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protocols Namespace Reference

The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP. More...

Namespaces

 abinitio
 
 analysis
 
 anchored_design
 
 antibody
 
 antibody2
 
 backrub
 
 boinc
 
 branch_angle
 
 canonical_sampling
 
 cartesian
 
 checkpoint
 
 cluster
 
 coarse_rna
 
 comparative_modeling
 
 constraints_additional
 
 contact_map
 
 ddg
 
 ddG
 
 design_opt
 
 dna
 
 docking
 
 domain_assembly
 
 electron_density
 
 elscripts
 
 enzdes
 
 evaluation
 
 features
 
 fibril
 
 filters
 
 fldsgn
 
 flexpack
 
 flexpep_docking
 
 floppy_tail
 
 flxbb
 
 forge
 
 frag_picker
 
 frags
 
 genetic_algorithm
 
 geometry
 
 grafting
 
 hotspot_hashing
 
 hybridization
 
 id
 
 idealize
 
 init
 
 inputter
 
 jd2
 
 jobdist
 
 jumping
 
 kinmatch
 
 ligand_docking
 
 loop_build
 
 loophash
 
 loops
 
 MakeRotLib
 
 match
 
 medal
 
 motifs
 
 moves
 
 mpi
 
 multistate_design
 
 noesy_assign
 
 nonlocal
 
 optimize_weights
 
 outputter
 
 pack_daemon
 
 pb_potential
 
 pmut_scan
 
 pockets
 
 protein_interface_design
 
 qsar
 
 rbsegment_relax
 
 relax
 
 rigid
 
 rna
 
 rosetta_scripts
 
 rotamer_recovery
 
 RotamerDump
 
 sasa_scores
 
 scoring
 
 seeded_abinitio
 
 sic_dock
 
 simple_filters
 
 simple_moves
 
 sparta
 
 star
 
 surface_docking
 
 swa
 
 symmetric_docking
 
 toolbox
 
 topology_broker
 
 ub_e2c
 
 unfolded_state_energy_calculator
 
 viewer
 
 vip
 
 wum
 
 wum2
 

Classes

class  LoopRebuild
 The loop-rebuild protocol. More...
 
class  LoopRefine
 class LoopRefine for fullatom loop refinement More...
 
class  RBSegmentRelaxImpl
 

Typedefs

typedef
utility::pointer::owning_ptr
< AntibodyModeler > 
AntibodyModelerOP
 
typedef
utility::pointer::owning_ptr
< AntibodyModeler const > 
AntibodyModelerCOP
 
typedef
utility::pointer::owning_ptr
< RBSegmentRelaxImpl
RBSegmentRelaxImplOP
 

Functions

void print_ddgs (std::string ddg_out, std::string label, ddgs delta_e_components, ddgs, double 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")
 
static
numeric::random::RandomGenerator 
RG (431111)
 
void Tokenize (const std::string &str, utility::vector1< std::string > &tokens, const std::string &delimiters=" ")
 Helper function tokenizes a str. More...
 
int RBSegmentRelax_main ()
 

Detailed Description

The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.

FIX THIS.

Restrict design to residues matching user-specified SASA criteria in the monomeric, bound, or unbound state.

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?

unit headers

unit headeers

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:

initialization protocols for symmetrical docking

Inserts a Fragment into a Pose, similar to old Rosetta++ main_frag_trial algorithm.

set of fragments for a certain alignment frame

Hold chi- tensor information for the Pseudocontact Shift calculation.

MPI Headers.

STL Headers.

Boost headers.

Numeric headers.

general functions for generating typical kinds of Loops sets.

kinematic closure move

TODO make this a .fwd.

TODO .fwd fails (why?)

Project Headings.

C++ headers.

metric for Gunn moves

Cost computation for Gunn Moves.

Project headers.

Unit Headers.

Utility headers.

class to compute projection of a protein structure to principal component (PCA) eigenvectors ( as defined in file )

Replace pack_region_ala_pose_ with a PoseOP to remove this header.

stores movable_jumps info for replica docking

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

Where is the ddGMover.fwd.hh include?

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.

LoopRelaxThreadingMover.hh.

