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protocols::moves Namespace Reference

Classes

class  ChangeFoldTreeMover
 
class  CompositionMover
 
class  CycleMover
 CycleMover iterates through its vector of Movers one at a time over many calls to apply(). More...
 
class  CyclicMover
 A simple class for cycling between movers in consecutive calls to apply() More...
 
class  DsspMover
 
class  DsspMoverCreator
 
class  DualMonteCarlo
 
class  EXCN_Converged
 
class  FastLinearFunc
 
class  FilterMover
 
class  FilterReportAsPoseExtraScoresMover
 This Mover runs a Filter and dumps the report_sm value to Pose's extra scores (for later JD reporting) To do the same for all filters, use WriteFiltersToPose. More...
 
class  FilterReportAsPoseExtraScoresMoverCreator
 
class  FilterReporterMover
 A FilterMover that also calls report() on apply() More...
 
class  GeometricFunc
 Ramps rapidly from the starting value to the final value. Not 1 at x=1. Doesn't really finish at (1,1). func(x) = 1 - exp( -1 * x * inv_xval_at_0p5 * 0.6931 );. More...
 
class  IfMover
 
class  IfMoverCreator
 
class  InvGeometricFunc
 Ramps slowly from the starting value to the final value Non-zero for x = 0. Doesn't really start at (0,0). func(x) = exp( -1 * ( 1 - x ) / ( 1 - xval_at_0p5 ) * 0.6931 );. More...
 
class  IteratedConvergenceMover
 A mover that repeatedly applies a sub-mover (up to a given maximum) until the given filter returns values within a certain delta for a given number of cycles. More...
 
class  IteratedConvergenceMoverCreator
 
class  JumpOutMover
 
class  LinearFunc
 
class  MCShowMover
 
class  MonteCarlo
 This object is responsible for all of the major functions needed in a Monte Carlo simulation. Its main purpose is to apply the Metropolis Criterion on a pose, based on a ScoreFunction, temperature, and the previously accepted pose. It stores the lowest-energy pose ecountered, the last-accepted pose in the simulation, and various other statistics. More...
 
class  MonteCarloExceptionConverge
 
class  MonteCarloUtil
 the MCResetMover applies a monte carlo reset More...
 
class  MoveMapMover
 
class  Mover
 
class  MoverApplyingMover
 
class  MoverContainer
 
class  MoverCreator
 Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class. More...
 
class  MoverFactory
 
class  MoverForPoseList
 
class  MoverRegistrator
 This templated class will register an instance of an MoverCreator (class T) with the MoverFactory. It will ensure that no MoverCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
 
class  MoverStatistics
 
class  NullMover
 
class  PDBDumpMover
 
class  PoseCondition
 
class  ProfilerMover
 
class  PyMOLMover
 Special Mover designed to send Pose information into PyMOL instance running. More...
 
class  PyMOLMoverCreator
 
class  PyMOLObserver
 Special Observer which apply PyMOLMover if Pose is changed. More...
 
class  RampingFunc
 
class  RampingMover
 
class  RampingMoverCreator
 
class  RandomMover
 RandomMover picks a random move and applies it. More...
 
class  RandomMoverCreator
 
class  RepeatMover
 A Mover that repeats an input Mover a user-specified number of times. More...
 
class  ReplicaExchangeMC
 
class  ResId
 
class  SequenceMover
 A Mover that iterates through a vector of Movers, applying each one sequentially. More...
 
class  SimulatedTempering
 
class  StructureRestrictor
 
class  SwitchMover
 SwitchMover can hold multiple movers and execute only the requested one. More...
 
class  SwitchMoverCreator
 
class  TrialCounter
 
class  TrialMover
 A TrialMover applies a Mover and then accepts or rejects the move according to a MonteCarlo object. More...
 
class  UDPSocketClient
 PyMOLMover helper class. Handle low level UDP transactions stuff. This is a port of original Python version of UDP socket client written writen for PyRosetta. More...
 
class  VectorPoseMover
 A simple class used for a mover that acts on a vector of poses More...
 
class  WhileMover
 

Typedefs

typedef
utility::pointer::shared_ptr
< ChangeFoldTreeMover
ChangeFoldTreeMoverOP
 
typedef
utility::pointer::shared_ptr
< ChangeFoldTreeMover const > 
ChangeFoldTreeMoverCOP
 
typedef
utility::pointer::shared_ptr
< CompositionMover
CompositionMoverOP
 
typedef
utility::pointer::shared_ptr
< CompositionMover const > 
CompositionMoverCOP
 
typedef
utility::pointer::shared_ptr
< CyclicMover
CyclicMoverOP
 
typedef
utility::pointer::shared_ptr
< CyclicMover const > 
CyclicMoverCOP
 
typedef
utility::pointer::shared_ptr
< DsspMover
DsspMoverOP
 
typedef
utility::pointer::shared_ptr
< DualMonteCarlo
DualMonteCarloOP
 
typedef
utility::pointer::shared_ptr
< DualMonteCarlo const > 
DualMonteCarloCOP
 
typedef
utility::pointer::shared_ptr
< FilterMover
FilterMoverOP
 
typedef
utility::pointer::shared_ptr
< FilterReportAsPoseExtraScoresMover
FilterReportAsPoseExtraScoresMoverOP
 
typedef
utility::pointer::shared_ptr
< FilterReportAsPoseExtraScoresMover
const > 
FilterReportAsPoseExtraScoresMoverCOP
 
typedef
utility::pointer::shared_ptr
< FilterReporterMover
FilterReporterMoverOP
 
typedef
utility::pointer::shared_ptr
< FilterReporterMover const > 
FilterReporterMoverCOP
 
typedef
utility::pointer::shared_ptr
< IteratedConvergenceMover
IteratedConvergenceMoverOP
 
typedef
utility::pointer::shared_ptr
< IteratedConvergenceMover
const > 
IteratedConvergenceMoverCOP
 
typedef
utility::pointer::shared_ptr
< JumpOutMover
JumpOutMoverOP
 
typedef
utility::pointer::shared_ptr
< JumpOutMover const > 
JumpOutMoverCOP
 
typedef
utility::pointer::shared_ptr
< MonteCarlo
MonteCarloOP
 
typedef
utility::pointer::shared_ptr
< MonteCarlo const > 
MonteCarloCOP
 
typedef
utility::pointer::shared_ptr
< MonteCarloExceptionConverge
MonteCarloExceptionConvergeOP
 
typedef
utility::pointer::shared_ptr
< MonteCarloExceptionConverge
const > 
MonteCarloExceptionConvergeCOP
 
typedef
utility::pointer::shared_ptr
< MoveMapMover
MoveMapMoverOP
 
typedef
utility::pointer::shared_ptr
< MoveMapMover const > 
MoveMapMoverCOP
 
typedef
utility::pointer::shared_ptr
< Mover
MoverOP
 
typedef
utility::pointer::shared_ptr
< Mover const > 
MoverCOP
 
typedef
utility::pointer::weak_ptr
< Mover
MoverAP
 
typedef
utility::pointer::weak_ptr
< Mover const > 
MoverCAP
 
typedef std::map< std::string
const, MoverOP
Movers_map
 
typedef
utility::pointer::shared_ptr
< Movers_map
Movers_mapOP
 
typedef
utility::pointer::shared_ptr
< Movers_map const > 
Movers_mapCOP
 
typedef std::map< std::string,
std::string > 
MoverCache
 
typedef
utility::pointer::shared_ptr
< MoverCache
MoverCacheOP
 
typedef
utility::pointer::shared_ptr
< MoverApplyingMover
MoverApplyingMoverOP
 
typedef
utility::pointer::shared_ptr
< MoverApplyingMover const > 
MoverApplyingMoverCOP
 
typedef
utility::pointer::shared_ptr
< MoverContainer
MoverContainerOP
 
typedef
utility::pointer::shared_ptr
< MoverContainer const > 
MoverContainerCOP
 
typedef
utility::pointer::shared_ptr
< SequenceMover
SequenceMoverOP
 
typedef
utility::pointer::shared_ptr
< SequenceMover const > 
SequenceMoverCOP
 
typedef
utility::pointer::shared_ptr
< RandomMover
RandomMoverOP
 
typedef
utility::pointer::shared_ptr
< RandomMover const > 
RandomMoverCOP
 
typedef
utility::pointer::shared_ptr
< CycleMover
CycleMoverOP
 
typedef
utility::pointer::shared_ptr
< CycleMover const > 
CycleMoverCOP
 
typedef
utility::pointer::shared_ptr
< SwitchMover
SwitchMoverOP
 
typedef
utility::pointer::shared_ptr
< SwitchMover const > 
SwitchMoverCOP
 
typedef
utility::pointer::shared_ptr
< MoverCreator
MoverCreatorOP
 
typedef
utility::pointer::shared_ptr
< MoverCreator const > 
MoverCreatorCOP
 
typedef
utility::pointer::shared_ptr
< MoverFactory
MoverFactoryOP
 
typedef
utility::pointer::shared_ptr
< MoverFactory const > 
MoverFactoryCOP
 
typedef
utility::pointer::shared_ptr
< MoverForPoseList
MoverForPoseListOP
 
typedef
utility::pointer::shared_ptr
< MoverForPoseList const > 
MoverForPoseListCOP
 
