Namespaces
	mc_convergence_checks

Classes
class	_BoolMover

class	CanonicalSamplingMover

class	ChangeFoldTreeMover

class	CompositionMover

class	CyclicMover
	A simple class for cycling between movers in consecutive calls to apply() More...

class	DataMap
	general-purpose store for any reference-count derived object More...

class	DataMapObj
	templated class to make any data type compatible with ReferenceCounts and OPs. e.g., utility::pointer::owning_ptr< DataMapObj< bool > > stop; You can then place such constructs on the DataMap More...

class	DsspMover

class	DsspMoverCreator

class	FilterMover

class	IfMover

class	IfMoverCreator

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	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	EXCN_Converged

class	MonteCarloExceptionConverge

class	Mover
	: A mover is an object that can apply a conformational change to a pose More...

class	MoverContainer

class	SequenceMover
	A Mover that iterates through a vector of Movers, applying each one sequentially. More...

class	RandomMover
	RandomMover picks a random move and applies it. More...

class	CycleMover
	CycleMover iterates through its vector of Movers one at a time over many calls to apply(). More...

class	RandomMoverCreator

class	MoverCreator
	Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class. More...

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	MoverFactory

class	MoverStatistics

class	NullMover

class	PDBDumpMover

class	ProfilerMover

class	MCShowMover

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	PyMolMover

class	PyMolObserver

class	RampingFunc

class	LinearFunc

class	FastLinearFunc

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	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	RampingMover

class	RampingMoverCreator

class	RepeatMover
	A Mover that repeats an input Mover a user-specified number of times. More...

class	ReplicaExchangeMC

class	ResId

class	StructureRestrictor

class	TrialCounter

class	MonteCarloUtil
	the MCResetMover applies a monte carlo reset More...

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

class	WhileMover

class	PoseCondition

Typedefs
typedef utility::pointer::owning_ptr < CanonicalSamplingMover >	CanonicalSamplingMoverOP

typedef utility::pointer::owning_ptr < CanonicalSamplingMover const >	CanonicalSamplingMoverCOP

typedef utility::pointer::owning_ptr < ChangeFoldTreeMover >	ChangeFoldTreeMoverOP

typedef utility::pointer::owning_ptr < ChangeFoldTreeMover const >	ChangeFoldTreeMoverCOP

typedef utility::pointer::owning_ptr < CompositionMover >	CompositionMoverOP

typedef utility::pointer::owning_ptr < CompositionMover const >	CompositionMoverCOP

typedef utility::pointer::owning_ptr < CyclicMover >	CyclicMoverOP

typedef utility::pointer::owning_ptr < CyclicMover const >	CyclicMoverCOP

typedef utility::pointer::owning_ptr < DsspMover >	DsspMoverOP

typedef utility::pointer::owning_ptr < FilterMover >	FilterMoverOP

typedef utility::pointer::owning_ptr < IteratedConvergenceMover >	IteratedConvergenceMoverOP

typedef utility::pointer::owning_ptr < IteratedConvergenceMover const >	IteratedConvergenceMoverCOP

typedef utility::pointer::owning_ptr < JumpOutMover >	JumpOutMoverOP

typedef utility::pointer::owning_ptr < JumpOutMover const >	JumpOutMoverCOP

typedef utility::pointer::owning_ptr < MonteCarlo >	MonteCarloOP

typedef utility::pointer::owning_ptr < MonteCarlo const >	MonteCarloCOP

typedef utility::pointer::owning_ptr < MonteCarloExceptionConverge >	MonteCarloExceptionConvergeOP

typedef utility::pointer::owning_ptr < MonteCarloExceptionConverge const >	MonteCarloExceptionConvergeCOP

typedef utility::pointer::owning_ptr < Mover >	MoverOP

typedef utility::pointer::owning_ptr < Mover const >	MoverCOP

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::owning_ptr < MoverContainer >	MoverContainerOP