LoopRelaxMover.hh.

stupid test file for visual studio c++

The instance of CheckPointer contained by AbrelaxApplication should be replaced by a CheckPointerOP

Author
Oliver Lange
Oliver Lange Archive class to collect structures such that variances of scores can be computed to determine normalized weights
Oliver Lange (olang.nosp@m.e@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu)
Date
Wed Oct 20 12:08:31 2007
Detailed:
Author
Mike Tyka
James Thompson

C++ headers Utility headers Project headers

Author
ashworth

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?)

Author
ashworth
Andrew Leaver-Fay via code_writer.py (aleav.nosp@m.erfa.nosp@m.y@gma.nosp@m.il.c.nosp@m.om)
Zhe Zhang
Tim Jacobs
Tim jacobs
Sarel Fleishman (sarel.nosp@m.f@uw.nosp@m..edu)
Javier Castellanos ( javie.nosp@m.rcv@.nosp@m.uw.ed.nosp@m.u )

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

  1. CREATE THE FORWARD DECLARATION FILE
  2. #INCLUDE IT HERE

Package headers ObjexxFCL headers

Package headers Project headers Utility headers

Author
possu
Dominik Gront (dgron.nosp@m.t@ch.nosp@m.em.uw.nosp@m..edu.nosp@m..pl)
Oliver Lange ( olang.nosp@m.e@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu )
Date
Wed Aug 22 12:08:31 2007

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


#include <ObjexxFCL/format.hh> // apl needed? using namespace ObjexxFCL;

Project headers Utility headers C++ headers

Author
Oliver Lange

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.

Author
Daniel J. Mandell (dmand.nosp@m.ell@.nosp@m.itsa..nosp@m.ucsf.nosp@m..edu)
Date
Tues Jan 08 12:08:31 2008
Author
Amelie Stein (ameli.nosp@m.e.st.nosp@m.ein@u.nosp@m.csf..nosp@m.edu), Oct 2012 – next-generation KIC

ObjexxFCL headers

/protocols/match/downstream/SecMatchEvaluatorFactory.cc

Author
Kui Chan (kuich.nosp@m.an@u.nosp@m.w.edu), oct 09

This should probably be a pilot app, but the way Rosetta Scripts is set up, it can't be in the pilot apps

Utility headers C++ headers

Author
Sarel Fleishman

EVIL EVIL

Author
Rhiju Das

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

Detailed:
Parameters
@return
Remarks
References: JBNMR 2008 41:179-189 schmitz et all will explains the tensor convention used

Christophe Schmitz

Last Modified: June 2009
Author
Eva-Maria Strauch (evas0.nosp@m.1@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu), March 2011
Eva-Maria Strauch (evas0.nosp@m.1@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu)
Eva-Maria Strauch (evas0.nosp@m.1@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu), September 2011
Eva-Maria Strauch (evas0.nosp@m.1@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu), May 2011

Core headers Numeric headers Utility headers C++ Headers

Author
Ingemar Andre
Oliver Lange (olang.nosp@m.e@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu)
Date
Wed Oct 20 12:08:31 2007#include <protocols/abinitio/WobbleMover.fwd.hh>

modified for use inside CS-Rosetta by Oliver Lange

Author
Oliver Lange

modified for use inside CS-Rosetta by Oliver Lange

Author
Oliver Lange
James Thompson
Rhiju Das (rhiju.nosp@m.@sta.nosp@m.nford.nosp@m..edu, Parin Sripakdeevong (sripa.nosp@m.kap@.nosp@m.stanf.nosp@m.ord..nosp@m.edu)

project headers

package headers project headers

CatPiCalculator

Detailed:
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::toolbox::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.
Author
Steven Combs
Last Modified: October 22 2010

ExplicitWaterUnsatisfiedPolarsCalculator

Author
Chris King - dr.ch.nosp@m.ris..nosp@m.king@.nosp@m.gmai.nosp@m.l.com
Last Modified: 4.8.2011

PiPiCalculator

Detailed:
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::toolbox::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.
Author
Steven Combs
Last Modified: October 22 2010

RotamerRecovery

Detailed:
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:

total = 1

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

Authors
Author
James Thompson (original author)
Steven Combs (moved it to protocols for general use)
Last Modified: October 20 2010

