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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
|
Classes | |
| struct | f1prms |
Static Public Attributes | |
| static const std::string | _CT = "PolarSF" |
| static const std::string | _INCR |
| static const std::string | _R12FACTOR = "r12-factor" |
| static const std::string | _R12INCR = "r12-increment" |
| static const std::string | _DR12MIN = "dr12-minimum" |
| static const std::string | _DR12MAX = "dr12-maximum" |
| static const std::string | _A1 = "a1" |
| static const std::string | _DA1MIN = "da1-minimum" |
| static const std::string | _DA1MAX = "da1-maximum" |
| static const std::string | _A2 = "a2" |
| static const std::string | _DA2MIN = "da2-minimum" |
| static const std::string | _DA2MAX = "da2-maximum" |
| static const std::string | _INCMETAL = "inc-metal" |
| static const std::string | _INCHBD = "inc-HBD" |
| static const std::string | _INCHBA = "inc-HBA" |
| static const std::string | _INCGUAN = "inc-guan" |
| static const std::string | _GUAN_PLANE = "guan-plane" |
| static const std::string | _ABS_DR12 = "abs-dr12" |
| static const std::string | _LP_OSP2 = "lp-osp2" |
| static const std::string | _LP_PHI = "lp-phi" |
| static const std::string | _LP_DPHIMIN = "lp-dphi-minimum" |
| static const std::string | _LP_DPHIMAX = "lp-dphi-maximum" |
| static const std::string | _LP_DTHETAMIN = "lp-dtheta-minimum" |
| static const std::string | _LP_DTHETAMAX = "lp-dtheta-maximum" |
 Static Public Attributes inherited from rxdock::BaseSF | |
| static const std::string | _CT = "BaseSF" |
| static const std::string | _WEIGHT = "weight" |
| static const std::string | _RANGE = "range" |
| static const std::string | _SYSTEM_SF = "rxdock.score.system" |
| static const std::string | _INTRA_SF = "rxdock.score.intra" |
| Static Public Attributes inherited from rxdock::BaseObject | |
| static const std::string | _CT = "BaseObject" |
| static const std::string | _CLASS = "CLASS" |
| static const std::string | _NAME = "NAME" |
| static const std::string | _ENABLED = "ENABLED" |
| Static Public Attributes inherited from rxdock::AnnotationHandler | |
| static const std::string | _ANNOTATION_FIELD = "annotations" |
Protected Member Functions | |
| InteractionCenterList | CreateAcceptorInteractionCenters (const AtomList &atomList) const |
| InteractionCenterList | CreateDonorInteractionCenters (const AtomList &atomList) const |
| void | BuildIntraMap (const InteractionCenterList &ICList1, const InteractionCenterList &ICList2, InteractionListMap &intns) const |
| void | BuildIntraMap (const InteractionCenterList &ICList, InteractionListMap &intns) const |
| double | IntraScore (const InteractionCenterList &posList, const InteractionCenterList &negList, const InteractionListMap &prtIntns, bool attr) const |
| void | Partition (const InteractionCenterList &posList, const InteractionCenterList &negList, const InteractionListMap &intns, InteractionListMap &prtIntns, double dist=0.0) const |
| f1prms | GetRprms () const |
| f1prms | GetA1prms () const |
| f1prms | GetA2prms () const |
| double | PolarScore (const InteractionCenter *intn, const InteractionCenterList &intnList, const f1prms &Rprms, const f1prms &A1prms, const f1prms &A2prms) const |
| void | OwnParameterUpdated (const std::string &strName) |
| Protected Member Functions inherited from rxdock::BaseSF | |
| BaseSF (const std::string &strClass, const std::string &strName) | |
| virtual double | RawScore () const =0 |
| void | ParameterUpdated (const std::string &strName) |
| void | AddToParentMapEntry (StringVariantMap &scoreMap, double rs) const |
| Protected Member Functions inherited from rxdock::BaseObject | |
| BaseObject (const std::string &strClass, const std::string &strName) | |
| void | ParameterUpdated (const std::string &strName) |
| Protected Member Functions inherited from rxdock::ParamHandler | |
| void | AddParameter (const std::string &strName, const Variant &vValue) |
| void | DeleteParameter (const std::string &strName) |
| void | ClearParameters () |
| virtual void | ParameterUpdated (const std::string &strName) |
| Protected Member Functions inherited from rxdock::AnnotationHandler | |
| void | AddAnnotation (AnnotationPtr spAnnotation) const |
| void | ClearAnnotationList () const |
| void | EnableAnnotations (bool bEnabled) const |
Friends | |
| void | to_json (json &j, const PolarSF &polarSF) |
| void | from_json (const json &j, PolarSF &polarSF) |
Additional Inherited Members | |
| Public Member Functions inherited from rxdock::BaseSF | |
| std::string | GetFullName () const |
| double | GetWeight () const |
| void | SetWeight (double) |
| double | GetRange () const |
| RBTDLL_EXPORT void | SetRange (double) |
| RBTDLL_EXPORT double | Score () const |
| virtual void | ScoreMap (StringVariantMap &scoreMap) const |
| virtual void | Add (BaseSF *) |
| virtual void | Remove (BaseSF *) |
| virtual bool | isAgg () const |
| virtual unsigned int | GetNumSF () const |
| virtual BaseSF * | GetSF (unsigned int iSF) const |
| void | Orphan () |
| BaseSF * | GetParentSF () const |
| Public Member Functions inherited from rxdock::BaseObject | |
| std::string | GetClass () const |
| std::string | GetName () const |
| void | SetName (const std::string &) |
| virtual std::string | GetFullName () const |
| void | Enable () |
| void | Disable () |
| bool | isEnabled () const |
| virtual void | Register (WorkSpace *) |
| virtual void | Unregister () |
| WorkSpace * | GetWorkSpace () const |
| virtual void | Deleted (Subject *theDeletedSubject) |
| virtual void | HandleRequest (RequestPtr spRequest) |
| virtual void | Print (std::ostream &s) const |
| Public Member Functions inherited from rxdock::ParamHandler | |
| unsigned int | GetNumParameters () const |
| Variant | GetParameter (const std::string &strName) const |
| bool | isParameterValid (const std::string &strName) const |
| std::vector< std::string > | GetParameterNames () const |
| StringVariantMap | GetParameters () const |
| RBTDLL_EXPORT void | SetParameter (const std::string &strName, const Variant &vValue) |
| virtual void | Print (std::ostream &s) const |
| Public Member Functions inherited from rxdock::Observer | |
| virtual void | Update (Subject *theChangedSubject)=0 |
| virtual void | Deleted (Subject *theDeletedSubject)=0 |
| virtual void | HandleRequest (RequestPtr spRequest) |
| Public Member Functions inherited from rxdock::AnnotationHandler | |
| bool | isAnnotationEnabled () const |
| const AnnotationList & | GetAnnotationList () const |
| int | GetNumAnnotations () const |
| void | RenderAnnotationList (const std::string &strName, std::vector< std::string > &retVal) const |
1.9.7