typedef utility::pointer::owning_ptr < MoverContainer const >	MoverContainerCOP

typedef utility::pointer::owning_ptr < SequenceMover >	SequenceMoverOP

typedef utility::pointer::owning_ptr < SequenceMover const >	SequenceMoverCOP

typedef utility::pointer::owning_ptr < RandomMover >	RandomMoverOP

typedef utility::pointer::owning_ptr < RandomMover const >	RandomMoverCOP

typedef utility::pointer::owning_ptr < CycleMover >	CycleMoverOP

typedef utility::pointer::owning_ptr < CycleMover const >	CycleMoverCOP

typedef utility::pointer::owning_ptr < MoverCreator >	MoverCreatorOP

typedef utility::pointer::owning_ptr < MoverCreator const >	MoverCreatorCOP

typedef utility::pointer::owning_ptr < MoverFactory >	MoverFactoryOP

typedef utility::pointer::owning_ptr < MoverFactory const >	MoverFactoryCOP

typedef core::Real	Real

typedef utility::pointer::owning_ptr < NullMover >	NullMoverOP

typedef utility::pointer::owning_ptr < NullMover const >	NullMoverCOP

typedef utility::pointer::owning_ptr < PDBDumpMover >	PDBDumpMoverOP

typedef utility::pointer::owning_ptr < PDBDumpMover const >	PDBDumpMoverCOP

typedef utility::pointer::owning_ptr < ProfilerMover >	ProfilerMoverOP

typedef utility::pointer::owning_ptr < ProfilerMover const >	ProfilerMoverCOP

typedef utility::pointer::owning_ptr < MCShowMover >	MCShowMoverOP

typedef utility::pointer::owning_ptr < MCShowMover const >	MCShowMoverCOP

typedef utility::pointer::owning_ptr < PyMolMover >	PyMolMoverOP

typedef utility::pointer::owning_ptr < PyMolMover const >	PyMolMoverCOP

typedef utility::pointer::owning_ptr < PyMolObserver >	PyMolObserverOP

typedef utility::pointer::owning_ptr < PyMolObserver const >	PyMolObserverCOP

typedef utility::pointer::owning_ptr < RampingMover >	RampingMoverOP

typedef utility::pointer::owning_ptr < RampingMover const >	RampingMoverCOP

typedef utility::pointer::owning_ptr < RampingFunc >	RampingFuncOP

typedef utility::pointer::owning_ptr < RampingFunc const >	RampingFuncCOP

typedef utility::pointer::owning_ptr < RepeatMover >	RepeatMoverOP

typedef utility::pointer::owning_ptr < RepeatMover const >	RepeatMoverCOP

typedef utility::pointer::owning_ptr < ReplicaExchangeMC >	ReplicaExchangeMC_OP

typedef utility::pointer::owning_ptr < ReplicaExchangeMC const >	ReplicaExchangeMC_COP

typedef utility::pointer::owning_ptr < ResId >	ResIdOP

typedef utility::pointer::owning_ptr < ResId const >	ResIdCOP

typedef utility::pointer::owning_ptr < StructureRestrictor >	StructureRestrictorOP

typedef utility::pointer::owning_ptr < StructureRestrictor const >	StructureRestrictorCOP

typedef utility::pointer::owning_ptr < TemperatureController >	TemperatureControllerOP

typedef utility::pointer::owning_ptr < TemperatureController const >	TemperatureControllerCOP

typedef utility::pointer::access_ptr < TemperatureController >	TemperatureControllerAP

typedef utility::pointer::access_ptr < TemperatureController const >	TemperatureControllerCAP

typedef utility::pointer::owning_ptr < TrialMover >	TrialMoverOP

typedef utility::pointer::owning_ptr < TrialMover const >	TrialMoverCOP

typedef utility::pointer::owning_ptr < WhileMover >	WhileMoverOP

typedef utility::pointer::owning_ptr < WhileMover const >	WhileMoverCOP

typedef utility::pointer::owning_ptr < PoseCondition >	PoseConditionOP

typedef utility::pointer::owning_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 basic::Tracer	TR ("protocols.moves.DataMap")

static basic::Tracer	TR_hh ("protocols.moves.DataMap_hh")

template<class Ty >
Ty *	get_set_from_datamap (std::string const type, std::string const name, protocols::moves::DataMap &data)
	templated function for adding or getting an item from the datamap. Automatically checks whether an item of the requested type and name exists on the datamap. If so, returns the OP for that item, if not, instantiates that item on the datamap and returns the OP for it. More...

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

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

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

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

std::ostream &	operator<< (std::ostream &os, Mover const &mover)
	Test IO operator for debug and Python bindings. More...

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)

static numeric::random::RandomGenerator	RG (114)

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 ()

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...

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...

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, const utility::tag::TagPtr 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, const utility::tag::TagPtr 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::owning_ptr< CanonicalSamplingMover const > protocols::moves::CanonicalSamplingMoverCOP

Definition at line 28 of file CanonicalSamplingMover.fwd.hh.

typedef utility::pointer::owning_ptr< CanonicalSamplingMover > protocols::moves::CanonicalSamplingMoverOP

Definition at line 26 of file CanonicalSamplingMover.fwd.hh.

typedef utility::pointer::owning_ptr< ChangeFoldTreeMover const > protocols::moves::ChangeFoldTreeMoverCOP

Definition at line 26 of file ChangeFoldTreeMover.fwd.hh.

typedef utility::pointer::owning_ptr< ChangeFoldTreeMover > protocols::moves::ChangeFoldTreeMoverOP

Definition at line 24 of file ChangeFoldTreeMover.fwd.hh.

typedef utility::pointer::owning_ptr< CompositionMover const > protocols::moves::CompositionMoverCOP

Definition at line 24 of file CompositionMover.fwd.hh.

typedef utility::pointer::owning_ptr< CompositionMover > protocols::moves::CompositionMoverOP

Definition at line 22 of file CompositionMover.fwd.hh.

typedef utility::pointer::owning_ptr< CycleMover const > protocols::moves::CycleMoverCOP

Definition at line 38 of file MoverContainer.fwd.hh.

typedef utility::pointer::owning_ptr< CycleMover > protocols::moves::CycleMoverOP

Definition at line 36 of file MoverContainer.fwd.hh.

typedef utility::pointer::owning_ptr<CyclicMover const> protocols::moves::CyclicMoverCOP

Definition at line 23 of file CyclicMover.fwd.hh.

typedef utility::pointer::owning_ptr<CyclicMover> protocols::moves::CyclicMoverOP

Definition at line 21 of file CyclicMover.fwd.hh.

typedef utility::pointer::owning_ptr< DsspMover > protocols::moves::DsspMoverOP

Definition at line 23 of file DsspMover.fwd.hh.

typedef utility::pointer::owning_ptr< FilterMover > protocols::moves::FilterMoverOP

Definition at line 23 of file FilterMover.fwd.hh.

typedef utility::pointer::owning_ptr< IteratedConvergenceMover const > protocols::moves::IteratedConvergenceMoverCOP

Definition at line 24 of file IteratedConvergenceMover.fwd.hh.

typedef utility::pointer::owning_ptr< IteratedConvergenceMover > protocols::moves::IteratedConvergenceMoverOP

Definition at line 22 of file IteratedConvergenceMover.fwd.hh.

typedef utility::pointer::owning_ptr< JumpOutMover const > protocols::moves::JumpOutMoverCOP

Definition at line 27 of file JumpOutMover.fwd.hh.

typedef utility::pointer::owning_ptr< JumpOutMover > protocols::moves::JumpOutMoverOP

Definition at line 25 of file JumpOutMover.fwd.hh.

typedef utility::pointer::owning_ptr< MCShowMover const > protocols::moves::MCShowMoverCOP

Definition at line 34 of file OutputMovers.fwd.hh.

typedef utility::pointer::owning_ptr< MCShowMover > protocols::moves::MCShowMoverOP

Definition at line 32 of file OutputMovers.fwd.hh.

typedef utility::pointer::owning_ptr< MonteCarlo const > protocols::moves::MonteCarloCOP

Definition at line 29 of file MonteCarlo.fwd.hh.

typedef utility::pointer::owning_ptr< MonteCarloExceptionConverge const > protocols::moves::MonteCarloExceptionConvergeCOP

Definition at line 29 of file MonteCarloExceptionConverge.fwd.hh.

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

Definition at line 26 of file MonteCarloExceptionConverge.fwd.hh.

typedef utility::pointer::owning_ptr< MonteCarlo > protocols::moves::MonteCarloOP

Definition at line 26 of file MonteCarlo.fwd.hh.

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

Definition at line 42 of file Mover.fwd.hh.

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

Definition at line 43 of file Mover.fwd.hh.

typedef utility::pointer::owning_ptr< MoverContainer const > protocols::moves::MoverContainerCOP

Definition at line 26 of file MoverContainer.fwd.hh.

typedef utility::pointer::owning_ptr< MoverContainer > protocols::moves::MoverContainerOP

Definition at line 24 of file MoverContainer.fwd.hh.

typedef utility::pointer::owning_ptr< Mover const > protocols::moves::MoverCOP

Definition at line 31 of file Mover.fwd.hh.

typedef utility::pointer::owning_ptr< MoverCreator const > protocols::moves::MoverCreatorCOP

Definition at line 41 of file MoverCreator.hh.

typedef utility::pointer::owning_ptr< MoverCreator > protocols::moves::MoverCreatorOP

Definition at line 40 of file MoverCreator.hh.

typedef utility::pointer::owning_ptr< MoverFactory const > protocols::moves::MoverFactoryCOP

Definition at line 25 of file MoverFactory.fwd.hh.

typedef utility::pointer::owning_ptr< MoverFactory > protocols::moves::MoverFactoryOP

Definition at line 22 of file MoverFactory.fwd.hh.

typedef utility::pointer::owning_ptr< Mover > protocols::moves::MoverOP

Definition at line 29 of file Mover.fwd.hh.