using Real = core::Real
 
typedef
utility::pointer::shared_ptr
< NullMover
NullMoverOP
 
typedef
utility::pointer::shared_ptr
< NullMover const > 
NullMoverCOP
 
typedef
utility::pointer::shared_ptr
< PDBDumpMover
PDBDumpMoverOP
 
typedef
utility::pointer::shared_ptr
< PDBDumpMover const > 
PDBDumpMoverCOP
 
typedef
utility::pointer::shared_ptr
< ProfilerMover
ProfilerMoverOP
 
typedef
utility::pointer::shared_ptr
< ProfilerMover const > 
ProfilerMoverCOP
 
typedef
utility::pointer::shared_ptr
< MCShowMover
MCShowMoverOP
 
typedef
utility::pointer::shared_ptr
< MCShowMover const > 
MCShowMoverCOP
 
typedef
utility::pointer::shared_ptr
< PyMOLMover
PyMOLMoverOP
 
typedef
utility::pointer::shared_ptr
< PyMOLMover const > 
PyMOLMoverCOP
 
typedef
utility::pointer::shared_ptr
< PyMOLObserver
PyMOLObserverOP
 
typedef
utility::pointer::shared_ptr
< PyMOLObserver const > 
PyMOLObserverCOP
 
typedef
utility::pointer::shared_ptr
< RampingMover
RampingMoverOP
 
typedef
utility::pointer::shared_ptr
< RampingMover const > 
RampingMoverCOP
 
typedef
utility::pointer::shared_ptr
< RampingFunc
RampingFuncOP
 
typedef
utility::pointer::shared_ptr
< RampingFunc const > 
RampingFuncCOP
 
typedef
utility::pointer::shared_ptr
< RepeatMover
RepeatMoverOP
 
typedef
utility::pointer::shared_ptr
< RepeatMover const > 
RepeatMoverCOP
 
typedef
utility::pointer::shared_ptr
< ReplicaExchangeMC
ReplicaExchangeMC_OP
 
typedef
utility::pointer::shared_ptr
< ReplicaExchangeMC const > 
ReplicaExchangeMC_COP
 
typedef
utility::pointer::shared_ptr
< ResId
ResIdOP
 
typedef
utility::pointer::shared_ptr
< ResId const > 
ResIdCOP
 
typedef
utility::pointer::shared_ptr
< SimulatedTempering
SimulatedTemperingOP
 
typedef
utility::pointer::shared_ptr
< StructureRestrictor
StructureRestrictorOP
 
typedef
utility::pointer::shared_ptr
< StructureRestrictor const > 
StructureRestrictorCOP
 
typedef
utility::pointer::shared_ptr
< TrialCounter
TrialCounterOP
 
typedef
utility::pointer::shared_ptr
< TrialCounter const > 
TrialCounterCOP
 
typedef
utility::pointer::shared_ptr
< TrialMover
TrialMoverOP
 
typedef
utility::pointer::shared_ptr
< TrialMover const > 
TrialMoverCOP
 
typedef
utility::pointer::shared_ptr
< VectorPoseMover
VectorPoseMoverOP
 
typedef
utility::pointer::shared_ptr
< VectorPoseMover const > 
VectorPoseMoverCOP
 
typedef
utility::pointer::shared_ptr
< WhileMover
WhileMoverOP
 
typedef
utility::pointer::shared_ptr
< WhileMover const > 
WhileMoverCOP
 
typedef
utility::pointer::shared_ptr
< PoseCondition
PoseConditionOP
 
typedef
utility::pointer::shared_ptr
< PoseCondition const > 
PoseConditionCOP
 

Enumerations

enum  MCA { MCA_accepted_score_beat_low =3, MCA_accepted_score_beat_last =2, MCA_accepted_thermally =1, MCA_rejected =0 }
 
enum  MoverStatus {
  MS_SUCCESS = 0, FAIL_RETRY, FAIL_DO_NOT_RETRY, FAIL_BAD_INPUT,
  FAIL, MS_FAIL_RETRY = FAIL_RETRY, MS_FAIL_DO_NOT_RETRY = FAIL_DO_NOT_RETRY, MS_FAIL_BAD_INPUT = FAIL_BAD_INPUT,
  MS_FAIL = FAIL
}
 return status for movers - mover was successful, failed but can be retried, etc; used mostly by job dist. More...
 
enum  X11Colors {
  XC_first_color = 0, XC_black = XC_first_color, XC_AntiqueWhite = 1, XC_BlanchedAlmond = 2,
  XC_BlueViolet = 3, XC_CadetBlue = 4, XC_CornflowerBlue = 5, XC_DarkBlue = 6,
  XC_DarkCyan = 7, XC_DarkGoldenrod = 8, XC_DarkGray = 9, XC_DarkGreen = 10,
  XC_DarkGrey = 11, XC_DarkKhaki = 12, XC_DarkMagenta = 13, XC_DarkOliveGreen = 14,
  XC_DarkOrange = 15, XC_DarkOrchid = 16, XC_DarkRed = 17, XC_DarkSalmon = 18,
  XC_DarkSeaGreen = 19, XC_DarkSlateBlue = 20, XC_DarkSlateGray = 21, XC_DarkSlateGrey = 22,
  XC_DarkTurquoise = 23, XC_DarkViolet = 24, XC_DebianRed = 25, XC_DeepPink = 26,
  XC_DeepSkyBlue = 27, XC_DimGray = 28, XC_DimGrey = 29, XC_DodgerBlue = 30,
  XC_FloralWhite = 31, XC_ForestGreen = 32, XC_GhostWhite = 33, XC_GreenYellow = 34,
  XC_HotPink = 35, XC_IndianRed = 36, XC_LavenderBlush = 37, XC_LawnGreen = 38,
  XC_LemonChiffon = 39, XC_LightBlue = 40, XC_LightCoral = 41, XC_LightCyan = 42,
  XC_LightGoldenrod = 43, XC_LightGoldenrodYellow = 44, XC_LightGray = 45, XC_LightGreen = 46,
  XC_LightGrey = 47, XC_LightPink = 48, XC_LightSalmon = 49, XC_LightSeaGreen = 50,
  XC_LightSkyBlue = 51, XC_LightSlateBlue = 52, XC_LightSlateGray = 53, XC_LightSlateGrey = 54,
  XC_LightSteelBlue = 55, XC_LightYellow = 56, XC_LimeGreen = 57, XC_MediumAquamarine = 58,
  XC_MediumBlue = 59, XC_MediumOrchid = 60, XC_MediumPurple = 61, XC_MediumSeaGreen = 62,
  XC_MediumSlateBlue = 63, XC_MediumSpringGreen = 64, XC_MediumTurquoise = 65, XC_MediumVioletRed = 66,
  XC_MidnightBlue = 67, XC_MintCream = 68, XC_MistyRose = 69, XC_NavajoWhite = 70,
  XC_NavyBlue = 71, XC_OldLace = 72, XC_OliveDrab = 73, XC_OrangeRed = 74,
  XC_PaleGoldenrod = 75, XC_PaleGreen = 76, XC_PaleTurquoise = 77, XC_PaleVioletRed = 78,
  XC_PapayaWhip = 79, XC_PeachPuff = 80, XC_PowderBlue = 81, XC_RosyBrown = 82,
  XC_RoyalBlue = 83, XC_SaddleBrown = 84, XC_SandyBrown = 85, XC_SeaGreen = 86,
  XC_SkyBlue = 87, XC_SlateBlue = 88, XC_SlateGray = 89, XC_SlateGrey = 90,
  XC_SpringGreen = 91, XC_SteelBlue = 92, XC_VioletRed = 93, XC_WhiteSmoke = 94,
  XC_YellowGreen = 95, XC_aquamarine = 96, XC_azure = 97, XC_beige = 98,
  XC_bisque = 99, XC_AliceBlue = 100, XC_blue = 101, XC_blue1 = 102,
  XC_blue2 = 103, XC_blue3 = 104, XC_blue4 = 105, XC_brown = 106,
  XC_burlywood = 107, XC_chartreuse = 108, XC_chocolate = 109, XC_coral = 110,
  XC_cornsilk = 111, XC_cyan = 112, XC_firebrick = 113, XC_gainsboro = 114,
  XC_gold = 115, XC_goldenrod = 116, XC_gray = 117, XC_gray0 = 118,
  XC_gray10 = 119, XC_gray100 = 120, XC_gray20 = 121, XC_gray30 = 122,
  XC_gray40 = 123, XC_gray50 = 124, XC_gray60 = 125, XC_gray70 = 126,
  XC_gray80 = 127, XC_gray90 = 128, XC_green = 129, XC_green1 = 130,
  XC_green2 = 131, XC_green3 = 132, XC_green4 = 133, XC_honeydew = 134,
  XC_ivory = 135, XC_khaki = 136, XC_lavender = 137, XC_linen = 138,
  XC_magenta = 139, XC_maroon = 140, XC_moccasin = 141, XC_navy = 142,
  XC_orange = 143, XC_orchid = 144, XC_peru = 145, XC_pink = 146,
  XC_plum = 147, XC_purple = 148, XC_red = 149, XC_red1 = 150,
  XC_red2 = 151, XC_red3 = 152, XC_red4 = 153, XC_salmon = 154,
  XC_seashell = 155, XC_sienna = 156, XC_snow = 157, XC_snow1 = 158,
  XC_snow2 = 159, XC_snow3 = 160, XC_snow4 = 161, XC_tan = 162,
  XC_thistle = 163, XC_tomato = 164, XC_turquoise = 165, XC_violet = 166,
  XC_wheat = 167, XC_white = 168, XC_yellow = 169, XC_last_color
}
 
enum  StatsType { all_stats = 1, accept_reject, no_stats }
 A TrialMover applies a Mover and then accepts or rejects the move according to a MonteCarlo object. More...
 

