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Rosetta 3.5
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#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 () |
| 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... | |
| FragData & | fragment (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... | |
| BaseCacheUnit & | cache (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 |
Definition at line 189 of file EnzdesFlexBBProtocol.hh.
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Definition at line 191 of file EnzdesFlexBBProtocol.hh.
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Definition at line 192 of file EnzdesFlexBBProtocol.hh.
| 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 | ||
| ) |
Definition at line 1339 of file EnzdesFlexBBProtocol.cc.
References core::fragment::Frame::add_fragment(), assemble_enzdes_fragdata(), core::fragment::Frame::end(), frag_designabilities_, native_conf_, and positions_.
| protocols::enzdes::EnzdesFlexibleRegion::~EnzdesFlexibleRegion | ( | ) |
Definition at line 1373 of file EnzdesFlexBBProtocol.cc.
| void protocols::enzdes::EnzdesFlexibleRegion::apply_ranked_fragment | ( | core::pose::Pose & | pose, |
| core::Size | frag_rank | ||
| ) |
Definition at line 1790 of file EnzdesFlexBBProtocol.cc.
References core::fragment::Frame::apply(), and frag_designabilities_.
| core::fragment::FragDataOP protocols::enzdes::EnzdesFlexibleRegion::assemble_enzdes_fragdata | ( | core::pose::Pose const & | pose) |
Definition at line 1425 of file EnzdesFlexBBProtocol.cc.
References core::scoring::packstat::old::angles, core::chemical::ResidueType::atom_index(), core::fragment::Frame::end(), enzdes_protocol_, core::pose::Pose::residue_type(), and core::fragment::Frame::start().
Referenced by EnzdesFlexibleRegion(), and remap_resid().
| 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 |
Definition at line 1634 of file EnzdesFlexBBProtocol.cc.
References core::pack::create_packer_graph(), core::graph::delete_all_intragroup_edges(), design_targets_, core::pack::interaction_graph::EdgeBase::get_other_ind(), core::pack::interaction_graph::PDEdge::get_two_body_energy(), positions_, and core::pose::Pose::total_residue().
Referenced by sort_ensemble_by_designability().
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Definition at line 247 of file EnzdesFlexBBProtocol.hh.
Referenced by sort_ensemble_by_designability().
| bool protocols::enzdes::EnzdesFlexibleRegion::contains_catalytic_res | ( | ) | const |
Definition at line 1377 of file EnzdesFlexBBProtocol.cc.
References core::fragment::Frame::contains_seqpos(), and design_targets_.
| 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 | ||
| ) |
Definition at line 1820 of file EnzdesFlexBBProtocol.cc.
References core::fragment::Frame::add_fragment(), core::scoring::biggest_residue_deviation_no_super(), core::fragment::Frame::fragment_ptr(), core::scoring::is_protein_backbone(), core::scoring::is_protein_CA_or_CB(), core::fragment::Frame::length(), core::pose::Pose::omega(), core::pose::Pose::phi(), positions_, core::pose::Pose::psi(), core::pose::Pose::residue(), core::scoring::rmsd_no_super(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_xyz(), target_proximity_to_native_conformation_, target_proximity_to_other_conformations_, core::pose::Pose::total_residue(), and protocols::kinmatch::xyz().
| 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().
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requires that the pose was scored
Definition at line 2179 of file EnzdesFlexBBProtocol.cc.
References core::graph::Node::const_edge_list_begin(), core::graph::Node::const_edge_list_end(), core::fragment::Frame::contains_seqpos(), core::fragment::Frame::end(), core::pose::Pose::energies(), core::graph::Graph::get_node(), core::fragment::Frame::start(), core::scoring::Energies::tenA_neighbor_graph(), and twelve_A_neighbors_.
Referenced by sort_ensemble_by_designability().
| core::Real protocols::enzdes::EnzdesFlexibleRegion::get_region_mm_bend_score | ( | core::pose::Pose const & | pose) | const |
Definition at line 1806 of file EnzdesFlexBBProtocol.cc.
References core::fragment::Frame::end(), core::pose::Pose::energies(), core::scoring::mm_bend, core::scoring::Energies::residue_total_energies(), and core::fragment::Frame::start().
| core::Real protocols::enzdes::EnzdesFlexibleRegion::get_region_total_score | ( | core::pose::Pose const & | pose) | const |
Definition at line 2126 of file EnzdesFlexBBProtocol.cc.
