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	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

class	PyMolMoverCreator

class	PyMolObserver

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	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::owning_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 < 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 boost::shared_ptr< Mover >	MoverSP

typedef std::map< std::string const, MoverOP >	Movers_map

typedef std::map< std::string, std::string >	SerializableState

typedef boost::shared_ptr < SerializableState >	SerializableStateSP

typedef boost::shared_ptr < const SerializableState >	SerializableStateCSP

typedef boost::weak_ptr < SerializableState >	SerializableStateWP

typedef boost::weak_ptr< const SerializableState >	SerializableStateCWP

typedef std::map< std::string, std::string >	MoverCache

typedef boost::shared_ptr < MoverCache >	MoverCacheSP

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 < 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

typedef core::Real	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 }
	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
static thread_local basic::Tracer	TR ("protocols.moves.IfMover")

static thread_local basic::Tracer	TR ("protocols.moves.IteratedConvergenceMover")

std::ostream &	operator<< (std::ostream &os, MonteCarlo const &mc)

std::string	to_string (MCA const &mc_accepted)

static thread_local basic::Tracer	TR ("protocols.moves.Mover")

void	SerializableState_set (SerializableStateSP state, std::string key, std::string val)
	serializable set helper functions More...

void	SerializableState_set (SerializableStateSP state, std::string key, core::Real val)

std::string	SerializableState_get (SerializableStateSP state, std::string key)

std::ostream &	operator<< (std::ostream &os, MoverContainer const &mover)

static thread_local basic::Tracer	TR ("protocols.moves.MoverFactory")

MoverStatus	mstype_from_name (std::string const &name)

static thread_local basic::Tracer	TR ("protocols.moves.PyMolMover")

numeric::random::uniform_RG_OP	getRG ()

std::ostream &	operator<< (std::ostream &output, UDPSocketClient const &client)

std::ostream &	operator<< (std::ostream &output, PyMolMover const &mover)

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...

static thread_local 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 thread_local 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::owning_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< IteratedConvergenceMover > protocols::moves::IteratedConvergenceMoverOP

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< MonteCarloExceptionConverge const > protocols::moves::MonteCarloExceptionConvergeCOP

typedef utility::pointer::shared_ptr< MonteCarloExceptionConverge > protocols::moves::MonteCarloExceptionConvergeOP

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 boost::shared_ptr< MoverCache > protocols::moves::MoverCacheSP

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 boost::shared_ptr< Mover> protocols::moves::MoverSP

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 core::Real protocols::moves::Real

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 std::map< std::string, std::string > protocols::moves::SerializableState

typedef boost::shared_ptr< const SerializableState > protocols::moves::SerializableStateCSP

typedef boost::weak_ptr< const SerializableState > protocols::moves::SerializableStateCWP

typedef boost::shared_ptr< SerializableState > protocols::moves::SerializableStateSP

typedef boost::weak_ptr< SerializableState > protocols::moves::SerializableStateWP

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< 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

enum protocols::moves::MCA

Enumerator
MCA_accepted_score_beat_low
MCA_accepted_score_beat_last
MCA_accepted_thermally
MCA_rejected

enum protocols::moves::MoverStatus

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

Enumerator
MS_SUCCESS
FAIL_RETRY
FAIL_DO_NOT_RETRY
FAIL_BAD_INPUT

enum protocols::moves::StatsType

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

enum protocols::moves::X11Colors

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
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Function Documentation

PyMolObserverOP protocols::moves::AddPyMolObserver	(	core::pose::Pose &	p,
		bool	keep_history,
		core::Real	update_interval
	)

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...

References core::pose::Pose::attach_general_obs(), and protocols::moves::PyMolObserver::generalEvent().

Referenced by protocols::abinitio::AbrelaxMover::apply(), protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::abinitio::AbrelaxApplication::fold(), and protocols::jd2::JobDistributor::setup_pymol_observer().

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 core::pose::Pose::attach_conformation_obs(), and protocols::moves::PyMolObserver::conformationEvent().

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 core::pose::Pose::attach_energy_obs(), and protocols::moves::PyMolObserver::energyEvent().

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

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.

References utility_exit_with_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.

References utility_exit_with_message.

