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

#include <EnzdesFlexBBProtocol.hh>

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

Public Member Functions

 EnzdesFlexibleRegion (core::Size index_in, core::Size start, core::Size end, core::Size nr_res, core::pose::Pose const &pose, EnzdesFlexBBProtocolCAP enz_prot)
 ~EnzdesFlexibleRegion ()
core::Size no_ranked_frags () const
bool contains_catalytic_res () const
bool remodelable () const
core::Size remodel_min_length () const
core::Size remodel_max_length () const
toolbox::match_enzdes_util::EnzdesLoopInfoCOP enz_loop_info () const
core::Size index () const
void declare_remodelable (core::Size min_length, core::Size max_length)
core::Real deltaE_best (core::Size const frag_rank) const
core::fragment::FragDataOP assemble_enzdes_fragdata (core::pose::Pose const &pose)
utility::vector1< core::Size >
const & 
positions ()
core::Real extract_lig_designability_score (core::pose::Pose const &pose, core::pack::task::PackerTaskCOP task, core::Real &backgroundE)
core::Real get_region_mm_bend_score (core::pose::Pose const &pose) const
void apply_ranked_fragment (core::pose::Pose &pose, core::Size frag_rank)
void hack_fillup_frag_designabilities ()
void sort_ensemble_by_designability (core::pose::Pose const &ref_pose, core::scoring::ScoreFunctionOP scorefxn, core::pack::task::PackerTaskCOP task)
core::Real calculate_rotamer_set_design_targets_partition_sum (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, core::pack::task::PackerTaskCOP task) const
bool examine_new_loopconf (core::pose::Pose const &pose, core::pose::Pose &template_pose, utility::vector1< core::pose::PoseOP > &compare_poses, utility::vector1< core::Real > &rmsd_to_native)
bool minimize_region (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scorefxn, std::set< core::Size > const &chi_to_move, bool const including_CA_angles, core::Real min_tolerance)
core::Real get_region_total_score (core::pose::Pose const &pose) const
bool remap_resid (core::pose::Pose const &pose, core::id::SequenceMapping const &smap)
void scale_target_proximity_to_starting_conformation (core::Real factor)
void set_target_proximity_to_starting_conformation (core::Real proximity)
void scale_target_proximity_to_other_conformations (core::Real factor)

Static Public Member Functions

static bool compare_SizeRealPairs (SizeRealPair const &first, SizeRealPair const &second)

Protected Member Functions

void get_12A_neighbors (core::pose::Pose const &pose)
 requires that the pose was scored

Constructor & Destructor Documentation

protocols::enzdes::EnzdesFlexibleRegion::EnzdesFlexibleRegion ( core::Size  index_in,
core::Size  start,
core::Size  end,
core::Size  nr_res,
core::pose::Pose const &  pose,
EnzdesFlexBBProtocolCAP  enz_prot 
)
protocols::enzdes::EnzdesFlexibleRegion::~EnzdesFlexibleRegion ( )

Member Function Documentation

void protocols::enzdes::EnzdesFlexibleRegion::apply_ranked_fragment ( core::pose::Pose pose,
core::Size  frag_rank 
)
core::fragment::FragDataOP protocols::enzdes::EnzdesFlexibleRegion::assemble_enzdes_fragdata ( core::pose::Pose const &  pose)
core::Real protocols::enzdes::EnzdesFlexibleRegion::calculate_rotamer_set_design_targets_partition_sum ( core::pose::Pose const &  pose,
core::scoring::ScoreFunctionCOP  scorefxn,
core::pack::task::PackerTaskCOP  task 
) const
static bool protocols::enzdes::EnzdesFlexibleRegion::compare_SizeRealPairs ( SizeRealPair const &  first,
SizeRealPair const &  second 
) [inline, static]
bool protocols::enzdes::EnzdesFlexibleRegion::contains_catalytic_res ( ) const
void protocols::enzdes::EnzdesFlexibleRegion::declare_remodelable ( core::Size  min_length,
core::Size  max_length 
)
core::Real protocols::enzdes::EnzdesFlexibleRegion::deltaE_best ( core::Size const  frag_rank) const
toolbox::match_enzdes_util::EnzdesLoopInfoCOP protocols::enzdes::EnzdesFlexibleRegion::enz_loop_info ( ) const
bool protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf ( core::pose::Pose const &  pose,
core::pose::Pose template_pose,
utility::vector1< core::pose::PoseOP > &  compare_poses,
utility::vector1< core::Real > &  rmsd_to_native 
)
core::Real protocols::enzdes::EnzdesFlexibleRegion::extract_lig_designability_score ( core::pose::Pose const &  pose,
core::pack::task::PackerTaskCOP  task,
core::Real backgroundE 
)

function under heavy development, will prolly change a lot in the coming weeks/months

main idea: look at how the conformation of this region in the input pose interacts with

the ligand as well as the protein background, then combine the two numbers in some way

