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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 | |
| RBTDLL_EXPORT | Model (BaseMolecularFileSource *pMolSource) |
| RBTDLL_EXPORT | Model (AtomList &atomList, BondList &bondList) |
| Model (json j) | |
| std::string | GetName () const |
| int | GetNumTitles () const |
| std::vector< std::string > | GetTitleList () const |
| void | SetTitle (std::size_t index, const std::string &strTitle) |
| int | GetNumAtoms () const |
| AtomList | GetAtomList () const |
| int | GetNumBonds () const |
| BondList | GetBondList () const |
| int | GetNumSegments () const |
| SegmentMap | GetSegmentMap () const |
| int | GetNumRings () const |
| AtomListList | GetRingAtomLists () const |
| int | GetNumData () const |
| std::vector< std::string > | GetDataFieldList () const |
| StringVariantMap | GetDataMap () const |
| bool | isDataFieldPresent (const std::string &strDataField) const |
| RBTDLL_EXPORT Variant | GetDataValue (const std::string &strDataField) const |
| RBTDLL_EXPORT void | SetDataValue (const std::string &strDataField, const Variant &dataValue) |
| void | ClearDataField (const std::string &strDataField) |
| RBTDLL_EXPORT void | ClearAllDataFields (const std::string &strDataFieldPrefix) |
| void | ClearAllDataFields () |
| PseudoAtomPtr | AddPseudoAtom (const AtomList &atomList) |
| void | ClearPseudoAtoms () |
| void | UpdatePseudoAtoms () |
| unsigned int | GetNumPseudoAtoms () const |
| PseudoAtomList | GetPseudoAtomList () const |
| unsigned int | GetNumTetheredAtoms () const |
| AtomList | GetTetheredAtomList () const |
| double | GetOccupancy () const |
| bool | GetEnabled () const |
| RBTDLL_EXPORT void | SetOccupancy (double occupancy, double threshold=0.5) |
| void | UpdateCoords (BaseMolecularFileSource *pMolSource) |
| void | Translate (const Vector &vector) |
| void | Rotate (const Vector &axis, double thetaDeg) |
| void | Rotate (const Vector &axis, double thetaDeg, const Coord ¢er) |
| RBTDLL_EXPORT void | RotateBond (BondPtr spBond, double thetaDeg) |
| void | RotateBond (BondPtr spBond, double thetaDeg, AtomPtr spFixedAtom) |
| RBTDLL_EXPORT void | RotateBond (BondPtr spBond, double thetaDeg, bool bSwap) |
| void | SaveCoords (const std::string &coordName="") |
| RBTDLL_EXPORT void | RevertCoords (const std::string &coordName="") |
| std::map< std::string, int > | GetSavedCoordNames () const |
| int | GetNumSavedCoords () const |
| int | GetCurrentCoords () const |
| RBTDLL_EXPORT void | RevertCoords (int) |
| Coord | GetCenterOfMass () const |
| void | SetCenterOfMass (const Coord &c) |
| RBTDLL_EXPORT double | GetTotalMass () const |
| PrincipalAxes | GetPrincipalAxes () const |
| void | AlignPrincipalAxes (const PrincipalAxes &alignAxes=PrincipalAxes(), bool bAlignCOM=true) |
| RBTDLL_EXPORT void | SetFlexData (FlexData *pFlexData) |
| RBTDLL_EXPORT FlexData * | GetFlexData () const |
| RBTDLL_EXPORT ChromElement * | GetChrom () const |
| bool | isFlexible () const |
| const AtomRList & | GetFlexIntns (Atom *pAtom) const |
| BondList | GetFlexBonds () const |
| void | SelectFlexAtoms () |
| void | SelectFlexAtoms (Atom *pAtom) |
| void | SetAtomSelectionFlags (bool bSelected=true) |
| unsigned int | GetNumSelectedAtoms () |
| AtomList | GetSelectedAtomList () |
| void | SetAtomCyclicFlags (bool bCyclic=true) |
| unsigned int | GetNumCyclicAtoms () |
| AtomList | GetCyclicAtomList () |
| void | SetAtomUser1Flags (bool bUser1=true) |
| void | SetAtomUser1Values (double dUser1=0.0) |
| void | SetAtomUser2Values (double dUser2=0.0) |
| unsigned int | GetNumHBondAcceptorAtoms () |
| AtomList | GetHBondAcceptorAtomList () |
| unsigned int | GetNumHBondDonorAtoms () |
| AtomList | GetHBondDonorAtomList () |
| unsigned int | GetNumChargedAtoms () |
| AtomList | GetChargedAtomList () |
| unsigned int | GetNumPlanarAtoms () |
| AtomList | GetPlanarAtomList () |
| unsigned int | GetNumAtomsWithAtomicNo (int nAtomicNo) |
| AtomList | GetAtomListWithAtomicNo (int nAtomicNo) |
| unsigned int | GetNumAtomsWithFFType (std::string strFFType) |
| AtomList | GetAtomListWithFFType (std::string strFFType) |
| template<class Predicate > | |
| unsigned int | GetNumBonds (const Predicate &pred) |
| template<class Predicate > | |
| BondList | GetBondList (const Predicate &pred) |
| void | SetBondSelectionFlags (bool bSelected=true) |
| unsigned int | GetNumSelectedBonds () |
| BondList | GetSelectedBondList () |
| void | SetBondCyclicFlags (bool bCyclic=true) |
| unsigned int | GetNumCyclicBonds () |
| BondList | GetCyclicBondList () |
| void | GetMinMaxCoords (Coord &minCoord, Coord &maxCoord, bool bInit=true) |
| std::map< std::string, int > | GetAtomTypeMap () |
| std::map< std::string, int > | GetBondTypeMap () |
Friends | |
| class | ModelMutator |
| void | to_json (json &j, const Model &model) |
| void | from_json (const json &j, Model &model) |
1.9.7