| AddAtom(const REAL x, const REAL y, const REAL z, const ScatteringPower *pPow, const string &name, const bool updateDisplay=true) | ObjCryst::Molecule | |
| AddBond(MolAtom &atom1, MolAtom &atom2, const REAL length, const REAL sigma, const REAL delta, const REAL bondOrder=1., const bool updateDisplay=true) | ObjCryst::Molecule | |
| AddBondAngle(MolAtom &atom1, MolAtom &atom2, MolAtom &atom3, const REAL angle, const REAL sigma, const REAL delta, const bool updateDisplay=true) | ObjCryst::Molecule | |
| AddDihedralAngle(MolAtom &atom1, MolAtom &atom2, MolAtom &atom3, MolAtom &atom4, const REAL angle, const REAL sigma, const REAL delta, const bool updateDisplay=true) | ObjCryst::Molecule | |
| 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 | |
| AddRigidGroup(const RigidGroup &, const bool updateDisplay=true) | ObjCryst::Molecule | |
| AddSubRefObj(RefinableObj &) | ObjCryst::RefinableObj | protected |
| AsZMatrix(const bool keeporder) const | ObjCryst::Molecule | |
| BeginGlobalOptRandomMove() | ObjCryst::RefinableObj | |
| BeginOptimization(const bool allowApproximations=false, const bool enableRestraints=false) | ObjCryst::Molecule | virtual |
| BondAngleRandomChange(const StretchModeBondAngle &mode, const REAL amplitude, const bool respectRestraint=true) | ObjCryst::Molecule | |
| BondLengthRandomChange(const StretchModeBondLength &mode, const REAL amplitude, const bool respectRestraint=true) | ObjCryst::Molecule | |
| BuildConnectivityTable() const | ObjCryst::Molecule | |
| BuildFlipGroup() | ObjCryst::Molecule | |
| BuildMDAtomGroups() | ObjCryst::Molecule | |
| BuildRingList() | ObjCryst::Molecule | |
| BuildRotorGroup() | ObjCryst::Molecule | |
| BuildStretchModeBondAngle() | ObjCryst::Molecule | |
| BuildStretchModeBondLength() | ObjCryst::Molecule | |
| BuildStretchModeGroups() | ObjCryst::Molecule | |
| BuildStretchModeTorsion() | ObjCryst::Molecule | |
| BuildStretchModeTwist() | ObjCryst::Molecule | |
| ClearParamSet(const unsigned long id) const | ObjCryst::RefinableObj | |
| CreateCopy() const | ObjCryst::Molecule | virtual |
| CreateParamSet(const string name="") const | ObjCryst::RefinableObj | |
| DeRegisterClient(RefinableObj &) const | ObjCryst::RefinableObj | virtual |
| DihedralAngleRandomChange(const StretchModeTorsion &mode, const REAL amplitude, const bool respectRestraint=true) | ObjCryst::Molecule | |
| EndOptimization() | ObjCryst::Molecule | virtual |
| EraseAllParamSet() | ObjCryst::RefinableObj | |
| FindAtom(const string &name) | ObjCryst::Molecule | |
| FindAtom(const string &name) const | ObjCryst::Molecule | |
| FindBond(const MolAtom &, const MolAtom &) const | ObjCryst::Molecule | |
| FindBond(const MolAtom &, const MolAtom &) | ObjCryst::Molecule | |
| FindBondAngle(const MolAtom &at1, const MolAtom &at0, const MolAtom &at2) const | ObjCryst::Molecule | |
| FindDihedralAngle(const MolAtom &at1, const MolAtom &at2, const MolAtom &at3, const MolAtom &at4) const | ObjCryst::Molecule | |
| FindPar(const string &name) const | ObjCryst::RefinableObj | protected |
| FindPar(const REAL *) const | ObjCryst::RefinableObj | protected |
| FindParamSet(unsigned long id) const | ObjCryst::RefinableObj | protected |
| FixAllPar() | ObjCryst::RefinableObj | |
| FlipAtomGroup(const FlipGroup &) | ObjCryst::Molecule | |
| GetAtom(unsigned int i) (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetAtom(unsigned int i) const (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetAtom(const string &name) (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetAtom(const string &name) const (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetAtomList() const (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetAtomList() (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetAtomPositionClock() | ObjCryst::Molecule | |
| GetAtomPositionClock() const | ObjCryst::Molecule | |
| GetBondAngleList() const (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetBondAngleList() (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetBondList() const (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetBondList() (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetBondListClock() | ObjCryst::Molecule | |