SaltBridgeCalculator

Detailed:
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::toolbox::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.
Author
Steven Combs
Last Modified: October 22 2010

SequenceComparison

Detailed:
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
References:
"Native sequences are close to optimal" paper
Authors
Ron Jacak, Douglas Renfrew (renfr.nosp@m.ew@u.nosp@m.nc.ed.nosp@m.u) ( added rotamer recovery, cleanup ) Steven Combs (moved it into a general use class)
Last Modified: October 20 2010
Author
Jacob Bale (balej.nosp@m.@uw..nosp@m.edu)
Ken Jung

Typedef Documentation

Function Documentation

int protocols::ddG_main ( )
void protocols::print_ddgs ( std::string  ddg_out,
std::string  label,
ddgs  delta_e_components,
ddgs  ,
double  total_ddgs 
)

References 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 
)
static numeric::random::RandomGenerator protocols::RG ( 431111  )
static

Referenced by protocols::jd2::archive::VarianceStatisticsArchive::add_evaluated_structure(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::antibody::CDRH3Modeler::antibody_modeling_insert_ter(), protocols::toolbox::pose_metric_calculators::append_rsd_by_jump_near_atom(), protocols::swa::monte_carlo::RNA_O2StarMover::apply(), protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::apply(), protocols::antibody2::H3CterInsert::apply(), protocols::filters::StochasticFilter::apply(), protocols::antibody2::H3PerturbCCD::apply(), protocols::docking::ConformerSwitchMover::apply(), protocols::backrub::BackrubMover::apply(), protocols::backrub::BackrubSidechainMover::apply(), protocols::swa::rna::RNA_AnalyticLoopCloser::apply_solutions(), protocols::jd2::SilentFileJobOutputter::dump_pose(), protocols::simple_filters::ExternalEvaluator::ExternalEvaluator(), protocols::topology_broker::CoordConstraintClaimer::generate_constraints(), protocols::jd2::ShuffleFileSystemJobDistributor::get_new_job_id(), protocols::swa::monte_carlo::RNA_O2StarMover::get_random_o2star_residue(), protocols::swa::monte_carlo::RNA_O2StarMover::get_random_o2star_residue_near_moving_residue(), protocols::toolbox::KMedoid::init(), protocols::toolbox::GreedyKCenter::init(), protocols::topology_broker::StartStructClaimer::initialize_dofs(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::pass_metropolis(), protocols::anchored_design::AnchoredDesignMover::perturb_anchor(), protocols::anchored_design::AnchorMoversData::pick_new_cutpoint(), protocols::backrub::BackrubMover::random_angle(), protocols::dna::DNAParameters::random_basepair(), protocols::dna::DNAParameters::random_basestep(), protocols::canonical_sampling::MetropolisHastingsMover::random_mover(), protocols::hotspot_hashing::HotspotStubSet::random_stub(), protocols::anchored_design::AnchoredDesignMover::randomize_input_sequence(), protocols::swa::monte_carlo::RNA_O2StarMover::sample_near_o2star_torsion(), protocols::antibody::CDRH3Modeler::scored_frag_close(), protocols::topology_broker::RigidChunkClaimer::select_parts(), protocols::surface_docking::FullatomRelaxMover::setup_defaults(), protocols::canonical_sampling::ParallelTempering::shuffle_temperatures(), and protocols::canonical_sampling::SimulatedTempering::temperature_move().

void protocols::Tokenize ( const std::string &  str,
utility::vector1< std::string > &  tokens,
const std::string &  delimiters = " " 
)
static basic::Tracer protocols::TR ( "protocols.looprelax_protocols"  )
static