References core::fragment::Frame::end(), core::pose::Pose::energies(), core::scoring::Energies::residue_total_energy(), and core::fragment::Frame::start().
| void protocols::enzdes::EnzdesFlexibleRegion::hack_fillup_frag_designabilities | ( | ) |
Definition at line 1479 of file EnzdesFlexBBProtocol.cc.
References frag_designabilities_, index_, and core::fragment::Frame::nr_frags().
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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().
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Definition at line 208 of file EnzdesFlexBBProtocol.hh.
References frag_designabilities_.
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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 | ||
| ) |
Definition at line 2141 of file EnzdesFlexBBProtocol.cc.
References core::fragment::Frame::add_fragment(), core::fragment::Frame::align(), assemble_enzdes_fragdata(), core::fragment::Frame::clear(), core::fragment::Frame::end(), frag_designabilities_, core::fragment::Frame::init_length(), core::fragment::Frame::is_continuous(), core::fragment::Frame::length(), native_conf_, positions_, and core::fragment::Frame::start().
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Definition at line 221 of file EnzdesFlexBBProtocol.hh.
References remodel_max_length_.
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Definition at line 218 of file EnzdesFlexBBProtocol.hh.
References remodel_min_length_.
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Definition at line 214 of file EnzdesFlexBBProtocol.hh.
References remodelable_.
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Definition at line 328 of file EnzdesFlexBBProtocol.hh.
References target_proximity_to_other_conformations_.
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Definition at line 317 of file EnzdesFlexBBProtocol.hh.
References target_proximity_to_native_conformation_.
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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 | ||
| ) |
this function assumes that the pose is a poly ala pose of the residues to redesign
and that the backbone is in the native conformation
Definition at line 1494 of file EnzdesFlexBBProtocol.cc.
References core::fragment::Frame::apply(), calculate_rotamer_set_design_targets_partition_sum(), compare_SizeRealPairs(), protocols::toolbox::pose_manipulation::construct_poly_ala_pose(), core::fragment::Frame::contains_seqpos(), enzdes_protocol_, extract_lig_designability_score(), frag_designabilities_, get_12A_neighbors(), index_, core::fragment::Frame::length(), core::fragment::Frame::nr_frags(), core::pack::pack_rotamers_loop(), core::pack::pack_scorefxn_pose_handshake(), positions(), protocols::enzdes::enzutil::recreate_task(), protocols::enzdes::tr(), and twelve_A_neighbors_.
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Definition at line 353 of file EnzdesFlexBBProtocol.hh.
Referenced by calculate_rotamer_set_design_targets_partition_sum(), contains_catalytic_res(), and extract_lig_designability_score().
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Definition at line 366 of file EnzdesFlexBBProtocol.hh.
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Definition at line 351 of file EnzdesFlexBBProtocol.hh.
Referenced by assemble_enzdes_fragdata(), enz_loop_info(), and sort_ensemble_by_designability().
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Definition at line 357 of file EnzdesFlexBBProtocol.hh.
Referenced by apply_ranked_fragment(), deltaE_best(), EnzdesFlexibleRegion(), hack_fillup_frag_designabilities(), no_ranked_frags(), remap_resid(), and sort_ensemble_by_designability().
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Definition at line 343 of file EnzdesFlexBBProtocol.hh.
Referenced by enz_loop_info(), hack_fillup_frag_designabilities(), index(), and sort_ensemble_by_designability().
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Definition at line 348 of file EnzdesFlexBBProtocol.hh.
Referenced by EnzdesFlexibleRegion(), and remap_resid().
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Definition at line 345 of file EnzdesFlexBBProtocol.hh.
Referenced by calculate_rotamer_set_design_targets_partition_sum(), EnzdesFlexibleRegion(), examine_new_loopconf(), positions(), and remap_resid().
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Definition at line 365 of file EnzdesFlexBBProtocol.hh.
Referenced by declare_remodelable(), and remodel_max_length().
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Definition at line 365 of file EnzdesFlexBBProtocol.hh.
Referenced by declare_remodelable(), and remodel_min_length().
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Definition at line 364 of file EnzdesFlexBBProtocol.hh.
Referenced by declare_remodelable(), and remodelable().
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Definition at line 360 of file EnzdesFlexBBProtocol.hh.
Referenced by examine_new_loopconf(), scale_target_proximity_to_starting_conformation(), and set_target_proximity_to_starting_conformation().
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Definition at line 361 of file EnzdesFlexBBProtocol.hh.
Referenced by examine_new_loopconf(), and scale_target_proximity_to_other_conformations().
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Definition at line 359 of file EnzdesFlexBBProtocol.hh.
Referenced by get_12A_neighbors(), and sort_ensemble_by_designability().
1.8.4