Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Namespaces | Classes | Typedefs | Functions
protocols Namespace Reference

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

Namespaces

 aa_composition
 
 abinitio
 
 analysis
 
 anchored_design
 
 antibody
 
 antibody_legacy
 
 backbone_moves
 
 backrub
 
 boinc
 
 branch_angle
 
 buns
 
 calc_taskop_filters
 
 calc_taskop_movers
 
 canonical_sampling
 Algorithms for rigorously sampling native state ensembles. See disclaimer in detailed description.
 
 carbohydrates
 
 cartesian
 
 checkpoint
 
 chemically_conjugated_docking
 
 chromophore
 
 cluster
 
 comparative_modeling
 
 constel
 
 constraint_filters
 
 constraint_generator
 
 constraint_movers
 
 constraints_additional
 
 contact_map
 
 coupled_moves
 Protocol that combines backbone moves and sidechain moves in a single Monte Carlo step.
 
 cryst
 
 cutoutdomain
 
 cyclic_peptide
 
 cyclic_peptide_predict
 
 ddG
 
 ddg
 
 denovo_design
 
 design_opt
 
 dna
 
 dna_dock
 
 docking
 
 domain_assembly
 
 drug_design
 
 electron_density
 
 energy_based_clustering
 
 environment
 
 enzdes
 
 enzymatic_movers
 
 evaluation
 
 evolution
 
 farnesyl
 
 features
 
 fibril
 
 filters
 
 fldsgn
 
 flexpack
 
 flexpep_docking
 
 floppy_tail
 
 flxbb
 
 fold_from_loops
 
 forge
 
 frag_picker
 
 frags
 
 generalized_kinematic_closure
 
 genetic_algorithm
 
 geometry
 
 glycopeptide_docking
 
 grafting
 
 hbnet
 
 helical_bundle
 
 helical_bundle_predict
 
 helix_capper
 
 hotspot_hashing
 
 hybridization
 
 hydrate
 
 idealize
 
 indel
 
 indexed_structure_store
 
 init
 
 interface
 
 jd2
 
 jd3
 
 jobdist
 
 jumping
 
 kinematic_closure
 Implementation of the kinematic closure algorithm for sampling protein backbone conformations.
 
 kinmatch
 
 legacy_sewing
 
 ligand_docking
 
 loop_build
 
 loop_grower
 
 loop_modeler
 
 loop_modeling
 Framework for loop structure prediction.
 
 loophash
 
 loops
 
 magnesium
 
 mainchain_potential
 
 make_rot_lib
 
 match
 
 matdes
 
 md
 
 mean_field
 
 medal
 
 membrane
 
 membrane_benchmark
 
 metal_interface
 
 minimization_packing
 
 monte_carlo
 
 motif_grafting
 ...that lives inside of motif_grafting...
 
 motifs
 
 movers
 
 moves
 
 mpi_refinement
 
 multistage_rosetta_scripts
 
 multistate_design
 
 ncbb
 
 neighbor
 
 network
 
 nmr
 
 noesy_assign
 
 nonlocal
 
 normalmode
 
 optimize_weights
 
 pack_daemon
 
 pack_interface
 
 parser
 
 pb_potential
 
 pdbinfo_manipulations
 
 peptide_deriver
 
 pmut_scan
 
 pockets
 
 pose_creation
 
 pose_length_moves
 
 pose_metric_calculators
 
 pose_reporters
 
 pose_selectors
 
 protein_interface_design
 
 qsar
 
 quantum_annealing
 
 rbsegment_relax
 
 recces
 
 recon_design
 
 relax
 
 residue_optimization
 
 residue_selectors
 
 rigid
 
 rna
 
 rosetta_scripts
 
 rotamer_recovery
 
 RotamerDump
 
 rpc
 
 sasa_scores
 
 score_filters
 
 scoring
 
 seeded_abinitio
 
 sewing
 
 sic_dock
 
 simple_ddg
 
 simple_filters
 
 simple_moves
 
 simple_pose_metric_calculators
 
 simple_task_operations
 
 sparta
 
 splice
 
 ss_prediction
 
 star
 
 stepwise
 
 struct_fragment
 
 surface_docking
 
 switches
 
 symmetric_docking
 
 symmetry
 
 task_operations
 
 tcr
 
 testing
 
 toolbox
 
 topology_broker
 
 trajectory
 
 trRosetta
 
 trRosetta_protocols
 
 ub_e2c
 
 unfolded_state_energy_calculator
 
 vardist_solaccess
 
 viewer
 
 vip
 
 wum
 

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 ()
 

Detailed Description

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.

