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RxDock 0.1.0
A fast, versatile, and open-source program for docking ligands to proteins and nucleic acids
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RxDock 0.1.0
A fast, versatile, and open-source program for docking ligands to proteins and nucleic acids
|
Public Member Functions | |
| PseudoAtom (const AtomList &atomList, int nAtomId=-1, std::string strAtomName="PSEUDO") | |
| virtual std::ostream & | Print (std::ostream &s) const |
| unsigned int | GetNumAtoms () const |
| AtomList | GetAtomList () const |
| void | UpdateCoords () |
 Public Member Functions inherited from rxdock::Atom | |
| 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 | |
| void | to_json (json &j, const PseudoAtom &pseudoAtom) |
| void | from_json (const json &j, PseudoAtom &pseudoAtom) |
Additional Inherited Members | |
| Public Types inherited from rxdock::Atom | |
| enum | eHybridState { UNDEFINED = 0 , SP = 1 , SP2 = 2 , SP3 = 3 , AROM = 4 , TRI = 5 } |
|
virtual |
Reimplemented from rxdock::Atom.
1.9.7