Rosetta 3.4
Namespaces | Classes | Typedefs | Functions
protocols Namespace Reference

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

Namespaces

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

Classes

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

Typedefs

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

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.
int RBSegmentRelax_main (bool boinc_mode)

Detailed Description

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

FIX THIS.

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?

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.

ObjexxFCL headers.

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.

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 (olange@u.washington.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 (aleaverfay@gmail.com)
Tim jacobs
Sarel Fleishman (sarelf@uw.edu)

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 (dgront@chem.uw.edu.pl)
Oliver Lange ( olange@u.washington.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 (dmandell@itsa.ucsf.edu)
Date:
Tues Jan 08 12:08:31 2008

/protocols/match/downstream/SecMatchEvaluatorFactory.cc

Author:
Kui Chan (kuichan@uw.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:
Returns:
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 (evas01@u.washington.edu), March 2011
Eva-Maria Strauch (evas01@u.washington.edu)
Eva-Maria Strauch (evas01@u.washington.edu), September 2011
Eva-Maria Strauch (evas01@u.washington.edu), May 2011

Core headers Numeric headers Utility headers C++ Headers

Author:
Ingemar Andre
Oliver Lange (olange@u.washington.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@stanford.edu, Parin Sripakdeevong (sripakap@stanford.edu)

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.chris.king@gmail.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 (renfrew@unc.edu) ( added rotamer recovery, cleanup ) Steven Combs (moved it into a general use class)
Last Modified: October 20 2010
Author:
Tim Jacobs

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 ( bool  boinc_mode)
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]
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::backrub::BackrubMover::add_mainchain_segments(), protocols::backrub::BackrubMover::add_segment(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::antibody::CDRH3Modeler::antibody_modeling_insert_ter(), protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::surface_docking::SurfaceOrientMover::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::surface_docking::FaSlideAwayFromSurface::apply(), protocols::surface_docking::FaSlideIntoSurface::apply(), protocols::surface_docking::SlideIntoSurface::apply(), protocols::surface_docking::FullatomRelaxMover::apply(), protocols::surface_docking::CentroidRelaxMover::apply(), protocols::LoopRefine::apply(), protocols::LoopRebuild::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::flxbb::FilterStructs_TotalCharge::apply(), protocols::flxbb::FilterStructs_Packstat::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::flexpep_docking::FlexPepDockingLowRes::apply(), protocols::flexpep_docking::FlexPepDockingAbInitio::apply(), protocols::docking::DockMCMProtocol::apply(), protocols::docking::DockMCMCycle::apply(), protocols::docking::DockingProtocol::apply(), protocols::docking::DockingLowRes::apply(), protocols::docking::FaDockingSlideIntoContact::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::docking::DockingHighResLegacy::apply(), protocols::docking::ConformerSwitchMover::apply(), protocols::ddg::ddGMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::backrub::BackrubMover::apply(), protocols::antibody2::CDRH3Modeler2::apply(), protocols::antibody2::Ab_Assemble_Templates::apply(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::antibody::GraftMover::apply(), protocols::antibody::CDRH3Modeler::apply(), protocols::analysis::PackStatMover::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::analysis::InterfaceAnalyzerMover::apply(), protocols::docking::DockingInitialPerturbation::apply_body(), protocols::anchored_design::AnchorMoversData::autogenerate_constseq_frags(), protocols::anchored_design::AnchorMoversData::autogenerate_design_frags(), protocols::anchored_design::AnchorMoversData::autogenerate_frags(), protocols::antibody::CDRH3Modeler::build_centroid_loop(), protocols::antibody::CDRH3Modeler::build_fullatom_loop(), protocols::unfolded_state_energy_calculator::calc_all_averages(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_native_contacts(), protocols::ub_e2c::ubi_e2c_modeler::calc_interaction_energy(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_interface_metrics(), protocols::docking::DockingEnsemble::calculate_highres_ref_energy(), protocols::docking::DockingEnsemble::calculate_lowres_ref_energy(), 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::toolbox::KCluster::cluster(), protocols::cluster::APCluster::cluster(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_delta_hbond_unsat(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_packstat(), protocols::flxbb::constraints_NtoC(), protocols::flxbb::constraints_sheet(), protocols::docking::DockingHighResLegacy::define_loops(), protocols::antibody2::Ab_Info::detect_and_set_camelid_CDR_H3_stem_type(), protocols::antibody2::Ab_Info::detect_and_set_regular_CDR_H3_stem_type(), protocols::antibody2::Ab_ModelCDRH3::display_constraint_residues(), protocols::antibody2::Ab_Assemble_Templates::display_constraint_residues(), protocols::antibody::AntibodyModeler::display_constraint_residues(), protocols::docking::DockingEnsemble::DockingEnsemble(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), protocols::surface_docking::FullatomRelaxMover::FinalizeMovers(), protocols::surface_docking::CentroidRelaxMover::FinalizeMovers(), 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::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor::go(), protocols::toolbox::GreedyKCenter::init(), protocols::toolbox::KMedoid::init(), protocols::ub_e2c::ubi_e2c_modeler::init_d77_perturbation(), protocols::docking::DockingInitialPerturbation::init_from_options(), protocols::antibody::AntibodyModeler::init_from_options(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::docking::DockMCMCycle::init_mc(), 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::backrub::BackrubMover::initialize_simulation(), protocols::toolbox::KClusterData::KClusterData(), protocols::toolbox::KClusterData::load_silent_files(), protocols::antibody2::CDRH3Modeler2::loop_centroid_relax(), 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::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::master_go(), 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::flxbb::InterlockAroma::parse_my_tag(), protocols::flxbb::FlxbbDesign::parse_my_tag(), protocols::canonical_sampling::MetropolisHastingsMover::parse_my_tag(), protocols::toolbox::task_operations::ThreadSequenceOperation::parse_tag(), protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation::parse_tag(), protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation::parse_tag(), protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation::parse_tag(), protocols::toolbox::task_operations::JointSequenceOperation::parse_tag(), protocols::toolbox::task_operations::DesignAroundOperation::parse_tag(), protocols::flxbb::LayerDesignOperation::parse_tag(), protocols::anchored_design::AnchorMoversData::pick_new_cutpoints(), protocols::canonical_sampling::MetropolisHastingsMover::prepare_simulation(), protocols::antibody2::Ab_H3_perturb_ccd_build::read_and_store_fragments(), protocols::frags::TorsionFragmentLibrary::read_file(), protocols::antibody2::Ab_H3_cter_insert_mover::read_H3_cter_fragment(), protocols::antibody::read_H3_cter_fragment(), protocols::anchored_design::AnchorMoversData::read_options(), protocols::ub_e2c::ubi_e2c_modeler::restore_cter(), protocols::ub_e2c::ubi_e2c_modeler::restrict_to_interfacial_loop_packing(), protocols::antibody::CDRH3Modeler::scored_frag_close(), protocols::toolbox::SelectResiduesByLayer::SelectResiduesByLayer(), protocols::antibody2::CDRH3Modeler2::set_default(), protocols::antibody2::Ab_ModelCDRH3::set_default(), protocols::antibody2::Ab_Assemble_Templates::set_default(), protocols::ub_e2c::ubi_e2c_modeler::set_default(), protocols::antibody::GraftMover::set_default(), protocols::antibody::CDRH3Modeler::set_default(), protocols::antibody::AntibodyModeler::set_default(), 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::antibody::AntibodyModeler::set_snugdock_foldtree(), protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(), protocols::flxbb::DesignTask_Normal::setup(), protocols::flxbb::DesignTask_Layer::setup(), protocols::ub_e2c::ubi_e2c_modeler::setup_complex_fold_tree(), protocols::surface_docking::FullatomRelaxMover::setup_defaults(), protocols::surface_docking::CentroidRelaxMover::setup_defaults(), protocols::docking::setup_foldtree(), protocols::ub_e2c::ubi_e2c_modeler::setup_key_residues(), protocols::ub_e2c::ubi_e2c_modeler::setup_move_maps(), protocols::ub_e2c::ubi_e2c_modeler::setup_packer_task(), protocols::antibody::LoopRlxMover::setup_packer_task(), protocols::antibody::CDRH3Modeler::setup_packer_task(), protocols::antibody::AntibodyModeler::setup_packer_task(), protocols::ub_e2c::ubi_e2c_modeler::setup_simple_fold_tree(), protocols::antibody::AntibodyModeler::setup_simple_fold_tree(), protocols::surface_docking::SurfaceDockingProtocol::setupFoldTree(), protocols::antibody::simple_fold_tree(), protocols::antibody::simple_one_loop_fold_tree(), protocols::surface_docking::SurfaceDockingProtocol::SurfaceDockingProtocol(), protocols::surface_docking::SurfaceParameters::SurfaceParameters(), protocols::ub_e2c::ubi_e2c_modeler::trim_cter(), protocols::flexpep_docking::FlexPepDockingFlags::updateChains(), protocols::flexpep_docking::FlexPepDockingFlags::updateChainsAndAnchors_fromParamsFile(), protocols::toolbox::GreedyKCenter::whoami(), protocols::toolbox::KMedoid::whoami(), protocols::canonical_sampling::MetropolisHastingsMover::wind_down_simulation(), and protocols::branch_angle::BranchAngleOptimizer::write_database().

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