ObjCryst::Crystal Member List

This is the complete list of members for ObjCryst::Crystal, including all inherited members.

AddBondValenceRo(const ScatteringPower &, const ScatteringPower &, const REAL ro) (defined in ObjCryst::Crystal)	ObjCryst::Crystal
AddOption(RefObjOpt *opt)	ObjCryst::RefinableObj	protected
AddPar(const RefinablePar &newRefPar)	ObjCryst::RefinableObj
AddPar(RefinablePar *newRefPar)	ObjCryst::RefinableObj
AddPar(RefinableObj &newRefParList, const bool copyParam=false)	ObjCryst::RefinableObj
AddRestraint(Restraint *pNewRestraint)	ObjCryst::RefinableObj
AddScatterer(Scatterer *scatt)	ObjCryst::Crystal
AddScatteringPower(ScatteringPower *scattPow)	ObjCryst::Crystal
AddSubRefObj(RefinableObj &)	ObjCryst::RefinableObj	protected
BeginGlobalOptRandomMove()	ObjCryst::RefinableObj
BeginOptimization(const bool allowApproximations=false, const bool enableRestraints=false)	ObjCryst::Crystal	virtual
CalcBondValenceSum() const	ObjCryst::Crystal	private
CalcDistTable(const bool fast) const	ObjCryst::Crystal	private
CalcDynPopCorr(const REAL overlapDist=1., const REAL mergeDist=.0) const	ObjCryst::Crystal
CIFOutput(ostream &os, double mindist=0.5) const	ObjCryst::Crystal	virtual
ClearParamSet(const unsigned long id) const	ObjCryst::RefinableObj
ConnectAtoms(const REAL min_relat_dist=0.4, const REAL max_relat_dist=1.3, const bool warnuser_fail=false)	ObjCryst::Crystal
CreateParamSet(const string name="") const	ObjCryst::RefinableObj
Crystal()	ObjCryst::Crystal
Crystal(const REAL a, const REAL b, const REAL c, const string &SpaceGroupId)	ObjCryst::Crystal
Crystal(const REAL a, const REAL b, const REAL c, const REAL alpha, const REAL beta, const REAL gamma, const string &SpaceGroupId)	ObjCryst::Crystal
Crystal(const Crystal &oldCryst)	ObjCryst::Crystal
DeRegisterClient(RefinableObj &) const	ObjCryst::RefinableObj	virtual
EndOptimization()	ObjCryst::RefinableObj	virtual
EraseAllParamSet()	ObjCryst::RefinableObj
FindPar(const string &name) const	ObjCryst::RefinableObj	protected
FindPar(const REAL *) const	ObjCryst::RefinableObj	protected
FindParamSet(unsigned long id) const	ObjCryst::RefinableObj	protected
FindScatterer(const string &scattName) const	ObjCryst::Crystal	private
FixAllPar()	ObjCryst::RefinableObj
FractionalToOrthonormalCoords(REAL &x, REAL &y, REAL &z) const	ObjCryst::UnitCell
GetBMatrix() const	ObjCryst::UnitCell
GetBondValenceCost() const	ObjCryst::Crystal
GetBondValenceRoList() (defined in ObjCryst::Crystal)	ObjCryst::Crystal
GetBondValenceRoList() const (defined in ObjCryst::Crystal)	ObjCryst::Crystal
GetBumpMergeCost() const	ObjCryst::Crystal
GetBumpMergeParList() const (defined in ObjCryst::Crystal)	ObjCryst::Crystal
GetBumpMergeParList() (defined in ObjCryst::Crystal)	ObjCryst::Crystal
GetClassName() const	ObjCryst::Crystal	virtual
GetClientRegistry() const	ObjCryst::RefinableObj	virtual
GetClientRegistry()	ObjCryst::RefinableObj	virtual
GetClockLatticePar() const	ObjCryst::UnitCell
GetClockMaster() const	ObjCryst::RefinableObj
GetClockMetricMatrix() const	ObjCryst::UnitCell
GetClockScattCompList() const	ObjCryst::Crystal
GetClockScattererList() const	ObjCryst::Crystal
GetDynPopCorr(const Scatterer *pscatt, unsigned int component) const	ObjCryst::Crystal
GetGeneGroup(const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const	ObjCryst::Crystal	virtual