| GetBondListClock() const | ObjCryst::Molecule | |
| GetCenterAtom() const | ObjCryst::Molecule | |
| GetClassName() const | ObjCryst::Molecule | virtual |
| GetClientRegistry() const | ObjCryst::RefinableObj | virtual |
| GetClientRegistry() | ObjCryst::RefinableObj | virtual |
| GetClockMaster() const | ObjCryst::RefinableObj | |
| GetClockScattCompList() const | ObjCryst::Scatterer | protected |
| GetClockScatterer() const | ObjCryst::Scatterer | |
| GetClockScatterer() | ObjCryst::Scatterer | |
| GetColour() const | ObjCryst::Scatterer | virtual |
| GetColourRGB() const | ObjCryst::Scatterer | virtual |
| GetComponentName(const int i) const | ObjCryst::Molecule | virtual |
| GetConnectivityTable() | ObjCryst::Molecule | |
| GetCrystal() const | ObjCryst::Scatterer | |
| GetCrystal() | ObjCryst::Scatterer | |
| GetDihedralAngleList() const (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetDihedralAngleList() (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetGeneGroup(const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const | ObjCryst::RefinableObj | virtual |
| GetLogLikelihood() const | ObjCryst::Molecule | virtual |
| GetLSQCalc(const unsigned int) const | ObjCryst::Molecule | virtual |
| GetLSQDeriv(const unsigned int n, RefinablePar &par) | ObjCryst::Molecule | virtual |
| GetLSQObs(const unsigned int) const | ObjCryst::Molecule | virtual |
| GetLSQWeight(const unsigned int) const | ObjCryst::Molecule | virtual |
| GetName() const | ObjCryst::RefinableObj | virtual |
| GetNbComponent() const | ObjCryst::Molecule | virtual |
| GetNbLSQFunction() const | ObjCryst::Molecule | virtual |
| GetNbOption() const | ObjCryst::RefinableObj | |
| GetNbPar() const | ObjCryst::RefinableObj | |
| GetNbParNotFixed() const | ObjCryst::RefinableObj | |
| GetOccupancy() const | ObjCryst::Scatterer | |
| GetOption(const unsigned int i) | ObjCryst::RefinableObj | |
| GetOption(const unsigned int i) const | ObjCryst::RefinableObj | |
| 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 | |
| GetParIndex(const string &name, const bool nothrow=false) const | ObjCryst::RefinableObj | |
| GetParIndex(const REAL *, const bool nothrow=false) 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 |
| GetRigidGroupClock() | ObjCryst::Molecule | |
| GetRigidGroupClock() const | ObjCryst::Molecule | |
| GetRigidGroupList() const | ObjCryst::Molecule | |
| GetRigidGroupList() | ObjCryst::Molecule | |
| GetScatteringComponentList() const | ObjCryst::Molecule | virtual |
| GetStretchModeBondAngleList() (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetStretchModeBondAngleList() const (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetStretchModeBondLengthList() (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetStretchModeBondLengthList() const (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetStretchModeTorsionList() (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetStretchModeTorsionList() const (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| GetSubObjRegistry() | ObjCryst::RefinableObj | |
| GetSubObjRegistry() const | ObjCryst::RefinableObj | |
| GetX() const | ObjCryst::Scatterer | |
| GetY() const | ObjCryst::Scatterer | |
| GetZ() const | ObjCryst::Scatterer | |
| 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 displayEnantiomer=false, const bool displayNames=false) const | ObjCryst::Molecule | virtual |
| GlobalOptRandomMove(const REAL mutationAmplitude, const RefParType *type) | ObjCryst::Molecule | virtual |
| InitOptions() | ObjCryst::Molecule | |
| InitRefParList() | ObjCryst::Molecule | virtual |
| InitRGBColour() | ObjCryst::Scatterer | protectedvirtual |
| IsBeingRefined() const | ObjCryst::RefinableObj | |
| mAsZMatrix | ObjCryst::Molecule | mutable |
| mAutoOptimizeConformation | ObjCryst::Molecule | |
| mBaseRotationAmplitude (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| mClientObjRegistry | ObjCryst::RefinableObj | mutableprotected |
