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:
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