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Public Member Functions
BuildingBlock Class Reference

#include <buildingblock.hh>

Public Member Functions

 BuildingBlock ()
 
 BuildingBlock (const BuildingBlock &block)
 
bool Match (const ost::mol::ResidueHandle &handle, bool match_connectivity, String &info) const
 
void Connect (ost::mol::ResidueHandle &handle, ost::mol::XCSEditor &ed)
 
std::vector< StringGetAtoms () const
 
std::vector< StringGetTypes () const
 
std::vector< RealGetCharges () const
 
std::vector< RealGetMasses () const
 
String GetType (const String &name) const
 
Real GetCharge (const String &name) const
 
Real GetMass (const String &name) const
 
std::vector< InteractionPtrGetBonds () const
 
std::vector< InteractionPtrGetAngles () const
 
std::vector< InteractionPtrGetDihedrals () const
 
std::vector< InteractionPtrGetImpropers () const
 
std::vector< InteractionPtrGetCMaps () const
 
std::vector< InteractionPtrGetExclusions () const
 
std::vector< InteractionPtrGetConstraints () const
 
void AddAtom (const String &name, const String &type, Real charge, Real mass=std::numeric_limits< Real >::quiet_NaN())
 
void AddBond (InteractionPtr p, bool replace_existing=false)
 
void AddAngle (InteractionPtr p, bool replace_existing=false)
 
void AddDihedral (InteractionPtr p, bool replace_existing=false)
 
void AddImproper (InteractionPtr p, bool replace_existing=false)
 
void AddExclusion (InteractionPtr p, bool replace_existing=false)
 
void AddCMap (InteractionPtr p, bool replace_existing=false)
 
void AddConstraint (InteractionPtr p, bool replace_existing=false)
 
void RemoveAtom (const String &name)
 
void ReplaceAtom (const String &name, const String &new_name, const String &new_type, Real new_charge, Real new_mass=std::numeric_limits< Real >::quiet_NaN())
 
void RemoveInteractionsToPrev ()
 
void RemoveInteractionsToNext ()
 
template<typename DS >
void Serialize (DS &ds)
 

Detailed Description

Definition at line 43 of file buildingblock.hh.

Constructor & Destructor Documentation

BuildingBlock ( )
inline

Definition at line 45 of file buildingblock.hh.

BuildingBlock ( const BuildingBlock block)

Member Function Documentation

void AddAngle ( InteractionPtr  p,
bool  replace_existing = false 
)
void AddAtom ( const String name,
const String type,
Real  charge,
Real  mass = std::numeric_limits< Real >::quiet_NaN() 
)
void AddBond ( InteractionPtr  p,
bool  replace_existing = false 
)
void AddCMap ( InteractionPtr  p,
bool  replace_existing = false 
)
void AddConstraint ( InteractionPtr  p,
bool  replace_existing = false 
)
void AddDihedral ( InteractionPtr  p,
bool  replace_existing = false 
)
void AddExclusion ( InteractionPtr  p,
bool  replace_existing = false 
)
void AddImproper ( InteractionPtr  p,
bool  replace_existing = false 
)
void Connect ( ost::mol::ResidueHandle handle,
ost::mol::XCSEditor ed 
)
std::vector<InteractionPtr> GetAngles ( ) const
inline

Definition at line 73 of file buildingblock.hh.

std::vector<String> GetAtoms ( ) const
inline

Definition at line 57 of file buildingblock.hh.

std::vector<InteractionPtr> GetBonds ( ) const
inline

Definition at line 71 of file buildingblock.hh.

Real GetCharge ( const String name) const
std::vector<Real> GetCharges ( ) const
inline

Definition at line 61 of file buildingblock.hh.

std::vector<InteractionPtr> GetCMaps ( ) const
inline

Definition at line 79 of file buildingblock.hh.

std::vector<InteractionPtr> GetConstraints ( ) const
inline

Definition at line 83 of file buildingblock.hh.

std::vector<InteractionPtr> GetDihedrals ( ) const
inline

Definition at line 75 of file buildingblock.hh.

std::vector<InteractionPtr> GetExclusions ( ) const
inline

Definition at line 81 of file buildingblock.hh.

std::vector<InteractionPtr> GetImpropers ( ) const
inline

Definition at line 77 of file buildingblock.hh.

Real GetMass ( const String name) const
std::vector<Real> GetMasses ( ) const
inline

Definition at line 63 of file buildingblock.hh.

String GetType ( const String name) const
std::vector<String> GetTypes ( ) const
inline

Definition at line 59 of file buildingblock.hh.

bool Match ( const ost::mol::ResidueHandle handle,
bool  match_connectivity,
String info 
) const
void RemoveAtom ( const String name)
void RemoveInteractionsToNext ( )
void RemoveInteractionsToPrev ( )
void ReplaceAtom ( const String name,
const String new_name,
const String new_type,
Real  new_charge,
Real  new_mass = std::numeric_limits< Real >::quiet_NaN() 
)
void Serialize ( DS &  ds)
inline

Definition at line 120 of file buildingblock.hh.


The documentation for this class was generated from the following file: