OpenStructure
 All Data Structures Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Macros Groups Pages
Namespaces | Data Structures | Typedefs | Enumerations | Functions
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, StringPropertyMap
 
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

typedef boost::shared_ptr<BlockModifier> BlockModifierPtr

Definition at line 38 of file block_modifiers.hh.

typedef boost::shared_ptr<BuildingBlock> BuildingBlockPtr

Definition at line 40 of file buildingblock.hh.

typedef boost::shared_ptr<CHARMMData> CHARMMDataPtr

Definition at line 44 of file ff_reader.hh.

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

Definition at line 52 of file simulation.hh.

typedef boost::shared_ptr<FFReader> FFReaderPtr

Definition at line 43 of file ff_reader.hh.

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

Definition at line 42 of file forcefield.hh.

typedef boost::shared_ptr<GromacsBlockModifier> GromacsBlockModifierPtr

Definition at line 45 of file gromacs_block_modifiers.hh.

typedef boost::shared_ptr<GromacsData> GromacsDataPtr

Definition at line 41 of file ff_reader.hh.

Definition at line 41 of file gromacs_block_modifiers.hh.

typedef boost::shared_ptr<GromacsTerminiConstructor> GromacsTerminiConstructorPtr

Definition at line 44 of file gromacs_block_modifiers.hh.

Definition at line 45 of file heuristic_block_modifiers.hh.

Definition at line 41 of file heuristic_block_modifiers.hh.

typedef boost::shared_ptr<HeuristicTerminiConstructor> HeuristicTerminiConstructorPtr

Definition at line 44 of file heuristic_block_modifiers.hh.

typedef boost::shared_ptr<HydrogenConstructor> HydrogenConstructorPtr

Definition at line 34 of file block_modifiers.hh.

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

Definition at line 49 of file simulation.hh.

typedef boost::shared_ptr<Interaction> InteractionPtr

Definition at line 39 of file interaction.hh.

typedef boost::shared_ptr<Observer> ObserverPtr

Definition at line 46 of file observer.hh.

typedef std::map<String,String> PropertyMap

Definition at line 93 of file settings.hh.

typedef boost::shared_ptr<ResidueNames> ResidueNamesPtr

Definition at line 39 of file forcefield.hh.

typedef boost::shared_ptr<Settings> SettingsPtr

Definition at line 46 of file settings.hh.

typedef boost::shared_ptr<Simulation> SimulationPtr

Definition at line 53 of file simulation.hh.

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

Definition at line 51 of file system_creator.hh.

typedef boost::shared_ptr<TerminiConstructor> TerminiConstructorPtr

Definition at line 37 of file block_modifiers.hh.

typedef boost::shared_ptr<TerminiExceptions> TerminiExceptionsPtr

Definition at line 48 of file settings.hh.

typedef boost::shared_ptr<TopologyCreator> TopologyCreatorPtr

Definition at line 44 of file topology_creator.hh.

typedef boost::shared_ptr<Topology> TopologyPtr

Definition at line 48 of file topology.hh.

typedef boost::shared_ptr<TrajObserver> TrajObserverPtr

Definition at line 48 of file observer.hh.

typedef boost::shared_ptr<TrajWriter> TrajWriterPtr

Definition at line 49 of file observer.hh.

Enumeration Type Documentation

Enumerator
GromacsBlockModifiers 
HeuristicBlockModifiers 

Definition at line 40 of file block_modifiers.hh.

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.

Enumerator
NoCutoff 
CutoffNonPeriodic 
CutoffPeriodic 
Ewald 
PME 

Definition at line 57 of file settings.hh.

enum Platform
Enumerator
Reference 
OpenCL 
CUDA 
CPU 

Definition at line 50 of file settings.hh.

Function Documentation

def ost.mol.mm.LoadAMBERForcefield ( )

Definition at line 25 of file __init__.py.

def ost.mol.mm.LoadCHARMMForcefield ( )

Definition at line 28 of file __init__.py.