Functions

std::ostream & operator<< (std::ostream &os, FilterReportAsPoseExtraScoresMover const &mover)
 
static basic::Tracer TR ("protocols.moves.IfMover")
 
static basic::Tracer TR ("protocols.moves.IteratedConvergenceMover")
 
std::ostream & operator<< (std::ostream &os, MonteCarlo const &mc)
 
std::string to_string (MCA const &mc_accepted)
 
static basic::Tracer TR ("protocols.moves.Mover")
 
std::string complex_type_name_for_mover (std::string const &mover_name)
 
void xsd_type_definition_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &mover_type, std::string const &description, utility::tag::AttributeList const &attributes)
 Define the XML schema definition for a Mover that contains no subtags but may contain any number of attributes (aka options). More...
 
void xsd_type_definition_w_attributes_and_repeatable_subelements (utility::tag::XMLSchemaDefinition &xsd, std::string const &mover_type, std::string const &description, utility::tag::AttributeList const &attributes, utility::tag::XMLSchemaSimpleSubelementList const &subelements)
 Define the XML schema definition for a Mover that contains subtags attributes (aka options). More...
 
std::ostream & operator<< (std::ostream &os, MoverContainer const &mover)
 
static basic::Tracer TR ("protocols.moves.MoverFactory")
 
MoverStatus mstype_from_name (std::string const &name)
 
static basic::Tracer TR ("protocols.moves.PyMOLMover")
 
numeric::random::uniform_RG_OP getRG ()
 
std::ostream & operator<< (std::ostream &output, UDPSocketClient const &client)
 
utility::vector1< numeric::Real > get_energies (core::pose::Pose const &pose, core::scoring::ScoreType energy_type)
 Returns a list of energies of type energy_type from the pose. More...
 
std::ostream & operator<< (std::ostream &output, PyMOLMover const &mover)
 End Xiyao's Code. More...
 
PyMOLObserverOP get_pymol_observer (core::pose::Pose &pose)
 (Internal) helper function to create a PyMOLObserver and add it to the given pose NOTE: You NEED to adjust the observer type and call attach() on the return - by default a new PyMOLObserver isn't attached/observing. More...
 
PyMOLObserverOP AddPyMOLObserver (core::pose::Pose &p, bool keep_history=false, core::Real update_interval=0)
 Helper function that create PyMOLObserver Object and add it to the give Pose. This is the most likely the only function that you need to call... More...
 
PyMOLObserverOP AddPyMOLObserver_to_energies (core::pose::Pose &p, bool keep_history=false, core::Real update_interval=0)
 Helper function that create PyMOLObserver Object and add it to the give Pose energies object so pymol only updates on energy changes. More...
 
PyMOLObserverOP AddPyMOLObserver_to_conformation (core::pose::Pose &p, bool keep_history=false, core::Real update_interval=0)
 Helper function that create PyMOLObserver Object and add it to the give Pose conformation object so pymol only updates on conformation changes. More...
 
PyMOLObserver::ObserverType operator| (PyMOLObserver::ObserverType &l, PyMOLObserver::ObserverType &r)
 
static basic::Tracer TR ("protocols.moves.RampingMover")
 
std::ostream & operator<< (std::ostream &os, RepeatMover const &mover)
 
void modify_ResId_based_object (utility::pointer::ReferenceCountOP const obj, core::Size const resid)
 Checks whether a referencecount object is a derived from ResId and if so, sets its resid. More...
 
static basic::Tracer tr ("protocols.TrialMover")
 
std::ostream & operator<< (std::ostream &os, TrialMover const &mover)
 
protocols::moves::MoverOP find_mover_or_die (const std::string &mover_name, utility::tag::TagCOP tag, const protocols::moves::Movers_map &movers)
 Searches <movers> for the named mover, returning it if it exists, otherwise halts execution with an error message. More...
 
protocols::filters::FilterOP find_filter_or_die (const std::string &filter_name, utility::tag::TagCOP tag, const protocols::filters::Filters_map &filters)
 Searches <filters> for the named filter, returning it if it exists, otherwise halts execution with an error message. More...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< ChangeFoldTreeMover const > protocols::moves::ChangeFoldTreeMoverCOP
typedef utility::pointer::shared_ptr< ChangeFoldTreeMover > protocols::moves::ChangeFoldTreeMoverOP
typedef utility::pointer::shared_ptr< CompositionMover const > protocols::moves::CompositionMoverCOP
typedef utility::pointer::shared_ptr< CompositionMover > protocols::moves::CompositionMoverOP
typedef utility::pointer::shared_ptr< CycleMover const > protocols::moves::CycleMoverCOP
typedef utility::pointer::shared_ptr< CycleMover > protocols::moves::CycleMoverOP
typedef utility::pointer::shared_ptr<CyclicMover const> protocols::moves::CyclicMoverCOP
typedef utility::pointer::shared_ptr<CyclicMover> protocols::moves::CyclicMoverOP
typedef utility::pointer::shared_ptr< DsspMover > protocols::moves::DsspMoverOP
typedef utility::pointer::shared_ptr< DualMonteCarlo const > protocols::moves::DualMonteCarloCOP
typedef utility::pointer::shared_ptr< DualMonteCarlo > protocols::moves::DualMonteCarloOP
typedef utility::pointer::shared_ptr< FilterMover > protocols::moves::FilterMoverOP
typedef utility::pointer::shared_ptr<FilterReporterMover const> protocols::moves::FilterReporterMoverCOP
typedef utility::pointer::shared_ptr<FilterReporterMover> protocols::moves::FilterReporterMoverOP
typedef utility::pointer::shared_ptr< IteratedConvergenceMover const > protocols::moves::IteratedConvergenceMoverCOP
typedef utility::pointer::shared_ptr< JumpOutMover const > protocols::moves::JumpOutMoverCOP
typedef utility::pointer::shared_ptr< JumpOutMover > protocols::moves::JumpOutMoverOP
typedef utility::pointer::shared_ptr< MCShowMover const > protocols::moves::MCShowMoverCOP
typedef utility::pointer::shared_ptr< MCShowMover > protocols::moves::MCShowMoverOP
typedef utility::pointer::shared_ptr< MonteCarlo const > protocols::moves::MonteCarloCOP
typedef utility::pointer::shared_ptr< MonteCarlo > protocols::moves::MonteCarloOP
typedef utility::pointer::shared_ptr< MoveMapMover const > protocols::moves::MoveMapMoverCOP
typedef utility::pointer::shared_ptr< MoveMapMover > protocols::moves::MoveMapMoverOP
typedef utility::pointer::weak_ptr< Mover > protocols::moves::MoverAP
typedef utility::pointer::shared_ptr< MoverApplyingMover const > protocols::moves::MoverApplyingMoverCOP
typedef utility::pointer::shared_ptr< MoverApplyingMover > protocols::moves::MoverApplyingMoverOP
typedef std::map< std::string, std::string > protocols::moves::MoverCache
typedef utility::pointer::shared_ptr< MoverCache > protocols::moves::MoverCacheOP
typedef utility::pointer::weak_ptr< Mover const > protocols::moves::MoverCAP
typedef utility::pointer::shared_ptr< MoverContainer const > protocols::moves::MoverContainerCOP
typedef utility::pointer::shared_ptr< MoverContainer > protocols::moves::MoverContainerOP
typedef utility::pointer::shared_ptr< Mover const > protocols::moves::MoverCOP
typedef utility::pointer::shared_ptr< MoverCreator const > protocols::moves::MoverCreatorCOP
typedef utility::pointer::shared_ptr< MoverCreator > protocols::moves::MoverCreatorOP
typedef utility::pointer::shared_ptr< MoverFactory const > protocols::moves::MoverFactoryCOP
typedef utility::pointer::shared_ptr< MoverFactory > protocols::moves::MoverFactoryOP
typedef utility::pointer::shared_ptr< MoverForPoseList const > protocols::moves::MoverForPoseListCOP
typedef utility::pointer::shared_ptr< MoverForPoseList > protocols::moves::MoverForPoseListOP
typedef utility::pointer::shared_ptr< Mover > protocols::moves::MoverOP
typedef std::map< std::string const, MoverOP > protocols::moves::Movers_map
typedef utility::pointer::shared_ptr< Movers_map const > protocols::moves::Movers_mapCOP
typedef utility::pointer::shared_ptr< Movers_map > protocols::moves::Movers_mapOP
typedef utility::pointer::shared_ptr< NullMover const > protocols::moves::NullMoverCOP
typedef utility::pointer::shared_ptr< NullMover > protocols::moves::NullMoverOP
typedef utility::pointer::shared_ptr< PDBDumpMover const > protocols::moves::PDBDumpMoverCOP
typedef utility::pointer::shared_ptr< PDBDumpMover > protocols::moves::PDBDumpMoverOP
typedef utility::pointer::shared_ptr< PoseCondition const > protocols::moves::PoseConditionCOP
typedef utility::pointer::shared_ptr< PoseCondition > protocols::moves::PoseConditionOP
typedef utility::pointer::shared_ptr< ProfilerMover const > protocols::moves::ProfilerMoverCOP
typedef utility::pointer::shared_ptr< ProfilerMover > protocols::moves::ProfilerMoverOP
typedef utility::pointer::shared_ptr< PyMOLMover const > protocols::moves::PyMOLMoverCOP
typedef utility::pointer::shared_ptr< PyMOLMover > protocols::moves::PyMOLMoverOP
typedef utility::pointer::shared_ptr< PyMOLObserver const > protocols::moves::PyMOLObserverCOP
typedef utility::pointer::shared_ptr< PyMOLObserver > protocols::moves::PyMOLObserverOP
typedef utility::pointer::shared_ptr< RampingFunc const > protocols::moves::RampingFuncCOP
typedef utility::pointer::shared_ptr< RampingFunc > protocols::moves::RampingFuncOP
typedef utility::pointer::shared_ptr< RampingMover const > protocols::moves::RampingMoverCOP
typedef utility::pointer::shared_ptr< RampingMover > protocols::moves::RampingMoverOP
typedef utility::pointer::shared_ptr< RandomMover const > protocols::moves::RandomMoverCOP
typedef utility::pointer::shared_ptr< RandomMover > protocols::moves::RandomMoverOP
typedef utility::pointer::shared_ptr< RepeatMover const > protocols::moves::RepeatMoverCOP
typedef utility::pointer::shared_ptr< RepeatMover > protocols::moves::RepeatMoverOP
typedef utility::pointer::shared_ptr< ReplicaExchangeMC const > protocols::moves::ReplicaExchangeMC_COP
typedef utility::pointer::shared_ptr< ReplicaExchangeMC > protocols::moves::ReplicaExchangeMC_OP
typedef utility::pointer::shared_ptr< ResId const > protocols::moves::ResIdCOP
typedef utility::pointer::shared_ptr< ResId > protocols::moves::ResIdOP
typedef utility::pointer::shared_ptr< SequenceMover const > protocols::moves::SequenceMoverCOP
typedef utility::pointer::shared_ptr< SequenceMover > protocols::moves::SequenceMoverOP
typedef utility::pointer::shared_ptr<SimulatedTempering> protocols::moves::SimulatedTemperingOP
typedef utility::pointer::shared_ptr< StructureRestrictor const > protocols::moves::StructureRestrictorCOP
typedef utility::pointer::shared_ptr< StructureRestrictor > protocols::moves::StructureRestrictorOP
typedef utility::pointer::shared_ptr< SwitchMover const > protocols::moves::SwitchMoverCOP
typedef utility::pointer::shared_ptr< SwitchMover > protocols::moves::SwitchMoverOP
typedef utility::pointer::shared_ptr< TrialCounter const > protocols::moves::TrialCounterCOP
typedef utility::pointer::shared_ptr< TrialCounter > protocols::moves::TrialCounterOP
typedef utility::pointer::shared_ptr< TrialMover const > protocols::moves::TrialMoverCOP
typedef utility::pointer::shared_ptr< TrialMover > protocols::moves::TrialMoverOP
typedef utility::pointer::shared_ptr<VectorPoseMover const> protocols::moves::VectorPoseMoverCOP
typedef utility::pointer::shared_ptr<VectorPoseMover> protocols::moves::VectorPoseMoverOP
typedef utility::pointer::shared_ptr< WhileMover const > protocols::moves::WhileMoverCOP
typedef utility::pointer::shared_ptr< WhileMover > protocols::moves::WhileMoverOP

Enumeration Type Documentation

Enumerator
MCA_accepted_score_beat_low 
MCA_accepted_score_beat_last 
MCA_accepted_thermally 
MCA_rejected 

return status for movers - mover was successful, failed but can be retried, etc; used mostly by job dist.

Documention for individual codes from SML, and reflects the original intent behind them (more than current usage)

Enumerator
MS_SUCCESS 

MS_SUCCESS: job succeeds.

FAIL_RETRY 

FAIL_RETRY: The job failed in a "science-y" way (rather than a "programmatic" way). E.g. this particular docking run failed an RMSD filter, but there's no reason to believe it's not just trapped in a bad region of conformational space due to the stochasticity of Monte Carlo.

FAIL_DO_NOT_RETRY 

FAIL_DO_NOT_RETRY: This particular job should not be re-attempted, but there wasn't anything structurally wrong with it - it was a valid job, but its output is uninteresting, so toss it and move on.

FAIL_BAD_INPUT 

FAIL_BAD_INPUT: This job has something structurally wrong with it/its input and can never be completed. Other jobs of the same input (same InnerJob / stuff that differs only by its nstruct index) will by definition fail in the same fashion, so short-circuit those failures and pre-emptively cancel those jobs when possible. This probably means there is a user input problem.

FAIL 

FAIL: ??? Unknown usage (not obeyed by JD2).

MS_FAIL_RETRY 
MS_FAIL_DO_NOT_RETRY 
MS_FAIL_BAD_INPUT 
MS_FAIL 

A TrialMover applies a Mover and then accepts or rejects the move according to a MonteCarlo object.

: Each derived class should define its own apply() statement the apply (mc) which requires a monte carlo object and only keeps the move if the monte carlo test allows it

Author
Monica Berrondo
Enumerator
all_stats 
accept_reject 
no_stats 
Enumerator
XC_first_color 
XC_black 
XC_AntiqueWhite 
XC_BlanchedAlmond 
XC_BlueViolet 
XC_CadetBlue 
XC_CornflowerBlue 
XC_DarkBlue 
XC_DarkCyan 
XC_DarkGoldenrod 
XC_DarkGray 
XC_DarkGreen 
XC_DarkGrey 
XC_DarkKhaki 
XC_DarkMagenta 
XC_DarkOliveGreen 
XC_DarkOrange 
XC_DarkOrchid 
XC_DarkRed 
XC_DarkSalmon 
XC_DarkSeaGreen 
XC_DarkSlateBlue 
XC_DarkSlateGray 
XC_DarkSlateGrey 
XC_DarkTurquoise 
XC_DarkViolet 
XC_DebianRed 
XC_DeepPink 
XC_DeepSkyBlue 
XC_DimGray 
XC_DimGrey 
XC_DodgerBlue 
XC_FloralWhite 
XC_ForestGreen 
XC_GhostWhite 
XC_GreenYellow 
XC_HotPink 
XC_IndianRed 
XC_LavenderBlush 
XC_LawnGreen 
XC_LemonChiffon 
XC_LightBlue 
XC_LightCoral 
XC_LightCyan 
XC_LightGoldenrod 
XC_LightGoldenrodYellow 
XC_LightGray 
XC_LightGreen 
XC_LightGrey 
XC_LightPink 
XC_LightSalmon 
XC_LightSeaGreen 
XC_LightSkyBlue 
XC_LightSlateBlue 
XC_LightSlateGray 
XC_LightSlateGrey 
XC_LightSteelBlue 
XC_LightYellow 
XC_LimeGreen 
XC_MediumAquamarine 
XC_MediumBlue 
XC_MediumOrchid 
XC_MediumPurple 
XC_MediumSeaGreen 
XC_MediumSlateBlue 
XC_MediumSpringGreen 
XC_MediumTurquoise 
XC_MediumVioletRed 
XC_MidnightBlue 
XC_MintCream 
XC_MistyRose 
XC_NavajoWhite 
XC_NavyBlue 
XC_OldLace 
XC_OliveDrab 
XC_OrangeRed 
XC_PaleGoldenrod 
XC_PaleGreen 
XC_PaleTurquoise 
XC_PaleVioletRed 
XC_PapayaWhip 
XC_PeachPuff 
XC_PowderBlue 
XC_RosyBrown 
XC_RoyalBlue 
XC_SaddleBrown 
XC_SandyBrown 
XC_SeaGreen 
XC_SkyBlue 
XC_SlateBlue 
XC_SlateGray 
XC_SlateGrey 
XC_SpringGreen 
XC_SteelBlue 
XC_VioletRed 
XC_WhiteSmoke 
XC_YellowGreen 
XC_aquamarine 
XC_azure 
XC_beige 
XC_bisque 
XC_AliceBlue 
XC_blue 
XC_blue1 
XC_blue2 
XC_blue3 
XC_blue4 
XC_brown 
XC_burlywood 
XC_chartreuse 
XC_chocolate 
XC_coral 
XC_cornsilk 
XC_cyan 
XC_firebrick 
XC_gainsboro 
XC_gold 
XC_goldenrod 
XC_gray 
XC_gray0 
XC_gray10 
XC_gray100 
XC_gray20 
XC_gray30 
XC_gray40 
XC_gray50 
XC_gray60 
XC_gray70 
XC_gray80 
XC_gray90 
XC_green 
XC_green1 
XC_green2 
XC_green3 
XC_green4 
XC_honeydew 
XC_ivory 
XC_khaki 
XC_lavender 
XC_linen 
XC_magenta 
XC_maroon 
XC_moccasin 
XC_navy 
XC_orange 
XC_orchid 
XC_peru 
XC_pink 
XC_plum 
XC_purple 
XC_red 
XC_red1 
XC_red2 
XC_red3 
XC_red4 
XC_salmon 
XC_seashell 
XC_sienna 
XC_snow 
XC_snow1 
XC_snow2 
XC_snow3 
XC_snow4 
XC_tan 
XC_thistle 
XC_tomato 
XC_turquoise 
XC_violet 
XC_wheat 
XC_white 
XC_yellow 
XC_last_color 

Function Documentation

PyMOLObserverOP protocols::moves::AddPyMOLObserver ( core::pose::Pose p,
bool  keep_history,
core::Real  update_interval 
)
PyMOLObserverOP protocols::moves::AddPyMOLObserver_to_conformation ( core::pose::Pose p,
bool  keep_history,
core::Real  update_interval 
)

Helper function that create PyMOLObserver Object and add it to the give Pose conformation object so pymol only updates on conformation changes.

References protocols::moves::PyMOLObserver::conformation_observer, and get_pymol_observer().

Referenced by protocols::jd2::JobDistributor::setup_pymol_observer().

PyMOLObserverOP protocols::moves::AddPyMOLObserver_to_energies ( core::pose::Pose p,
bool  keep_history,
core::Real  update_interval 
)

Helper function that create PyMOLObserver Object and add it to the give Pose energies object so pymol only updates on energy changes.

References protocols::moves::PyMOLObserver::energy_observer, and get_pymol_observer().