LoopRelaxMover.hh.

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

demo program for implementing loop relax + FA relax

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.

LoopRelaxThreadingMover.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
Author
Sarel Fleishman (sarel.nosp@m.f@uw.nosp@m..edu)
Oliver Lange
Mike Tyka
Mike Tyka
James Thompson

C++ headers Utility headers Project headers

Author
Gideon Lapidoth
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m..wash.nosp@m.ingt.nosp@m.on.ed.nosp@m.u)
Chris King (chris.nosp@m.k1@u.nosp@m.w.edu)
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)

Run quick relax on separated partners; this emulates unbound docking

Author
JKLeman (julia.nosp@m..koe.nosp@m.hler1.nosp@m.982@.nosp@m.gmail.nosp@m..com)
Zhe Zhang
fpd
Javier Castellanos (javie.nosp@m.rcv@.nosp@m.ue.ed.nosp@m.u)
Christoffer Norn ( chnor.nosp@m.n@gm.nosp@m.ail.c.nosp@m.om )
Tim jacobs
Tim Jacobs
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


Author
Frank DiMaio
Alex Ford (forda.nosp@m.s@uw.nosp@m..edu)

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"

Author
Sam DeLuca samue.nosp@m.l.l..nosp@m.deluc.nosp@m.a@va.nosp@m.nderb.nosp@m.ilt..nosp@m.edu
Detailed: The base class is somewhat messy, so there are a few derived classes in protocols/jd3/DerivedNodeManagers.hh that simplify some of these interfaces by specializing for certain cases. Features include:

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

Author
Jack Maguire, jackm.nosp@m.agui.nosp@m.re144.nosp@m.4@gm.nosp@m.ail.c.nosp@m.om

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()

Author
Roland A. Pache, PhD
Srivatsan Raman
James Thompson
Mike Tyka
Daniel J. Mandell
Roland A. Pache, PhD
Kale Kundert
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
Kyle Barlow (kb@ky.nosp@m.leba.nosp@m.rlow..nosp@m.com)

A class to save and output matcher data, if matches are scored

Author
Kyle Barlow (kb@ky.nosp@m.leba.nosp@m.rlow..nosp@m.com)
Jacob Bale (balej.nosp@m.@uw..nosp@m.edu)
jacob bale (balej.nosp@m.@uw..nosp@m.edu)
Aliza Rubenstein (aliza.nosp@m..rub.nosp@m.enste.nosp@m.in@g.nosp@m.mail..nosp@m.com)
arubenstein

Uses SmallMover and ShearMover with adjustable maximum dihedral angle changes, then repacking and a single round of minimization

Author
JKLeman (julia.nosp@m..koe.nosp@m.hler1.nosp@m.982@.nosp@m.gmail.nosp@m..com)

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

Author
JKLeman (julia.nosp@m..koe.nosp@m.hler1.nosp@m.982@.nosp@m.gmail.nosp@m..com)

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

Author
JKLeman (julia.nosp@m..koe.nosp@m.hler1.nosp@m.982@.nosp@m.gmail.nosp@m..com)

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

Author
JKLeman (julia.nosp@m..koe.nosp@m.hler1.nosp@m.982@.nosp@m.gmail.nosp@m..com)

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

Author
JKLeman (julia.nosp@m..koe.nosp@m.hler1.nosp@m.982@.nosp@m.gmail.nosp@m..com)

