RxDock 0.1.0
A fast, versatile, and open-source program for docking ligands to proteins and nucleic acids
Loading...
Searching...
No Matches
Public Types | Public Member Functions | Friends | List of all members
rxdock::Atom Class Reference
Inheritance diagram for rxdock::Atom:
rxdock::PseudoAtom

Public Types

enum  eHybridState {
  UNDEFINED = 0 , SP = 1 , SP2 = 2 , SP3 = 3 ,
  AROM = 4 , TRI = 5
}
 

Public Member Functions

RBTDLL_EXPORT Atom (int nAtomId, int nAtomicNo=6, std::string strAtomName="C", std::string strSubunitId="1", std::string strSubunitName="RES", std::string strSegmentName="SEG1", eHybridState eState=UNDEFINED, unsigned int nHydrogens=0, int nFormalCharge=0)
 
 Atom (json j)
 
 Atom (const Atom &atom)
 
Atom & operator= (const Atom &atom)
 
virtual std::ostream & Print (std::ostream &s) const
 
RBTDLL_EXPORT bool GetEnabled () const
 
int GetAtomId () const
 
void SetAtomId (const int nAtomId)
 
int GetAtomicNo () const
 
void SetAtomicNo (const int nAtomicNo)
 
std::string GetName () const
 
void SetAtomName (const std::string &strAtomName)
 
RBTDLL_EXPORT std::string GetFullAtomName () const
 
std::string GetSubunitId () const
 
void SetSubunitId (const std::string &strSubunitId)
 
std::string GetSubunitName () const
 
void SetSubunitName (const std::string &strSubunitName)
 
std::string GetSegmentName () const
 
void SetSegmentName (const std::string &strSegmentName)
 
eHybridState GetHybridState () const
 
void SetHybridState (const eHybridState eState)
 
unsigned int GetNumImplicitHydrogens () const
 
void SetNumImplicitHydrogens (const unsigned int nHydrogens)
 
int GetFormalCharge () const
 
void SetFormalCharge (const int nFormalCharge)
 
bool GetCyclicFlag () const
 
void SetCyclicFlag (bool bCyclic=true)
 
bool GetSelectionFlag () const
 
void SetSelectionFlag (bool bSelected=true)
 
void InvertSelectionFlag ()
 
bool GetUser1Flag () const
 
void SetUser1Flag (bool bUser1=true)
 
double GetUser1Value () const
 
void SetUser1Value (double dUser1=0.0)
 
double GetUser2Value () const
 
void SetUser2Value (double dUser2=0.0)
 
Model * GetModelPtr () const
 
void SetModelPtr (Model *pModel=nullptr)
 
unsigned int GetNumBonds () const
 
const BondMap & GetBondMap () const
 
bool AddBond (Bond *pBond)
 
bool RemoveBond (Bond *pBond)
 
unsigned int GetNumCyclicBonds () const
 
BondMap GetCyclicBondMap () const
 
int GetTotalFormalBondOrder () const
 
int GetMaxFormalBondOrder () const
 
const Coord & GetCoords () const
 
double GetX () const
 
double GetY () const
 
double GetZ () const
 
void SetCoords (const Coord &coord)
 
void SetCoords (const double x, const double y, const double z)
 
void SetX (const double x)
 
void SetY (const double y)
 
void SetZ (const double z)
 
double GetPartialCharge () const
 
void SetPartialCharge (const double dPartialCharge)
 
double GetGroupCharge () const
 
void SetGroupCharge (const double dGroupCharge)
 
double GetAtomicMass () const
 
void SetAtomicMass (const double dAtomicMass)
 
double GetVdwRadius () const
 
void SetVdwRadius (const double dVdwRadius)
 
std::string GetFFType () const
 
void SetFFType (const std::string &strFFType)
 
PMFType GetPMFType () const
 
void SetPMFType (PMFType aType)
 
TriposAtomType::eType GetTriposType () const
 
void SetTriposType (TriposAtomType::eType aType)
 
void SaveCoords (unsigned int coordNum=0)
 
void RevertCoords (unsigned int coordNum=0)
 
void Translate (const Vector &vector)
 
void Translate (const double vx, const double vy, const double vz)
 
void RotateUsingQuat (const Quat &q)
 
unsigned int GetCoordinationNumber () const
 
unsigned int GetCoordinationNumber (int nAtomicNo) const
 
unsigned int GetCoordinationNumber (const std::string &strFFType) const
 
unsigned int GetCoordinationNumber (eHybridState e) const
 

Friends

RBTDLL_EXPORT friend std::ostream & operator<< (std::ostream &s, const Atom &atom)
 
void to_json (json &j, const Atom &atom)
 
void from_json (const json &j, Atom &atom)
 
The documentation for this class was generated from the following files:
Generated by doxygen 1.9.7