Referenced by protocols::jd2::JobDistributor::setup_pymol_observer().

std::string protocols::moves::complex_type_name_for_mover ( std::string const &  mover_name)

Referenced by protocols::multistage_rosetta_scripts::MRSJobQueen::append_common_tag_subelements(), protocols::rigid::UniformRigidBodyMover::complex_type_gen(), protocols::grafting::AnchoredGraftMover::complex_type_generator_for_anchored_graft_mover(), protocols::simple_moves::BackboneMover::complex_type_generator_for_backbone_mover(), protocols::relax::FastRelax::complex_type_generator_for_fast_relax(), protocols::minimization_packing::MinMover::complex_type_generator_for_min_mover(), protocols::minimization_packing::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover(), protocols::minimization_packing::RotamerTrialsMover::complex_type_generator_for_rotamer_trials_mover(), protocols::legacy_sewing::LegacyAssemblyMover::define_assembly_mover_ct_gen(), protocols::loop_modeling::LoopMover::define_composition_schema(), protocols::monte_carlo::GenericMonteCarloMover::define_composition_schema(), protocols::simple_ddg::ddG::define_ddG_schema(), protocols::moves::MoverFactory::define_mover_xml_schema(), protocols::simple_moves::WaterBoxMover::define_water_box_mover_schema(), protocols::calc_taskop_movers::DesignRepackMover::get_xsd_complex_type(), protocols::protein_interface_design::movers::HotspotHasherMover::provide_xml_schema(), protocols::ligand_docking::ComputeLigandRDF::provide_xml_schema(), protocols::simple_moves::SetupMetalsMover::provide_xml_schema(), protocols::rosetta_scripts::MultipleOutputWrapper::provide_xml_schema(), protocols::rosetta_scripts::MultiplePoseMover::provide_xml_schema(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::provide_xml_schema(), protocols::grafting::CCDEndsGraftMover::provide_xml_schema(), protocols::sewing::movers::AppendAssemblyMover::provide_xml_schema(), protocols::protein_interface_design::movers::PlaceStubMover::provide_xml_schema(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::provide_xml_schema(), protocols::sewing::movers::LigandBindingAssemblyMover::provide_xml_schema(), protocols::sewing::hashing::AlignmentFileGeneratorMover::provide_xml_schema(), protocols::sewing::movers::AssemblyMover::provide_xml_schema(), protocols::grafting::AnchoredGraftMover::provide_xml_schema(), protocols::canonical_sampling::MetricRecorder::provide_xml_schema(), protocols::fold_from_loops::NubInitioMover::provide_xml_schema(), protocols::canonical_sampling::MetropolisHastingsMover::provide_xml_schema(), protocols::simple_moves::SmallMover::provide_xml_schema(), protocols::simple_moves::ShearMover::provide_xml_schema(), protocols::generalized_kinematic_closure::GeneralizedKIC::provide_xml_schema(), protocols::design_opt::GreedyOptMutationMover::root_node_for_greedy_opt(), protocols::rosetta_scripts::RosettaScriptsParser::write_ROSETTASCRIPTS_complex_type(), xsd_type_definition_w_attributes(), and xsd_type_definition_w_attributes_and_repeatable_subelements().

protocols::filters::FilterOP protocols::moves::find_filter_or_die ( const std::string &  filter_name,
const utility::tag::TagCOP  ,
const protocols::filters::Filters_map filters 
)

Searches <filters> for the named filter, returning it if it exists, otherwise halts execution with an error message.

Referenced by protocols::moves::IfMover::parse_my_tag().

protocols::moves::MoverOP protocols::moves::find_mover_or_die ( const std::string &  mover_name,
const utility::tag::TagCOP  ,
const protocols::moves::Movers_map movers 
)

Searches <movers> for the named mover, returning it if it exists, otherwise halts execution with an error message.

Referenced by protocols::moves::IfMover::parse_my_tag(), protocols::moves::RandomMover::parse_my_tag(), and protocols::moves::SwitchMover::parse_my_tag().

utility::vector1< numeric::Real > protocols::moves::get_energies ( core::pose::Pose const &  pose,
core::scoring::ScoreType  energy_type 
)
PyMOLObserverOP protocols::moves::get_pymol_observer ( core::pose::Pose pose)

(Internal) helper function to create a PyMOLObserver and add it to the given pose NOTE: You NEED to adjust the observer type and call attach() on the return - by default a new PyMOLObserver isn't attached/observing.

References core::pose::Pose::observer_cache(), core::pose::datacache::PYMOL_OBSERVER, and core::pose::datacache::ObserverCache::set().

Referenced by AddPyMOLObserver(), AddPyMOLObserver_to_conformation(), and AddPyMOLObserver_to_energies().

numeric::random::uniform_RG_OP protocols::moves::getRG ( )

We using independent numeric::random::rg() which is not connected to RNG system because we do not want PyMOL to interfere with other Rosetta systems. I.e creating and using PyMOL mover should not change any trajectories of the running program even in production mode.

References RG().

Referenced by protocols::moves::UDPSocketClient::UDPSocketClient().

void protocols::moves::modify_ResId_based_object ( utility::pointer::ReferenceCountOP const  obj,
core::Size const  resid 
)

Checks whether a referencecount object is a derived from ResId and if so, sets its resid.

a recursive function that sets the resid of obj to the resid parameter. If the type of obj is a CompoundFilter or a DockDesignMover then each of the members of these containers are probed to see whether they are ResId types. Recursion ensures that any nesting structure would be supported. Non-ResId objects will pass through this function without being changed.

Referenced by protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), protocols::rosetta_scripts::ParsedProtocol::set_resid(), and protocols::filters::CompoundFilter::set_resid().

MoverStatus protocols::moves::mstype_from_name ( std::string const &  name)
std::ostream & protocols::moves::operator<< ( std::ostream &  os,
RepeatMover const &  mover 
)
std::ostream & protocols::moves::operator<< ( std::ostream &  os,
FilterReportAsPoseExtraScoresMover const &  mover 
)
std::ostream & protocols::moves::operator<< ( std::ostream &  output,
UDPSocketClient const &  client 
)
std::ostream& protocols::moves::operator<< ( std::ostream &  os,
TrialMover const &  mover 
)
std::ostream& protocols::moves::operator<< ( std::ostream &  os,
MoverContainer const &  mover 
)
std::ostream & protocols::moves::operator<< ( std::ostream &  os,
MonteCarlo const &  mc 
)
std::ostream & protocols::moves::operator<< ( std::ostream &  output,
PyMOLMover const &  mover 
)

End Xiyao's Code.

References protocols::moves::PyMOLMover::show().

PyMOLObserver::ObserverType protocols::moves::operator| ( PyMOLObserver::ObserverType &  l,
PyMOLObserver::ObserverType &  r 
)
inline
std::string protocols::moves::to_string ( MCA const &  mc_accepted)
static basic::Tracer protocols::moves::TR ( "protocols.moves.IteratedConvergenceMover"  )
static
static basic::Tracer protocols::moves::tr ( "protocols.TrialMover"  )
static
static basic::Tracer protocols::moves::TR ( "protocols.moves.MoverFactory"  )
static
static basic::Tracer protocols::moves::TR ( "protocols.moves.IfMover"  )
static
static basic::Tracer protocols::moves::TR ( "protocols.moves.Mover"  )
static
static basic::Tracer protocols::moves::TR ( "protocols.moves.RampingMover"  )
static
static basic::Tracer protocols::moves::TR ( "protocols.moves.PyMOLMover"  )
static
void protocols::moves::xsd_type_definition_w_attributes ( utility::tag::XMLSchemaDefinition &  xsd,
std::string const &  mover_type,
std::string const &  description,
utility::tag::AttributeList const &  attributes 
)

Define the XML schema definition for a Mover that contains no subtags but may contain any number of attributes (aka options).

References complex_type_name_for_mover().

