Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
protocols::enzdes::EnzdesBaseProtocol Class Reference

#include <EnzdesBaseProtocol.hh>

Inheritance diagram for protocols::enzdes::EnzdesBaseProtocol:
Inheritance graph

Public Member Functions

 EnzdesBaseProtocol ()
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
utility::vector1< core::Sizecatalytic_res (core::pose::Pose const &pose) const
std::set< core::Size > const & design_targets (core::pose::Pose const &pose) const
utility::vector1< core::Sizerb_min_jumps () const
void rb_min_jumps (utility::vector1< core::Size > const)
bool is_catalytic_position (core::pose::Pose const &pose, core::Size const seqpos) const
core::chemical::ResidueTypeSetCAP restype_set () const
void generate_explicit_ligand_rotamer_poses (core::pose::Pose const &orig_pose, utility::vector1< core::pose::PoseOP > &ligrot_poses, core::scoring::ScoreFunctionCOP scofx)
core::scoring::ScoreFunctionCOP reduced_scorefxn () const
core::scoring::ScoreFunctionOP reduced_scorefxn ()
core::Real design_targets_score (core::pose::Pose const &pose) const
virtual void remap_resid (core::pose::Pose const &pose, core::id::SequenceMapping const &smap)
void remove_enzdes_constraints (core::pose::Pose &pose, bool keep_covalent) const
void add_pregenerated_enzdes_constraints (core::pose::Pose &pose) const
void cst_minimize (core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool cst_opt=false)
core::pack::task::PackerTaskOP create_enzdes_pack_task (core::pose::Pose &pose, bool design=true)
void setup_sequence_recovery_cache (core::pose::Pose &pose, core::pack::task::PackerTask const &task) const
void set_all_jumps_minimizable (bool const &setting)
void set_minimize_options (bool const &min_sc, bool const &min_bb, bool const &min_rb, bool const &min_lig, bool backrub=false)
void set_fix_cataa (bool const &setting)
core::kinematics::MoveMapOP create_enzdes_movemap (core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool min_all_jumps=false)
void enzdes_pack (core::pose::Pose &pose, core::pack::task::PackerTaskCOP, core::scoring::ScoreFunctionCOP scorefxn, core::Size cycles, bool minimize_after_packing, bool pack_unconstrained, bool favor_native)
void set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
void setup_bbmin_ft_and_csts (core::pose::Pose &pose, utility::vector1< bool > allow_move_bb, core::Size jump_id)
- 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 apply (core::pose::Pose &pose) override
 Main Method. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
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...

Static Public Member Functions

static void register_options ()
- 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

void setup_enzdes_constraints (core::pose::Pose &pose, bool allow_missing_remark_blocks) const
void enable_constraint_scoreterms ()
void disable_constraint_scoreterms ()
 function to disable constraint scoring terms: @NOTE: this will leave eventual covalent connections set up by EnzConstraintIO untouched. More...
bool exchange_ligands_in_pose (core::pose::Pose &pose, bool check_bb_clashes, core::scoring::ScoreFunctionCOP scofx)
bool native_needs_load () const
 Do we need to (lazily) load the native pose? More...
void set_native_needs_load (bool const setting)
 Set whether the native needs loading. 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...

Protected Attributes

core::scoring::ScoreFunctionOP reduced_sfxn_
std::set< core::Sizedesign_targets_
bool include_all_design_targets_in_design_interface_

Private Member Functions

void read_ligand_superposition_file (std::string filename)

Private Attributes

core::chemical::ResidueTypeSetCAP restype_set_
core::scoring::EnergyMap constraint_weights_
core::Real bb_min_allowed_dev_
core::Real loop_bb_min_allowed_dev_
bool lig_superposition_file_read_
std::pair< std::string, std::string > res_to_superimpose_
utility::vector1< std::pair< std::string, std::string > > atoms_to_superimpose_on_
bool chi_min_
bool bb_min_
bool rb_min_
bool minimize_ligand_torsions_
bool bb_backrub_
bool min_all_jumps_
bool minimize_all_ligand_torsions_
core::Real lig_min_stddev_
bool native_needs_load_ = false
 Do we need to load a native pose? More...
bool exclude_protein_protein_fa_elec_
bool fix_catalytic_aa_
utility::vector1< core::Sizerb_min_jumps_

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

Constructor & Destructor Documentation

◆ EnzdesBaseProtocol()

protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol ( )

Member Function Documentation

◆ add_pregenerated_enzdes_constraints()

void protocols::enzdes::EnzdesBaseProtocol::add_pregenerated_enzdes_constraints ( core::pose::Pose pose) const

