make_packer_task_ligand_only (core::pose::Pose const &pose, int jump_id, bool ligand_protonation) const
 Just ligand, not the receptor. More...
void find_interface_rsds (core::pose::Pose const &pose, int jump_id, core::Real padding, ObjexxFCL::FArray1D_bool &is_interface) const
void find_interface_backbone (core::pose::Pose const &pose, int jump_id, core::Real cutoff_dist, utility::vector1< bool > &is_interface, utility::vector1< bool > &is_around_interface) const
core::scoring::constraints::ConstraintOP restrain_ligand_nbr_atom (core::pose::Pose &pose, core::Size lig_id, core::Real stddev_Angstroms) const
void setup_bbmin_foldtree (core::pose::Pose &pose, core::Size const &jump_id, core::Real cutoff_dist, core::Real stddev_Angstroms)
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Protected Attributes

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_

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::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...

Detailed Description

Shared functionality for protocols that dock ligands.

Includes score function setup, interface definitions, and ligand flexibility.

Constructor & Destructor Documentation

protocols::ligand_docking::LigandBaseProtocol::LigandBaseProtocol ( )
protocols::ligand_docking::LigandBaseProtocol::~LigandBaseProtocol ( )

Member Function Documentation

void protocols::ligand_docking::LigandBaseProtocol::apply ( core::pose::Pose pose)
core::Vector protocols::ligand_docking::LigandBaseProtocol::choose_desired_centroid ( core::pose::Pose const &  pose,
core::Size  jump_id,
utility::vector1< core::Vector start_from_pts 
void protocols::ligand_docking::LigandBaseProtocol::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
void protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds ( core::pose::Pose const &  pose,
int  jump_id,
core::Real  padding,
ObjexxFCL::FArray1D_bool &  is_interface 
) const
core::Size protocols::ligand_docking::LigandBaseProtocol::get_ligand_id ( core::pose::Pose const &  pose) const
core::Size protocols::ligand_docking::LigandBaseProtocol::get_ligand_id ( core::pose::Pose const &  pose,
core::Size  jump_id 
) const
core::Size protocols::ligand_docking::LigandBaseProtocol::get_ligand_jump_id ( core::pose::Pose const &  pose) const
std::string protocols::ligand_docking::LigandBaseProtocol::get_name ( ) const
void protocols::ligand_docking::LigandBaseProtocol::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
core::scoring::ScoreFunctionOP protocols::ligand_docking::LigandBaseProtocol::get_scorefxn ( )
core::scoring::ScoreFunctionCOP protocols::ligand_docking::LigandBaseProtocol::get_scorefxn ( ) const

References scorefxn_.

core::kinematics::MoveMapOP protocols::ligand_docking::LigandBaseProtocol::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 protocols::ligand_docking::LigandBaseProtocol::make_packer_task ( core::pose::Pose const &  pose,
ObjexxFCL::FArray1D_bool const &  allow_repack,
bool  ligand_protonation 
) const
core::pack::task::PackerTaskOP protocols::ligand_docking::LigandBaseProtocol::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.

References find_interface_rsds(), make_packer_task(), and core::pose::Pose::total_residue().

core::pack::task::PackerTaskOP protocols::ligand_docking::LigandBaseProtocol::make_packer_task_ligand_only ( core::pose::Pose const &  pose,
int  jump_id,
bool  ligand_protonation 
) const
core::scoring::ScoreFunctionOP protocols::ligand_docking::LigandBaseProtocol::make_tweaked_scorefxn ( std::string const &  weights_tag,
bool  estat_exclude_protein,
bool  estat_upweight,
bool  hbonds_downweight 
void protocols::ligand_docking::LigandBaseProtocol::move_ligand_to_desired_centroid ( core::pose::Pose pose,
core::Size  jump_id,
utility::vector1< core::Vector start_from_pts 
void protocols::ligand_docking::LigandBaseProtocol::move_ligand_to_desired_centroid ( core::pose::Pose pose,
core::Size  jump_id,
core::Vector  desired_centroid 
void protocols::ligand_docking::LigandBaseProtocol::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

have zero effect on the non-mobile regions. for every contiguous string of mobile regions, the downstream non-mobile stretch will be connected to the upstream non-mobile stretch through a jump. further, a cutpoint will be introduced into every mobile stretch. the ligand will be connected to the nearest non-mobile residue. Note: every contiguous stretch in the mobile regions must be at least 4 residues long

References core::kinematics::FoldTree::add_edge(), core::pose::add_variant_type_to_pose_residue(), core::kinematics::FoldTree::begin(), protocols::loops::Loop::cut(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::delete_extra_vertices(), numeric::xyzVector< class >::distance_squared(), core::kinematics::FoldTree::end(), utility::exit(), core::pose::Pose::fold_tree(), get_ligand_id(), core::conformation::Residue::has(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_terminus(), l, loops, max(), min, protocols::ligand_docking::my_RG, core::conformation::Residue::nbr_atom_xyz(), nres, core::kinematics::FoldTree::num_jump(), protocols::make_rot_lib::PEPTIDE, numeric::random::RandomGenerator::random_range(), core::pose::Pose::residue(), runtime_assert, protocols::loops::Loop::start(), protocols::loops::start, protocols::loops::Loop::stop(), protocols::loops::stop, core::pose::Pose::total_residue(), protocols::ligand_docking::TR, utility_exit_with_message, and core::conformation::Residue::xyz().

Referenced by setup_bbmin_foldtree(), and protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts().

core::scoring::constraints::ConstraintOP protocols::ligand_docking::LigandBaseProtocol::restrain_ligand_nbr_atom ( core::pose::Pose pose,
core::Size  lig_id,
core::Real  stddev_Angstroms 
) const

Depends on atomtree topology; atomtree setup should be finished before calling this. Returns the newly created Constraint for future reference, but also adds it to the Pose.

References core::pose::Pose::add_constraint(), core::pose::Pose::atom_tree(), core::scoring::coordinate_constraint, core::pose::Pose::residue(), core::kinematics::AtomTree::root(), scorefxn_, and protocols::ligand_docking::TR.

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

void protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas ( core::pose::Pose pose,
utility::vector1< bool > const &  is_restrained,
core::scoring::func::FuncOP  restr_func 
) const
void protocols::ligand_docking::LigandBaseProtocol::setup_bbmin_foldtree ( core::pose::Pose pose,
core::Size const &  jump_id,
core::Real  cutoff_dist,
core::Real  stddev_Angstroms 

This function actually alters both the pose, and the jump_id to be docked. The pose will have chainbreak variant types and distance constraints added.

References find_interface_backbone(), get_ligand_id(), nres, reorder_foldtree_around_mobile_regions(), restrain_protein_Calphas(), and core::pose::Pose::total_residue().

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

Member Data Documentation

core::Real protocols::ligand_docking::LigandBaseProtocol::bb_interface_cutoff_
core::scoring::ScoreFunctionOP protocols::ligand_docking::LigandBaseProtocol::hard_scorefxn_
core::Real protocols::ligand_docking::LigandBaseProtocol::sc_interface_padding_
core::scoring::ScoreFunctionOP protocols::ligand_docking::LigandBaseProtocol::scorefxn_
core::scoring::ScoreFunctionOP protocols::ligand_docking::LigandBaseProtocol::soft_scorefxn_
core::pack::rotamer_set::UnboundRotamersOperationOP protocols::ligand_docking::LigandBaseProtocol::unboundrot_
bool protocols::ligand_docking::LigandBaseProtocol::use_soft_rep_

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