Referenced by protocols::surface_docking::SurfaceDockingProtocol::abinitio(), protocols::LoopRebuild::acceptable_rmsd_change(), protocols::swa::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::backrub::BackrubMover::add_mainchain_segments(), protocols::toolbox::task_operations::JointSequenceOperation::add_pdb(), protocols::backrub::BackrubMover::add_segment(), protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::antibody::CDRH3Modeler::antibody_modeling_insert_ter(), protocols::analysis::PackStatMover::apply(), protocols::swa::monte_carlo::RNA_AddOrDeleteMover::apply(), protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::swa::monte_carlo::RNA_AddMover::apply(), protocols::protein_interface_design::movers::PlacementMinimizationMover::apply(), protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply(), protocols::antibody2::GraftCDRLoopsProtocol::apply(), protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::antibody2::AntibodyModelerProtocol::apply(), protocols::antibody2::RefineBetaBarrel::apply(), protocols::antibody2::SnugDockProtocol::apply(), protocols::forge::constraints::RemoveCsts::apply(), protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation::apply(), protocols::antibody2::H3CterInsert::apply(), protocols::surface_docking::SurfaceOrientMover::apply(), protocols::canonical_sampling::MetropolisHastingsMover::apply(), protocols::antibody2::SnugDock::apply(), protocols::flexpep_docking::FlexPepDockingLowRes::apply(), protocols::floppy_tail::FloppyTailMover::apply(), protocols::surface_docking::SlideIntoSurface::apply(), protocols::antibody2::ModelCDRH3::apply(), protocols::antibody2::RefineOneCDRLoopCentroid::apply(), protocols::flexpep_docking::FlexPepDockingAbInitio::apply(), protocols::antibody2::H3PerturbCCD::apply(), protocols::antibody2::LHRepulsiveRamp::apply(), protocols::toolbox::task_operations::RestrictNativeResiduesOperation::apply(), protocols::docking::ConformerSwitchMover::apply(), protocols::docking::DockingInitialPerturbation::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::LoopRebuild::apply(), protocols::surface_docking::FullatomRelaxMover::apply(), protocols::surface_docking::CentroidRelaxMover::apply(), protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation::apply(), protocols::antibody2::H3RefineCCD::apply(), protocols::antibody2::LHRepulsiveRampLegacy::apply(), protocols::analysis::InterfaceAnalyzerMover::apply(), protocols::antibody::GraftMover::apply(), protocols::antibody2::RefineOneCDRLoop::apply(), protocols::surface_docking::FaSlideIntoSurface::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::docking::DockingHighResLegacy::apply(), protocols::docking::DockMCMProtocol::apply(), protocols::docking::DockingLowRes::apply(), protocols::backrub::BackrubMover::apply(), protocols::docking::DockMCMCycle::apply(), protocols::antibody::CDRH3Modeler::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::surface_docking::FaSlideAwayFromSurface::apply(), protocols::ddg::ddGMover::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::docking::DockingProtocol::apply(), protocols::docking::FaDockingSlideIntoContact::apply(), protocols::flxbb::FilterStructs_Packstat::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::flxbb::FilterStructs_TotalCharge::apply(), protocols::LoopRefine::apply(), protocols::docking::DockingInitialPerturbation::apply_body(), protocols::ub_e2c::ubi_e2c_modeler::assign_CSPs(), protocols::ub_e2c::ubi_e2c_modeler::assign_non_CSPs(), protocols::anchored_design::AnchorMoversData::autogenerate_constseq_frags(), protocols::anchored_design::AnchorMoversData::autogenerate_design_frags(), protocols::anchored_design::AnchorMoversData::autogenerate_frags(), protocols::flexpep_docking::FlexPepDockingProtocol::backrub_move(), protocols::LoopRebuild::barcode_extend_stems(), protocols::antibody::CDRH3Modeler::build_centroid_loop(), protocols::flxbb::FlxbbDesign::build_design_taskset(), protocols::antibody::CDRH3Modeler::build_fullatom_loop(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::LoopRebuild::build_random_loops(), protocols::unfolded_state_energy_calculator::calc_all_averages(), protocols::analysis::InterfaceAnalyzerMover::calc_centroid_dG(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_native_contacts(