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Rosetta
2020.37
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Rosetta
2020.37
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The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP. More...
Classes | |
| class | LoopRebuild |
| The loop-rebuild protocol. More... | |
| class | LoopRefine |
| class LoopRefine for fullatom loop refinement More... | |
| class | RBSegmentRelaxImpl |
Typedefs | |
| typedef utility::pointer::shared_ptr < AntibodyModeler > | AntibodyModelerOP |
| typedef utility::pointer::shared_ptr < AntibodyModeler const > | AntibodyModelerCOP |
| typedef utility::pointer::shared_ptr < RBSegmentRelaxImpl > | RBSegmentRelaxImplOP |
Functions | |
| void | print_ddgs (std::string const &ddg_out, std::string const &label, ddgs const &delta_e_components, ddgs const &, core::Real total_ddgs) |
| void | read_in_mutations (utility::vector1< mutations > &res_to_mut, std::string filename, pose::Pose &pose) |
| int | ddG_main () |
| static basic::Tracer | TR ("protocols.looprelax_protocols") |
| void | Tokenize (const std::string &str, utility::vector1< std::string > &tokens, const std::string &delimiters=" ") |
| Helper function tokenizes a str. More... | |
| int | RBSegmentRelax_main () |
The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
FIX THIS.
unit headers
unit headeers
Restrict design to residues with electron density correlation above threshold value.
Restrict design to residues matching user-specified SASA criteria in the monomeric, bound, or unbound state.
Sample a set of mutations each time packer is generated.
initialization protocols for symmetrical docking
Utility functions useful in Splice mover.
Splice forward declarations header.
Clarifications of variables used:
samples rotamers from a pre-computed db
Set of functions from Sparta class that don't actually manipulate any state in the class and have thus been removed.
Problems found during porting:
set of fragments for a certain alignment frame
swaps both BBangles and residue types
swaps both fragment xyz and amino acid
Inserts a Fragment into a Pose, similar to old Rosetta++ main_frag_trial algorithm.
Hold chi- tensor information for the Pseudocontact Shift calculation.
EVIL.
Definition of types SHOBuriedUnsatisfiedPolarsCalculatorOP and SHOBuriedUnsatisfiedPolarsCalculatorCOP.
Calculator for buried unsatisfied polar atoms under the SHO solvation model.
Compare the sequences between a native and designed protein.
How many salt bridge interactions are there?
Compare the rotamer recovery between a native protein and a list of other proteins.
How many pi-pi interactiosn are there? pi-stacking considered are T-stacking and offset.
This Calculator tries to solvate all polar groups by docking explicit TP5 water molecules, then counts unsatisfied hydrogen bonds using the same criteria in BuriedUnsatisfiedHydrogenBondCalculator.
How many cation-pi interactions are there?
A class to generate pharmacophore from RNA binding proteins.
MPI Headers.
STL Headers.
A class to determine the neighborhood of a set of residues.
Implementation of the Neighborhood class.
This is a protocol...
Does translation and rotation of a pose or the membrane.
Optimizes the protein embedding in the membrane.
Optimizes the membrane position given the high-res score function.
Does a quick relax of a membrane protein.
Declarations and simple accessor/mutator definitions for RotProb, simple class to encapsulate rotamer data and probability of rotamer occurring.
Forward declarations for RotProb.
Declarations and simple accessor/mutator definitions for RotMatrix (a conformational matrix used for mean-field theory calculations).
Forward declarations for RotMatrix.
Method definitions for RotMatrix.
Declarations and simple accessor/mutator definitions for ResHashMap.
Forward declarations for ResHashMap - a data structure that stores Residue hash keys and corresponding rot_ind values.
Method definitions for ResHashMap.
Declarations and simple accessor/mutator definitions for MeanField.
Forward declarations for MeanField.
Declarations and simple accessor/mutator definitions for jagged_array. Generally copied from utility::vector1.
Declarations and simple accessor/mutator definitions for FlexBBMeanField.
Forward declarations for FlexBBMeanField.
Declarations and simple accessor/mutator definitions for FlexBBDesignMeanField.
Forward declarations for FlexBBDesignMeanField.
Declarations and simple accessor/mutator definitions for DesignMeanField.
Forward declarations for DesignMeanField.
Declarations and simple accessor/mutator definitions for AAProb.
Forward declarations for AAProb.
Declarations and simple accessor/mutator definitions for AAMatrix.
Forward declarations for AAMatrix.
Method definitions for AAMatrix.
this is a modified version of chris king's PointMutationCalculator with additional functionality that is currently not compatible with all of the ParetoOpt functionality. please note that this has been checked into master in its current state in response to requests from others to use this modified version of chris king's GreedyOptMutationMover. although this is still a somewhat developmental piece of code, it has currently been left in src/protocols/matdes/ to avoid issues with intra-library level dependencies.
This is a modified version of Chris King's GreedyOptMutationMover with additional functionality that is currently not compatible with all of the ParetoOpt functionality. Please note that this has been checked into master in its current state in response to requests from others to use this modified version of Chris King's GreedyOptMutationMover. Although this is still a somewhat developmental piece of code, it has currently been left in src/protocols/matdes/ to avoid issues with intra-library level dependencies.
Declarations and simple accessor/mutator definitions for MatchScoreWriter.
Forward declarations for MatchScoreWriter.
Boost headers.
Numeric headers.
general functions for generating typical kinds of Loops sets.
kinematic closure move
TODO make this a .fwd.
Project Headings.
Temp will be removed when requirement files are in place.
C++ headers.
#include <ObjexxFCL/format.hh> // apl needed?
metric for Gunn moves
Cost computation for Gunn Moves.
ObjexxFCL headers.
Project headers.
Unit Headers.
Utility headers.
class to compute projection of a protein structure to principal component (PCA) eigenvectors ( as defined in file )
Check if the ligand's pocket is stable by removing the ligand, relaxing the structure and calculating rms to the starting structure.
Replace pack_region_ala_pose_ with a PoseOP to remove this header.
This represents the symmetry info needed for dealing with symmetric density maps. Symmetry is detected from the map directly, without a model.
stores movable_jumps info for replica docking
Mover partners apart and relax them separately.
This class will create instances of Mover ConformerSwitchMover for the MoverFactory.
very simple–pulls apart non-DNA (i.e. protein and friends) from DNA to facilitate DNA binding score calculation
A helper class for setting up trigonal planarly-coordinated metals like Zn or Cu.
A helper class for setting up tetrahedrally-coordinated metals like Zn or Cu.
A helper class for setting up square planarly-coordinated metals like Ni.
A helper class for setting up octahedrally-coordinated metals.
File format example:
Project Headers.
Unit headers.
simple mover for stealing side chains from one pose and sticking them on another pose.
simple mover that applies another Mover, and then recovers the input sidechains from the input Pose.
demo program for implementing loop relax + FA relax
stupid test file for visual studio c++
The instance of CheckPointer contained by AbrelaxApplication should be replaced by a CheckPointerOP
C++ headers Utility headers Project headers
sets an appropriate fold tree for a non-DNA/DNA interface (including multichain non-DNA and/or DNA) and then simply separates non-DNA chain(s) from the DNA chain(s) with a single translation. More basic than RigidBodyMover (which maybe needs a new base class?)
Run quick relax on separated partners; this emulates unbound docking
Package headers
Package headers Utility headers Numeric headers
Package headers Numeric headers
Package headers Project headers ObjexxFCL headers Utility headers Numeric headers C++ headers
Package headers Project headers
Package headers Project headers C++ headers
Package headers Project headers Utility headers C++ headers TEMP
C++ headers
Package headers CREATE THE .FWD.HH FILE Project headers ObjexxFCL headers
Unit headers
Package headers ObjexxFCL headers
Package headers Project headers Utility headers
Code duplication alert: TorsionFragment is going to be phased out Please avoid writing any new code using these classes: look in core/fragment/ instead look in /protocols/abinitio/FragmentMover for usage examples
Project headers Utility headers C++ headers
} In this scheme, jobs will be created for all combinations of rpoteins and ligands, and the job will be tagged with "group_name" using a job string/real pair, in the form "input_group_name group_name_a"
Underlying data structure resembles a 2D vector. Each row (outer dimension) represents a different partition and each partition holds a sorted vector of results that is pruned to make sure it has no more than the maximum number of elements allowed. elements that are pruned out are added to a list of job results to discard.
To get the most out of this class, call:
1) get_next_local_jobid() during JobQueen::determine_job_list()
2) note_job_completed() during JobQueen::note_job_completed()
3) register_result() during JobQueen::completed_job_summary()
4) append_job_results_that_should_be_discarded() during JobQueen::job_results_that_should_be_discarded()
5) get_nth_job_result_id() during JobQueen::determine_job_list() for downstream job dag nodes
This class was designed to help job queen developers keep track of the sources for their jobs.
The underlying data in this class are represented by a directed acyclic graph alternating between job nodes and results nodes. Consider this example:
Job1 -|– Result 1 -|– Job 3 — Result 1 ......| | ......| |– Job 4 -|- Result 1 ......| | ......|– Result 2 |- Result 2
Job2 -|– Result 1 -|– Job 5 ....................| ....................|– Job 6
Let's say Nobs 1 & 2 come from the first node in the job DAG and the rest come from the second job DAG node. We can use this to:
1) Track the original input source (<Job> tag, most likely) for each job.
2) Find job results to discard. Maybe we originally wanted to keep result { Job1, Result2 } but now we can delete all of the jobs from DAG node 1 that do not have offspring such as { Job1, Result2 }. The garbage_collection() method helps us find those job results.
Jobs are represented using JGJobNodes and results with JGResultNodes. This does not have to be a tree; you can have a JGJobNode with multiple parents (JGResultNodes).
