Rosetta Protocols  2014.35
Public Member Functions | Static Public Member Functions | Private Types | Private Attributes | List of all members
protocols::enzdes::EnzdesFlexibleRegion Class Reference

#include <EnzdesFlexBBProtocol.hh>

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 () const
 
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)
 
std::set< core::Sizeget_10A_neighbors (core::pose::Pose const &pose) const
 requires that the pose was scored More...
 
- Public Member Functions inherited from core::fragment::Frame
virtual ~Frame ()
 
 Frame ()
 
 Frame (core::Size begin, core::Size end, core::Size nr_res)
 
 Frame (core::Size start, core::Size length)
 
 Frame (core::Size start)
 
 Frame (core::Size start, FragDataCOP const &frag1)
 
 Frame (core::Size start, core::Size length, SingleResidueFragDataOP srfd)
 
virtual FrameOP clone () const
 
virtual FrameOP clone_with_frags () const
 
virtual FrameOP clone_with_template ()
 
virtual std::string type () const
 
core::Size add_fragment (FragDataCOP new_frag)
 
bool add_fragment (FragDataCOPs new_frags)
 
FragData const & fragment (core::Size frag_num) const
 
FragDataCOP fragment_ptr (core::Size frag_num) const
 
bool is_valid () const
 
core::Size apply (kinematics::MoveMap const &, core::Size frag_num, pose::Pose &pose) const
 
core::Size apply (core::Size frag_num, pose::Pose &pose) const
 
core::Size apply_ss (kinematics::MoveMap const &, core::Size frag_num, std::string &ss) const
 
bool steal (pose::Pose const &pose)
 
core::Size is_applicable (kinematics::MoveMap const &) const
 
virtual core::Size seqpos (core::Size intra_pos) const
 
core::Size frag_id (core::Size frag_num) const
 
void fragment_as_pose (core::Size frag_num, pose::Pose &pose, chemical::ResidueTypeSetCAP restype_set) const
 
virtual bool is_continuous () const
 
core::Size nr_frags () const
 
void clear ()
 
bool contains_seqpos (core::Size seqpos) const
 
core::Size start () const
 
virtual void shift_to (core::Size setting)
 
virtual void shift_by (int offset)
 
core::Size end () const
 
core::Size stop () const
 
virtual bool moves_residue (core::Size pos) const
 
core::Size nr_res_affected (kinematics::MoveMap const &mm) const
 
core::Size length () const
 
BaseCacheUnitcache (std::string tag, BaseCacheUnitOP const &new_cache) const
 
void clone_cache_data (Frame const &source, core::Size sid, core::Size nid)
 
virtual void show_classic (std::ostream &out) const
 
virtual void show (std::ostream &out) const
 
virtual void show_header (std::ostream &out) const
 
virtual void read (std::istream &in)
 
bool is_mergeable (Frame const &other) const
 
bool merge (Frame const &other)
 
virtual bool align (core::id::SequenceMapping const &map)
 
FrameOP generate_sub_frame (Size length, Size start=1) const
 

Static Public Member Functions

static bool compare_SizeRealPairs (SizeRealPair const &first, SizeRealPair const &second)
 
- Static Public Member Functions inherited from core::fragment::Frame
static std::string _static_type_name ()
 

Private Types

typedef std::pair< core::Size,
core::Real
SizeRealPair
 
typedef core::fragment::Frame Super
 

Private Attributes

core::Size index_
 
utility::vector1< core::Sizepositions_
 
core::fragment::FragDataOP native_conf_
 
EnzdesFlexBBProtocolCAP enzdes_protocol_
 
std::set< core::Size > const & design_targets_
 
utility::vector1< SizeRealPairfrag_designabilities_
 
core::Real target_proximity_to_native_conformation_
 
core::Real target_proximity_to_other_conformations_
 
bool remodelable_
 
core::Size remodel_min_length_
 
core::Size remodel_max_length_
 
utility::vector1< std::stringdesired_remodel_ss_strings_
 

Additional Inherited Members

- Protected Member Functions inherited from core::fragment::Frame
virtual void show_fragments (std::ostream &out) const
 
virtual bool is_compatible (FragDataCOP new_frag) const
 
void init_length (core::Size start, core::Size end, core::Size length)
 

Member Typedef Documentation

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 
)
inlinestatic
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::fragment::Frame::contains_seqpos(), design_targets_, core::scoring::EnergyEdge::dot(), core::fragment::Frame::end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::fragment::Frame::length(), core::fragment::Frame::start(), and core::scoring::Energies::weights().

Referenced by sort_ensemble_by_designability().

std::set< core::Size > protocols::enzdes::EnzdesFlexibleRegion::get_10A_neighbors ( core::pose::Pose const &  pose) const
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

References index_.

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(), protocols::loops::loop_closure::ccd::backward, core::kinematics::FoldTree::begin(), core::scoring::chainbreak, core::kinematics::FoldTree::check_fold_tree(), core::kinematics::MoveMap::clear(), core::fragment::Frame::clear(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::delete_extra_vertices(), core::fragment::Frame::end(), core::kinematics::FoldTree::end(), core::pose::Pose::energies(), core::pose::Pose::fold_tree(), movemap, 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(), runtime_assert, core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::fragment::Frame::start(), core::fragment::Frame::steal(), core::scoring::Energies::total_energies(), protocols::enzdes::tr, and utility_exit_with_message.

core::Size protocols::enzdes::EnzdesFlexibleRegion::no_ranked_frags ( ) const
inline

References frag_designabilities_.

utility::vector1< core::Size > const& protocols::enzdes::EnzdesFlexibleRegion::positions ( ) const
inline

References positions_.

Referenced by sort_ensemble_by_designability().

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

References remodel_max_length_.

core::Size protocols::enzdes::EnzdesFlexibleRegion::remodel_min_length ( ) const
inline

References remodel_min_length_.

bool protocols::enzdes::EnzdesFlexibleRegion::remodelable ( ) const
inline

References remodelable_.

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 
)

Member Data Documentation

std::set< core::Size > const& protocols::enzdes::EnzdesFlexibleRegion::design_targets_
private
utility::vector1< std::string > protocols::enzdes::EnzdesFlexibleRegion::desired_remodel_ss_strings_
private
EnzdesFlexBBProtocolCAP protocols::enzdes::EnzdesFlexibleRegion::enzdes_protocol_
private
utility::vector1< SizeRealPair > protocols::enzdes::EnzdesFlexibleRegion::frag_designabilities_
private
core::Size protocols::enzdes::EnzdesFlexibleRegion::index_
private
core::fragment::FragDataOP protocols::enzdes::EnzdesFlexibleRegion::native_conf_
private
utility::vector1< core::Size > protocols::enzdes::EnzdesFlexibleRegion::positions_
private
core::Size protocols::enzdes::EnzdesFlexibleRegion::remodel_max_length_
private
core::Size protocols::enzdes::EnzdesFlexibleRegion::remodel_min_length_
private
bool protocols::enzdes::EnzdesFlexibleRegion::remodelable_
private

Referenced by declare_remodelable(), and remodelable().

core::Real protocols::enzdes::EnzdesFlexibleRegion::target_proximity_to_native_conformation_
private
core::Real protocols::enzdes::EnzdesFlexibleRegion::target_proximity_to_other_conformations_
private

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