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

Definition at line 34 of file Mover.fwd.hh.

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

Definition at line 32 of file Mover.fwd.hh.

typedef utility::pointer::owning_ptr< NullMover const > protocols::moves::NullMoverCOP

Definition at line 25 of file NullMover.fwd.hh.

typedef utility::pointer::owning_ptr< NullMover > protocols::moves::NullMoverOP

Definition at line 23 of file NullMover.fwd.hh.

typedef utility::pointer::owning_ptr< PDBDumpMover const > protocols::moves::PDBDumpMoverCOP

Definition at line 26 of file OutputMovers.fwd.hh.

typedef utility::pointer::owning_ptr< PDBDumpMover > protocols::moves::PDBDumpMoverOP

Definition at line 24 of file OutputMovers.fwd.hh.

typedef utility::pointer::owning_ptr< PoseCondition const > protocols::moves::PoseConditionCOP

Definition at line 30 of file WhileMover.fwd.hh.

typedef utility::pointer::owning_ptr< PoseCondition > protocols::moves::PoseConditionOP

Definition at line 28 of file WhileMover.fwd.hh.

typedef utility::pointer::owning_ptr< ProfilerMover const > protocols::moves::ProfilerMoverCOP

Definition at line 30 of file OutputMovers.fwd.hh.

typedef utility::pointer::owning_ptr< ProfilerMover > protocols::moves::ProfilerMoverOP

Definition at line 28 of file OutputMovers.fwd.hh.

typedef utility::pointer::owning_ptr< PyMolMover const > protocols::moves::PyMolMoverCOP

Definition at line 24 of file PyMolMover.fwd.hh.

typedef utility::pointer::owning_ptr< PyMolMover > protocols::moves::PyMolMoverOP

Definition at line 22 of file PyMolMover.fwd.hh.

typedef utility::pointer::owning_ptr< PyMolObserver const > protocols::moves::PyMolObserverCOP

Definition at line 28 of file PyMolMover.fwd.hh.

typedef utility::pointer::owning_ptr< PyMolObserver > protocols::moves::PyMolObserverOP

Definition at line 26 of file PyMolMover.fwd.hh.

typedef utility::pointer::owning_ptr< RampingFunc const > protocols::moves::RampingFuncCOP

Definition at line 30 of file RampingMover.fwd.hh.

typedef utility::pointer::owning_ptr< RampingFunc > protocols::moves::RampingFuncOP

Definition at line 28 of file RampingMover.fwd.hh.

typedef utility::pointer::owning_ptr< RampingMover const > protocols::moves::RampingMoverCOP

Definition at line 26 of file RampingMover.fwd.hh.

typedef utility::pointer::owning_ptr< RampingMover > protocols::moves::RampingMoverOP

Definition at line 24 of file RampingMover.fwd.hh.

typedef utility::pointer::owning_ptr< RandomMover const > protocols::moves::RandomMoverCOP

Definition at line 34 of file MoverContainer.fwd.hh.

typedef utility::pointer::owning_ptr< RandomMover > protocols::moves::RandomMoverOP

Definition at line 32 of file MoverContainer.fwd.hh.

typedef core::Real protocols::moves::Real

Definition at line 53 of file MoverStatistics.cc.

typedef utility::pointer::owning_ptr< RepeatMover const > protocols::moves::RepeatMoverCOP

Definition at line 39 of file RepeatMover.fwd.hh.

typedef utility::pointer::owning_ptr< RepeatMover > protocols::moves::RepeatMoverOP

Definition at line 37 of file RepeatMover.fwd.hh.

typedef utility::pointer::owning_ptr< ReplicaExchangeMC const > protocols::moves::ReplicaExchangeMC_COP

Definition at line 25 of file ReplicaExchangeMC.fwd.hh.

typedef utility::pointer::owning_ptr< ReplicaExchangeMC > protocols::moves::ReplicaExchangeMC_OP

Definition at line 23 of file ReplicaExchangeMC.fwd.hh.

typedef utility::pointer::owning_ptr< ResId const > protocols::moves::ResIdCOP

Definition at line 26 of file ResId.fwd.hh.

typedef utility::pointer::owning_ptr< ResId > protocols::moves::ResIdOP

Definition at line 24 of file ResId.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceMover const > protocols::moves::SequenceMoverCOP

Definition at line 30 of file MoverContainer.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceMover > protocols::moves::SequenceMoverOP

Definition at line 28 of file MoverContainer.fwd.hh.

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

Definition at line 36 of file Mover.fwd.hh.

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

Definition at line 38 of file Mover.fwd.hh.

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

Definition at line 40 of file Mover.fwd.hh.

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

Definition at line 37 of file Mover.fwd.hh.

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

Definition at line 39 of file Mover.fwd.hh.

typedef utility::pointer::owning_ptr< StructureRestrictor const > protocols::moves::StructureRestrictorCOP

Definition at line 28 of file StructureRestrictor.fwd.hh.

typedef utility::pointer::owning_ptr< StructureRestrictor > protocols::moves::StructureRestrictorOP

Definition at line 26 of file StructureRestrictor.fwd.hh.

typedef utility::pointer::access_ptr< TemperatureController > protocols::moves::TemperatureControllerAP

Definition at line 28 of file TemperatuerController.fwd.hh.

typedef utility::pointer::access_ptr< TemperatureController const > protocols::moves::TemperatureControllerCAP

Definition at line 29 of file TemperatuerController.fwd.hh.

typedef utility::pointer::owning_ptr< TemperatureController const > protocols::moves::TemperatureControllerCOP

Definition at line 27 of file TemperatuerController.fwd.hh.

typedef utility::pointer::owning_ptr< TemperatureController > protocols::moves::TemperatureControllerOP

Definition at line 25 of file TemperatuerController.fwd.hh.

typedef utility::pointer::owning_ptr< TrialMover const > protocols::moves::TrialMoverCOP

Definition at line 26 of file TrialMover.fwd.hh.

typedef utility::pointer::owning_ptr< TrialMover > protocols::moves::TrialMoverOP

Definition at line 24 of file TrialMover.fwd.hh.

typedef utility::pointer::owning_ptr< WhileMover const > protocols::moves::WhileMoverCOP

Definition at line 26 of file WhileMover.fwd.hh.

typedef utility::pointer::owning_ptr< WhileMover > protocols::moves::WhileMoverOP

Definition at line 24 of file WhileMover.fwd.hh.

Enumeration Type Documentation

enum protocols::moves::MCA

Enumerator
MCA_accepted_score_beat_low
MCA_accepted_score_beat_last
MCA_accepted_thermally
MCA_rejected

Definition at line 25 of file MonteCarloStatus.hh.

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

Definition at line 28 of file MoverStatus.hh.

enum protocols::moves::StatsType

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

Detailed::: 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

Authors: Monica Berrondo

Last Modified: August 16 2007

Enumerator
all_stats
accept_reject
no_stats

Definition at line 67 of file TrialMover.hh.

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
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

Definition at line 60 of file PyMolMover.hh.

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...

Definition at line 372 of file PyMolMover.cc.

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

Referenced by protocols::abinitio::AbrelaxApplication::fold(), and protocols::jd2::JobDistributor::go_main().

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

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

Definition at line 44 of file util.cc.

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::TagPtr	,
		const protocols::moves::Movers_map &	movers
	)

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

Definition at line 34 of file util.cc.

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

template<class Ty >

Ty* protocols::moves::get_set_from_datamap	(	std::string const	type,
		std::string const	name,
		protocols::moves::DataMap &	data
	)

templated function for adding or getting an item from the datamap. Automatically checks whether an item of the requested type and name exists on the datamap. If so, returns the OP for that item, if not, instantiates that item on the datamap and returns the OP for it.

Definition at line 109 of file DataMap.hh.

References protocols::moves::DataMap::add(), protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), and TR_hh().

Referenced by protocols::protein_interface_design::movers::Splice::parse_my_tag(), and protocols::simple_moves::GenericMonteCarloMover::parse_my_tag().

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

We using independent 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.

Definition at line 68 of file PyMolMover.cc.

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.

Definition at line 73 of file ResId.cc.

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)

Definition at line 21 of file MoverStatus.cc.

References FAIL_BAD_INPUT, FAIL_DO_NOT_RETRY, FAIL_RETRY, and MS_SUCCESS.

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