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

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 )

References FAIL_BAD_INPUT, FAIL_DO_NOT_RETRY, FAIL_RETRY, MS_SUCCESS, and utility_exit_with_message.

Referenced by protocols::protein_interface_design::movers::LoopOver::parse_my_tag().

std::ostream & protocols::moves::operator<<	(	std::ostream &	os,
		RepeatMover const &	mover
	)

References protocols::moves::Mover::get_current_tag(), protocols::moves::RepeatMover::get_mover(), protocols::moves::RepeatMover::get_name(), protocols::moves::RepeatMover::get_nmoves(), and protocols::moves::Mover::get_type().

std::ostream & protocols::moves::operator<<	(	std::ostream &	output,
		UDPSocketClient const &	client
	)

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

std::ostream& protocols::moves::operator<<	(	std::ostream &	os,
		MoverContainer const &	mover
	)

References protocols::moves::Mover::get_current_tag(), protocols::moves::MoverContainer::get_mover(), protocols::moves::Mover::get_name(), protocols::moves::Mover::get_type(), and protocols::moves::MoverContainer::size().

std::ostream& protocols::moves::operator<<	(	std::ostream &	os,
		TrialMover const &	mover
	)

References protocols::moves::MoverStatistics::acceptance_rate(), protocols::moves::Mover::get_current_tag(), protocols::moves::TrialMover::get_name(), protocols::moves::Mover::get_type(), protocols::moves::TrialMover::mc_, protocols::moves::TrialMover::mover(), protocols::moves::TrialMover::num_accepts(), and protocols::moves::TrialMover::stats_.

std::ostream & protocols::moves::operator<<	(	std::ostream &	output,
		PyMolMover const &	mover
	)

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

std::ostream & protocols::moves::operator<<	(	std::ostream &	os,
		MonteCarlo const &	mc
	)

References protocols::moves::MonteCarlo::last_accepted_score(), protocols::moves::MonteCarlo::lowest_score(), protocols::moves::MonteCarlo::temperature(), and protocols::moves::MonteCarlo::total_trials().

std::string protocols::moves::SerializableState_get	(	SerializableStateSP	state,
		std::string	key
	)

void protocols::moves::SerializableState_set	(	SerializableStateSP	state,
		std::string	key,
		std::string	val
	)

serializable set helper functions

void protocols::moves::SerializableState_set	(	SerializableStateSP	state,
		std::string	key,
		core::Real	val
	)

References utility::to_string().

std::string protocols::moves::to_string ( MCA const & mc_accepted )

References protocols::init::init(), MCA_accepted_score_beat_last, MCA_accepted_score_beat_low, MCA_accepted_thermally, and MCA_rejected.

Referenced by protocols::optimize_weights::IterativeOptEDriver::collect_decoy_discrimination_data(), protocols::docking::membrane::MPDockingMover::finalize_setup(), protocols::stepwise::monte_carlo::get_move_type_string(), protocols::stepwise::sampler::StepWiseSamplerOneTorsion::get_name(), protocols::moves::MonteCarlo::mc_accepted_string(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::optimize_weights::IterativeOptEDriver::setup_pdbnames_next_round(), and protocols::moves::MonteCarlo::show_state().

static thread_local basic::Tracer protocols::moves::TR ( "protocols.moves.IteratedConvergenceMover" )

static

static thread_local basic::Tracer protocols::moves::TR ( "protocols.moves.MoverFactory" )

static

static thread_local basic::Tracer protocols::moves::tr ( "protocols.TrialMover" )

static

Referenced by protocols::moves::TrialMover::acceptance_rate(), protocols::moves::SequenceMover::apply(), and protocols::moves::TrialCounter::show().

static thread_local basic::Tracer protocols::moves::TR ( "protocols.moves.IfMover" )

static

static thread_local basic::Tracer protocols::moves::TR ( "protocols.moves.RampingMover" )

static

static thread_local basic::Tracer protocols::moves::TR ( "protocols.moves.Mover" )

static

static thread_local basic::Tracer protocols::moves::TR ( "protocols.moves.PyMolMover" )

static

Classes

Typedefs

Enumerations

Functions

Typedef Documentation

Enumeration Type Documentation

Function Documentation