| mClockAtomList (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| mClockAtomPosition (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| mClockAtomScattPow (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| mClockBondAngleList (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| mClockBondList (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| mClockConnectivityTable (defined in ObjCryst::Molecule) | ObjCryst::Molecule | mutable |
| mClockDihedralAngleList (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| mClockFlipGroup (defined in ObjCryst::Molecule) | ObjCryst::Molecule | mutable |
| mClockLogLikelihood (defined in ObjCryst::Molecule) | ObjCryst::Molecule | mutable |
| mClockMaster | ObjCryst::RefinableObj | protected |
| mClockMDAtomGroup (defined in ObjCryst::Molecule) | ObjCryst::Molecule | mutable |
| mClockOrientation (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| mClockRigidGroup (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| mClockRingList (defined in ObjCryst::Molecule) | ObjCryst::Molecule | mutable |
| mClockRotorGroup (defined in ObjCryst::Molecule) | ObjCryst::Molecule | mutable |
| mClockScattCompList | ObjCryst::Scatterer | mutableprotected |
| mClockScatterer | ObjCryst::Scatterer | protected |
| mClockStretchModeBondAngle (defined in ObjCryst::Molecule) | ObjCryst::Molecule | mutable |
| mClockStretchModeBondLength (defined in ObjCryst::Molecule) | ObjCryst::Molecule | mutable |
| mClockStretchModeTorsion (defined in ObjCryst::Molecule) | ObjCryst::Molecule | mutable |
| mClockStretchModeTwist (defined in ObjCryst::Molecule) | ObjCryst::Molecule | mutable |
| mColourName | ObjCryst::Scatterer | protected |
| mColourRGB | ObjCryst::Scatterer | protected |
| mConnectivityTable | ObjCryst::Molecule | mutable |
| mDeleteRefParInDestructor | ObjCryst::RefinableObj | protected |
| mDeleteSubObjInDestructor | ObjCryst::Molecule | |
| mFlexModel | ObjCryst::Molecule | |
| mIsSelfOptimizing (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| mLastLogLike (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| mLocalParamSet (defined in ObjCryst::Molecule) | ObjCryst::Molecule | |
| mLogLikelihood | ObjCryst::Molecule | mutable |
| mLogLikelihoodScale | ObjCryst::Molecule | |
| mLSQCalc | ObjCryst::Molecule | mutable |
| mLSQDeriv | ObjCryst::RefinableObj | mutableprotected |
| mLSQObs | ObjCryst::Molecule | mutable |
| mLSQWeight | ObjCryst::Molecule | mutable |
| mMDMoveEnergy | ObjCryst::Molecule | |
| mMDMoveFreq | ObjCryst::Molecule | |
| mMoleculeCenter | ObjCryst::Molecule | |
| mName | ObjCryst::RefinableObj | protected |
| mNbRefParNotFixed | ObjCryst::RefinableObj | mutableprotected |
| mOccupancy | ObjCryst::Scatterer | protected |
| MolecularDynamicsEvolve(std::map< MolAtom *, XYZ > &v0, const unsigned nbStep, const REAL dt, const std::vector< MolBond * > &vb, const std::vector< MolBondAngle * > &va, const std::vector< MolDihedralAngle * > &vd, std::map< RigidGroup *, std::pair< XYZ, XYZ > > &vr, REAL nrj0=0) | ObjCryst::Molecule | |
| Molecule(Crystal &cryst, const string &name="") | ObjCryst::Molecule | |
| Molecule(const Molecule &old) | ObjCryst::Molecule | |
| mOptimizationDepth | ObjCryst::RefinableObj | protected |
| mOptimizeOrientation | ObjCryst::Molecule | |
| mOptionRegistry | ObjCryst::RefinableObj | protected |
| mpCenterAtom | ObjCryst::Molecule | |
| mpCryst | ObjCryst::Scatterer | protected |
| mQuat | ObjCryst::Molecule | |
| mRandomConformChangeNbAccept (defined in ObjCryst::Molecule) | ObjCryst::Molecule | mutable |
| mRandomConformChangeNbTest (defined in ObjCryst::Molecule) | ObjCryst::Molecule | mutable |
| mRandomConformChangeTemp (defined in ObjCryst::Molecule) | ObjCryst::Molecule | mutable |
| mRandomMoveIsDone | ObjCryst::RefinableObj | protected |
| mRefParListClock | ObjCryst::RefinableObj | protected |
| mRefparNotFixedIndex | ObjCryst::RefinableObj | mutableprotected |
| mScattCompList | ObjCryst::Molecule | mutable |
| mSubObjRegistry | ObjCryst::RefinableObj | protected |
| mvAtomBond | ObjCryst::Molecule | |
| mvFlipGroup | ObjCryst::Molecule | mutable |
| mvMDAtomGroup | ObjCryst::Molecule | mutable |
| mvMDFullAtomGroup | ObjCryst::Molecule | mutable |