To keep this up to date (only on node 0, of course), make sure to:
1) call JobGenealogist::register_new_job() inside JobQueen::determine_job_list()
2) call JobGenealogist::note_job_completed() inside JobQueen::note_job_completed()
3) call JobGenealogist::discard_job_result() for every job result id returned in JobQueen::job_results_that_should_be_discarded()
this class replaces the frag_close routines in jumping_pairings.cc the short loop is copied into a special purpose pose that just contains the loop-fragment with the hope that things are speeded up... which may or may not be true! only the linear chainbreak score is used.
ObjexxFCL headers
/protocols/match/downstream/SecMatchEvaluatorFactory.cc
A class to save and output matcher data, if matches are scored
Uses SmallMover and ShearMover with adjustable maximum dihedral angle changes, then repacking and a single round of minimization
Optimizes the membrane position given the smooth high-res score function; scans the center along the normal around the initial center in 0.1A steps; scans the normal in 0.2degree steps along arches over the x-axis, y-axis, xy-direction, -xy-direction; outcome is deterministic
Optimizes the membrane position given the smooth high-res score function; scans the center along the normal around the initial center in 0.1A steps; scans the normal in 0.2 degree steps along arches over the x-axis, y-axis, xy-direction, -xy-direction; outcome is deterministic
Optimizes the protein embedding in the membrane given the smooth high-res score function; transforms the protein into the membrane, optimizes the membrane position (flexible), and uses the optimized embedding to reposition the protein in the membrane
Translates along a vector and rotates a pose or membrane around the axis perpendicular to both vectors. Works for both fixed protein/flexible membrane or fixed membrane/flexible protein Takes the jump number as input, default is the membrane jump
Core headers Numeric headers Utility headers C++ Headers
SimulatedTempering
Carries out Markov Chain Monte Carlo with temperature jumps to mimic replica exchange.
Obeys detailed balance.
For speed, check_boltzmann() does not copy pose back to previous pose, but demands that external sampler 'back-update' pose (see, e.g., recces::RECCES_Mover) – note difference with Rosetta's standard MonteCarlo class!
In use for, e.g., RECCES, developed by Fang-Chieh Chou and Das lab for calculating folding energetics of small RNA motifs.
See: Chou et al. (2016), PNAS 113:30. http://dx.doi.org/10.1073/pnas.1523335113
This should probably be a pilot app, but the way Rosetta Scripts is set up, it can't be in the pilot apps
For example of using RosettaCloud API please see main/source/src/apps/pilot/sergey/cloud_demo.cc
https://ui.graylab.jhu.edu/execution/summaries - list of all summaries already created on your account
https://ui.graylab.jhu.edu/execution/es/0 - magic link to the latest summary (re-bound latest ES on page refresh)
Relevant command line options:
-cloud:auth - specify user name and password (visit https://ui.graylab.jhu.edu/settings to get credentials for your account)
-cloud:key - specify key to use when process query Cloud server for new ExecutionSummary ID. Default is empty string (no key) which mean always create a new ES instance Specifying key is a way to have somewhat permanent ES instance. The downside of using it is that each new run override the previous one (but this could be desirable when debugging)
-cloud:clean - delete all previously posted files upon ES instance creation. If you using key option above for debugging then you most likely want to set -clean to true as well.
-cloud:block - specify what to do in post_* when network queue is full: blocking will pause main thread execution until some network operation is finished while setting block to false will instruct post_* function to drop new request without delaying main thread.
Utility headers C++ headers
Not much detailed here. Iterate through the carbons of aromatic rings and compare that to the distance of the polar hydrogens in basic residues...histidine not considered. Default distance is 3.2A. Wait, you want to know how to use this? Well, within your protocol, you need to do the following: First, create the calculator. To do this, see below: core::pose::metrics::PoseMetricCalculatorOP cat_pi_calculator = new protocols::pose_metric_calculators::SaltBridgeCalculator(); Then you must register this so that the pose understands it. See below: core::pose::metrics::CalculatorFactory::Instance().register_calculator( "cat_pi_metric", cat_pi_calculator ); To actually get the metric, you have to print it. For example: core::pose::Pose pose; pose.print_metric("cat_pi_metric", "cat_pi") Where cat_pi_metric is the name that it is registered under and "cat_pi" is the key, seen below.
ExplicitWaterUnsatisfiedPolarsCalculator
Not much detailed here. Iterate through the carbons of aromatic rings and compare that to the distance of the aromatic hydrogens. Default distance is 3.2A. Wait, you want to know how to use this? Well, within your protocol, you need to do the following: First, create the calculator. To do this, see below: core::pose::metrics::PoseMetricCalculatorOP pi_pi_calculator = new protocols::pose_metric_calculators::SaltBridgeCalculator(); Then you must register this so that the pose understands it. See below: core::pose::metrics::CalculatorFactory::Instance().register_calculator( "pi_pi_metric", pi_pi_calculator ); To actually get the metric, you have to print it. For example: core::pose::Pose pose; pose.print_metric("pi_pi_metric", "pi_pi") Where pi_pi_metric is the name that it is registered under and "pi_pi" is the key, seen below.
This is an implementation taken from James Thompson. I am not even sure he knows I stole it from him. The main function that is called is the get_rotamer_recovery() function. You can pass this function a native pdb and a list of altered pdbs, or just 1 native and 1 alterd pdb. The rotamer recovery will be output to the screen. Output looks like:
resi_idx nat_bb_bin pct_bb nat_rot1 pct_rot1 nat_rot2 pct_rot2 nat_rot3 pct_rot3 nat_rot4 pct_rot4 1 E 1.0000 1 1.0000 2 1.0000 1 1.0000 999 0.0000 2 B 1.0000 2 1.0000 1 1.0000 999 0.0000 999 0.0000 Where the # total is how many proteins compared. resi_idx = residue index nat_bb_bin = dssp naming for bb pct_bb = how many match the bb bins? nat_rot1 = chi 1 pct_rot1 = how many are correct If 999 appears, that means that the amino acid does not have that chi angle
Not much detailed here. Iterate through the oxygens of acidic residues and compare that to the distance of the polar hydrogens in basic residues. Default distance is 3.2A. Wait, you want to know how to use this? Well, within your protocol, you need to do the following: First, create the calculator. To do this, see below: core::pose::metrics::PoseMetricCalculatorOP sb_calculator = new protocols::pose_metric_calculators::SaltBridgeCalculator(); Then you must register this so that the pose understands it. See below: core::pose::metrics::CalculatorFactory::Instance().register_calculator( "sb_metric", sb_calculator ); To actually get the metric, you have to print it. For example: core::pose::Pose pose; pose.print_metric("sb_metric", "salt_bridge") Where sb_metric is the name that it is registered under and "salt_bridge" is the key, seen below.
This is an implementation taken from Ron Jacak, Douglas Renfrew, Matt O Mera. The main function that is called is the get_sequence_recovery() function. You can pass this function a list of native pdbs and designed pdbs, or just 1 native and 1 designed pdb. The sequence recovery will be output in a file called sequencerecovery.txt along with a substitution matrix in a file called submatrix.txt
Decides whether or not to run fragment insertions, RNA jump moves docking, 'chunk' moves, etc.
This class should not have to know details of MonteCarlo or simulated tempering scheme – have that handled outside.
TODO: Better unify RNA & RNP docking movers. [perhaps set those up at beginning, and only update rot/trans mags in here?]
Stick everything related to running scores, pose info, 6D jump information, etc. here.
-- rhiju, 2016-2017.
Where the # total is how many proteins compared. resi_idx = residue index nat_bb_bin = dssp naming for bb pct_bb = fraction matching backbone bins nat_rot1 = chi 1 pct_rot1 = fraction matching chi bins If 999 appears, that means that the amino acid does not have that chi angle
| return |
Christophe Schmitz
| return |
| return |
Christophe Schmitz , Kala Bharath Pilla
Computes the change in entropy of the denatured state caused by forcing certain disulfide bonds, according to random flight configurational statistics (Gaussian approximation).
See "Analysis and Classification of Disulphide Connectivity in Proteins: The Entropic effect of Cross-Linkage", PM Harrison & MJE Sternberg, J Mol Biol 1994 244, 448-463
Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias Jakob P. Ulmschneider, JCP, VOl 118, 9, 2003
modified for use inside CS-Rosetta by Oliver Lange
modified for use inside CS-Rosetta by Oliver Lange
How about some ASCII art to show all the atoms at play?
C1' C1' C1' C1'
/ \ moving_suite / \ / \ chainbreak_suite / \ ... O4 C2' O4 C2' O4 C2' O4 C2' | | | | | | OVU | OVL1 OVL2 | | C4’—C3'—O3'—P—O5'—C5'—C4'–C3'- ... –C4'—C3'—O3'—P—O5'—C5'—C4'–C3' delt eps zeta alph bet gam deta delt eps zeta alph bet gam delt X D1 D2 D3 P1–P1 X X P2–P2 D4 P3–P3 X
X = fixed (sugar) P = pivot torsions D = driver torsions
TODO: Generalize to cyclized cutpoints. TODO: Test that driver torsions vs. pivot torsions agree in cyclic dinucleotide. TODO: Check possibly incorrect O3' atom.