GetLatticePar() const	ObjCryst::UnitCell
GetLatticePar(const int whichPar) const	ObjCryst::UnitCell
GetLogLikelihood() const	ObjCryst::Crystal	virtual
GetLSQ_FullDeriv(const unsigned int, std::set< RefinablePar * > &vPar)	ObjCryst::RefinableObj	virtual
GetLSQCalc(const unsigned int) const	ObjCryst::RefinableObj	virtual
GetLSQDeriv(const unsigned int, RefinablePar &)	ObjCryst::RefinableObj	virtual
GetLSQObs(const unsigned int) const	ObjCryst::RefinableObj	virtual
GetLSQWeight(const unsigned int) const	ObjCryst::RefinableObj	virtual
GetMasterClockScatteringPower() const	ObjCryst::Crystal
GetMinDistanceTable(const REAL minDistance=0.1) const	ObjCryst::Crystal
GetName() const	ObjCryst::RefinableObj	virtual
GetNbLSQFunction() const	ObjCryst::RefinableObj	virtual
GetNbOption() const	ObjCryst::RefinableObj
GetNbPar() const	ObjCryst::RefinableObj
GetNbParNotFixed() const	ObjCryst::RefinableObj
GetNbScatterer() const	ObjCryst::Crystal
GetOption(const unsigned int i)	ObjCryst::RefinableObj
GetOption(const unsigned int i) const	ObjCryst::RefinableObj
GetOrthMatrix() const	ObjCryst::UnitCell
GetOrthonormalCoords(const REAL x, const REAL y, const REAL z) const	ObjCryst::UnitCell
GetPar(const long i)	ObjCryst::RefinableObj
GetPar(const long i) const	ObjCryst::RefinableObj
GetPar(const string &name)	ObjCryst::RefinableObj
GetPar(const string &name) const	ObjCryst::RefinableObj
GetPar(const REAL *)	ObjCryst::RefinableObj
GetPar(const REAL *) const	ObjCryst::RefinableObj
GetParamSet(const unsigned long setId) const	ObjCryst::RefinableObj
GetParamSet(const unsigned long setId)	ObjCryst::RefinableObj
GetParamSet_ParNotFixedHumanValue(const unsigned long setId, const long parNumber) const	ObjCryst::RefinableObj
GetParamSetName(const unsigned long setId) const	ObjCryst::RefinableObj
GetParNotFixed(const long i)	ObjCryst::RefinableObj
GetParNotFixed(const long i) const	ObjCryst::RefinableObj
GetRefParListClock() const	ObjCryst::RefinableObj
GetRestraintCost() const	ObjCryst::RefinableObj	virtual
GetScatt(const string &scattName)	ObjCryst::Crystal
GetScatt(const string &scattName) const	ObjCryst::Crystal
GetScatt(const long scattIndex)	ObjCryst::Crystal
GetScatt(const long scattIndex) const	ObjCryst::Crystal
GetScattererRegistry()	ObjCryst::Crystal
GetScattererRegistry() const	ObjCryst::Crystal
GetScatteringComponentList() const	ObjCryst::Crystal	virtual
GetScatteringPower(const string &name)	ObjCryst::Crystal
GetScatteringPower(const string &name) const	ObjCryst::Crystal
GetScatteringPowerRegistry()	ObjCryst::Crystal
GetScatteringPowerRegistry() const	ObjCryst::Crystal
GetSpaceGroup() const	ObjCryst::UnitCell
GetSpaceGroup()	ObjCryst::UnitCell
GetSubObjRegistry()	ObjCryst::RefinableObj
GetSubObjRegistry() const	ObjCryst::RefinableObj
GetUseDynPopCorr() const	ObjCryst::Crystal
GetVolume() const	ObjCryst::UnitCell
GLInitDisplayList(const bool onlyIndependentAtoms=false, const REAL xMin=-.1, const REAL xMax=1.1, const REAL yMin=-.1, const REAL yMax=1.1, const REAL zMin=-.1, const REAL zMax=1.1, const bool displayNames=false, const bool hideHydrogens=false) const	ObjCryst::Crystal	virtual
GlobalOptRandomMove(const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst)	ObjCryst::Crystal	virtual
