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< String > | GetAtoms () const |
std::vector< String > | GetTypes () const |
std::vector< Real > | GetCharges () const |
std::vector< Real > | GetMasses () const |
String | GetType (const String &name) const |
Real | GetCharge (const String &name) const |
Real | GetMass (const String &name) const |
std::vector< InteractionPtr > | GetBonds () const |
std::vector< InteractionPtr > | GetAngles () const |
std::vector< InteractionPtr > | GetDihedrals () const |
std::vector< InteractionPtr > | GetImpropers () const |
std::vector< InteractionPtr > | GetCMaps () const |
std::vector< InteractionPtr > | GetExclusions () const |
std::vector< InteractionPtr > | GetConstraints () 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
Member Function Documentation
void AddAtom |
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const String & |
name, |
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const String & |
type, |
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Real |
charge, |
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Real |
mass = std::numeric_limits< Real >::quiet_NaN() | |
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void AddConstraint |
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InteractionPtr |
p, |
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bool |
replace_existing = false | |
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std::vector<String> GetAtoms |
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const [inline] |
std::vector<Real> GetCharges |
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const [inline] |
std::vector<Real> GetMasses |
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const [inline] |
std::vector<String> GetTypes |
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const [inline] |
void RemoveAtom |
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const String & |
name |
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void RemoveInteractionsToNext |
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void RemoveInteractionsToPrev |
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void ReplaceAtom |
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const String & |
name, |
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const String & |
new_name, |
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const String & |
new_type, |
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Real |
new_charge, |
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Real |
new_mass = std::numeric_limits< Real >::quiet_NaN() | |
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) |
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void Serialize |
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DS & |
ds |
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[inline] |
The documentation for this class was generated from the following file: