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protocols::enzdes::EnzdesFlexibleRegion Class Reference

#include <EnzdesFlexBBProtocol.hh>

Inheritance diagram for protocols::enzdes::EnzdesFlexibleRegion:
Inheritance graph

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 () override
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, core::Size const threads_to_request) 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
 ~Frame () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. 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, FragDataCOP const &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 () const
 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 (FragDataCOP new_frag)
 add a fragment .. return new frag_nr More...
bool add_fragment (FragDataCOPs 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...
FragDataCOP fragment_ptr (core::Size frag_num) const
 accessor for underlying FragData More...
bool is_valid () const
 accessor for underlying FragData as owning ptr 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...
virtual void shift_to (core::Size setting)
 set start position More...
virtual void shift_by (int offset)
 shift frame by offset relative to current start position ( change end accordingly ) 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) const
 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 ()

Private Types

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

Private Member Functions

 EnzdesFlexibleRegion ()
 Private default constructor – You must use the parameterized constructor to create! More...

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::string > desired_remodel_ss_strings_

Additional Inherited Members

- 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...
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)

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 ( )
protocols::enzdes::EnzdesFlexibleRegion::EnzdesFlexibleRegion ( )

Private default constructor – You must use the parameterized constructor to create!

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,
core::Size const  threads_to_request 
) const
static bool protocols::enzdes::EnzdesFlexibleRegion::compare_SizeRealPairs ( SizeRealPair const &  first,
SizeRealPair const &  second 
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

References frag_designabilities_.

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

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

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

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::carbohydrates::backward, core::scoring::chainbreak, core::kinematics::FoldTree::check_fold_tree(), core::fragment::Frame::clear(), core::kinematics::FoldTree::clone(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::delete_extra_vertices(), 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

References frag_designabilities_.

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

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

References remodel_max_length_.

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

References remodel_min_length_.

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

References remodelable_.

void protocols::enzdes::EnzdesFlexibleRegion::scale_target_proximity_to_other_conformations ( core::Real  factor)
void protocols::enzdes::EnzdesFlexibleRegion::scale_target_proximity_to_starting_conformation ( core::Real  factor)
void protocols::enzdes::EnzdesFlexibleRegion::set_target_proximity_to_starting_conformation ( core::Real  proximity)
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_
utility::vector1< std::string > protocols::enzdes::EnzdesFlexibleRegion::desired_remodel_ss_strings_
EnzdesFlexBBProtocolCAP protocols::enzdes::EnzdesFlexibleRegion::enzdes_protocol_
utility::vector1< SizeRealPair > protocols::enzdes::EnzdesFlexibleRegion::frag_designabilities_
core::Size protocols::enzdes::EnzdesFlexibleRegion::index_
core::fragment::FragDataOP protocols::enzdes::EnzdesFlexibleRegion::native_conf_
utility::vector1< core::Size > protocols::enzdes::EnzdesFlexibleRegion::positions_
core::Size protocols::enzdes::EnzdesFlexibleRegion::remodel_max_length_
core::Size protocols::enzdes::EnzdesFlexibleRegion::remodel_min_length_
bool protocols::enzdes::EnzdesFlexibleRegion::remodelable_

Referenced by declare_remodelable(), and remodelable().

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

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