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), protocols::ub_e2c::ubi_e2c_modeler::calc_interaction_energy(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_interface_metrics(), protocols::protein_interface_design::ReportPSSMDifferences::calculate(), protocols::docking::DockingEnsemble::calculate_highres_ref_energy(), protocols::docking::DockingEnsemble::calculate_lowres_ref_energy(), protocols::swa::protein::StepWiseProteinCCD_Closer::CCD_loop_close(), protocols::swa::protein::StepWiseProteinCCD_Closer::CCD_loop_close_sample_omega_recursively(), protocols::antibody::CDRH3Modeler::CDR_H3_filter(), protocols::ub_e2c::ubi_e2c_modeler::centroid_filter(), protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation(), protocols::surface_docking::CentroidRelaxMover::CentroidRelaxMover(), protocols::flexpep_docking::FlexPepDockingProtocol::check_filters(), protocols::cluster::APCluster::cluster(), protocols::toolbox::KCluster::cluster(), protocols::grafting::GraftMoverBase::combine_movemaps(), protocols::toolbox::SelectResiduesByLayer::compute(), protocols::toolbox::task_operations::LayerOperations::compute(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_delta_hbond_unsat(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_packstat(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc(), protocols::ub_e2c::ubi_e2c_modeler::compute_swap_trim_CSPs(), protocols::ub_e2c::ubi_e2c_modeler::compute_trim_CSPs(), protocols::flxbb::constraints_NtoC(), protocols::flxbb::constraints_sheet(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoASP(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoGLU(), protocols::docking::DockingHighResLegacy::define_loops(), protocols::grafting::delete_region(), protocols::antibody2::AntibodyInfo::detect_and_set_camelid_CDR_H3_stem_type(), protocols::antibody2::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type(), protocols::antibody2::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule(), protocols::antibody::Antibody::detect_camelid_CDR_H3_stem_type(), protocols::antibody::Antibody::detect_regular_CDR_H3_stem_type(), protocols::antibody::AntibodyModeler::display_constraint_residues(), protocols::antibody2::GraftCDRLoopsProtocol::display_constraint_residues(), protocols::antibody2::AntibodyModelerProtocol::display_constraint_residues(), protocols::docking::DockingEnsemble::DockingEnsemble(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), protocols::LoopRebuild::extend_barcode_regions_if_chain_break(), protocols::swa::StepWiseScreener::filter_and_output(), protocols::swa::protein::StepWiseProteinScreener::filter_and_output(), protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), protocols::antibody2::RefineOneCDRLoopCentroid::finalize_setup(), protocols::antibody2::CDRsMinPackMin::finalize_setup(), protocols::antibody2::RefineBetaBarrel::finalize_setup(), protocols::antibody2::GraftCDRLoopsProtocol::finalize_setup(), protocols::antibody2::LHRepulsiveRampLegacy::finalize_setup(), protocols::antibody2::AntibodyModelerProtocol::finalize_setup(), protocols::docking::DockingProtocol::finalize_setup(), protocols::surface_docking::CentroidRelaxMover::FinalizeMovers(), protocols::surface_docking::FullatomRelaxMover::FinalizeMovers(), protocols::flxbb::find_ligands(), protocols::floppy_tail::FloppyTailMover::FloppyTailMover(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_filter(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_mode_perturbation(), protocols::surface_docking::FullatomRelaxMover::FullatomRelaxMover(), protocols::forge::constraints::NtoC_RCG::generate_remodel_constraints(), protocols::surface_docking::SurfaceParameters::GenerateSurfaceParameters(), protocols::branch_angle::get_branching_atoms2(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_sample_phi_only(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_phi_only(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_sample_psi_only(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_psi_only(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor::go(), protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), protocols::antibody2::AntibodyInfo::identify_CDR_from_a_sequence(), protocols::toolbox::KMedoid::init(), protocols::toolbox::GreedyKCenter::init(), protocols::ub_e2c::ubi_e2c_modeler::init_d77_perturbation(), protocols::antibody::AntibodyModeler::init_from_options(), protocols::docking::DockingInitialPerturbation::init_from_options(), protocols::antibody2::GraftCDRLoopsProtocol::init_from_options(), protocols::antibody2::AntibodyModelerProtocol::init_from_options(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::docking::DockMCMCycle::init_mc(), 