AddBondValenceRo(const ScatteringPower &, const ScatteringPower &, const REAL ro) | ObjCryst::Crystal | |
AddOption(RefObjOpt *opt) | ObjCryst::RefinableObj | [protected] |
AddPar(const RefinablePar &newRefPar) | ObjCryst::RefinableObj | |
AddPar(RefinablePar *newRefPar) | ObjCryst::RefinableObj | |
AddPar(RefinableObj &newRefParList) | 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 REAL asymUnitMargin=4) const | ObjCryst::Crystal | [private] |
CalcDynPopCorr(const REAL overlapDist=1., const REAL mergeDist=.0) const | ObjCryst::Crystal | |
CIFOutput(ostream &os) const | ObjCryst::Crystal | [virtual] |
ClearParamSet(const unsigned long id) const | ObjCryst::RefinableObj | |
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() | ObjCryst::Crystal | |
GetBondValenceRoList() const | ObjCryst::Crystal | |
GetBumpMergeCost() const | ObjCryst::Crystal | |
GetBumpMergeParList() const | ObjCryst::Crystal | |
GetBumpMergeParList() | ObjCryst::Crystal | |
GetClassName() const | ObjCryst::Crystal | [virtual] |
GetClockLatticePar() const | ObjCryst::UnitCell | |
GetClockMaster() const | ObjCryst::RefinableObj | |
GetClockMetricMatrix() const | ObjCryst::UnitCell | |
GetClockScattCompList() const | ObjCryst::Crystal | |
GetClockScattererList() 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] |
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 | |
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 | |
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 | 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 | [private, virtual] |
InitOptions() | ObjCryst::Crystal | [private, virtual] |
InitRefParList() | ObjCryst::UnitCell | [protected] |
IsBeingRefined() const | ObjCryst::RefinableObj | |
mBondValenceCalcClock | ObjCryst::Crystal | [mutable, private] |
mBondValenceCost | ObjCryst::Crystal | [mutable, private] |
mBondValenceCostClock | ObjCryst::Crystal | [mutable, private] |
mBondValenceCostScale | ObjCryst::Crystal | [private] |
mBondValenceParClock | ObjCryst::Crystal | [private] |
mBumpMergeCost | ObjCryst::Crystal | [mutable, private] |
mBumpMergeCostClock | ObjCryst::Crystal | [mutable, private] |
mBumpMergeParClock | ObjCryst::Crystal | [private] |
mBumpMergeScale | ObjCryst::Crystal | [private] |
mClientObjRegistry | ObjCryst::RefinableObj | [mutable, protected] |
mClockDynPopCorr | ObjCryst::Crystal | [mutable, private] |
mClockMaster | ObjCryst::RefinableObj | [protected] |
mClockNeighborTable | ObjCryst::Crystal | [mutable, private] |
mClockScattCompList | ObjCryst::Crystal | [mutable, private] |
mClockScattererList | ObjCryst::Crystal | [private] |
mDeleteRefParInDestructor | ObjCryst::RefinableObj | [protected] |
mDisplayEnantiomer | ObjCryst::Crystal | [private] |
mDistTableClock | ObjCryst::Crystal | [mutable, private] |
MillerToOrthonormalCoords(REAL &x, REAL &y, REAL &z) const | ObjCryst::UnitCell | |
mIsbeingRefined | ObjCryst::RefinableObj | [protected] |
mLatticeClock | ObjCryst::Crystal | [private] |
mLSQDeriv | ObjCryst::RefinableObj | [mutable, protected] |
mMasterClockScatteringPower | ObjCryst::Crystal | [private] |
mName | ObjCryst::RefinableObj | [protected] |
mNbRefParNotFixed | ObjCryst::RefinableObj | [mutable, protected] |
mOptionRegistry | ObjCryst::RefinableObj | [protected] |
mRandomMoveIsDone | ObjCryst::RefinableObj | [protected] |
mRefParListClock | ObjCryst::RefinableObj | [protected] |
mRefparNotFixedIndex | ObjCryst::RefinableObj | [mutable, protected] |
mScattCompList | ObjCryst::Crystal | [mutable, private] |
mScattererRegistry | ObjCryst::Crystal | [private] |
mScatteringPowerRegistry | ObjCryst::Crystal | [private] |
mSubObjRegistry | ObjCryst::RefinableObj | [protected] |
mUseDynPopCorr | ObjCryst::Crystal | [private] |
mvBondValenceCalc | ObjCryst::Crystal | [mutable, private] |
mvBondValenceRo | ObjCryst::Crystal | [private] |
mvBumpMergePar | ObjCryst::Crystal | [private] |
mvDistTableSq | ObjCryst::Crystal | [mutable, private] |
mvpRefPar | ObjCryst::RefinableObj | [protected] |
mvpRestraint | ObjCryst::RefinableObj | [protected] |
mvpSavedValuesSet | ObjCryst::RefinableObj | [mutable, protected] |
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 | [protected, virtual] |
PrepareForRefinement() const | ObjCryst::RefinableObj | |
Print(ostream &os=cout) const | ObjCryst::Crystal | [virtual] |
ObjCryst::RefinableObj::Print() const | ObjCryst::RefinableObj | [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 &) | ObjCryst::Crystal | |
RemoveBumpMergeDistance(const ScatteringPower &scatt1, const ScatteringPower &scatt2) | ObjCryst::Crystal | |
RemovePar(RefinablePar *refPar) | ObjCryst::RefinableObj | |
RemoveRestraint(Restraint *pRestraint) | ObjCryst::RefinableObj | |
RemoveScatterer(Scatterer *scatt) | ObjCryst::Crystal | |
RemoveScatteringPower(ScatteringPower *scattPow) | 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 | |
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 | |
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 | |