project headers
package headers project headers
| typedef utility::pointer::shared_ptr< AntibodyModeler const > protocols::AntibodyModelerCOP |
| typedef utility::pointer::shared_ptr< AntibodyModeler > protocols::AntibodyModelerOP |
| typedef utility::pointer::shared_ptr< RBSegmentRelaxImpl > protocols::RBSegmentRelaxImplOP |
| int protocols::ddG_main | ( | ) |
References core::chemical::aa_unk, protocols::ddg::ddGMover::apply(), protocols::scoring::Interface::calculate(), core::pack::task::TaskFactory::create_packer_task(), core::scoring::ScoreFunctionFactory::create_score_function(), protocols::ddg::ddGMover::ddG(), protocols::ddg::ddGMover::debug_output(), protocols::scoring::Interface::distance(), protocols::ddg::ddGMover::dump_pdbs(), protocols::abinitio::filename(), protocols::ddg::ddGMover::get_delta_energy_components(), protocols::ddg::ddGMover::get_mutant_averaged_score_components(), core::scoring::get_score_function(), protocols::ddg::ddGMover::get_wt_averaged_score_components(), protocols::scoring::Interface::is_interface(), protocols::ddg::ddGMover::is_interface_ddg(), protocols::ddg::ddGMover::is_mutant_calc_complete(), protocols::ddg::ddGMover::is_wt_calc_complete(), core::simple_metrics::metrics::mean, protocols::mean_field::min(), protocols::ddg::ddGMover::mutation_label(), protocols::ddg::ddGMover::neighbor_cutoff(), protocols::ddg::ddGMover::num_iterations(), core::conformation::membrane::out, core::pack::task::parse_resfile(), core::import_pose::PDB_file, protocols::protein_interface_design::point_mutation(), core::import_pose::pose_from_file(), protocols::scoring::Interface::print(), print_ddgs(), read_in_mutations(), protocols::ddg::ddGMover::residues_to_mutate(), protocols::ddg::ddGMover::restrict_to_nbrs(), protocols::ddg::ddGMover::set_mean(), protocols::ddg::ddGMover::set_min(), protocols::ddg::ddGMover::set_min_cst(), core::scoring::TR(), protocols::ddg::ddGMover::wt_score_components(), and protocols::ddg::ddGMover::wt_unbound_score_components().
| void protocols::print_ddgs | ( | std::string const & | ddg_out, |
| std::string const & | label, | ||
| ddgs const & | delta_e_components, | ||
| ddgs const & | , | ||
| core::Real | total_ddgs | ||
| ) |
References core::chemical::element::F, and core::scoring::TR().
Referenced by ddG_main().
| int protocols::RBSegmentRelax_main | ( | ) |
| void protocols::read_in_mutations | ( | utility::vector1< mutations > & | res_to_mut, |
| std::string | filename, | ||
| pose::Pose & | pose | ||
| ) |
| void protocols::Tokenize | ( | const std::string & | str, |
| utility::vector1< std::string > & | tokens, | ||
| const std::string & | delimiters = " " |
||
| ) |
Helper function tokenizes a str.
|
static |
Referenced by protocols::monte_carlo::GenericMonteCarloMover::accept(), protocols::LoopRebuild::acceptable_rmsd_change(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_aa_virt_rsd_as_root(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_amide_bond_cyclic_constraints(), protocols::denovo_design::add_chain_from_pose(), protocols::denovo_design::components::FoldGraph::add_combined_solutions(), protocols::metal_interface::AddZincSiteConstraints::add_constraints(), protocols::pose_length_moves::PossibleLoop::add_coordinate_csts_from_lookback(), protocols::denovo_design::components::StructureData::add_covalent_bond(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_cutpoint_variants_at_termini(), protocols::grafting::add_cutpoint_variants_for_ccd(), protocols::denovo_design::components::FoldGraph::add_edge(), protocols::chemically_conjugated_docking::add_extra_bodies(), protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_helix_update_moves(), protocols::constraint_movers::CstInfoMover::add_info_for_csts(), protocols::backrub::BackrubMover::add_mainchain_segments(), protocols::membrane::symmetry::SymmetricAddMembraneMover::add_membrane_virtual(), protocols::membrane::AddMembraneMover::add_membrane_virtual(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_n_methylation(), protocols::denovo_design::architects::BetaSheetArchitect::add_orientations(), protocols::denovo_design::movers::add_overlap_to_loops(), protocols::denovo_design::components::add_paired_residues(), protocols::denovo_design::architects::BetaSheetArchitect::add_pairings(), protocols::denovo_design::components::FoldGraph::add_peptide_edge(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_protonated_H1_adenosine_variants(), protocols::denovo_design::architects::BetaSheetArchitect::add_register_shifts(), protocols::denovo_design::add_residues_to_pose(), protocols::analysis::InterfaceAnalyzerMover::add_score_info_to_pose(), protocols::sewing::data_storage::HashedSmartAssembly::add_segment(), protocols::backrub::BackrubMover::add_segment(), protocols::sewing::data_storage::SmartAssembly::add_segment(), protocols::denovo_design::components::add_segment(), protocols::denovo_design::components::StructureData::add_segment(), protocols::sewing::data_storage::SmartAssembly::add_segment_and_neighbors_to_local_segments(), protocols::denovo_design::components::add_segments_for_chain(), protocols::denovo_design::components::SheetDB::add_sheet(), protocols::denovo_design::components::SheetDB::add_sheets_from_pose(), protocols::denovo_design::components::SheetDB::add_sheets_from_spairs(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion(), protocols::denovo_design::components::add_to_pose(), protocols::hydrate::add_water_overcoordinated_hb_score(), protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), protocols::denovo_design::components::StructureData::alias(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::align_poses(), protocols::denovo_design::movers::AlignResiduesMover::align_residues(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::align_to_native_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::align_VDW_rep_screen_pose(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::analyze_and_filter(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::antibody_legacy::CDRH3Modeler::antibody_modeling_insert_ter(), protocols::backrub::append_fold_tree_to_file(), protocols::denovo_design::components::append_new_chain_from_template_segment(), protocols::denovo_design::components::append_new_residues(), protocols::denovo_design::components::append_residues_from_template_segment(), protocols::monte_carlo::ResetBaselineMover::apply(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::apply(), protocols::analysis::PackStatMover::apply(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::surface_docking::SurfaceOrientMover::apply(), protocols::stepwise::monte_carlo::mover::FromScratchMover::apply(), protocols::pose_length_moves::FixAllLoopsMover::apply(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser::apply(), protocols::carbohydrates::IdealizeAnomericHydrogens::apply(), protocols::denovo_design::constraints::FileConstraintGenerator::apply(), protocols::denovo_design::components::ExtendedPoseBuilder::apply(), protocols::magnesium::MgMonteCarlo::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::apply(), protocols::denovo_design::components::RandomTorsionPoseFolder::apply(), protocols::pose_length_moves::InsertResMover::apply(), protocols::constraint_movers::ConstraintSetMover::apply(), protocols::backrub::BackrubProtocol::apply(), protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(), protocols::stepwise::monte_carlo::mover::AddOrDeleteMover::apply(), protocols::rna::setup::RNA_MonteCarloJobDistributor::apply(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::apply(), protocols::rna::setup::RNA_CSA_JobDistributor::apply(), protocols::forge::constraints::RemoveRemodelCsts::apply(), protocols::membrane::HelixFromSequence::apply(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply(), protocols::denovo_design::movers::SealFoldTreeMover::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::constraint_movers::CstInfoMover::apply(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::apply(), protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::apply(), protocols::aa_composition::AddHelixSequenceConstraintsMover::apply(), protocols::farnesyl::SampleFarnesylMover::apply(), protocols::membrane::AqueousPoreFinder::apply(), protocols::membrane::benchmark::SampleTiltAngles::apply(), protocols::sewing::movers::AppendAssemblyMover::apply(), protocols::sewing::movers::LigandBindingAssemblyMover::apply(), protocols::membrane::MPLipidAccessibility::apply(), protocols::floppy_tail::FloppyTailMover::apply(), protocols::normalmode::NormalModeRelaxMover::apply(), protocols::aa_composition::AddMHCEpitopeConstraintMover::apply(), protocols::flexpep_docking::FlexPepDockingLowRes::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::analysis::simple_metrics::RunSimpleMetricsMover::apply(), protocols::ncbb::SecStructFinder::apply(), protocols::recces::scratch::ThermalSamplingMover::apply(), protocols::coupled_moves::CoupledMovesProtocol::apply(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::apply(), protocols::recces::scratch::ThermalMinimizer::apply(), protocols::flexpep_docking::FlexPepDockingAbInitio::apply(), protocols::aa_composition::ClearCompositionConstraintsMover::apply(), protocols::ncbb::ResidueReplacementRebuildMover::apply(), protocols::denovo_design::components::StructureDataPerturber::apply(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::apply(), protocols::LoopRebuild::apply(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply(), protocols::monte_carlo::MonteCarloReset::apply(), protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::apply(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::apply(), protocols::monte_carlo::MonteCarloTest::apply(), protocols::membrane_benchmark::PeptideOrientationMover::apply(), protocols::sewing::movers::AssemblyMover::apply(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::apply(), protocols::hydrate::Hydrate::apply(), protocols::surface_docking::CentroidRelaxMover::apply(), protocols::carbohydrates::GlycanTreeMinMover::apply(), protocols::denovo_design::filters::SSShapeComplementarityFilter::apply(), protocols::stepwise::modeler::StepWiseConnectionSampler::apply(), protocols::membrane::SetMembranePositionMover::apply(), protocols::stepwise::monte_carlo::mover::ResampleMover::apply(), protocols::carbohydrates::GlycanSampler::apply(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::apply(), protocols::enzymatic_movers::EnzymaticMover::apply(), protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::membrane::visualize::VisualizeEmbeddingMover::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::denovo_design::movers::RotateSegmentMover::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::grafting::CCDEndsGraftMover::apply(), protocols::membrane::OptimizeProteinEmbeddingMover::apply(), protocols::carbohydrates::SimpleGlycosylateMover::apply(), protocols::membrane::MembranePositionFromTopologyMover::apply(), protocols::membrane::MPMutateRelaxMover::apply(), protocols::backrub::BackrubMover::apply(), protocols::carbohydrates::LinkageConformerMover::apply(), protocols::carbohydrates::CreateGlycanSequonMover::apply(), protocols::carbohydrates::RingPlaneFlipMover::apply(), protocols::carbohydrates::TautomerizeAnomerMover::apply(), protocols::monte_carlo::GenericSimulatedAnnealer::apply(), protocols::membrane::OptimizeMembranePositionMover::apply(), protocols::antibody_legacy::CDRH3Modeler::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::membrane::AddMPLigandMover::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::membrane::MPQuickRelaxMover::apply(), protocols::membrane::visualize::VisualizeMembraneMover::apply(), protocols::denovo_design::movers::FastDesign::apply(), protocols::dna_dock::DNAClashCheckFilter::apply(), protocols::ddg::ddGMover::apply(), protocols::dna_dock::PropagateClashCheckFilter::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::membrane::FlipMover::apply(), protocols::membrane::TiltMover::apply(), protocols::membrane::TranslationMover::apply(), protocols::membrane::AddMembraneMover::apply(), protocols::membrane::SpinAroundPartnerMover::apply(), protocols::membrane::TransformIntoMembraneMover::apply(), protocols::monte_carlo::GenericMonteCarloMover::apply(), protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::flxbb::FilterStructs_Packstat::apply(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::apply(), protocols::membrane::RotationMover::apply(), protocols::antibody_legacy::LoopRlxMover::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::flxbb::FilterStructs_TotalCharge::apply(), protocols::LoopRefine::apply(), protocols::membrane::TranslationRotationMover::apply(), protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::apply(), protocols::analysis::InterfaceAnalyzerMover::apply_const(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_cutpoint_variants(), protocols::monte_carlo::GenericSimulatedAnnealer::apply_mover(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::apply_movers(), protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence(), protocols::normalmode::NormalModeRelaxMover::apply_on_pose(), protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_single_sequence(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::apply_solutions(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant(), protocols::pose_length_moves::ConnectChainsMover::assemble_missing_chain(), protocols::ub_e2c::ubi_e2c_modeler::assign_CSPs(), protocols::ub_e2c::ubi_e2c_modeler::assign_non_CSPs(), protocols::denovo_design::components::StructureDataFactory::attach_observer(), protocols::anchored_design::AnchorMoversData::autogenerate_constseq_frags(), protocols::anchored_design::AnchorMoversData::autogenerate_design_frags(), protocols::anchored_design::AnchorMoversData::autogenerate_frags(), protocols::denovo_design::connection::ConnectionArchitect::available_lower_termini(), protocols::denovo_design::components::StructureData::available_lower_termini(), protocols::denovo_design::connection::ConnectionArchitect::available_upper_termini(), protocols::denovo_design::components::StructureData::available_upper_termini(), protocols::membrane::average_antiparallel_embeddings(), protocols::toolbox::ResidueNetwork::average_shortest_path_length(), protocols::flexpep_docking::FlexPepDockingProtocol::backrub_move(), protocols::LoopRebuild::barcode_extend_stems(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), protocols::monte_carlo::GenericMonteCarloMover::boltzmann(), protocols::monte_carlo::GenericSimulatedAnnealer::boltzmann_result(), protocols::denovo_design::DisulfidizeMover::build_and_score_disulfide(), protocols::antibody_legacy::CDRH3Modeler::build_centroid_loop(), protocols::metal_interface::MatchGrafter::build_combined_pose_with_zinc_overlay(), protocols::flxbb::FlxbbDesign::build_design_taskset(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::build_full_model(), protocols::antibody_legacy::CDRH3Modeler::build_fullatom_loop(), protocols::tcr::TCRmodel::build_graft_model(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::build_in_phases(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::build_polymer(), protocols::LoopRebuild::build_random_loops(), protocols::denovo_design::components::FoldGraph::build_seg2node(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_closure_legacy(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_minimize_legacy(), protocols::unfolded_state_energy_calculator::calc_all_averages(), protocols::analysis::InterfaceAnalyzerMover::calc_centroid_dG(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), protocols::ub_e2c::ubi_e2c_modeler::calc_interaction_energy(), protocols::denovo_design::components::calc_paired_residues(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_and_regional_data(), protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::calculate(), protocols::quantum_annealing::InteractionGraphSummaryMetric::calculate(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::calculate(), protocols::helical_bundle_predict::HBP_SigmoidalTemperatureScheduleGenerator::calculate_current_temperature(), protocols::monte_carlo::MonteCarloInterface::calculate_score(), protocols::monte_carlo::GenericSimulatedAnnealer::calculate_temps(), protocols::sewing::hashing::Hasher::can_hash(), protocols::denovo_design::components::canonicalize(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::CCD_loop_close(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::CCD_loop_close_sample_omega_recursively(), protocols::antibody_legacy::CDRH3Modeler::CDR_H3_filter(), protocols::ub_e2c::ubi_e2c_modeler::centroid_filter(), protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::chain_break_screening_general(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::check_atom_bin_in_range(), protocols::denovo_design::components::SolutionPredicate::check_basic_connectivity(), protocols::denovo_design::components::StructureData::check_chains(), protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), protocols::denovo_design::DisulfidizeMover::check_disulfide_cb_distance(), protocols::denovo_design::DisulfidizeMover::check_disulfide_match_rt(), protocols::denovo_design::DisulfidizeMover::check_disulfide_score(), protocols::denovo_design::DisulfidizeMover::check_disulfide_seqpos(), protocols::flexpep_docking::FlexPepDockingProtocol::check_filters(), protocols::rna::setup::RNA_CSA_JobDistributor::check_for_closeness(), protocols::denovo_design::components::SolutionPredicate::check_for_unpaired_segments(), protocols::denovo_design::components::StructureData::check_improper_termini(), protocols::pose_length_moves::PossibleLoop::check_loop_abego(), protocols::stepwise::modeler::align::StepWisePoseAligner::check_matching_atom_names(), protocols::denovo_design::connection::AreConnectablePredicate::check_movable_groups(), protocols::denovo_design::components::StructureData::check_movable_groups(), protocols::membrane::AddMembraneMover::check_pdb_for_mem(), protocols::denovo_design::architects::BetaSheetArchitect::check_permutation(), protocols::denovo_design::components::StructureData::check_pose(), protocols::denovo_design::components::StructureData::check_pose_consistency(), protocols::stepwise::modeler::StepWiseMinimizer::check_pose_list(), protocols::denovo_design::DisulfidizeMover::check_residue_type(), protocols::denovo_design::components::StructureData::check_residues(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::check_screen(), protocols::denovo_design::components::FoldGraph::check_solution(), protocols::denovo_design::components::SolutionPredicate::check_start_segment(), protocols::denovo_design::components::SolutionPredicate::check_stop_segment(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::check_superimpose_res(), protocols::denovo_design::components::SolutionPredicate::check_template_poses(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_that_terminal_res_are_unstacked(), protocols::membrane::check_vector(), protocols::sewing::data_storage::SmartAssembly::chimerize(), protocols::sewing::hashing::LigandBindingResPlacer::choose_best_metal_coordinator(), protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::clean_fasta_file_contents(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::close_at_cutpoint(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::cluster(), protocols::cluster::APCluster::cluster(), protocols::toolbox::KCluster::cluster(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::cluster_pose_list(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::cluster_with_auto_tune(), protocols::grafting::combine_movemaps_post_insertion(), protocols::denovo_design::architects::BetaSheetArchitect::combine_permutations_rec(), protocols::multistage_rosetta_scripts::MRSJobQueen::completed_job_summary(), protocols::denovo_design::filters::SSPredictionFilter::compute(), protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute(), protocols::denovo_design::filters::SSShapeComplementarityFilter::compute(), protocols::denovo_design::filters::CavityVolumeFilter::compute(), protocols::toolbox::MulliganPNearEvaluator::compute(), protocols::denovo_design::components::DivideAndConqueror::compute_all_units(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::compute_best_allowed_aas(), protocols::denovo_design::components::FoldGraph::compute_best_solution(), protocols::denovo_design::filters::SSPredictionFilter::compute_boltz_sum(), protocols::denovo_design::connection::ConnectionArchitect::compute_connection_candidates(), protocols::denovo_design::filters::SSShapeComplementarityFilter::compute_from_selector(), protocols::denovo_design::filters::SSShapeComplementarityFilter::compute_from_ss_info(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_delta_hbond_unsat(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_packstat(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc(), protocols::denovo_design::filters::SSPredictionFilter::compute_mismatch_prob(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::compute_residue_subset(), protocols::analysis::InterfaceAnalyzerMover::compute_separated_sasa(), protocols::denovo_design::filters::PreProlineFilter::compute_simple(), protocols::membrane::MPLipidAccessibility::compute_slice_com(), protocols::denovo_design::filters::PreProlineFilter::compute_spline(), protocols::ub_e2c::ubi_e2c_modeler::compute_swap_trim_CSPs(), protocols::ub_e2c::ubi_e2c_modeler::compute_trim_CSPs(), protocols::denovo_design::connection::ConnectionArchitect::connect(), protocols::denovo_design::components::StructureData::connect_segments(), protocols::toolbox::ResidueNetwork::connectivity_index(), protocols::flxbb::constraints_NtoC(), protocols::flxbb::constraints_sheet(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoASP(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoGLU(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::copy_coords(), protocols::denovo_design::components::StructureData::copy_data(), protocols::denovo_design::movers::AlignResiduesMover::copy_residue(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::correctly_copy_HO2prime_positions(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::count_cis_peptide_bonds(), protocols::aa_composition::AddMHCEpitopeConstraintMover::create_constraint_from_file(), protocols::aa_composition::AddNetChargeConstraintMover::create_constraint_from_file(), protocols::aa_composition::AddCompositionConstraintMover::create_constraint_from_file(), protocols::aa_composition::AddMHCEpitopeConstraintMover::create_constraint_from_file_contents(), protocols::aa_composition::AddNetChargeConstraintMover::create_constraint_from_file_contents(), protocols::aa_composition::AddCompositionConstraintMover::create_constraint_from_file_contents(), protocols::denovo_design::movers::FastDesign::create_default_task_factory(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_false_movemap(), protocols::denovo_design::components::StructureDataFactory::create_from_cacheable_data(), protocols::toolbox::ResidueNetwork::create_from_pose(), protocols::denovo_design::components::StructureDataFactory::create_from_pose(), protocols::denovo_design::components::StructureDataFactory::create_from_remarks(), protocols::denovo_design::components::FoldGraph::create_loops(), protocols::denovo_design::components::FoldGraph::create_loops_dfs(), protocols::membrane::create_membrane_docking_foldtree_from_partners(), protocols::membrane::create_membrane_foldtree_from_anchors(), protocols::membrane::create_membrane_multi_partner_foldtree_anchor_tmcom(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::create_new_submotif(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::create_overlap_constraint_generator(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::create_pose_from_input_poses(), protocols::pose_length_moves::NearNativeLoopCloser::create_potential_loops(), protocols::stepwise::monte_carlo::mover::AddMover::create_residue_to_add(), protocols::carbohydrates::create_sequons(), protocols::membrane::create_specific_membrane_foldtree(), protocols::denovo_design::components::ExtendedPoseBuilder::create_template_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::create_VDW_screen_bin(), protocols::denovo_design::components::StructureData::declare_covalent_bond(), protocols::grafting::delete_region(), protocols::denovo_design::components::StructureData::delete_residue(), protocols::sewing::data_storage::SmartAssembly::delete_segment(), protocols::denovo_design::components::StructureData::delete_segment(), protocols::denovo_design::architects::HelixArchitect::design(), protocols::denovo_design::architects::BetaSheetArchitect::design(), protocols::denovo_design::architects::DeNovoMotifArchitect::design(), protocols::antibody_legacy::Antibody::detect_camelid_CDR_H3_stem_type(), protocols::antibody_legacy::Antibody::detect_regular_CDR_H3_stem_type(), protocols::multistage_rosetta_scripts::MRSJobQueen::determine_job_list(), protocols::multistage_rosetta_scripts::MRSJobQueen::determine_validity_of_stage_tags(), protocols::ncbb::SecStructMinimizeMultiFunc::dfunc(), protocols::toolbox::ResidueNetwork::dijkstras(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::disallow_aas(), protocols::antibody_legacy::AntibodyModeler::display_constraint_residues(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::display_progress(), protocols::denovo_design::components::DivideAndConqueror::divide_and_conquer(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::do_a_simulated_annealing_round(), protocols::stepwise::modeler::StepWiseMinimizer::do_clustering(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::do_cyclic_permutation(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::do_final_fastrelax(), protocols::stepwise::modeler::StepWiseMinimizer::do_full_minimizing(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::mainchain_potential::GenerateMainchainPotentialOptions::do_initialization_from_globals(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_option_checks(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::do_some_clustering(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::do_some_filtering(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_sugar_sampling(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_superimposition(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::do_test_move(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_the_modeler(), protocols::surface_docking::FullatomRelaxMover::dock_mcm_on_surface(), protocols::metal_interface::dump_chis(), protocols::stepwise::StepWiseSampleAndScreen::early_exit_check(), protocols::sewing::hashing::EdgeMapGenerator::edge_exists(), protocols::membrane::geometry::Embedding::Embedding(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::empty_pose_data_list(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::empty_sugar_modeling_list(), protocols::stepwise::modeler::protein::loop_close::enable_sampling_of_loop_takeoff(), protocols::stepwise::monte_carlo::mover::ensure_appropriate_foldtree_for_move(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), protocols::denovo_design::architects::BetaSheetArchitect::enumerate_permutations(), protocols::multistage_rosetta_scripts::MRSJobQueenChecker::estimate_number_of_bytes_needed_for_archiving(), protocols::metal_interface::AddZincSiteConstraints::evaluate_constraints(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), protocols::LoopRebuild::extend_barcode_regions_if_chain_break(), protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose(), protocols::denovo_design::extract_int(), protocols::denovo_design::components::extract_sheets_from_pose(), protocols::denovo_design::components::extract_sheets_from_strandlist(), protocols::normalmode::NormalModeRelaxMover::extrapolate_mode_on_crd(), protocols::normalmode::NormalModeRelaxMover::extrapolate_mode_on_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose(), protocols::membrane::scoring::FaWaterToBilayerEnergy::FaWaterToBilayerEnergy(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_appended_and_prepended_res_list(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_best_working_alignment(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_chain_boundaries(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::figure_out_fold_tree(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_gap_size_and_first_chain_break_res(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_gap_size_and_five_prime_chain_break_res(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_is_prepend_map(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_is_residue_prepend(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_jump_partners(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_jump_partners(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_last_appended_and_last_prepended_res(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_NUM_pose_list(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_offset(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_partition_definition(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_partition_definition(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_prepend_internal(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_working_sequence_and_mapping(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_working_sequence_and_mapping(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filter(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_and_save(), protocols::denovo_design::architects::BetaSheetArchitect::filter_permutations(), protocols::membrane::MPMutateRelaxMover::finalize_setup(), protocols::membrane::MPLipidAccessibility::finalize_setup(), protocols::scoring::VDW_GridEnergy::finalize_total_energy(), protocols::rna::AlignmentEnergy::finalize_total_energy(), protocols::denovo_design::DisulfidizeMover::find_current_disulfides(), protocols::denovo_design::components::FoldGraph::find_cutpoint_in_range(), protocols::aa_composition::find_helices_over_length(), protocols::flxbb::find_ligands(), protocols::denovo_design::components::find_orientations_and_lengths(), protocols::analysis::LoopAnalyzerMover::find_positions(), protocols::denovo_design::DisulfidizeMover::find_possible_disulfides(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::find_roots(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), protocols::flexpep_docking::FlexPepDockingProtocol::flip_in_pcs(), protocols::floppy_tail::FloppyTailMover::FloppyTailMover(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::fold_attempt(), protocols::denovo_design::components::FoldGraph::fold_tree(), protocols::denovo_design::components::FoldGraph::fold_tree_rec(), protocols::denovo_design::components::FoldGraph::FoldGraph(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::folding_score(), protocols::membrane::geometry::EmbeddingDef::from_span(), protocols::membrane::geometry::EmbeddingDef::from_span_positive_z(), protocols::membrane::geometry::Embedding::from_spans(), protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_filter(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_mode_perturbation(), protocols::denovo_design::components::IdealAbegoGenerator::generate(), protocols::sewing::movers::LigandBindingAssemblyMover::generate_assembly(), protocols::sewing::movers::AssemblyMover::generate_assembly(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), protocols::pose_length_moves::ConnectChainsMover::generate_best_final_pose(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), protocols::sewing::hashing::EdgeMapGenerator::generate_edge_file(), protocols::toolbox::DistanceResidueNetwork::generate_edges(), protocols::toolbox::CovalentResidueNetwork::generate_edges(), protocols::metal_interface::ZincHeterodimerMover::generate_factory(), protocols::mainchain_potential::GenerateMainchainPotential::generate_mainchain_potential(), protocols::metal_interface::ZincHeterodimerMover::generate_scorefunctions(), protocols::mainchain_potential::GenerateMainchainPotential::generate_sfxn(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::genkic_close(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_add_or_delete_element(), protocols::pose_length_moves::InsertResMover::get_additional_output(), protocols::normalmode::NormalModeRelaxMover::get_additional_output(), protocols::pose_length_moves::NearNativeLoopCloser::get_additional_output_with_rmsd(), protocols::membrane::get_anchor_points_for_tmcom(), protocols::sewing::hashing::BasisMapGenerator::get_basis_res_bounds(), protocols::branch_angle::get_branching_atoms2(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::get_C4_C3_distance_range(), protocols::sewing::data_storage::SmartSegment::get_c_terminal_parent(), protocols::membrane::get_chain_and_z(), protocols::constraint_movers::CstInfoMover::get_constraints_from_file(), protocols::constraint_movers::CstInfoMover::get_constraints_from_pose(), protocols::ncbb::SecStructMinimizeMultiFunc::get_dofs_map(), protocols::normalmode::NormalModeMultifunc::get_dofs_map(), protocols::network::NetworkQueue::get_execution_summary_id(), protocols::denovo_design::components::Picker::get_framelist(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::magnesium::MgMinimizer::get_mg_hoh_minimize_move_map(), protocols::stepwise::modeler::StepWiseMinimizer::get_move_map_and_atom_level_domain_map(), protocols::sewing::data_storage::SmartSegment::get_n_terminal_parent(), protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::get_next_solutions(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_previously_closed_cutpoint_from_imported_silent_file(), protocols::hydrate::get_ready_for_sew_packing(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz_average(), protocols::stepwise::monte_carlo::mover::ResampleMover::get_remodel_res(), protocols::sewing::data_storage::SmartSegment::get_residue(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_no_superimpose(), protocols::denovo_design::filters::SSShapeComplementarityFilter::get_sc_and_area(), protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::get_secstruct(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::get_secstruct(), protocols::membrane::get_secstruct(), protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::get_sheet_topology(), protocols::denovo_design::components::get_strand_residues(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::get_sugar_setup_scorefxns(), protocols::helical_bundle_predict::HBPHelix::get_torsions_for_helix(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_user_input_alignment_res_list(), protocols::pose_length_moves::AnalyzeLoopModeling::get_valid_resid(), protocols::pose_length_moves::PossibleLoop::get_valid_resid(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor::go(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), protocols::metal_interface::MatchGrafter::graft(), protocols::tcr::graft_cdr_to_fw(), protocols::denovo_design::components::graph_from_strandpairings(), protocols::sewing::hashing::Hasher::hash_segments(), protocols::sewing::hashing::Hasher::Hasher(), protocols::sasa_scores::help_load_data(), protocols::floppy_tail::FloppyTailMover::high_res(), protocols::hydrate::Hydrate::Hydrate(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), protocols::grafting::idealize_combined_pose(), protocols::carbohydrates::GlycanSampler::idealize_glycan_residues(), protocols::sewing::hashing::LigandBindingResPlacer::identify_possible_binders(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::import_and_set_up_native(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::Import_pose(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), protocols::stepwise::sampler::StepWiseSamplerComb::init(), protocols::stepwise::sampler::StepWiseSamplerSizedAny::init(), protocols::stepwise::sampler::StepWiseSamplerSizedComb::init(), protocols::surface_docking::CentroidRelaxMover::init(), protocols::surface_docking::SurfaceDockingProtocol::init(), protocols::enzymatic_movers::EnzymaticMover::init(), protocols::toolbox::KMedoid::init(), protocols::toolbox::GreedyKCenter::init(), protocols::ub_e2c::ubi_e2c_modeler::init_d77_perturbation(), protocols::membrane::HelixFromSequence::init_from_cmd(), protocols::membrane::MPMutateRelaxMover::init_from_cmd(), protocols::membrane::symmetry::SymmetricAddMembraneMover::init_from_cmd(), protocols::membrane::AddMembraneMover::init_from_cmd(), protocols::antibody_legacy::AntibodyModeler::init_from_options(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::carbohydrates::GlycanSampler::init_objects(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), protocols::ub_e2c::ubi_e2c_modeler::initial_cter_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::initial_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::initial_repack(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::initialize_checkpointing(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_euler_angle_grid_parameters(), protocols::flxbb::FlxbbDesign::initialize_filter(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::initialize_for_movie(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize_from_directory(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize_from_jump_library(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::initialize_from_options(), protocols::coupled_moves::CoupledMovesProtocol::initialize_from_options(), protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions::initialize_from_options_collection(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_generic_polymer_bond_sampler(), protocols::sewing::hashing::Hasher::initialize_hashmap(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_is_virtual_base(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_ligand_bond_sampler(), protocols::membrane::AddMembraneMover::initialize_membrane_residue(), protocols::stepwise::modeler::rna::o2prime::O2PrimePacker::initialize_o2prime_green_packer(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_phosphate_move_list(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_sampler(), protocols::backrub::BackrubMover::initialize_simulation(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_terminal_res(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_xyz_grid_parameters(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::input_struct_definition(), protocols::denovo_design::insert_peptide_edges(), protocols::grafting::GraftMoverBase::insert_piece(), protocols::grafting::insert_pose_into_pose(), protocols::flexpep_docking::FlexPepDockingFlags::is_ligand_present(), protocols::membrane::benchmark::MakeCanonicalHelix::is_valid(), protocols::sewing::hashing::Hasher::iterate_over_basis_pairs(), protocols::sewing::data_storage::SmartAssembly::iterate_over_basis_pairs(), protocols::multistage_rosetta_scripts::MRSJobQueen::jobs_that_should_be_output(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::just_simple_cycles(), protocols::toolbox::KClusterData::KClusterData(), protocols::stepwise::modeler::protein::loop_close::kic_close_loops_in_samples(), protocols::monte_carlo::linear_regression(), protocols::monte_carlo::GenericSimulatedAnnealer::load_checkpoint_file(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::load_native_pose_from_disk(), protocols::denovo_design::components::SheetDB::load_sheetlist_from_file(), protocols::toolbox::KClusterData::load_silent_files(), protocols::monte_carlo::GenericMonteCarloMover::load_trial_number_from_checkpoint(), protocols::anchored_design::AnchorMoversData::locate_anchor_loop(), protocols::denovo_design::calculators::CavityCalculator::lookup(), protocols::vardist_solaccess::VarSolDistSasaCalculator::lookup(), protocols::antibody_legacy::CDRH3Modeler::loop_centroid_relax(), protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax(), protocols::floppy_tail::FloppyTailMover::low_res(), protocols::sewing::hashing::LigandBindingResPlacer::make_aligned_residue(), protocols::denovo_design::DisulfidizeMover::make_disulfide(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::make_extended_pose(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_full_pose(), protocols::normalmode::NormalMode::make_Hessian_ANM(), protocols::normalmode::NormalMode::make_Hessian_TNM(), protocols::analysis::InterfaceAnalyzerMover::make_interface_set(), protocols::denovo_design::components::make_lengths_str(), protocols::tcr::TCRmodel::make_model(), protocols::analysis::InterfaceAnalyzerMover::make_multichain_interface_set(), protocols::membrane::MPMutateRelaxMover::make_mutations(), protocols::ncbb::ResidueReplacementRebuildMover::make_new_pose(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_pose(), protocols::denovo_design::components::StructureData::mark_disconnected(), protocols::flexpep_docking::FlexPepDockingProtocol::markInterfaceBySideChainContacts(), protocols::flexpep_docking::FlexPepDockingProtocol::markNativeInterface(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::master_go(), protocols::tcr::match_template_and_target_sequence(), protocols::denovo_design::components::StructureData::merge(), protocols::denovo_design::components::StructureData::merge_before(), protocols::denovo_design::components::StructureData::merge_segments(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::minimize_sugar(), protocols::denovo_design::architects::BetaSheetArchitect::modify_and_add_permutation(), protocols::denovo_design::components::modify_ft_for_residue_insertion(), protocols::ub_e2c::ubi_e2c_modeler::monoub_apply(), protocols::ub_e2c::ubi_e2c_modeler::monoub_assign_CSPs(), protocols::ub_e2c::ubi_e2c_modeler::monoub_calc_interaction_energy(), protocols::ub_e2c::ubi_e2c_modeler::monoub_centroid_filter(), protocols::ub_e2c::ubi_e2c_modeler::monoub_centroid_mode_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_fold_tree(), protocols::ub_e2c::ubi_e2c_modeler::monoub_fullatom_filter(), protocols::ub_e2c::ubi_e2c_modeler::monoub_fullatom_mode_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_initial_cter_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_initial_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_setup_key_residues(), protocols::ub_e2c::ubi_e2c_modeler::monoub_setup_move_maps(), protocols::rna::setup::RNA_MonteCarloJobDistributor::move_forward_to_next_model(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), protocols::analysis::InterfaceAnalyzerMover::mut_to_gly(), protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala(), protocols::pose_length_moves::NearNativeLoopCloser::NearNativeLoopCloser(), protocols::denovo_design::movers::new_jump_and_cutpoint(), protocols::denovo_design::components::FoldGraph::nodeidx(), protocols::normalmode::NormalModeMultifunc::NormalModeMultifunc(), protocols::multistage_rosetta_scripts::MRSJobQueen::note_job_completed(), protocols::denovo_design::components::StructureData::num_chains(), protocols::monte_carlo::GenericMonteCarloMover::num_designable(), protocols::denovo_design::components::StructureData::on_change(), protocols::denovo_design::components::StructureDataObserver::on_length_change(), protocols::denovo_design::components::StructureDataObserver::on_residue_delete(), protocols::ncbb::SecStructMinimizeMultiFunc::operator()(), protocols::denovo_design::connection::AreConnectablePredicate::operator()(), protocols::denovo_design::components::SolutionSorter::operator()(), protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), protocols::backrub::BackrubMover::optimize_branch_angles(), protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond(), protocols::membrane::OptimizeMembranePositionMover::optimize_membrane_center(), protocols::membrane::OptimizeMembranePositionMover::optimize_membrane_normal(), protocols::tcr::orient_tcr_chain(), protocols::surface_docking::FullatomRelaxMover::outer_loop_refinement_adsorbed(), protocols::stepwise::modeler::align::StepWisePoseAligner::output_atom_id_map(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::output_chainTORS(), protocols::metal_interface::AddZincSiteConstraints::output_constraints_file(), protocols::stepwise::StepWiseSampleAndScreen::output_counts(), protocols::stepwise::StepWiseSampleAndScreen::output_info_on_random_trials(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::output_moves(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_rep(), protocols::surface_docking::FullatomRelaxMover::output_solution_state(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::output_tags(), protocols::branch_angle::BranchAngleOptimizer::overall_params(), protocols::chemically_conjugated_docking::pack_extra_bodies(), protocols::magnesium::MgWaterHydrogenPacker::pack_mg_water_hydrogens_in_pose(), protocols::multistage_rosetta_scripts::MRSJobQueen::parse_common_tag(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::parse_extra_atom_list(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::parse_filters(), protocols::pose_length_moves::ConnectChainsMover::parse_input(), protocols::flxbb::LayerDesignOperation::parse_layer_secstruct_tag(), protocols::flxbb::LayerDesignOperation::parse_layer_tag(), protocols::sewing::hashing::LigandBindingResPlacer::parse_ligand_files(), protocols::sewing::hashing::AlignmentFileGeneratorMover::parse_ligands_tag(), protocols::denovo_design::parse_motif_string(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::parse_movers(), protocols::monte_carlo::ResetBaselineMover