◆ catalytic_res()

utility::vector1< core::Size > protocols::enzdes::EnzdesBaseProtocol::catalytic_res ( core::pose::Pose const &  pose) const

◆ create_enzdes_movemap()

core::kinematics::MoveMapOP protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap ( core::pose::Pose pose,
core::pack::task::PackerTaskCOP  task,
bool  min_all_jumps = false 

◆ create_enzdes_pack_task()

core::pack::task::PackerTaskOP protocols::enzdes::EnzdesBaseProtocol::create_enzdes_pack_task ( core::pose::Pose pose,
bool  design = true 

◆ cst_minimize()

void protocols::enzdes::EnzdesBaseProtocol::cst_minimize ( core::pose::Pose pose,
core::pack::task::PackerTaskCOP  task,
bool  cst_opt = false 

◆ design_targets()

std::set< core::Size > const & protocols::enzdes::EnzdesBaseProtocol::design_targets ( core::pose::Pose const &  pose) const

◆ design_targets_score()

core::Real protocols::enzdes::EnzdesBaseProtocol::design_targets_score ( core::pose::Pose const &  pose) const

◆ disable_constraint_scoreterms()

void protocols::enzdes::EnzdesBaseProtocol::disable_constraint_scoreterms ( )

◆ enable_constraint_scoreterms()

void protocols::enzdes::EnzdesBaseProtocol::enable_constraint_scoreterms ( )

◆ enzdes_pack()

void protocols::enzdes::EnzdesBaseProtocol::enzdes_pack ( core::pose::Pose pose,
core::pack::task::PackerTaskCOP  task,
core::scoring::ScoreFunctionCOP  scorefxn,
core::Size  cycles,
bool  minimize_after_packing,
bool  pack_unconstrained,
bool  favor_native 

◆ exchange_ligands_in_pose()

bool protocols::enzdes::EnzdesBaseProtocol::exchange_ligands_in_pose ( core::pose::Pose pose,
bool  check_bb_clashes,
core::scoring::ScoreFunctionCOP  scofx 

◆ generate_explicit_ligand_rotamer_poses()

void protocols::enzdes::EnzdesBaseProtocol::generate_explicit_ligand_rotamer_poses ( core::pose::Pose const &  orig_pose,
utility::vector1< core::pose::PoseOP > &  ligrot_poses,
core::scoring::ScoreFunctionCOP  scofx 

◆ get_name()

std::string protocols::enzdes::EnzdesBaseProtocol::get_name ( ) const

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

Implements protocols::moves::Mover.

Reimplemented in protocols::enzdes::SecondaryMatchProtocol, protocols::enzdes::EnzdesFlexBBProtocol, and protocols::enzdes::EnzdesFixBBProtocol.

◆ is_catalytic_position()

bool protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position ( core::pose::Pose const &  pose,
core::Size const  seqpos 
) const

◆ native_needs_load()

bool protocols::enzdes::EnzdesBaseProtocol::native_needs_load ( ) const

◆ rb_min_jumps() [1/2]

utility::vector1< core::Size > protocols::enzdes::EnzdesBaseProtocol::rb_min_jumps ( ) const

References rb_min_jumps_.

Referenced by create_enzdes_movemap().

◆ rb_min_jumps() [2/2]

void protocols::enzdes::EnzdesBaseProtocol::rb_min_jumps ( utility::vector1< core::Size > const  v)

References rb_min_jumps_.

◆ read_ligand_superposition_file()

void protocols::enzdes::EnzdesBaseProtocol::read_ligand_superposition_file ( std::string  filename)

◆ reduced_scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn ( )

References reduced_sfxn_.

◆ reduced_scorefxn() [2/2]

core::scoring::ScoreFunctionCOP protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn ( ) const

◆ register_options()

void protocols::enzdes::EnzdesBaseProtocol::register_options ( )

◆ remap_resid()

void protocols::enzdes::EnzdesBaseProtocol::remap_resid ( core::pose::Pose const &  pose,
core::id::SequenceMapping const &  smap 

◆ remove_enzdes_constraints()

void protocols::enzdes::EnzdesBaseProtocol::remove_enzdes_constraints ( core::pose::Pose pose,
bool  keep_covalent 
) const

◆ restype_set()

core::chemical::ResidueTypeSetCAP protocols::enzdes::EnzdesBaseProtocol::restype_set ( ) const

◆ set_all_jumps_minimizable()

void protocols::enzdes::EnzdesBaseProtocol::set_all_jumps_minimizable ( bool const &  setting)

References min_all_jumps_.