References core::graph::Node::const_edge_list_begin(), core::graph::Node::const_edge_list_end(), core::fragment::Frame::contains_seqpos(), core::scoring::EnergyEdge::dot(), core::fragment::Frame::end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::graph::Graph::get_node(), core::fragment::Frame::length(), core::fragment::Frame::start(), and core::scoring::Energies::weights().

Referenced by sort_ensemble_by_designability().

void protocols::enzdes::EnzdesFlexibleRegion::get_12A_neighbors ( core::pose::Pose const &  pose) [protected]
core::Real protocols::enzdes::EnzdesFlexibleRegion::get_region_mm_bend_score ( core::pose::Pose const &  pose) const
core::Real protocols::enzdes::EnzdesFlexibleRegion::get_region_total_score ( core::pose::Pose const &  pose) const
void protocols::enzdes::EnzdesFlexibleRegion::hack_fillup_frag_designabilities ( )
core::Size protocols::enzdes::EnzdesFlexibleRegion::index ( ) const [inline]
bool protocols::enzdes::EnzdesFlexibleRegion::minimize_region ( core::pose::Pose pose,
core::scoring::ScoreFunctionCOP  scorefxn,
std::set< core::Size > const &  chi_to_move,
bool const  including_CA_angles,
core::Real  min_tolerance 
)

minimize the backbone of this pose over the fragment residues, including the

bond angles around Calpha if desired. NOTE: CA ANGLE MINIMIZATION UNTESTED a chainbreak at the end of the region will be introduced. chainbreak weight will be set to 100 to make sure that it stays closed. in case the chainbreak score is higher after the min then before, function returns false. this might be the case when the input conformation has bad clashes, which is the case e.g. for some conformations that come out of remodel

References core::kinematics::FoldTree::add_edge(), core::pose::add_variant_type_to_pose_residue(), core::chemical::ResidueType::atom_index(), core::kinematics::FoldTree::begin(), core::scoring::chainbreak, core::kinematics::FoldTree::check_fold_tree(), core::fragment::Frame::clear(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::delete_extra_vertices(), core::kinematics::FoldTree::end(), core::fragment::Frame::end(), core::pose::Pose::energies(), core::pose::Pose::fold_tree(), core::fragment::Frame::nr_frags(), core::kinematics::FoldTree::num_jump(), core::id::PHI, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), core::fragment::Frame::start(), core::fragment::Frame::steal(), core::scoring::Energies::total_energies(), and protocols::enzdes::tr().

core::Size protocols::enzdes::EnzdesFlexibleRegion::no_ranked_frags ( ) const [inline]
utility::vector1< core::Size > const& protocols::enzdes::EnzdesFlexibleRegion::positions ( ) [inline]
bool protocols::enzdes::EnzdesFlexibleRegion::remap_resid ( core::pose::Pose const &  pose,
core::id::SequenceMapping const &  smap 
)
core::Size protocols::enzdes::EnzdesFlexibleRegion::remodel_max_length ( ) const [inline]
core::Size protocols::enzdes::EnzdesFlexibleRegion::remodel_min_length ( ) const [inline]
bool protocols::enzdes::EnzdesFlexibleRegion::remodelable ( ) const [inline]
void protocols::enzdes::EnzdesFlexibleRegion::scale_target_proximity_to_other_conformations ( core::Real  factor) [inline]
void protocols::enzdes::EnzdesFlexibleRegion::scale_target_proximity_to_starting_conformation ( core::Real  factor) [inline]
void protocols::enzdes::EnzdesFlexibleRegion::set_target_proximity_to_starting_conformation ( core::Real  proximity) [inline]
void protocols::enzdes::EnzdesFlexibleRegion::sort_ensemble_by_designability ( core::pose::Pose const &  ref_pose,
core::scoring::ScoreFunctionOP  scorefxn,
core::pack::task::PackerTaskCOP  task 
)

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