::parse_my_tag(), protocols::pose_length_moves::FixAllLoopsMover::parse_my_tag(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::parse_my_tag(), protocols::pose_selectors::ClusterPoseSelector::parse_my_tag(), protocols::denovo_design::filters::SSPredictionFilter::parse_my_tag(), protocols::pose_length_moves::InsertResMover::parse_my_tag(), protocols::pose_length_moves::AnalyzeLoopModeling::parse_my_tag(), protocols::pose_selectors::LogicalSelector::parse_my_tag(), protocols::forge::constraints::RemoveRemodelCsts::parse_my_tag(), protocols::constraint_movers::ConstraintSetMover::parse_my_tag(), protocols::constraint_movers::ResidueTypeConstraintMover::parse_my_tag(), protocols::aa_composition::AddMHCEpitopeConstraintMover::parse_my_tag(), protocols::ncbb::SecStructFinder::parse_my_tag(), protocols::aa_composition::AddNetChargeConstraintMover::parse_my_tag(), protocols::quantum_annealing::ExternalPackerResultLoader::parse_my_tag(), protocols::aa_composition::AddCompositionConstraintMover::parse_my_tag(), protocols::monte_carlo::MonteCarloRecover::parse_my_tag(), protocols::monte_carlo::MonteCarloReset::parse_my_tag(), protocols::monte_carlo::MonteCarloTest::parse_my_tag(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::parse_my_tag(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::parse_my_tag(), protocols::farnesyl::InstallFarnesylMover::parse_my_tag(), protocols::carbohydrates::RingPlaneFlipMover::parse_my_tag(), protocols::coupled_moves::CoupledMovesProtocol::parse_my_tag(), protocols::membrane_benchmark::PeptideOrientationMover::parse_my_tag(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::parse_my_tag(), protocols::flxbb::InterlockAroma::parse_my_tag(), protocols::sewing::movers::AssemblyMover::parse_my_tag(), protocols::sewing::movers::AppendAssemblyMover::parse_my_tag(), protocols::grafting::AnchoredGraftMover::parse_my_tag(), protocols::pose_selectors::TopNByProperty::parse_my_tag(), protocols::pose_length_moves::NearNativeLoopCloser::parse_my_tag(), protocols::membrane::AddMembraneMover::parse_my_tag(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::parse_my_tag(), protocols::sewing::movers::LigandBindingAssemblyMover::parse_my_tag(), protocols::pose_selectors::Filter::parse_my_tag(), protocols::flxbb::FlxbbDesign::parse_my_tag(), protocols::analysis::InterfaceAnalyzerMover::parse_my_tag(), protocols::monte_carlo::GenericMonteCarloMover::parse_my_tag(), protocols::denovo_design::components::parse_orientations(), protocols::multistage_rosetta_scripts::MRSJobQueen::parse_single_job_tag(), protocols::denovo_design::components::StructureData::parse_subtag(), protocols::denovo_design::architects::BetaSheetArchitect::parse_tag(), protocols::denovo_design::components::Segment::parse_tag(), protocols::flxbb::LayerDesignOperation::parse_tag(), protocols::monte_carlo::GenericMonteCarloMover::parse_task_operations(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_chain(), protocols::peptide_deriver::PeptideDeriverPoseOutputter::peptide_entry(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_last_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_nres(), protocols::enzymatic_movers::DNAMethyltransferaseMover::perform_reaction(), protocols::grafting::perturb_backbone_for_test(), protocols::kinematic_closure::perturbers::FragmentPerturber::perturb_subset(), protocols::denovo_design::components::Picker::pick_fragments_for_resid(), protocols::anchored_design::AnchorMoversData::pick_new_cutpoints(), protocols::sewing::data_storage::SmartAssembly::pick_random_starting_segment(), protocols::flexpep_docking::FlexPepDockingProtocol::place_peptide_on_binding_site(), protocols::multistage_rosetta_scripts::MRSJobQueen::pose_for_inner_job_derived(), protocols::denovo_design::components::pose_matches_description(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::pose_selection_by_full_score(), protocols::membrane::pose_tilt_angle_and_center_distance(), protocols::pose_length_moves::PossibleLoop::PossibleLoop(), protocols::network::post_decoy(), protocols::flexpep_docking::FlexPepDockingProtocol::prepack_only(), protocols::normalmode::NormalMode::prepare_coord(), protocols::stepwise::monte_carlo::mover::TransientCutpointHandler::prepare_fold_tree_for_erraser(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::prepare_ghost_pose(), protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::prepare_termini_for_remodel(), protocols::denovo_design::components::prepend_new_residues(), protocols::stepwise::legacy::modeler::rna::print_backbone_torsions(), protocols::multistage_rosetta_scripts::MRSJobQueen::print_job_lineage(), protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_packing(), protocols::hydrate::print_residues_near_water(), protocols::sewing::movers::AssemblyMover::print_statistics(), protocols::denovo_design::DisulfidizeMover::process_pose(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::proposal_probability(), protocols::denovo_design::components::prune_unpaired_residues(), protocols::rna::setup::RNA_CSA_JobDistributor::put_lock_on_silent_file(), protocols::carbohydrates::GlycanSampler::randomize_glycan_torsions(), protocols::flexpep_docking::FlexPepDockingProtocol::randomlySlidePeptideJump(), protocols::hydrate::read_body(), protocols::monte_carlo::GenericSimulatedAnnealer::read_checkpoint_line(), protocols::backrub::read_fold_tree_from_file(), protocols::antibody_legacy::read_H3_cter_fragment(), protocols::hydrate::read_header(), protocols::hydrate::read_hyfile(), protocols::scoring::VDW_CachedRepScreenInfo::read_in_VDW_rep_screen_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::read_in_VDW_rep_screen_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), protocols::sewing::hashing::ModelFileReader::read_model_file(), protocols::anchored_design::AnchorMoversData::read_options(), protocols::quantum_annealing::ExternalPackerResultLoader::read_packer_problem_file(), protocols::cyclic_peptide_predict::read_peptide_design_file(), protocols::quantum_annealing::ExternalPackerResultLoader::read_rotamer_selection_file(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::read_sequence(), protocols::denovo_design::rebuild_missing_atoms(), protocols::flexpep_docking::FlexPepDockingFlags::receptor_chain(), protocols::flexpep_docking::FlexPepDockingFlags::receptor_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::receptor_last_res(), protocols::flexpep_docking::FlexPepDockingFlags::receptor_nres(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::recluster_current_pose_list(), protocols::denovo_design::calculators::CavityCalculator::recompute(), protocols::vardist_solaccess::VarSolDistSasaCalculator::recompute(), protocols::sewing::data_storage::SmartAssembly::reconstitute_assembly_from_string(), protocols::monte_carlo::GenericMonteCarloMover::recover_low(), protocols::sewing::data_storage::SmartAssembly::recurse_revert_far_c_terminal_parent(), protocols::sewing::data_storage::SmartAssembly::recurse_revert_far_n_terminal_parent(), protocols::flexpep_docking::FlexPepDockingFlags::ref_start_struct(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::reference_xyz_consistency_check(), protocols::surface_docking::FullatomRelaxMover::refinement_cycle(), protocols::analysis::InterfaceAnalyzerMover::register_calculators(), protocols::ddg::ddGMover::relax_wildtype_structure(), protocols::denovo_design::remove_all_jump_atoms(), protocols::monte_carlo::GenericSimulatedAnnealer::remove_checkpoint_file(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::remove_cutpoints(), protocols::denovo_design::movers::SealFoldTreeMover::remove_cutpoints(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::remove_cutpoints(), protocols::hydrate::remove_high_energy_water_molecules(), protocols::denovo_design::remove_missing_jump_atoms(), protocols::hydrate::remove_non_buried_wat(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::monte_carlo::GenericMonteCarloMover::remove_trigger(), protocols::denovo_design::components::reorder_chains(), protocols::surface_docking::FullatomRelaxMover::reorient_and_slide_into_surface(), protocols::monte_carlo::replace_file(), protocols::denovo_design::components::StructureDataPerturber::replace_segments(), protocols::pose_reporters::FilterReporter::report_property(), protocols::pose_reporters::RMSDReporter::report_property(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::reroot_fold_tree(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::reroot_fold_tree(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model(), protocols::monte_carlo::GenericMonteCarloMover::reset(), protocols::sewing::data_storage::SmartAssembly::reset_chimaera_contacts(), protocols::ub_e2c::ubi_e2c_modeler::restore_cter(), protocols::ub_e2c::ubi_e2c_modeler::restrict_to_interfacial_loop_packing(), protocols::denovo_design::components::StructureData::retrieve_remarks(), protocols::grafting::return_region(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_add_move(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move(), protocols::denovo_design::components::reverse_orientations(), protocols::sewing::data_storage::SmartAssembly::revert(), protocols::flexpep_docking::FlexPepDockingProtocol::rigidbody_monte_carlo_minimize(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::RNA_VDW_BinChecker(), protocols::membrane::rsd_closest_to_chain_com(), protocols::membrane::rsd_closest_to_chain_tm_com(), protocols::stepwise::StepWiseSampleAndScreen::run(), protocols::mainchain_potential::GenerateMainchainPotential::run(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::run(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::run(), protocols::recces::RECCES_Mover::run_sampler(), protocols::carbohydrates::run_shear_min_pack(), protocols::stepwise::monte_carlo::mover::AddMover::sample_by_monte_carlo_internal(), protocols::farnesyl::SampleFarnesylMover::sample_farnesyl(), protocols::farnesyl::InstallFarnesylMover::sample_first(), protocols::farnesyl::InstallFarnesylMover::sample_second(), protocols::farnesyl::InstallFarnesylMover::sample_third(), protocols::stepwise::modeler::StepWiseModeler::sampling_successful(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::save_moves(), protocols::denovo_design::components::StructureData::save_remarks(), protocols::monte_carlo::GenericSimulatedAnnealer::scale_temperatures(), protocols::sewing::hashing::Hasher::score_basis_pair(), protocols::monte_carlo::GenericSimulatedAnnealer::score_pose(), protocols::analysis::InterfaceAnalyzerMover::score_separated_chains(), protocols::antibody_legacy::CDRH3Modeler::scored_frag_close(), protocols::ncbb::SecStructMinimizeMultiFunc::SecStructMinimizeMultiFunc(), protocols::denovo_design::components::FoldGraph::segment(), protocols::sewing::hashing::BasisMapGenerator::segs_can_chimerize(), protocols::denovo_design::components::FoldGraph::select_best_solution(), protocols::LoopRebuild::select_one_loop(), protocols::pose_selectors::ClusterPoseSelector::select_poses(), protocols::pose_selectors::LogicalSelector::select_poses(), protocols::pose_selectors::TopNByProperty::select_poses(), protocols::pose_selectors::Filter::select_poses(), protocols::denovo_design::components::StructureData::set_alias(), protocols::stepwise::modeler::rna::sugar::SugarModeling::set_base_and_pucker_state(), protocols::hydrate::set_bb_movemap(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