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::flxbb::FlxbbDesign::initialize_filter(), protocols::swa::StepWiseResidueSampler::initialize_green_packer(), protocols::swa::protein::StepWiseProteinPacker::initialize_green_packer(), protocols::swa::protein::StepWiseProteinResidueSampler::initialize_green_packer(), protocols::backrub::BackrubMover::initialize_simulation(), protocols::grafting::GraftMoverBase::insert_piece(), protocols::grafting::insert_pose_into_pose(), protocols::toolbox::KClusterData::KClusterData(), protocols::toolbox::task_operations::LayerOperations::LayerOperations(), protocols::sasa_scores::load_avge_polynomial_coefficients(), protocols::docking::DockingEnsemble::load_ensemble(), protocols::protein_interface_design::ReportPSSMDifferences::load_pssm_data(), protocols::sasa_scores::load_sasapack_polynomial_coefficients(), protocols::toolbox::KClusterData::load_silent_files(), protocols::anchored_design::AnchorMoversData::locate_anchor_loop(), protocols::antibody::CDRH3Modeler::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_fa_relax(), protocols::analysis::InterfaceAnalyzerMover::make_interface_set(), protocols::analysis::InterfaceAnalyzerMover::make_separated_pose(), protocols::flexpep_docking::FlexPepDockingProtocol::markNativeInterface(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::master_go(), 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::analysis::InterfaceAnalyzerMover::mut_to_gly(), protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), protocols::backrub::BackrubMover::optimize_branch_angles(), protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond(), protocols::branch_angle::BranchAngleOptimizer::overall_params(), protocols::toolbox::task_operations::DesignAroundOperation::parse_def(), protocols::protein_interface_design::movers::SubroutineMover::parse_my_tag(), protocols::protein_interface_design::movers::PlacementMinimizationMover::parse_my_tag(), protocols::forge::constraints::RemoveCsts::parse_my_tag(), protocols::analysis::InterfaceAnalyzerMover::parse_my_tag(), protocols::canonical_sampling::MetropolisHastingsMover::parse_my_tag(), protocols::flxbb::InterlockAroma::parse_my_tag(), protocols::docking::DockingInitialPerturbation::parse_my_tag(), protocols::flxbb::FlxbbDesign::parse_my_tag(), protocols::toolbox::task_operations::ProteinCore::parse_tag(), protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::parse_tag(), protocols::toolbox::task_operations::DesignAroundOperation::parse_tag(), protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation::parse_tag(), protocols::toolbox::task_operations::ThreadSequenceOperation::parse_tag(), protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation::parse_tag(), protocols::toolbox::task_operations::RestrictNativeResiduesOperation::parse_tag(), protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation::parse_tag(), protocols::flxbb::LayerDesignOperation::parse_tag(), protocols::protein_interface_design::ParserJobInputter::ParserJobInputter(), protocols::grafting::GraftMoverBase::perturb_backbone_for_test(), protocols::anchored_design::AnchorMoversData::pick_new_cutpoints(), protocols::protein_interface_design::ParserJobInputter::pose_from_job(), protocols::flexpep_docking::FlexPepDockingProtocol::prepack_only(), protocols::swa::protein::StepWiseProteinScreener::prepare_ghost_pose(), protocols::canonical_sampling::MetropolisHastingsMover::prepare_simulation(), protocols::flexpep_docking::FlexPepDockingProtocol::randomlySlidePeptideJump(), protocols::antibody2::H3PerturbCCD::read_and_store_fragments(), protocols::frags::TorsionFragmentLibrary::read_file(), protocols::antibody2::H3CterInsert::read_H3_cter_fragment(), protocols::antibody::read_H3_cter_fragment(), protocols::anchored_design::AnchorMoversData::read_options(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::ddg::ddGMover::relax_wildtype_structure(), protocols::ub_e2c::ubi_e2c_modeler::restore_cter(), protocols::ub_e2c::ubi_e2c_modeler::restrict_to_interfacial_loop_packing(), protocols::grafting::return_region(), protocols::flexpep_docking::FlexPepDockingProtocol::rigidbody_monte_carlo_minimize(), protocols::swa::StepWiseResidueSampler::sample_residues(), protocols::swa::protein::StepWiseProteinPacker::sample_residues(), protocols::antibody::CDRH3Modeler::scored_frag_close(), protocols::LoopRebuild::select_one_loop(), protocols::toolbox::SelectResiduesByLayer::SelectResiduesByLayer(), protocols::ub_e2c::ubi_e2c_modeler::set_default(), protocols::antibody2::AntibodyModelerProtocol::set_default(), protocols::antibody2::GraftCDRLoopsProtocol::set_default(), protocols::antibody::AntibodyModeler::set_default(), protocols::antibody::GraftMover::set_default(), protocols::antibody2::RefineOneCDRLoopCentroid::set_default(), protocols::antibody::CDRH3Modeler::set_default(), protocols::flxbb::LayerDesignOperation::set_default_layer_residues(), protocols::grafting::GraftMoverBase::set_default_movemap(), protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(), protocols::docking::DockingHighResLegacy::set_dock_min_protocol(), protocols::docking::DockingHighResLegacy::set_dock_ppk_protocol(), protocols::ub_e2c::ubi_e2c_modeler::set_e2g2_diubi_fold_tree(), protocols::grafting::GraftMoverBase::set_regions_from_movemap(), protocols::antibody::AntibodyModeler::set_snugdock_foldtree(), protocols::anchored_design::AnchorMoversData::set_unset_packertask_factory(), protocols::anchored_design::AnchorMoversData::set_unset_scorefunctions(), protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(), protocols::flxbb::DesignTask_Normal::setup(), protocols::flxbb::DesignTask_Layer::setup(), protocols::antibody2::AntibodyInfo::setup_CDRsInfo(), protocols::ub_e2c::ubi_e2c_modeler::setup_complex_fold_tree(), protocols::ddg::ddGMover::setup_constraints(), protocols::docking::DockingProtocol::setup_constraints(), protocols::surface_docking::CentroidRelaxMover::setup_defaults(), protocols::surface_docking::FullatomRelaxMover::setup_defaults(), protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree(), protocols::docking::setup_foldtree(), protocols::ub_e2c::ubi_e2c_modeler::setup_key_residues(), protocols::ub_e2c::ubi_e2c_modeler::setup_move_maps(), protocols::antibody2::SnugDockProtocol::setup_objects(), protocols::antibody2::SnugDock::setup_objects(), protocols::ub_e2c::ubi_e2c_modeler::setup_packer_task(), protocols::antibody::AntibodyModeler::setup_packer_task(), protocols::antibody::CDRH3Modeler::setup_packer_task(), protocols::antibody::LoopRlxMover::setup_packer_task(), protocols::ddg::ddGMover::setup_packer_task_for_mutations(), protocols::docking::DockingHighResLegacy::setup_packing(), protocols::ub_e2c::ubi_e2c_modeler::setup_simple_fold_tree(), protocols::antibody::AntibodyModeler::setup_simple_fold_tree(), protocols::grafting::GraftMoverBase::setup_single_loop_double_arm_remodeling_foldtree(), protocols::grafting::GraftMoverBase::setup_single_loop_single_arm_remodeling_foldtree(), protocols::surface_docking::SurfaceDockingProtocol::setupFoldTree(), protocols::antibody::simple_fold_tree(), protocols::antibody::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::protein_interface_design::star_fold_tree(), protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics(), protocols::grafting::GraftMoverBase::superimpose_overhangs_heavy(), protocols::surface_docking::SurfaceDockingProtocol::SurfaceDockingProtocol(), protocols::surface_docking::SurfaceParameters::SurfaceParameters(), protocols::flexpep_docking::FlexPepDockingLowRes::to_centroid(), protocols::flexpep_docking::FlexPepDockingAbInitio::to_centroid(), protocols::flexpep_docking::FlexPepDockingProtocol::torsions_monte_carlo_minimize(), protocols::ub_e2c::ubi_e2c_modeler::trim_cter(), protocols::flexpep_docking::FlexPepDockingFlags::updateChains(), protocols::flexpep_docking::FlexPepDockingFlags::updateChainsAndAnchors_fromParamsFile(), protocols::toolbox::KMedoid::whoami(), protocols::toolbox::GreedyKCenter::whoami(), protocols::canonical_sampling::MetropolisHastingsMover::wind_down_simulation(), protocols::branch_angle::BranchAngleOptimizer::write_database(), and protocols::flxbb::LayerDesignOperation::write_pymol_script().