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

Author
Andrea Bazzoli (bazzo.nosp@m.li@k.nosp@m.u.edu)

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

Author
Nir London
Yuval Sedan (yuval.nosp@m..sed.nosp@m.an@ma.nosp@m.il.h.nosp@m.uji.a.nosp@m.c.il)
Orly Marcu (orly..nosp@m.marc.nosp@m.u@mai.nosp@m.l.hu.nosp@m.ji.ac.nosp@m..il)
Date
Jul. 30, 2014
Author
Nir London
Yuval Sedan (yuval.nosp@m..sed.nosp@m.an@ma.nosp@m.il.h.nosp@m.uji.a.nosp@m.c.il)
Date
Jul. 30, 2014
Author
Yuval Sedan (yuval.nosp@m..sed.nosp@m.an@ma.nosp@m.il.h.nosp@m.uji.a.nosp@m.c.il)
Date
Sep. 21, 2014
Author
Ragul Gowthaman (ragul.nosp@m.@ku..nosp@m.edu)
Yan Xia (seanx.nosp@m.iay@.nosp@m.ku.ed.nosp@m.u)

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.

Author
Steven Combs

ExplicitWaterUnsatisfiedPolarsCalculator

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

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.

Author
Steven Combs

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

Author
James Thompson (original author)
Steven Combs (moved it to protocols for general use)

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.

Author
Steven Combs

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
Author
Ron Jacak, Douglas Renfrew (renfr.nosp@m.ew@n.nosp@m.yu.ed.nosp@m.u) ( added rotamer recovery, cleanup ) Steven Combs (moved it into a general use class)
Sarel Fleishman
Mike Tyka
Srivatsan Raman
James Thompson
Daniel J. Mandell
Detailed:
RNA_DeNovoMasterMover (factored out of RNA_FragmentMonteCarlo)

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?]

Author
Rhiju Das
Kalli Kappel
Detailed:

Stick everything related to running scores, pose info, 6D jump information, etc. here.

        -- rhiju, 2016-2017.
Author
Luki Goldschmidt (lugo@.nosp@m.uw.e.nosp@m.du)

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

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

Christophe Schmitz

Parameters
return
Remarks
References: C Schmitz et.al. J Mol Biol. Mar 9, 2012; 416(5): 668–677 ; Yagi H et.al Structure, 2013, 21(6):883-890
JBNMR 2008 41:179-189 schmitz et all will explains the tensor convention used Christophe Schmitz , Kala Bharath Pilla
Parameters
return
Remarks
References: C Schmitz et.al. J Mol Biol. Mar 9, 2012; 416(5): 668–677 ; Yagi H et.al Structure, 2013, 21(6):883-890,
JBNMR 2008 41:179-189 schmitz et all will explains the tensor convention used

Christophe Schmitz , Kala Bharath Pilla

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

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

Author
Hahnbeom Park
TJ Brunette (tjbru.nosp@m.nett.nosp@m.e@gma.nosp@m.il.c.nosp@m.om)

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

Author
TJ Brunette (olang.nosp@m.e@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu)
Date
3/22/10
Author
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>
Author
Kale Kundert (kale..nosp@m.kund.nosp@m.ert@u.nosp@m.csf..nosp@m.edu)

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
Gideon Lapidoth (glapi.nosp@m.doth.nosp@m.@gmai.nosp@m.l.co.nosp@m.m)

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.

Author
Ingemar Andre
Samuel Schmitz (Samue.nosp@m.l.Sc.nosp@m.hmitz.nosp@m.@van.nosp@m.derbi.nosp@m.lt.e.nosp@m.du)
Patrick Conway