Referenced by protocols::simple_moves::AddResidueLabelMoverCreator::provide_xml_schema(), protocols::constraint_movers::ClearConstraintsMover::provide_xml_schema(), protocols::loop_modeling::utilities::PrepareForCentroid::provide_xml_schema(), protocols::vardist_solaccess::LoadVarSolDistSasaCalculatorMover::provide_xml_schema(), protocols::simple_moves::SaveSequenceToCommentsMover::provide_xml_schema(), protocols::simple_moves::ResetFoldTree::provide_xml_schema(), protocols::simple_moves::RepeatPropagationMover::provide_xml_schema(), protocols::simple_moves::FavorSymmetricSequence::provide_xml_schema(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::provide_xml_schema(), protocols::simple_moves::AddPDBInfoMover::provide_xml_schema(), protocols::simple_moves::ReportXYZ::provide_xml_schema(), protocols::protein_interface_design::movers::PatchdockTransform::provide_xml_schema(), protocols::ligand_docking::WriteLigandMolFile::provide_xml_schema(), protocols::protein_interface_design::movers::PeptideStapleDesignMover::provide_xml_schema(), protocols::ligand_docking::RandomConformers::provide_xml_schema(), protocols::protein_interface_design::movers::ShoveResidueMover::provide_xml_schema(), protocols::protein_interface_design::movers::SubroutineMover::provide_xml_schema(), protocols::protein_interface_design::movers::TopologyBrokerMover::provide_xml_schema(), protocols::simple_moves::AddJobPairData::provide_xml_schema(), protocols::electron_density::ScaleMapIntensities::provide_xml_schema(), protocols::symmetry::DetectSymmetry::provide_xml_schema(), protocols::monte_carlo::ResetBaselineMover::provide_xml_schema(), protocols::protein_interface_design::movers::BuildAlaPose::provide_xml_schema(), protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle::provide_xml_schema(), protocols::protein_interface_design::movers::SetTemperatureFactor::provide_xml_schema(), protocols::protein_interface_design::movers::TaskAwareCsts::provide_xml_schema(), protocols::simple_moves::SequenceProfileMover::provide_xml_schema(), protocols::electron_density::ReportFSC::provide_xml_schema(), protocols::simple_moves::VirtualRootMover::provide_xml_schema(), protocols::cutoutdomain::CutOutDomain::provide_xml_schema(), protocols::protein_interface_design::movers::FavorNativeResiduePreCycle::provide_xml_schema(), protocols::rbsegment_relax::MakeStarTopologyMover::provide_xml_schema(), protocols::simple_moves::PDBReloadMover::provide_xml_schema(), protocols::cyclic_peptide::DeclareBond::provide_xml_schema(), protocols::relax::RepeatProteinRelax::provide_xml_schema(), protocols::simple_moves::DeleteChainMover::provide_xml_schema(), protocols::calc_taskop_movers::ForceDisulfidesMover::provide_xml_schema(), protocols::loop_build::LoopmodelWrapper::provide_xml_schema(), protocols::fldsgn::SheetRemodelConstraintGenerator::provide_xml_schema(), protocols::protein_interface_design::movers::LoopOver::provide_xml_schema(), protocols::simple_moves::LoadUnboundRotMover::provide_xml_schema(), protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover::provide_xml_schema(), protocols::pose_length_moves::FixAllLoopsMover::provide_xml_schema(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::provide_xml_schema(), protocols::protein_interface_design::movers::RandomMutation::provide_xml_schema(), protocols::simple_moves::PSSM2BfactorMover::provide_xml_schema(), protocols::loops::FoldTreeFromLoops::provide_xml_schema(), protocols::simple_moves::WriteSSEMover::provide_xml_schema(), protocols::task_operations::StoreTaskMover::provide_xml_schema(), protocols::carbohydrates::IdealizeAnomericHydrogens::provide_xml_schema(), protocols::pose_creation::MergePDBatOverlapMover::provide_xml_schema(), protocols::protein_interface_design::movers::BestHotspotCstMover::provide_xml_schema(), protocols::protein_interface_design::movers::InterfaceRecapitulationMover::provide_xml_schema(), protocols::protein_interface_design::movers::SpinMover::provide_xml_schema(), protocols::simple_moves::FavorSequenceProfile::provide_xml_schema(), protocols::matdes::SchemePlaceMotifsMover::provide_xml_schema(), protocols::simple_moves::DumpPdb::provide_xml_schema(), protocols::task_operations::StoreCombinedStoredTasksMover::provide_xml_schema(), protocols::protein_interface_design::movers::AddChainBreak::provide_xml_schema(), protocols::ligand_docking::Rotates::provide_xml_schema(), protocols::stepwise::monte_carlo::mover::FromScratchMover::provide_xml_schema(), protocols::simple_moves::LoadPDBMover::provide_xml_schema(), protocols::abinitio::DomainAssembly::provide_xml_schema(), protocols::protein_interface_design::movers::PlaceOnLoop::provide_xml_schema(), protocols::residue_selectors::StoreResidueSubsetMover::provide_xml_schema(), protocols::rosetta_scripts::SavePoseMover::provide_xml_schema(), protocols::simple_moves::AlignChainMover::provide_xml_schema(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::provide_xml_schema(), protocols::simple_moves::SuperimposeMover::provide_xml_schema(), protocols::splice::RotLibOut::provide_xml_schema(), protocols::stepwise::monte_carlo::mover::ResampleMover::provide_xml_schema(), protocols::symmetric_docking::SymFoldandDockSlideTrialMover::provide_xml_schema(), protocols::pose_creation::MakeJunctionsMover::provide_xml_schema(), protocols::pose_length_moves::InsertResMover::provide_xml_schema(), protocols::protein_interface_design::movers::SetupHotspotConstraintsMover::provide_xml_schema(), protocols::ligand_docking::AddHydrogens::provide_xml_schema(), protocols::legacy_sewing::LegacyAddStartnodeFragments::provide_xml_schema(), protocols::ligand_docking::LigandDesign::provide_xml_schema(), protocols::simple_moves::SwitchChainOrderMover::provide_xml_schema(), protocols::cyclic_peptide::FlipChiralityMover::provide_xml_schema(), protocols::ligand_docking::GrowLigand::provide_xml_schema(), protocols::simple_moves::ModifyVariantTypeMover::provide_xml_schema(), protocols::features::InterfaceDdGMover::provide_xml_schema(), protocols::simple_moves::ContingentAcceptMover::provide_xml_schema(), protocols::simple_moves::StructProfileMover::provide_xml_schema(), protocols::motifs::MotifDnaPacker::provide_xml_schema(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::provide_xml_schema(), protocols::struct_fragment::StructFragmentMover::provide_xml_schema(), protocols::matdes::ExtractSubposeMover::provide_xml_schema(), protocols::enzdes::BackboneSampler::provide_xml_schema(), protocols::cryst::ReportGradientsMover::provide_xml_schema(), protocols::fold_from_loops::movers::SavePDBInfoMover::provide_xml_schema(), protocols::protein_interface_design::movers::LoopLengthChange::provide_xml_schema(), protocols::dna::DnaInterfaceMinMover::provide_xml_schema(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::provide_xml_schema(), protocols::electron_density::SetupForDensityScoringMover::provide_xml_schema(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::provide_xml_schema(), protocols::fold_from_loops::movers::MoveMapFactoryToNamedMoveMapMover::provide_xml_schema(), protocols::pose_length_moves::AnalyzeLoopModeling::provide_xml_schema(), protocols::rbsegment_relax::OptimizeThreadingMover::provide_xml_schema(), protocols::ligand_docking::SlideTogether::provide_xml_schema(), protocols::stepwise::monte_carlo::mover::DeleteMover::provide_xml_schema(), protocols::minimization_packing::SaneMinMover::provide_xml_schema(), protocols::protein_interface_design::movers::LoopFinder::provide_xml_schema(), protocols::protein_interface_design::movers::SetAtomTree::provide_xml_schema(), protocols::stepwise::monte_carlo::mover::AddMover::provide_xml_schema(), protocols::ligand_docking::FinalMinimizer::provide_xml_schema(), protocols::dna::DesignProteinBackboneAroundDNA::provide_xml_schema(), protocols::dna::SeparateDnaFromNonDna::provide_xml_schema(), protocols::loops::loop_mover::LoopCM::provide_xml_schema(), protocols::constraint_movers::ResidueTypeConstraintMover::provide_xml_schema(), protocols::constraint_movers::ConstraintSetMover::provide_xml_schema(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::provide_xml_schema(), protocols::qsar::RenderGridsToKinemage::provide_xml_schema(), protocols::splice::RBOutMover::provide_xml_schema(), protocols::simple_moves::AddChainMover::provide_xml_schema(), protocols::ligand_docking::MinimizeBackbone::provide_xml_schema(), protocols::docking::DockingPrepackProtocol::provide_xml_schema(), protocols::moves::DsspMover::provide_xml_schema(), protocols::moves::IfMover::provide_xml_schema(), protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMover::provide_xml_schema(), protocols::dna::DnaInterfaceMultiStateDesign::provide_xml_schema(), protocols::simple_moves::sidechain_moves::SetChiMover::provide_xml_schema(), protocols::simple_moves::SwitchResidueTypeSetMover::provide_xml_schema(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover::provide_xml_schema(), protocols::enzymatic_movers::GlycosyltransferaseMover::provide_xml_schema(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::provide_xml_schema(), protocols::pose_length_moves::ConnectChainsMover::provide_xml_schema(), protocols::forge::constraints::NtoCConstraintGenerator::provide_xml_schema(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::provide_xml_schema(), protocols::membrane::OptimizeProteinEmbeddingMover::provide_xml_schema(), protocols::pose_creation::MakePolyXMover::provide_xml_schema(), protocols::simple_moves::MembraneTopology::provide_xml_schema(), protocols::membrane::benchmark::MakeCanonicalHelix::provide_xml_schema(), protocols::minimization_packing::symmetry::TaskAwareSymMinMover::provide_xml_schema(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::provide_xml_schema(), protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMover::provide_xml_schema(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::provide_xml_schema(), protocols::grafting::simple_movers::DeleteRegionMover::provide_xml_schema(), protocols::simple_moves::FindConsensusSequence::provide_xml_schema(), protocols::splice::TailSegmentMover::provide_xml_schema(), protocols::protein_interface_design::movers::LoopRemodel::provide_xml_schema(), protocols::abinitio::abscript::StructPerturberCM::provide_xml_schema(), protocols::symmetric_docking::SymFoldandDockRbTrialMover::provide_xml_schema(), protocols::grafting::simple_movers::InsertPoseIntoPoseMover::provide_xml_schema(), protocols::ligand_docking::InterfaceScoreCalculator::provide_xml_schema(), protocols::constraint_generator::RemoveConstraints::provide_xml_schema(), protocols::aa_composition::ClearCompositionConstraintsMover::provide_xml_schema(), protocols::forge::constraints::RemoveRemodelCsts::provide_xml_schema(), protocols::electron_density::VoxelSpacingRefinementMover::provide_xml_schema(), protocols::flexpep_docking::FlexPepDockingProtocol::provide_xml_schema(), protocols::splice::RBInMover::provide_xml_schema(), protocols::denovo_design::movers::SetResidueAliasMover::provide_xml_schema(), protocols::abinitio::abscript::FragmentCM::provide_xml_schema(), protocols::loops::loop_mover::refine::RepackTrial::provide_xml_schema(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::provide_xml_schema(), protocols::denovo_design::movers::AddSegmentDataMover::provide_xml_schema(), protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::provide_xml_schema(), protocols::ligand_docking::Transform::provide_xml_schema(), protocols::abinitio::abscript::AbscriptLoopCloserCM::provide_xml_schema(), protocols::enzdes::AddOrRemoveMatchCsts::provide_xml_schema(), protocols::grafting::simple_movers::ReplaceRegionMover::provide_xml_schema(), protocols::relax::membrane::MPRangeRelaxMover::provide_xml_schema(), protocols::abinitio::abscript::FragmentJumpCM::provide_xml_schema(), protocols::simple_moves::Tumble::provide_xml_schema(), protocols::simple_moves::WriteFiltersToPose::provide_xml_schema(), protocols::docking::DockMinMover::provide_xml_schema(), protocols::hotspot_hashing::movers::PlaceSurfaceProbe::provide_xml_schema(), protocols::membrane::OptimizeMembranePositionMover::provide_xml_schema(), protocols::mean_field::GenMeanFieldMover::provide_xml_schema(), protocols::coupled_moves::CoupledMovesProtocol::provide_xml_schema(), protocols::loops::loop_mover::refine::ShearMinCCDTrial::provide_xml_schema(), protocols::minimization_packing::TaskAwareMinMover::provide_xml_schema(), protocols::ligand_docking::Translate::provide_xml_schema(), protocols::symmetry::SetupForSymmetryMover::provide_xml_schema(), protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::provide_xml_schema(), protocols::moves::IteratedConvergenceMover::provide_xml_schema(), protocols::canonical_sampling::SilentTrajectoryRecorder::provide_xml_schema(), protocols::ligand