Init(const REAL a, const REAL b, const REAL c, const REAL alpha, const REAL beta, const REAL gamma, const string &SpaceGroupId, const string &name)	ObjCryst::Crystal	virtual
InitOptions()	ObjCryst::Crystal	privatevirtual
InitRefParList()	ObjCryst::UnitCell	protected
IsBeingRefined() const	ObjCryst::RefinableObj
mBondValenceCalcClock	ObjCryst::Crystal	mutableprivate
mBondValenceCost	ObjCryst::Crystal	mutableprivate
mBondValenceCostClock	ObjCryst::Crystal	mutableprivate
mBondValenceCostScale	ObjCryst::Crystal	private
mBondValenceParClock	ObjCryst::Crystal	private
mBumpMergeCost	ObjCryst::Crystal	mutableprivate
mBumpMergeCostClock	ObjCryst::Crystal	mutableprivate
mBumpMergeParClock	ObjCryst::Crystal	private
mBumpMergeScale	ObjCryst::Crystal	private
mClientObjRegistry	ObjCryst::RefinableObj	mutableprotected
mClockDynPopCorr	ObjCryst::Crystal	mutableprivate
mClockMaster	ObjCryst::RefinableObj	protected
mClockNeighborTable	ObjCryst::Crystal	mutableprivate
mClockScattCompList	ObjCryst::Crystal	mutableprivate
mClockScattererList	ObjCryst::Crystal	private
mDeleteRefParInDestructor	ObjCryst::RefinableObj	protected
mDeleteSubObjInDestructor (defined in ObjCryst::Crystal)	ObjCryst::Crystal	private
mDisplayEnantiomer	ObjCryst::Crystal	private
mDistTableClock	ObjCryst::Crystal	mutableprivate
mDistTableMaxDistance	ObjCryst::Crystal	mutableprivate
MillerToOrthonormalCoords(REAL &x, REAL &y, REAL &z) const	ObjCryst::UnitCell
mLatticeClock	ObjCryst::Crystal	private
mLSQ_FullDeriv	ObjCryst::RefinableObj	mutableprotected
mLSQDeriv	ObjCryst::RefinableObj	mutableprotected
mMasterClockScatteringPower	ObjCryst::Crystal	private
mName	ObjCryst::RefinableObj	protected
mNbRefParNotFixed	ObjCryst::RefinableObj	mutableprotected
mOptimizationDepth	ObjCryst::RefinableObj	protected
mOptionRegistry	ObjCryst::RefinableObj	protected
mRandomMoveIsDone	ObjCryst::RefinableObj	protected
mRefParListClock	ObjCryst::RefinableObj	protected
mRefparNotFixedIndex	ObjCryst::RefinableObj	mutableprotected
mScattCompList	ObjCryst::Crystal	mutableprivate
mScattererRegistry	ObjCryst::Crystal	private
mScatteringPowerRegistry	ObjCryst::Crystal	private
mSubObjRegistry	ObjCryst::RefinableObj	protected
mUseDynPopCorr	ObjCryst::Crystal	private
mvBondValenceCalc	ObjCryst::Crystal	mutableprivate
mvBondValenceRo	ObjCryst::Crystal	private
mvBumpMergePar	ObjCryst::Crystal	private
mvDistTableSq	ObjCryst::Crystal	mutableprivate
mvpRefPar	ObjCryst::RefinableObj	protected
mvpRestraint	ObjCryst::RefinableObj	protected
mvpSavedValuesSet	ObjCryst::RefinableObj	mutableprotected
operator=(const RefinableObj &old)	ObjCryst::RefinableObj
OrthonormalToFractionalCoords(REAL &x, REAL &y, REAL &z) const	ObjCryst::UnitCell
OrthonormalToMillerCoords(REAL &x, REAL &y, REAL &z) const	ObjCryst::UnitCell
POVRayDescription(ostream &os, const CrystalPOVRayOptions &options) const	ObjCryst::Crystal
Prepare()	ObjCryst::RefinableObj	protectedvirtual
PrepareForRefinement() const	ObjCryst::RefinableObj
Print(ostream &os=cout) const	ObjCryst::Crystal	virtual
Print() const (defined in ObjCryst::UnitCell)	ObjCryst::UnitCell	virtual
PrintMinDistanceTable(const REAL minDistance=0.1, ostream &os=cout) const	ObjCryst::Crystal
RandomizeConfiguration()	ObjCryst::RefinableObj	virtual
RefinableObj()	ObjCryst::RefinableObj
RefinableObj(const bool internalUseOnly)	ObjCryst::RefinableObj
