RxDock 0.1.0
A fast, versatile, and open-source program for docking ligands to proteins and nucleic acids
Loading...
Searching...
No Matches
Public Member Functions | Static Public Attributes | Protected Member Functions | List of all members
rxdock::PMFIdxSF Class Reference

#include <PMFIdxSF.h>

Inheritance diagram for rxdock::PMFIdxSF:
rxdock::BaseInterSF rxdock::BaseIdxSF rxdock::AnnotationHandler rxdock::BaseSF rxdock::BaseSF rxdock::BaseObject rxdock::BaseObject rxdock::ParamHandler rxdock::Observer rxdock::RequestHandler rxdock::ParamHandler rxdock::Observer rxdock::RequestHandler

Public Member Functions

 PMFIdxSF (const std::string &strName="pmf")
 
virtual ~PMFIdxSF ()
 
virtual void Update (Subject *theChangedSubject)
 
- Public Member Functions inherited from rxdock::BaseInterSF
ModelPtr GetReceptor () const
 
ModelPtr GetLigand () const
 
ModelList GetSolvent () const
 
virtual void Update (Subject *theChangedSubject)
 
- 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
 
virtual void Update (Subject *theChangedSubject)=0
 
virtual void Deleted (Subject *theDeletedSubject)=0
 
virtual void HandleRequest (RequestPtr spRequest)
 
- Public Member Functions inherited from rxdock::BaseIdxSF
double GetGridStep () const
 
void SetGridStep (double step)
 
double GetBorder () const
 
void SetBorder (double border)
 
- 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
 

Static Public Attributes

static const std::string _CT = "PMFIdxSF"
 
static const std::string _PMFDIR = "pmf-directory"
 
static const std::string _CC_CUTOFF = "C-C-cutoff"
 
static const std::string _SLOPE = "slope"
 
- Static Public Attributes inherited from rxdock::BaseInterSF
static const std::string _CT = "BaseInterSF"
 
- 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::BaseIdxSF
static const std::string _CT = "BaseIdxSF"
 
static const std::string _GRIDSTEP = "grid-step"
 
static const std::string _BORDER = "border"
 
- Static Public Attributes inherited from rxdock::AnnotationHandler
static const std::string _ANNOTATION_FIELD = "annotations"
 

Protected Member Functions

virtual void SetupReceptor ()
 
virtual void SetupLigand ()
 
virtual void SetupScore ()
 
virtual double RawScore (void) const
 
double GetLinearCloseRangeValue (double aDist, PMFType aRecType, PMFType aLigType) const
 
- Protected Member Functions inherited from rxdock::BaseInterSF
virtual void SetupReceptor ()=0
 
virtual void SetupLigand ()=0
 
virtual void SetupSolvent ()
 
virtual void SetupScore ()=0
 
- 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::BaseIdxSF
InteractionGridPtr CreateInteractionGrid () const
 
NonBondedGridPtr CreateNonBondedGrid () const
 
NonBondedHHSGridPtr CreateNonBondedHHSGrid () const
 
double GetMaxError () const
 
double GetCorrectedRange () const
 
void OwnParameterUpdated (const std::string &strName)
 
- Protected Member Functions inherited from rxdock::AnnotationHandler
void AddAnnotation (AnnotationPtr spAnnotation) const
 
void ClearAnnotationList () const
 
void EnableAnnotations (bool bEnabled) const
 

Detailed Description

PMFIdxSF class for PMF scoring.

Constructor & Destructor Documentation

◆ PMFIdxSF()

PMFIdxSF::PMFIdxSF ( const std::string &  strName = "pmf")

The only one constructor

◆ ~PMFIdxSF()

PMFIdxSF::~PMFIdxSF ( )
virtual

The virtual destructor

Member Function Documentation

◆ GetLinearCloseRangeValue()

double PMFIdxSF::GetLinearCloseRangeValue ( double  aDist,
PMFType  aRecType,
PMFType  aLigType 
) const
protected

Estimate value for short distances instead of using plateau in PMFs

◆ RawScore()

double PMFIdxSF::RawScore ( void  ) const
protectedvirtual

RawScore(void) returning with the actual PMF score

Implements rxdock::BaseSF.

◆ SetupLigand()

void PMFIdxSF::SetupLigand ( )
protectedvirtual

determine PMF types for all ligand atoms

Implements rxdock::BaseInterSF.

◆ SetupReceptor()

void PMFIdxSF::SetupReceptor ( )
protectedvirtual

Setting up receptor means atom typing for all the receptor atoms and create NonBondedGrid for NN

SetupReceptor: determine PMF atom types for all receptor atoms create NonBondedGrid of nearest neighbours

Implements rxdock::BaseInterSF.

◆ SetupScore()

void PMFIdxSF::SetupScore ( )
protectedvirtual

Setting up scores

Implements rxdock::BaseInterSF.

◆ Update()

void PMFIdxSF::Update ( Subject *  theChangedSubject)
virtual

Observer functionalities pure virtual, so it must be overloaded.

Reimplemented from rxdock::BaseInterSF.

Member Data Documentation

◆ _CT

const std::string PMFIdxSF::_CT = "PMFIdxSF"
static

This string serves as a name for the weight factor of the PMF score. Should be read from the .prm file.

◆ _PMFDIR

const std::string PMFIdxSF::_PMFDIR = "pmf-directory"
static

String pointing to the dir with PMF tables

The documentation for this class was generated from the following files:
Generated by doxygen 1.9.7