ost::mol::mm Namespace Reference

Namespaces
	antechamber
	impl

Data Structures
class	HydrogenConstructor
class	TerminiConstructor
class	BlockModifier
class	BuildingBlock
class	GromacsData
class	CHARMMData
class	MMPreprocessor
class	FFReader
struct	ResidueNames
class	Forcefield
class	GromacsPositionRuleEvaluator
class	GromacsHydrogenConstructor
class	GromacsBlockModifier
class	HeuristicHydrogenConstructor
class	HeuristicBlockModifier
class	Index
class	Index< 1 >
class	Index< 2 >
class	Index< 3 >
class	Index< 4 >
class	Index< 5 >
class	Index< 6 >
class	Index< 7 >
class	IndexIterator
class	Interaction
class	Modeller
class	Observer
class	TrajObserver
class	TrajWriter
class	TerminiExceptions
struct	Settings
class	Simulation
class	StateExtractor
class	Steep
class	SystemCreator
class	Topology
class	TopologyCreator

Typedefs
typedef boost::shared_ptr< HydrogenConstructor >	HydrogenConstructorPtr
typedef boost::shared_ptr< TerminiConstructor >	TerminiConstructorPtr
typedef boost::shared_ptr< BlockModifier >	BlockModifierPtr
typedef boost::shared_ptr< BuildingBlock >	BuildingBlockPtr
typedef boost::shared_ptr< GromacsData >	GromacsDataPtr
typedef boost::shared_ptr< FFReader >	FFReaderPtr
typedef boost::shared_ptr< CHARMMData >	CHARMMDataPtr
typedef boost::shared_ptr< ResidueNames >	ResidueNamesPtr
typedef boost::shared_ptr< ost::mol::mm::Forcefield >	ForcefieldPtr
typedef boost::shared_ptr< GromacsHydrogenConstructor >	GromacsHydrogenConstructorPtr
typedef boost::shared_ptr< GromacsTerminiConstructor >	GromacsTerminiConstructorPtr
typedef boost::shared_ptr< GromacsBlockModifier >	GromacsBlockModifierPtr
typedef boost::shared_ptr< HeuristicHydrogenConstructor >	HeuristicHydrogenConstructorPtr
typedef boost::shared_ptr< HeuristicTerminiConstructor >	HeuristicTerminiConstructorPtr
typedef boost::shared_ptr< HeuristicBlockModifier >	HeuristicBlockModifierPtr
typedef boost::shared_ptr< Interaction >	InteractionPtr
typedef boost::shared_ptr< Observer >	ObserverPtr
typedef boost::shared_ptr< TrajObserver >	TrajObserverPtr
typedef boost::shared_ptr< TrajWriter >	TrajWriterPtr
typedef boost::shared_ptr< Settings >	SettingsPtr
typedef boost::shared_ptr< TerminiExceptions >	TerminiExceptionsPtr
typedef std::map< String, String >	PropertyMap
typedef boost::shared_ptr< OpenMM::Integrator >	IntegratorPtr
typedef boost::shared_ptr< OpenMM::Context >	ContextPtr
typedef boost::shared_ptr< Simulation >	SimulationPtr
typedef boost::shared_ptr< OpenMM::System >	SystemPtr
typedef boost::shared_ptr< Topology >	TopologyPtr
typedef boost::shared_ptr< TopologyCreator >	TopologyCreatorPtr

Enumerations
enum	BlockModifierType { GromacsBlockModifiers , HeuristicBlockModifiers }
enum	FuncType {   Invalid , HarmonicBond , HarmonicAngle , UreyBradleyAngle ,   PeriodicDihedral , PeriodicImproper , HarmonicImproper , CMap ,   LJ , LJPair , GBSA , DistanceConstraint ,   Exclusion , HarmonicPositionRestraint , HarmonicDistanceRestraint }
enum	Platform { Reference , OpenCL , CUDA , CPU }
enum	NonbondedMethod {   NoCutoff , CutoffNonPeriodic , CutoffPeriodic , Ewald ,   PME }

Functions
def	LoadAMBERForcefield ()
def	LoadCHARMMForcefield ()

Typedef Documentation

BlockModifierPtr

typedef boost::shared_ptr<BlockModifier> BlockModifierPtr

Definition at line 38 of file block_modifiers.hh.

BuildingBlockPtr

typedef boost::shared_ptr<BuildingBlock> BuildingBlockPtr

Definition at line 41 of file buildingblock.hh.

CHARMMDataPtr

typedef boost::shared_ptr<CHARMMData> CHARMMDataPtr

Definition at line 44 of file ff_reader.hh.

ContextPtr

typedef boost::shared_ptr<OpenMM::Context> ContextPtr

Definition at line 52 of file simulation.hh.

FFReaderPtr

typedef boost::shared_ptr<FFReader> FFReaderPtr

Definition at line 43 of file ff_reader.hh.

ForcefieldPtr

typedef boost::shared_ptr<ost::mol::mm::Forcefield> ForcefieldPtr

Definition at line 42 of file forcefield.hh.

GromacsBlockModifierPtr

typedef boost::shared_ptr<GromacsBlockModifier> GromacsBlockModifierPtr

Definition at line 45 of file gromacs_block_modifiers.hh.

GromacsDataPtr

typedef boost::shared_ptr<GromacsData> GromacsDataPtr

Definition at line 42 of file ff_reader.hh.

GromacsHydrogenConstructorPtr

typedef boost::shared_ptr<GromacsHydrogenConstructor> GromacsHydrogenConstructorPtr

Definition at line 43 of file gromacs_block_modifiers.hh.

GromacsTerminiConstructorPtr

typedef boost::shared_ptr<GromacsTerminiConstructor> GromacsTerminiConstructorPtr

Definition at line 44 of file gromacs_block_modifiers.hh.

HeuristicBlockModifierPtr

typedef boost::shared_ptr<HeuristicBlockModifier> HeuristicBlockModifierPtr

Definition at line 45 of file heuristic_block_modifiers.hh.

HeuristicHydrogenConstructorPtr

typedef boost::shared_ptr<HeuristicHydrogenConstructor> HeuristicHydrogenConstructorPtr

Definition at line 43 of file heuristic_block_modifiers.hh.

HeuristicTerminiConstructorPtr

typedef boost::shared_ptr<HeuristicTerminiConstructor> HeuristicTerminiConstructorPtr

Definition at line 44 of file heuristic_block_modifiers.hh.

HydrogenConstructorPtr

typedef boost::shared_ptr<HydrogenConstructor> HydrogenConstructorPtr

Definition at line 36 of file block_modifiers.hh.

IntegratorPtr

typedef boost::shared_ptr<OpenMM::Integrator> IntegratorPtr

Definition at line 51 of file simulation.hh.

InteractionPtr

typedef boost::shared_ptr<Interaction> InteractionPtr

Definition at line 40 of file interaction.hh.

ObserverPtr

typedef boost::shared_ptr<Observer> ObserverPtr

Definition at line 47 of file observer.hh.

PropertyMap

typedef std::map<String,String> PropertyMap

Definition at line 93 of file settings.hh.

ResidueNamesPtr

typedef boost::shared_ptr<ResidueNames> ResidueNamesPtr

Definition at line 41 of file forcefield.hh.

SettingsPtr

typedef boost::shared_ptr<Settings> SettingsPtr

Definition at line 47 of file settings.hh.

SimulationPtr

typedef boost::shared_ptr<Simulation> SimulationPtr

Definition at line 53 of file simulation.hh.

SystemPtr

typedef boost::shared_ptr<OpenMM::System> SystemPtr

Definition at line 51 of file system_creator.hh.

TerminiConstructorPtr

typedef boost::shared_ptr<TerminiConstructor> TerminiConstructorPtr

Definition at line 37 of file block_modifiers.hh.

TerminiExceptionsPtr

typedef boost::shared_ptr<TerminiExceptions> TerminiExceptionsPtr

Definition at line 48 of file settings.hh.

TopologyCreatorPtr

typedef boost::shared_ptr<TopologyCreator> TopologyCreatorPtr

Definition at line 45 of file topology_creator.hh.

TopologyPtr

typedef boost::shared_ptr<Topology> TopologyPtr

Definition at line 49 of file topology.hh.

TrajObserverPtr

typedef boost::shared_ptr<TrajObserver> TrajObserverPtr

Definition at line 48 of file observer.hh.

TrajWriterPtr

typedef boost::shared_ptr<TrajWriter> TrajWriterPtr

Definition at line 49 of file observer.hh.

Enumeration Type Documentation

BlockModifierType

enum BlockModifierType

Enumerator
GromacsBlockModifiers
HeuristicBlockModifiers

Definition at line 40 of file block_modifiers.hh.

FuncType

enum FuncType

Enumerator
Invalid
HarmonicBond
HarmonicAngle
UreyBradleyAngle
PeriodicDihedral
PeriodicImproper
HarmonicImproper
CMap
LJ
LJPair
GBSA
DistanceConstraint
Exclusion
HarmonicPositionRestraint
HarmonicDistanceRestraint

Definition at line 42 of file interaction.hh.

NonbondedMethod

enum NonbondedMethod

Enumerator
NoCutoff
CutoffNonPeriodic
CutoffPeriodic
Ewald
PME

Definition at line 57 of file settings.hh.

Platform

enum Platform

Enumerator
Reference
OpenCL
CUDA
CPU

Definition at line 50 of file settings.hh.

Function Documentation

LoadAMBERForcefield()

def ost.mol.mm.LoadAMBERForcefield

(

)

Definition at line 25 of file __init__.py.

LoadCHARMMForcefield()

def ost.mol.mm.LoadCHARMMForcefield

(

)

Definition at line 28 of file __init__.py.