Rosetta 3.4
Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes
protocols::enzdes::EnzdesBaseProtocol Class Reference

#include <EnzdesBaseProtocol.hh>

Inheritance diagram for protocols::enzdes::EnzdesBaseProtocol:
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List of all members.

Public Member Functions

 EnzdesBaseProtocol ()
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
utility::vector1< Sizecatalytic_res (core::pose::Pose const &pose) const
std::set< Size > const & design_targets (core::pose::Pose const &pose) 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) const
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) const
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) const
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) const

Static Public Member Functions

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.

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: : this will leave eventual covalent connections set up by EnzConstraintIO untouched.
bool exchange_ligands_in_pose (core::pose::Pose &pose, bool check_bb_clashes, core::scoring::ScoreFunctionCOP scofx)

Protected Attributes

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

Constructor & Destructor Documentation

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

Member Function Documentation

void protocols::enzdes::EnzdesBaseProtocol::add_pregenerated_enzdes_constraints ( core::pose::Pose pose) const
utility::vector1< core::Size > protocols::enzdes::EnzdesBaseProtocol::catalytic_res ( core::pose::Pose const &  pose) const
core::kinematics::MoveMapOP protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap ( core::pose::Pose pose,
core::pack::task::PackerTaskCOP  task,
bool  min_all_jumps = false 
) const
core::pack::task::PackerTaskOP protocols::enzdes::EnzdesBaseProtocol::create_enzdes_pack_task ( core::pose::Pose pose,
bool  design = true 
)
void protocols::enzdes::EnzdesBaseProtocol::cst_minimize ( core::pose::Pose pose,
core::pack::task::PackerTaskCOP  task,
bool  cst_opt = false 
) const
std::set< core::Size > const & protocols::enzdes::EnzdesBaseProtocol::design_targets ( core::pose::Pose const &  pose) const
core::Real protocols::enzdes::EnzdesBaseProtocol::design_targets_score ( core::pose::Pose const &  pose) const
void protocols::enzdes::EnzdesBaseProtocol::disable_constraint_scoreterms ( ) [protected]

function to disable constraint scoring terms: : this will leave eventual covalent connections set up by EnzConstraintIO untouched.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::scoring::res_type_constraint, and protocols::ligand_docking::LigandBaseProtocol::scorefxn_.

void protocols::enzdes::EnzdesBaseProtocol::enable_constraint_scoreterms ( ) [protected]
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 
) const
bool protocols::enzdes::EnzdesBaseProtocol::exchange_ligands_in_pose ( core::pose::Pose pose,
bool  check_bb_clashes,
core::scoring::ScoreFunctionCOP  scofx 
) [protected]
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 
)
std::string protocols::enzdes::EnzdesBaseProtocol::get_name ( ) const [virtual]
bool protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position ( core::pose::Pose const &  pose,
core::Size const  seqpos 
) const
core::scoring::ScoreFunctionCOP protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn ( ) const
core::scoring::ScoreFunctionOP protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn ( )

References reduced_sfxn_.

void protocols::enzdes::EnzdesBaseProtocol::register_options ( ) [static]

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.

Reimplemented from protocols::moves::Mover.

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

void protocols::enzdes::EnzdesBaseProtocol::remap_resid ( core::pose::Pose const &  pose,
core::id::SequenceMapping const &  smap 
) [virtual]
void protocols::enzdes::EnzdesBaseProtocol::remove_enzdes_constraints ( core::pose::Pose pose,
bool  keep_covalent 
) const
core::chemical::ResidueTypeSetCAP protocols::enzdes::EnzdesBaseProtocol::restype_set ( ) const [inline]
void protocols::enzdes::EnzdesBaseProtocol::set_all_jumps_minimizable ( bool const &  setting) [inline]
void protocols::enzdes::EnzdesBaseProtocol::set_fix_cataa ( bool const &  setting) [inline]
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 
) [inline]
void protocols::enzdes::EnzdesBaseProtocol::set_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn)
void protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts ( core::pose::Pose pose,
utility::vector1< bool allow_move_bb,
core::Size  jump_id 
) const
void protocols::enzdes::EnzdesBaseProtocol::setup_enzdes_constraints ( core::pose::Pose pose,
bool  allow_missing_remark_blocks 
) const [protected]
void protocols::enzdes::EnzdesBaseProtocol::setup_sequence_recovery_cache ( core::pose::Pose pose,
core::pack::task::PackerTask const &  task 
) const

Member Data Documentation


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