::set_cluster_rmsd(), protocols::denovo_design::movers::FastDesign::set_constraint_weight(), protocols::ub_e2c::ubi_e2c_modeler::set_default(), protocols::antibody_legacy::AntibodyModeler::set_default(), protocols::antibody_legacy::GraftMover::set_default(), protocols::antibody_legacy::CDRH3Modeler::set_default(), protocols::tcr::TCRmodel::set_default(), protocols::flxbb::LayerDesignOperation::set_default_layer_residues(), protocols::grafting::AnchoredGraftMover::set_default_movemap(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_default_rama_table_type(), protocols::sewing::movers::AssemblyMover::set_default_requirements(), protocols::hydrate::set_dew_waters_not_to_be_included(), protocols::ub_e2c::ubi_e2c_modeler::set_e2g2_diubi_fold_tree(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_fixed_res(), protocols::denovo_design::architects::BlueprintArchitect::set_helix_pairings(), protocols::denovo_design::components::ResidueDihedrals::set_in_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_jump_point_pair_list(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_mainchain_torsions(), protocols::denovo_design::components::set_map_data(), protocols::normalmode::NormalModeRelaxMover::set_mode(), protocols::normalmode::NormalModeMultifunc::set_modes(), protocols::denovo_design::connection::ConnectionArchitect::set_motifs(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_native_alignment_res(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_octahedral_metal_positions_from_string_vector(), protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_output_filename(), protocols::enzymatic_movers::EnzymaticMover::set_pose_reactive_sites(), protocols::sewing::hashing::EdgeMapGenerator::set_private_data(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_rama_table_type_by_res(), protocols::normalmode::NormalModeRelaxMover::set_random_mode(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_reference_xyz(), protocols::grafting::AnchoredGraftMover::set_regions_from_flexibility(), protocols::grafting::AnchoredGraftMover::set_regions_from_movemap(), protocols::recces::scratch::ThermalSamplingMover::set_residue_sampling_from_pose_and_movemap(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_sample_cis_pro_frequency(), protocols::surface_docking::SurfaceDockingProtocol::set_secondary_structure(), protocols::antibody_legacy::AntibodyModeler::set_snugdock_foldtree(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_square_planar_metal_positions_from_string_vector(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_square_pyramidal_metal_positions_from_string_vector(), protocols::denovo_design::components::StructureData::set_ss(), protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_symmetrize_output(), protocols::hydrate::set_task_and_movemap(), protocols::hydrate::set_task_with_de_novo_water_using_resfile(), protocols::denovo_design::components::Segment::set_template_pose(), protocols::denovo_design::architects::BlueprintArchitect::set_template_segments(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_tetrahedral_metal_positions_from_string_vector(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_trigonal_planar_metal_positions_from_string_vector(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_trigonal_pyramidal_metal_positions_from_string_vector(), protocols::anchored_design::AnchorMoversData::set_unset_packertask_factory(), protocols::anchored_design::AnchorMoversData::set_unset_scorefunctions(), protocols::sewing::movers::AppendAssemblyMover::set_up_assembly(), protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_cterm_isopeptide_cyclization_mover(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_design_taskoperations(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_n_to_c_cyclization_mover(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_native(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_nterm_isopeptide_cyclization_mover(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::set_up_scorefunction(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_sidechain_isopeptide_cyclization_mover(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_terminal_disulfide_cyclization_mover(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_terminal_disulfide_variants(), protocols::hydrate::set_water_info_and_add_de_novo_water(), protocols::mainchain_potential::GenerateMainchainPotentialOptions::set_write_potentials_for_individual_scoreterms(), protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(), protocols::flxbb::DesignTask_Normal::setup(), protocols::flxbb::DesignTask_Layer::setup(), protocols::surface_docking::SurfaceDockingProtocol::setup_abinitio(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_additional_cutpoint_closed(), protocols::stepwise::legacy::modeler::rna::setup_bulge_jump_point(), protocols::tcr::setup_cdr_template_from_db(), protocols::ub_e2c::ubi_e2c_modeler::setup_complex_fold_tree(), protocols::ddg::ddGMover::setup_constraints(), protocols::carbohydrates::GlycanSampler::setup_default_task_factory(), protocols::surface_docking::CentroidRelaxMover::setup_defaults(), protocols::surface_docking::FullatomRelaxMover::setup_defaults(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_disulfides(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_floating_base_jump_to_anchor(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree(), protocols::membrane::setup_foldtree_from_anchors(), protocols::analysis::InterfaceAnalyzerMover::setup_for_dock_chains(), protocols::tcr::setup_fw_template_from_db(), protocols::ub_e2c::ubi_e2c_modeler::setup_key_residues(), protocols::carbohydrates::TautomerizeAnomerMover::setup_movable_reducing_ends(), protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs(), protocols::ub_e2c::ubi_e2c_modeler::setup_move_maps(), protocols::grafting::AnchoredGraftMover::setup_movemap_and_regions(), protocols::surface_docking::CentroidRelaxMover::setup_movers(), protocols::carbohydrates::GlycanSampler::setup_movers(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::ub_e2c::ubi_e2c_modeler::setup_packer_task(), protocols::antibody_legacy::AntibodyModeler::setup_packer_task(), protocols::antibody_legacy::CDRH3Modeler::setup_packer_task(), protocols::antibody_legacy::LoopRlxMover::setup_packer_task(), protocols::ddg::ddGMover::setup_packer_task_for_mutations(), protocols::denovo_design::filters::SSShapeComplementarityFilter::setup_sc(), protocols::denovo_design::filters::SSShapeComplementarityFilter::setup_sc_hh(), protocols::denovo_design::filters::SSShapeComplementarityFilter::setup_sc_hss(), protocols::analysis::InterfaceAnalyzerMover::setup_scorefxn(), protocols::ub_e2c::ubi_e2c_modeler::setup_simple_fold_tree(), protocols::antibody_legacy::AntibodyModeler::setup_simple_fold_tree(), protocols::grafting::setup_single_loop_double_arm_remodeling_foldtree(), protocols::grafting::setup_single_loop_single_arm_remodeling_foldtree(), protocols::denovo_design::filters::PreProlineFilter::setup_spline(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_sugar_conformations(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::setup_sugar_modeling(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::setup_sugar_modeling_list(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::setup_tag_to_source_map(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_working_pose(), protocols::stepwise::modeler::StepWiseMinimizer::setup_vary_bond_geometry(), protocols::magnesium::MgHydrater::setup_virtual_waters_around_magnesiums(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_working_native_pose(), protocols::denovo_design::components::SolutionSorter::shared_mgs(), protocols::denovo_design::components::SheetDB::sheet_list(), protocols::membrane::geometry::EmbeddingDef::show(), protocols::membrane::geometry::Embedding::show(), protocols::ncbb::SecStructFinder::show_current_dihedrals(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::show_scores(), protocols::hydrate::show_water_hb_network(), protocols::antibody_legacy::simple_fold_tree(), protocols::antibody_legacy::simple_one_loop_fold_tree(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::slave_add_unfolded_energy_data(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::slave_set_energy_terms(), protocols::denovo_design::slide_jump(), protocols::stepwise::monte_carlo::mover::ResampleMover::slide_jump_randomly(), protocols::flexpep_docking::FlexPepDockingProtocol::SlideIntoContact(), protocols::sewing::data_storage::SmartAssembly::SmartAssembly(), protocols::normalmode::NormalMode::solve(), protocols::membrane::split_topology_by_jump(), protocols::denovo_design::components::Picker::ss_key(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::StepWiseRNA_CombineLongLoopFilterer(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::StepWiseWorkingParametersSetup(), protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics(), protocols::denovo_design::components::StructureDataFactory::StructureDataFactory(), protocols::denovo_design::components::StructureData::substitute_variables(), protocols::grafting::superimpose_overhangs_heavy(), protocols::sewing::data_storage::SmartAssembly::switch_segment(), protocols::denovo_design::symmetric_fold_tree(), protocols::membrane::symmetry::symmetrize_spans(), protocols::denovo_design::components::StructureData::termini(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::test_all_moves_recursively(), protocols::flexpep_docking::FlexPepDockingLowRes::to_centroid(), protocols::flexpep_docking::FlexPepDockingAbInitio::to_centroid(), protocols::sewing::data_storage::SmartAssembly::to_pose(), protocols::flexpep_docking::FlexPepDockingProtocol::torsions_monte_carlo_minimize(), protocols::sewing::hashing::Hasher::transform_segments(), protocols::sewing::data_storage::SmartAssembly::transform_segments(), protocols::ub_e2c::ubi_e2c_modeler::trim_cter(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::UBQ_GTPaseMover(), protocols::chemically_conjugated_docking::ubq_ras_rotation_angle(), protocols::sewing::data_storage::SmartAssembly::unchimerize_ligand_segment(), protocols::toolbox::GreedyKCenter::update(), protocols::rna::setup::RNA_CSA_JobDistributor::update_bank(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::update_fold_tree_at_virtual_sugars(), protocols::denovo_design::components::StructureData::update_numbering(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::update_pose_list(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), protocols::flexpep_docking::FlexPepDockingFlags::updateChains(), protocols::flexpep_docking::FlexPepDockingFlags::updateChainsAndAnchors_fromParamsFile(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen_with_act_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants(), protocols::toolbox::KMedoid::whoami(), protocols::toolbox::GreedyKCenter::whoami(), protocols::branch_angle::BranchAngleOptimizer::write_database(), protocols::sewing::hashing::EdgeMapGenerator::write_edges_for_segment(), protocols::coupled_moves::CoupledMovesProtocol::write_info_to_log(), protocols::mainchain_potential::GenerateMainchainPotential::write_last_generated_to_disk(), protocols::rna::setup::RNA_CSA_JobDistributor::write_out_round_silent_file(), and protocols::flxbb::LayerDesignOperation::write_pymol_script().
1.8.7