_docking::HighResDocker::provide_xml_schema(), protocols::splice::AlignEndsMover::provide_xml_schema(), protocols::docking::ConformerSwitchMover::provide_xml_schema(), protocols::matdes::SymDofMover::provide_xml_schema(), protocols::environment::CoMTrackerCM::provide_xml_schema(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::provide_xml_schema(), protocols::canonical_sampling::PDBTrajectoryRecorder::provide_xml_schema(), protocols::protein_interface_design::movers::TryRotamers::provide_xml_schema(), protocols::loophash::LoopHashMoverWrapper::provide_xml_schema(), protocols::simple_moves::ShortBackrubMover::provide_xml_schema(), protocols::evolution::NucleotideMutation::provide_xml_schema(), protocols::indexed_structure_store::movers::DirectSegmentLookupMover::provide_xml_schema(), protocols::denovo_design::movers::ExtendChainMover::provide_xml_schema(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::provide_xml_schema(), protocols::pose_creation::ExtendedPoseMover::provide_xml_schema(), protocols::protein_interface_design::movers::DisulfideMover::provide_xml_schema(), protocols::denovo_design::movers::AlignResiduesMover::provide_xml_schema(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::provide_xml_schema(), protocols::simple_moves::ScoreMover::provide_xml_schema(), protocols::aa_composition::AddNetChargeConstraintMover::provide_xml_schema(), protocols::membrane::benchmark::SampleTiltAngles::provide_xml_schema(), protocols::monte_carlo::MonteCarloReset::provide_xml_schema(), protocols::abinitio::abscript::ConstraintPreparer::provide_xml_schema(), protocols::canonical_sampling::TrialCounterObserver::provide_xml_schema(), protocols::simple_moves::PoseFromPoseResourceMover::provide_xml_schema(), protocols::membrane::SpinAroundPartnerMover::provide_xml_schema(), protocols::monte_carlo::MonteCarloRecover::provide_xml_schema(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::provide_xml_schema(), protocols::abinitio::abscript::RigidChunkCM::provide_xml_schema(), protocols::aa_composition::AddHelixSequenceConstraintsMover::provide_xml_schema(), protocols::relax::LocalRelax::provide_xml_schema(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::provide_xml_schema(), protocols::simple_moves::MSDMover::provide_xml_schema(), protocols::membrane::visualize::VisualizeEmbeddingMover::provide_xml_schema(), protocols::monte_carlo::MonteCarloTest::provide_xml_schema(), protocols::ncbb::NcbbDockDesignProtocol::provide_xml_schema(), protocols::cyclic_peptide::SymmetricCycpepAlign::provide_xml_schema(), protocols::membrane::AddMembraneSpanConstraint::provide_xml_schema(), protocols::membrane::AddMembraneSpanTermZConstraint::provide_xml_schema(), protocols::ncbb::oop::OopDockDesignProtocol::provide_xml_schema(), protocols::relax::AtomCoordinateCstMover::provide_xml_schema(), protocols::ligand_docking::TransformEnsemble::provide_xml_schema(), protocols::simple_moves::DumpSingleResidueRotamers::provide_xml_schema(), protocols::ligand_docking::Rotate::provide_xml_schema(), protocols::aa_composition::AddMHCEpitopeConstraintMover::provide_xml_schema(), protocols::membrane::TiltMover::provide_xml_schema(), protocols::minimization_packing::DisulfideOptimizationMover::provide_xml_schema(), protocols::rna::movers::RNAIdealizeMover::provide_xml_schema(), protocols::moves::FilterReportAsPoseExtraScoresMover::provide_xml_schema(), protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::provide_xml_schema(), protocols::simple_moves::ReportEffectivePKA::provide_xml_schema(), protocols::docking::DockSetupMover::provide_xml_schema(), protocols::constraint_movers::CstInfoMover::provide_xml_schema(), protocols::backbone_moves::local_backbone_mover::LocalBackboneMover::provide_xml_schema(), protocols::membrane::MPLipidAccessibility::provide_xml_schema(), protocols::forge::constraints::InvrotTreeRCG::provide_xml_schema(), protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::provide_xml_schema(), protocols::grafting::simple_movers::KeepRegionMover::provide_xml_schema(), protocols::farnesyl::SampleFarnesylMover::provide_xml_schema(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::provide_xml_schema(), protocols::docking::DockMCMProtocol::provide_xml_schema(), protocols::membrane::MembranePositionFromTopologyMover::provide_xml_schema(), protocols::enzdes::EnzRepackMinimize::provide_xml_schema(), protocols::calc_taskop_movers::ConsensusDesignMover::provide_xml_schema(), protocols::cryst::UpdateCrystInfo::provide_xml_schema(), protocols::simple_moves::ConvertVirtualToRealMover::provide_xml_schema(), protocols::antibody::snugdock::SnugDock::provide_xml_schema(), protocols::pose_creation::MergePDBMover::provide_xml_schema(), protocols::farnesyl::InstallFarnesylMover::provide_xml_schema(), protocols::hybridization::BackboneTorsionPerturbation::provide_xml_schema(), protocols::hybridization::BackboneTorsionSampler::provide_xml_schema(), protocols::simple_moves::ConvertRealToVirtualMover::provide_xml_schema(), protocols::simple_moves::DeleteChainsMover::provide_xml_schema(), protocols::membrane::SetMembranePositionMover::provide_xml_schema(), protocols::enzdes::PackRotamersMoverPartGreedy::provide_xml_schema(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::provide_xml_schema(), protocols::electron_density::BfactorFittingMover::provide_xml_schema(), protocols::membrane::FlipMover::provide_xml_schema(), protocols::flxbb::InterlockAroma::provide_xml_schema(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::provide_xml_schema(), protocols::antibody::constraints::ParatopeSiteConstraintMover::provide_xml_schema(), protocols::relax::membrane::MPFastRelaxMover::provide_xml_schema(), protocols::simple_moves::StorePoseSnapshot::provide_xml_schema(), protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover::provide_xml_schema(), protocols::ligand_docking::HighResEnsemble::provide_xml_schema(), protocols::ncbb::oop::OopCreatorMover::provide_xml_schema(), protocols::cyclic_peptide::TryDisulfPermutations::provide_xml_schema(), protocols::antibody::AntibodyNumberingConverterMover::provide_xml_schema(), protocols::simple_moves::bin_transitions::InitializeByBins::provide_xml_schema(), protocols::symmetric_docking::membrane::MPSymDockMover::provide_xml_schema(), protocols::analysis::GlycanInfoMover::provide_xml_schema(), protocols::recces::scratch::ThermalMinimizer::provide_xml_schema(), protocols::membrane::AddMPLigandMover::provide_xml_schema(), protocols::minimization_packing::RotamerTrialsMinMover::provide_xml_schema(), protocols::simple_moves::SimpleThreadingMover::provide_xml_schema(), protocols::docking::DockingHighResLegacy::provide_xml_schema(), protocols::forge::constraints::InverseRotamersRCG::provide_xml_schema(), protocols::membrane::visualize::VisualizeMembraneMover::provide_xml_schema(), protocols::md::CartesianMD::provide_xml_schema(), protocols::loop_build::LoopMover_SlidingWindow::provide_xml_schema(), protocols::hbnet::HBNetStapleInterface::provide_xml_schema(), protocols::kinematic_closure::KicMover::provide_xml_schema(), protocols::recces::scratch::ThermalSamplingMover::provide_xml_schema(), protocols::ligand_docking::ProtLigEnsemble::provide_xml_schema(), protocols::docking::membrane::MPDockingSetupMover::provide_xml_schema(), protocols::simple_moves::PeriodicBoxMover::provide_xml_schema(), protocols::ncbb::SecStructMinimizeMover::provide_xml_schema(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::provide_xml_schema(), protocols::backrub::BackrubProtocol::provide_xml_schema(), protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::provide_xml_schema(), protocols::contact_map::ContactMap::provide_xml_schema(), protocols::denovo_design::movers::BridgeChainsMover::provide_xml_schema(), protocols::simple_moves::MutateResidue::provide_xml_schema(), protocols::fldsgn::potentials::SetAACompositionPotential::provide_xml_schema(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::provide_xml_schema(), protocols::antibody::design::AntibodyDesignProtocol::provide_xml_schema(), protocols::rna::movers::ErraserMinimizerMover::provide_xml_schema(), protocols::rotamer_recovery::RotamerRecoveryMover::provide_xml_schema(), protocols::dna::DnaInterfacePacker::provide_xml_schema(), protocols::helical_bundle::PerturbBundleHelix::provide_xml_schema(), protocols::cyclic_peptide::CrosslinkerMover::provide_xml_schema(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::provide_xml_schema(), protocols::simple_moves::CopyRotamerMover::provide_xml_schema(), protocols::minimization_packing::BoltzmannRotamerMover::provide_xml_schema(), protocols::membrane::TransformIntoMembraneMover::provide_xml_schema(), protocols::minimization_packing::MinPackMover::provide_xml_schema(), protocols::idealize::IdealizeMover::provide_xml_schema(), protocols::canonical_sampling::SimulatedTempering::provide_xml_schema(), protocols::simple_moves::BBGaussianMover::provide_xml_schema(), protocols::loophash::LoopHashDiversifier::provide_xml_schema(), protocols::docking::membrane::MPDockingMover::provide_xml_schema(), protocols::docking::DockingInitialPerturbation::provide_xml_schema(), protocols::simple_moves::ChangeAndResetFoldTreeMover::provide_xml_schema(), protocols::pose_length_moves::NearNativeLoopCloser::provide_xml_schema(), protocols::cryst::RecomputeDensityMapMover::provide_xml_schema(), protocols::cryst::CrystRMS::provide_xml_schema(), protocols::simple_moves::bin_transitions::PerturbByBins::provide_xml_schema(), protocols::simple_moves::CoupledMover::provide_xml_schema(), protocols::canonical_sampling::ParallelTempering::provide_xml_schema(), protocols::antibody::constraints::CDRDihedralConstraintMover::provide_xml_schema(), protocols::fldsgn::CircularPermutation::provide_xml_schema(), protocols::legacy_sewing::LegacyAssemblyConstraintsMover::provide_xml_schema(), protocols::fldsgn::potentials::SetSecStructEnergies::provide_xml_schema(), protocols::canonical_sampling::HamiltonianExchange::provide_xml_schema(), protocols::cryst::LoadDensityMapMover::provide_xml_schema(), protocols::cryst::MakeLayerMover::provide_xml_schema(), protocols::carbohydrates::LinkageConformerMover::provide_xml_schema(), protocols::symmetry::ExtractAsymmetricUnitMover::provide_xml_schema(), protocols::helical_bundle::MakeBundleHelix::provide_xml_schema(), protocols::symmetric_docking::SymDockProtocol::provide_xml_schema(), protocols::helical_bundle::FitSimpleHelix::provide_xml_schema(), protocols::calc_taskop_movers::CreateSequenceMotifMover::provide_xml_schema(), protocols::simple_moves::sidechain_moves::SidechainMCMover::provide_xml_schema(), protocols::moves::RampingMover::provide_xml_schema(), protocols::enzdes::PredesignPerturbMover::provide_xml_schema(), protocols::carbohydrates::CreateGlycanSequonMover::provide_xml_schema(), protocols::antibody::AntibodyCDRGrafter::provide_xml_schema(), protocols::cryst::FitBfactorsMover::provide_xml_schema(), protocols::moves::RandomMover::provide_xml_schema(), protocols::carbohydrates::GlycanTreeModeler::provide_xml_schema(), protocols::docking::DockingSlideIntoContact::provide_xml_schema(), protocols::comparative_modeling::LoopRelaxMover::provide_xml_schema(), protocols::symmetry::ExtractAsymmetricPoseMover::provide_xml_schema(), protocols::docking::DockingProtocol::provide_xml_schema(), protocols::backrub::BackrubSidechainMover::provide_xml_schema(), protocols::forge::remodel::ResidueVicinityRCG::provide_xml_schema(), protocols::denovo_design::DisulfidizeMover::provide_xml_schema(), protocols::cryst::DockLatticeMover::provide_xml_schema(), protocols::cryst::UpdateSolventMover::provide_xml_schema(), protocols::fldsgn::BluePrintBDR::provide_xml_schema(), protocols::antibody::design::AntibodyDesignMover::provide_xml_schema(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::provide_xml_schema(), protocols::cryst::TagPoseWithRefinementStatsMover::provide_xml_schema(), protocols::simple_moves::sidechain_moves::SidechainMover::provide_xml_schema(), protocols::moves::SwitchMover::provide_xml_schema(), protocols::rigid::RigidBodyPerturbNoCenterMover::provide_xml_schema(), protocols::enzdes::UpdateEnzdesHeaderMover::provide_xml_schema(), protocols::cryst::SetRefinementOptionsMover::provide_xml_schema(), protocols::cryst::MakeLatticeMover::provide_xml_schema(), protocols::backrub::BackrubMover::provide_xml_schema(), protocols::moves::PyMOLMover::provide_xml_schema(), protocols::motif_grafting::movers::MotifGraftMover::provide_xml_schema(), protocols::rigid::RigidBodyTiltMover::provide_xml_schema(), protocols::analysis::InterfaceAnalyzerMover::provide_xml_schema(), protocols::rigid::RigidBodyTransMover::provide_xml_schema(), protocols::forge::remodel::RemodelMover::provide_xml_schema(), and protocols::hbnet::HBNet::provide_xml_schema().

void protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements ( utility::tag::XMLSchemaDefinition &  xsd,
std::string const &  mover_type,
std::string const &  description,
utility::tag::AttributeList const &  attributes,
utility::tag::XMLSchemaSimpleSubelementList const &  subelements 
)

Define the XML schema definition for a Mover that contains subtags attributes (aka options).

References complex_type_name_for_mover().

Referenced by protocols::cyclic_peptide::CreateAngleConstraint::provide_xml_schema(), protocols::seeded_abinitio::DefineMovableLoops::provide_xml_schema(), protocols::protein_interface_design::movers::VLB::provide_xml_schema(), protocols::ligand_docking::CompoundTranslate::provide_xml_schema(), protocols::seeded_abinitio::CoordinateCst::provide_xml_schema(), protocols::cyclic_peptide::CreateDistanceConstraint::provide_xml_schema(), protocols::seeded_abinitio::SwapSegment::provide_xml_schema(), protocols::protein_interface_design::movers::PrepackMover::provide_xml_schema(), protocols::cyclic_peptide::CreateTorsionConstraint::provide_xml_schema(), protocols::seeded_abinitio::CAcstGenerator::provide_xml_schema(), protocols::seeded_abinitio::CloseFold::provide_xml_schema(), protocols::seeded_abinitio::SeedSetupMover::provide_xml_schema(), protocols::rbsegment_relax::IdealizeHelicesMover::provide_xml_schema(), protocols::seeded_abinitio::GrowPeptides::provide_xml_schema(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::provide_xml_schema(), protocols::simple_moves::RandomOmegaFlipMover::provide_xml_schema(), protocols::protein_interface_design::movers::BackrubDDMover::provide_xml_schema(), protocols::seeded_abinitio::SegmentHybridizer::provide_xml_schema(), protocols::simple_moves::RandomTorsionMover::provide_xml_schema(), protocols::splice::SpliceOutTail::provide_xml_schema(), protocols::environment::EnvMover::provide_xml_schema(), protocols::cyclic_peptide::PeptideCyclizeMover::provide_xml_schema(), protocols::splice::SpliceInTail::provide_xml_schema(), protocols::protein_interface_design::movers::MapHotspot::provide_xml_schema(), protocols::protein_interface_design::movers::PlacementMinimizationMover::provide_xml_schema(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::provide_xml_schema(), protocols::protein_interface_design::movers::DockWithHotspotMover::provide_xml_schema(), protocols::rigid::RollMover::provide_xml_schema(), protocols::constraint_generator::AddConstraints::provide_xml_schema(), protocols::splice::SpliceOutAntibody::provide_xml_schema(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::provide_xml_schema(), protocols::seeded_abinitio::SeedFoldTree::provide_xml_schema(), protocols::loop_grower::FragmentExtension::provide_xml_schema(), protocols::simple_moves::RingConformationMover::provide_xml_schema(), protocols::splice::SpliceOut::provide_xml_schema(), protocols::splice::SpliceIn::provide_xml_schema(), protocols::carbohydrates::RingPlaneFlipMover::provide_xml_schema(), protocols::task_operations::StoreCompoundTaskMover::provide_xml_schema(), protocols::normalmode::NormalModeMinimizer::provide_xml_schema(), protocols::fldsgn::MatchResiduesMover::provide_xml_schema(), protocols::protein_interface_design::movers::PlacementAuctionMover::provide_xml_schema(), protocols::environment::ScriptCM::provide_xml_schema(), protocols::splice::SpliceInAntibody::provide_xml_schema(), protocols::aa_composition::AddCompositionConstraintMover::provide_xml_schema(), protocols::ligand_docking::StartFrom::provide_xml_schema(), protocols::minimization_packing::PertMinMover::provide_xml_schema(), protocols::abinitio::abscript::AbscriptMover::provide_xml_schema(), protocols::analysis::LoopAnalyzerMover::provide_xml_schema(), protocols::cryst::SetCrystWeightMover::provide_xml_schema(), protocols::features::TrajectoryReportToDB::provide_xml_schema(), protocols::hybridization::CartesianSampler::provide_xml_schema(), protocols::simple_moves::DisulfideInsertionMover::provide_xml_schema(), protocols::cyclic_peptide::PeptideStubMover::provide_xml_schema(), protocols::match::MatcherMover::provide_xml_schema(), protocols::analysis::simple_metrics::RunSimpleMetricsMover::provide_xml_schema(), protocols::nonlocal::SingleFragmentMover::provide_xml_schema(), protocols::normalmode::NormalModeRelaxMover::provide_xml_schema(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::provide_xml_schema(), protocols::carbohydrates::GlycanTreeMinMover::provide_xml_schema(), protocols::membrane::symmetry::SymmetricAddMembraneMover::provide_xml_schema(), protocols::symmetry::SetupNCSMover::provide_xml_schema(), protocols::rosetta_scripts::ParsedProtocol::provide_xml_schema(), protocols::helical_bundle::PerturbBundle::provide_xml_schema(), protocols::simple_moves::SetTorsion::provide_xml_schema(), protocols::hybridization::HybridizeProtocol::provide_xml_schema(), protocols::carbohydrates::SimpleGlycosylateMover::provide_xml_schema(), protocols::carbohydrates::GlycanTreeSampler::provide_xml_schema(), protocols::membrane::AddMembraneMover::provide_xml_schema(), protocols::flxbb::FlxbbDesign::provide_xml_schema(), protocols::helical_bundle::MakeBundle::provide_xml_schema(), protocols::splice::Splice::provide_xml_schema(), protocols::features::ReportToDB::provide_xml_schema(), protocols::helical_bundle::BundleGridSampler::provide_xml_schema(), and protocols::helical_bundle::BackboneGridSampler::provide_xml_schema().