RefinableObj(const RefinableObj &old)	ObjCryst::RefinableObj
RegisterClient(RefinableObj &) const	ObjCryst::RefinableObj	virtual
RemoveBondValenceRo(const ScatteringPower &, const ScatteringPower &) (defined in ObjCryst::Crystal)	ObjCryst::Crystal
RemoveBumpMergeDistance(const ScatteringPower &scatt1, const ScatteringPower &scatt2)	ObjCryst::Crystal
RemovePar(RefinablePar *refPar)	ObjCryst::RefinableObj
RemoveRestraint(Restraint *pRestraint)	ObjCryst::RefinableObj
RemoveScatterer(Scatterer *scatt, const bool del=true)	ObjCryst::Crystal
RemoveScatteringPower(ScatteringPower *scattPow, const bool del=true)	ObjCryst::Crystal
RemoveSubRefObj(RefinableObj &)	ObjCryst::RefinableObj	protected
ResetDynPopCorr() const	ObjCryst::Crystal
ResetParList()	ObjCryst::RefinableObj
RestoreParamSet(const unsigned long id)	ObjCryst::RefinableObj
SaveParamSet(const unsigned long id) const	ObjCryst::RefinableObj
SetApproximationFlag(const bool allow)	ObjCryst::RefinableObj	virtual
SetBumpMergeDistance(const ScatteringPower &scatt1, const ScatteringPower &scatt2, const REAL dist=1.5)	ObjCryst::Crystal
SetBumpMergeDistance(const ScatteringPower &scatt1, const ScatteringPower &scatt2, const REAL dist, const bool allowMerge)	ObjCryst::Crystal
SetDeleteRefParInDestructor(const bool b)	ObjCryst::RefinableObj
SetDeleteSubObjInDestructor(const bool b)	ObjCryst::Crystal
SetGlobalOptimStep(const RefParType *type, const REAL step)	ObjCryst::RefinableObj
SetLimitsAbsolute(const string &parName, const REAL min, const REAL max)	ObjCryst::RefinableObj
SetLimitsAbsolute(const RefParType *type, const REAL min, const REAL max)	ObjCryst::RefinableObj
SetLimitsProportional(const string &parName, const REAL min, const REAL max)	ObjCryst::RefinableObj
SetLimitsProportional(const RefParType *type, const REAL min, const REAL max)	ObjCryst::RefinableObj
SetLimitsRelative(const string &parName, const REAL min, const REAL max)	ObjCryst::RefinableObj
SetLimitsRelative(const RefParType *type, const REAL min, const REAL max)	ObjCryst::RefinableObj
SetName(const string &name)	ObjCryst::RefinableObj	virtual
SetParIsFixed(const long parIndex, const bool fix)	ObjCryst::RefinableObj
SetParIsFixed(const string &parName, const bool fix)	ObjCryst::RefinableObj
SetParIsFixed(const RefParType *type, const bool fix)	ObjCryst::RefinableObj
SetParIsUsed(const string &parName, const bool use)	ObjCryst::RefinableObj
SetParIsUsed(const RefParType *type, const bool use)	ObjCryst::RefinableObj
SetUseDynPopCorr(const int use)	ObjCryst::Crystal
TagNewBestConfig() const	ObjCryst::RefinableObj	virtual
UnFixAllPar()	ObjCryst::RefinableObj
UnitCell()	ObjCryst::UnitCell
UnitCell(const REAL a, const REAL b, const REAL c, const string &SpaceGroupId)	ObjCryst::UnitCell
UnitCell(const REAL a, const REAL b, const REAL c, const REAL alpha, const REAL beta, const REAL gamma, const string &SpaceGroupId)	ObjCryst::UnitCell
UnitCell(const UnitCell &oldCryst)	ObjCryst::UnitCell
UpdateDisplay() const	ObjCryst::RefinableObj	virtual
VBumpMergePar typedef	ObjCryst::Crystal
XMLInput(istream &is, const XMLCrystTag &tag)	ObjCryst::Crystal	virtual
XMLOutput(ostream &os, int indent=0) const	ObjCryst::Crystal	virtual
~Crystal()	ObjCryst::Crystal
~RefinableObj()	ObjCryst::RefinableObj	virtual
~UnitCell()	ObjCryst::UnitCell