◆ set_fix_cataa()

void protocols::enzdes::EnzdesBaseProtocol::set_fix_cataa ( bool const &  setting)

References fix_catalytic_aa_.

◆ set_minimize_options()

void protocols::enzdes::EnzdesBaseProtocol::set_minimize_options ( bool const &  min_sc,
bool const &  min_bb,
bool const &  min_rb,
bool const &  min_lig,
bool  backrub = false 

◆ set_native_needs_load()

void protocols::enzdes::EnzdesBaseProtocol::set_native_needs_load ( bool const  setting)

◆ set_scorefxn()

void protocols::enzdes::EnzdesBaseProtocol::set_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn)

◆ setup_bbmin_ft_and_csts()

void protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts ( core::pose::Pose pose,
utility::vector1< bool >  allow_move_bb,
core::Size  jump_id 

◆ setup_enzdes_constraints()

void protocols::enzdes::EnzdesBaseProtocol::setup_enzdes_constraints ( core::pose::Pose pose,
bool  allow_missing_remark_blocks 
) const

◆ setup_sequence_recovery_cache()

void protocols::enzdes::EnzdesBaseProtocol::setup_sequence_recovery_cache ( core::pose::Pose pose,
core::pack::task::PackerTask const &  task 
) const

Member Data Documentation

◆ atoms_to_superimpose_on_

utility::vector1< std::pair< std::string, std::string > > protocols::enzdes::EnzdesBaseProtocol::atoms_to_superimpose_on_

◆ bb_backrub_

bool protocols::enzdes::EnzdesBaseProtocol::bb_backrub_

◆ bb_min_

bool protocols::enzdes::EnzdesBaseProtocol::bb_min_

◆ bb_min_allowed_dev_

core::Real protocols::enzdes::EnzdesBaseProtocol::bb_min_allowed_dev_

◆ chi_min_

bool protocols::enzdes::EnzdesBaseProtocol::chi_min_

◆ constraint_weights_

core::scoring::EnergyMap protocols::enzdes::EnzdesBaseProtocol::constraint_weights_

◆ design_targets_

std::set< core::Size > protocols::enzdes::EnzdesBaseProtocol::design_targets_

◆ exclude_protein_protein_fa_elec_

bool protocols::enzdes::EnzdesBaseProtocol::exclude_protein_protein_fa_elec_

Referenced by EnzdesBaseProtocol().

◆ fix_catalytic_aa_

bool protocols::enzdes::EnzdesBaseProtocol::fix_catalytic_aa_

◆ include_all_design_targets_in_design_interface_

bool protocols::enzdes::EnzdesBaseProtocol::include_all_design_targets_in_design_interface_

◆ lig_min_stddev_

core::Real protocols::enzdes::EnzdesBaseProtocol::lig_min_stddev_

◆ lig_superposition_file_read_

bool protocols::enzdes::EnzdesBaseProtocol::lig_superposition_file_read_

◆ loop_bb_min_allowed_dev_

core::Real protocols::enzdes::EnzdesBaseProtocol::loop_bb_min_allowed_dev_

◆ min_all_jumps_

bool protocols::enzdes::EnzdesBaseProtocol::min_all_jumps_

◆ minimize_all_ligand_torsions_

bool protocols::enzdes::EnzdesBaseProtocol::minimize_all_ligand_torsions_

◆ minimize_ligand_torsions_

bool protocols::enzdes::EnzdesBaseProtocol::minimize_ligand_torsions_

◆ native_needs_load_

bool protocols::enzdes::EnzdesBaseProtocol::native_needs_load_ = false

Do we need to load a native pose?

Referenced by EnzdesBaseProtocol(), native_needs_load(), and set_native_needs_load().

◆ rb_min_

bool protocols::enzdes::EnzdesBaseProtocol::rb_min_

◆ rb_min_jumps_

utility::vector1< core::Size > protocols::enzdes::EnzdesBaseProtocol::rb_min_jumps_

Referenced by EnzdesBaseProtocol(), and rb_min_jumps().

◆ reduced_sfxn_

core::scoring::ScoreFunctionOP protocols::enzdes::EnzdesBaseProtocol::reduced_sfxn_

◆ res_to_superimpose_

std::pair< std::string, std::string > protocols::enzdes::EnzdesBaseProtocol::res_to_superimpose_

◆ restype_set_

core::chemical::ResidueTypeSetCAP protocols::enzdes::EnzdesBaseProtocol::restype_set_

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