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protocols::enzdes::EnzdesFlexibleRegion Class Reference

#include <EnzdesFlexBBProtocol.hh>

Inheritance diagram for protocols::enzdes::EnzdesFlexibleRegion:
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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)
 
- Public Member Functions inherited from core::fragment::Frame
virtual ~Frame ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
 
 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, FragDataOP frag1)
 
 Frame (core::Size start, core::Size length, SingleResidueFragDataOP srfd)
 
virtual FrameOP clone () const
 clone method, new frame with same alignment position, fragments are not copied! More...
 
virtual FrameOP clone_with_frags ()
 clone method, new frame with same alignment position, fragments are not copied! More...
 
virtual FrameOP clone_with_template ()
 clone method, new frame with same alignment position, one fragments is copied as template ( valid() == false ) More...
 
virtual std::string type () const
 type() is specifying the output name of the Frame in FragmentIO ("FRAME", "JUMPFRAME", etc) More...
 
core::Size add_fragment (FragDataOP new_frag)
 add a fragment .. return new frag_nr More...
 
bool add_fragment (FragDataList new_frags)
 add all fragments in list More...
 
FragData const & fragment (core::Size frag_num) const
 delete a fragment: Attention: all data in the FragCache is invalidated ( and deleted ) it would be complicated to change this behaviour. Thus, it is desirable to avoid using delete_fragment() altogether. Faster: Make a new Frame and add all fragments you are interested in. More...
 
FragDatafragment (core::Size frag_num)
 accessor for underlying FragData More...
 
FragDataCOP fragment_ptr (core::Size frag_num) const
 accessor for underlying FragData as owning ptr More...
 
FragDataOP fragment_ptr (core::Size frag_num)
 accessor for underlying FragData as owning ptr More...
 
bool is_valid () const
 a frame is considered valid if at least one fragment is contained and this fragment is also valid (not an empty template fragment) More...
 
core::Size apply (kinematics::MoveMap const &, core::Size frag_num, pose::Pose &pose) const
 insert fragment frag_num into pose More...
 
core::Size apply (core::Size frag_num, pose::Pose &pose) const
 insert fragment frag_num into pose — ignore movemap More...
 
core::Size apply_ss (kinematics::MoveMap const &, core::Size frag_num, std::string &ss) const
 change ss-string according to sec-struct info in fragments More...
 
bool steal (pose::Pose const &pose)
 obtain fragment from pose at frame position More...
 
core::Size is_applicable (kinematics::MoveMap const &) const
 is the Frame applicable to the pose with the given movemap? More...
 
virtual core::Size seqpos (core::Size intra_pos) const
 translate intra-frame position into sequence position. (trivial for base-class) More...
 
core::Size frag_id (core::Size frag_num) const
 a unique id for every fragment in the list. his is silly, but would enable later on to avoid cache_clearence on deletion of FragData entries in this case, we would require that the ID of a certain fragment never changes, even if the position in FragList changes More...
 
void fragment_as_pose (core::Size frag_num, pose::Pose &pose, chemical::ResidueTypeSetCAP restype_set) const
 returns a (small) pose with fragment ( continous from seqpos 1 ... nr_res_affected() ) More...
 
virtual bool is_continuous () const
 true if frame is continuous (always true for base class) More...
 
core::Size nr_frags () const
 number of fragments attached to this frame More...
 
void clear ()
 remove all valid fragments, a template fragment will be left over More...
 
bool contains_seqpos (core::Size seqpos) const
 whether this fragment contains a certain position More...
 
core::Size start () const
 first seqpos of this frame More...
 
void shift_to (core::Size setting)
 set start position More...
 
core::Size end () const
 last sequence position affected by this frame More...
 
core::Size stop () const
 /// More...
 
virtual bool moves_residue (core::Size pos) const
 
core::Size nr_res_affected (kinematics::MoveMap const &mm) const
 number of residues affected by this frame More...
 
core::Size length () const
 number of residues in this frame ( for continuous frames it is the same as end()-start() + 1 ) More...
 
BaseCacheUnitcache (std::string tag, BaseCacheUnitOP const &new_cache) const
 return handle to cached data stored under "tag" shouldn't be called directly More...
 
void clone_cache_data (Frame const &source, core::Size sid, core::Size nid)
 copies all entries in the Frame-Cache for fragment "sid" of Frame "source" to fragment "nid" of "this" frame More...
 
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)
 change frames residue numbers accoriding to map More...
 
FrameOP generate_sub_frame (Size length, Size start=1)
 generate_sub_frame of length from start ( internal numbers ) More...
 

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 ()
 

Protected Member Functions

void get_12A_neighbors (core::pose::Pose const &pose)
 requires that the pose was scored More...
 
- Protected Member Functions inherited from core::fragment::Frame
virtual void show_fragments (std::ostream &out) const
 NOT IMPLEMENTED YET: generate_sub_frame according to mapping ( residue numbers ) returns NULL if mapping invalid. More...
 
virtual bool is_compatible (FragDataCOP new_frag) const
 is a FragData object compatible with the already stored ones ? you can only add instances of FragData to the same Frame that are compatible, i.e., that contain the same class of FragData, e.g., based on BBTorsionSRFD, if you want to have different fragment for other dof's at the same sequence position create a new Frame. Users of the fragment-core are aware that multiple Frames for the same sequence position may exist. More...
 
void init_length (core::Size start, core::Size end, core::Size length)
 

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_
 
std::set< core::Sizetwelve_A_neighbors_
 
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::string > desired_remodel_ss_strings_
 

Detailed Description

Definition at line 189 of file EnzdesFlexBBProtocol.hh.

Member Typedef Documentation

Definition at line 191 of file EnzdesFlexBBProtocol.hh.

Definition at line 192 of file EnzdesFlexBBProtocol.hh.

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 ( )

Definition at line 1373 of file EnzdesFlexBBProtocol.cc.

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

Definition at line 247 of file EnzdesFlexBBProtocol.hh.

Referenced by sort_ensemble_by_designability().

bool protocols::enzdes::EnzdesFlexibleRegion::contains_catalytic_res ( ) const
void protocols::enzdes::EnzdesFlexibleRegion::declare_remodelable ( core::Size  min_length,
core::Size  max_length 
)

Definition at line 1403 of file EnzdesFlexBBProtocol.cc.

References remodel_max_length_, remodel_min_length_, and remodelable_.

core::Real protocols::enzdes::EnzdesFlexibleRegion::deltaE_best ( core::Size const  frag_rank) const

Definition at line 1414 of file EnzdesFlexBBProtocol.cc.

References frag_designabilities_.

toolbox::match_enzdes_util::EnzdesLoopInfoCOP protocols::enzdes::EnzdesFlexibleRegion::enz_loop_info ( ) const

Definition at line 1388 of file EnzdesFlexBBProtocol.cc.

References enzdes_protocol_, and index_.

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

Definition at line 1725 of file EnzdesFlexBBProtocol.cc.

References core::graph::Node::const_edge_list_begin(), core::graph::Node::const_edge_list_end(), 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::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

Definition at line 228 of file EnzdesFlexBBProtocol.hh.

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

Definition at line 1959 of file EnzdesFlexBBProtocol.cc.

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

Definition at line 208 of file EnzdesFlexBBProtocol.hh.

References frag_designabilities_.

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

Definition at line 253 of file EnzdesFlexBBProtocol.hh.

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

Definition at line 221 of file EnzdesFlexBBProtocol.hh.

References remodel_max_length_.

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

Definition at line 218 of file EnzdesFlexBBProtocol.hh.

References remodel_min_length_.

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

Definition at line 214 of file EnzdesFlexBBProtocol.hh.

References remodelable_.

void protocols::enzdes::EnzdesFlexibleRegion::scale_target_proximity_to_other_conformations ( core::Real  factor)
inline

Definition at line 328 of file EnzdesFlexBBProtocol.hh.

References target_proximity_to_other_conformations_.

void protocols::enzdes::EnzdesFlexibleRegion::scale_target_proximity_to_starting_conformation ( core::Real  factor)
inline

Definition at line 317 of file EnzdesFlexBBProtocol.hh.

References target_proximity_to_native_conformation_.

void protocols::enzdes::EnzdesFlexibleRegion::set_target_proximity_to_starting_conformation ( core::Real  proximity)
inline

Definition at line 322 of file EnzdesFlexBBProtocol.hh.

References target_proximity_to_native_conformation_.

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

Definition at line 366 of file EnzdesFlexBBProtocol.hh.

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

Definition at line 348 of file EnzdesFlexBBProtocol.hh.

Referenced by EnzdesFlexibleRegion(), and remap_resid().

utility::vector1< core::Size > protocols::enzdes::EnzdesFlexibleRegion::positions_
private
core::Size protocols::enzdes::EnzdesFlexibleRegion::remodel_max_length_
private

Definition at line 365 of file EnzdesFlexBBProtocol.hh.

Referenced by declare_remodelable(), and remodel_max_length().

core::Size protocols::enzdes::EnzdesFlexibleRegion::remodel_min_length_
private

Definition at line 365 of file EnzdesFlexBBProtocol.hh.

Referenced by declare_remodelable(), and remodel_min_length().

bool protocols::enzdes::EnzdesFlexibleRegion::remodelable_
private

Definition at line 364 of file EnzdesFlexBBProtocol.hh.

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
std::set< core::Size > protocols::enzdes::EnzdesFlexibleRegion::twelve_A_neighbors_
private

Definition at line 359 of file EnzdesFlexBBProtocol.hh.

Referenced by get_12A_neighbors(), and sort_ensemble_by_designability().


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