project headers

package headers project headers

Typedef Documentation

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

Function Documentation

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 
)
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 basic::Tracer protocols::TR ( "protocols.looprelax_protocols"  )
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::analysis::PackStatMover::apply(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::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::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::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::constraint_movers::ConstraintSetMover::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::metal_interface::RemoveMetalConnectionsMover::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::denovo_design::components::ExtendedPoseBuilder::apply(), protocols::membrane::SetMembranePositionMover::apply(), protocols::stepwise::monte_carlo::mover::ResampleMover::apply(), protocols::carbohydrates::GlycanSampler::apply(), protocols::denovo_design::movers::FoldArchitectMover::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::carbohydrates::LinkageConformerMover::apply(), protocols::carbohydrates::CreateGlycanSequonMover::apply(), protocols::carbohydrates::RingPlaneFlipMover::apply(), protocols::carbohydrates::TautomerizeAnomerMover::apply(), protocols::backrub::BackrubMover::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::glycopeptide_docking::GlycopeptideDockingProtocol::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::trRosetta_protocols::movers::trRosettaProtocolMover::apply(), protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::apply(), protocols::monte_carlo::GenericMonteCarloMover::apply(), protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::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::FoldArchitectMover::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::FoldArchitectMover::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::glycopeptide_docking::calculate_additional_glycosylation_metrics(), protocols::helical_bundle_predict::HBP_SigmoidalTemperatureScheduleGenerator::calculate_current_temperature(), protocols::glycopeptide_docking::calculate_sampled_distance(), 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::FoldArchitectMover::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::PoseArchitect::design(), protocols::denovo_design::architects::HelixArchitect::design(), protocols::denovo_design::architects::MotifArchitect::design(), protocols::denovo_design::architects::BetaSheetArchitect::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::FoldArchitectMover::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::FoldArchitectMover::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::FoldArchitectMover::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::glycopeptide_docking::glycosylate_residues(), 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::StepWiseSamplerSizedAny::init(), protocols::stepwise::sampler::StepWiseSamplerComb::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::monte_carlo::MonteCarloInterface::init_interface_analyzer(), 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_protein_bond_sampler(), 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::FoldArchitectMover::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::backrub::BackrubMover::parse_movemap_factory(), protocols::denovo_design::movers::FoldArchitectMover::parse_movers(), protocols::monte_carlo::ResetBaselineMover::parse_my_tag(), protocols::pose_length_moves::FixAllLoopsMover::parse_my_tag(), protocols::pose_selectors::ClusterPoseSelector::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::constraint_movers::AddConstraintsToCurrentConformationMover::parse_my_tag(), protocols::forge::constraints::RemoveRemodelCsts::parse_my_tag(), protocols::constraint_movers::ResidueTypeConstraintMover::parse_my_tag(), protocols::constraint_movers::ConstraintSetMover::parse_my_tag(), protocols::ncbb::SecStructFinder::parse_my_tag(), protocols::aa_composition::AddMHCEpitopeConstraintMover::parse_my_tag(), protocols::aa_composition::AddNetChargeConstraintMover::parse_my_tag(), protocols::aa_composition::AddCompositionConstraintMover::parse_my_tag(), protocols::quantum_annealing::ExternalPackerResultLoader::parse_my_tag(), protocols::monte_carlo::MonteCarloRecover::parse_my_tag(), protocols::backrub::BackrubMover::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::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::glycopeptide_docking::record_pose_metrics(), 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::movers::SealFoldTreeMover::remove_cutpoints(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::remove_cutpoints(), protocols::denovo_design::movers::FoldArchitectMover::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::metal_interface::RemoveMetalConnectionsMover::remove_variant_types_from_res(), protocols::denovo_design::components::reorder_chains(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), 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::IdealAbegoGenerator::retrieve_loop_abegos(), 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::denovo_design::filters::SSPredictionFilter::set_blueprint_file(), 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::analysis::InterfaceAnalyzerMover::set_pack_input(), protocols::analysis::InterfaceAnalyzerMover::set_pack_separated(), 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::LigandBindingAssemblyMover::set_up_assembly(), protocols::sewing::movers::AppendAssemblyMover::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::denovo_design::movers::FoldArchitectMover::setup_from_xml_tag(), protocols::tcr::setup_fw_template_from_db(), protocols::glycopeptide_docking::setup_glycosylation_foldtree(), 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::glycopeptide_docking::write_debug_pdb(), 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().