| mvpAtom | ObjCryst::Molecule | |
| mvpBond | ObjCryst::Molecule | |
| mvpBondAngle | ObjCryst::Molecule | |
| mvpDihedralAngle | ObjCryst::Molecule | |
| mvpRefPar | ObjCryst::RefinableObj | protected |
| mvpRestraint | ObjCryst::RefinableObj | protected |
| mvpSavedValuesSet | ObjCryst::RefinableObj | mutableprotected |
| mvpStretchModeFree | ObjCryst::Molecule | mutable |
| mvpStretchModeNotFree | ObjCryst::Molecule | mutable |
| mvRigidGroup | ObjCryst::Molecule | |
| mvRing | ObjCryst::Molecule | mutable |
| mvRotorGroupInternal | ObjCryst::Molecule | mutable |
| mvRotorGroupTorsion | ObjCryst::Molecule | mutable |
| mvRotorGroupTorsionSingleChain | ObjCryst::Molecule | mutable |
| mvStretchModeBondAngle | ObjCryst::Molecule | mutable |
| mvStretchModeBondLength | ObjCryst::Molecule | mutable |
| mvStretchModeTorsion | ObjCryst::Molecule | mutable |
| mvStretchModeTwist | ObjCryst::Molecule | mutable |
| mXYZ | ObjCryst::Scatterer | protected |
| operator string() const | ObjCryst::Scatterer | |
| operator=(const RefinableObj &old) | ObjCryst::RefinableObj | |
| OptimizeConformation(const long nbTrial=10000, const REAL stopCost=0.) | ObjCryst::Molecule | |
| OptimizeConformationSteepestDescent(const REAL maxStep=0.1, const unsigned nbStep=1) | ObjCryst::Molecule | |
| POVRayDescription(ostream &os, const CrystalPOVRayOptions &options) const | ObjCryst::Molecule | virtual |
| Prepare() | ObjCryst::RefinableObj | protectedvirtual |
| PrepareForRefinement() const | ObjCryst::RefinableObj | |
| Print() const | ObjCryst::Molecule | virtual |
| RandomizeConfiguration() | ObjCryst::Molecule | virtual |
| RefinableObj() | ObjCryst::RefinableObj | |
| RefinableObj(const bool internalUseOnly) | ObjCryst::RefinableObj | |
| RefinableObj(const RefinableObj &old) | ObjCryst::RefinableObj | |
| RegisterClient(RefinableObj &) const | ObjCryst::RefinableObj | virtual |
| RemoveAtom(MolAtom &, const bool del=true) | ObjCryst::Molecule | |
| RemoveBond(const MolBond &, const bool del=true) | ObjCryst::Molecule | |
| RemoveBondAngle(const MolBondAngle &, const bool del=true) | ObjCryst::Molecule | |
| RemoveDihedralAngle(const MolDihedralAngle &, const bool del=true) | ObjCryst::Molecule | |
| RemovePar(RefinablePar *refPar) | ObjCryst::RefinableObj | |
| RemoveRestraint(Restraint *pRestraint) | ObjCryst::RefinableObj | |
| RemoveRigidGroup(const RigidGroup &group, const bool updateDisplay=true, const bool del=true) | ObjCryst::Molecule | |
| RemoveSubRefObj(RefinableObj &) | ObjCryst::RefinableObj | protected |
| ResetParList() | ObjCryst::RefinableObj | |
| ResetRigidGroupsPar() const | ObjCryst::Molecule | |
| RestoreParamSet(const unsigned long id) | ObjCryst::RefinableObj | |
| RestraintStatus(ostream &os) const | ObjCryst::Molecule | |
| RigidifyWithDihedralAngles() | ObjCryst::Molecule | |
| RotateAtomGroup(const MolAtom &at1, const MolAtom &at2, const set< MolAtom * > &atoms, const REAL angle, const bool keepCenter=true) | ObjCryst::Molecule | |
| RotateAtomGroup(const MolAtom &at, const REAL vx, const REAL vy, const REAL vz, const set< MolAtom * > &atoms, const REAL angle, const bool keepCenter=true) | ObjCryst::Molecule | |
| SaveParamSet(const unsigned long id) const | ObjCryst::RefinableObj | |
| Scatterer() | ObjCryst::Scatterer | |
| Scatterer(const Scatterer &old) | ObjCryst::Scatterer | |
| SetApproximationFlag(const bool allow) | ObjCryst::RefinableObj | virtual |
| SetCenterAtom(const MolAtom &at) | ObjCryst::Molecule | |
| SetCrystal(Crystal &) | ObjCryst::Scatterer | |
| SetDeleteRefParInDestructor(const bool b) | ObjCryst::RefinableObj | |
| SetDeleteSubObjInDestructor(const bool b) | ObjCryst::Molecule | |
| 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 |
| SetOccupancy(const REAL occupancy) | ObjCryst::Scatterer | 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 | |
| SetX(const REAL x) | ObjCryst::Scatterer | virtual |
| SetY(const REAL y) | ObjCryst::Scatterer | virtual |
| SetZ(const REAL z) | ObjCryst::Scatterer | virtual |
| TagNewBestConfig() const | ObjCryst::Molecule | virtual |
| TranslateAtomGroup(const set< MolAtom * > &atoms, const REAL dx, const REAL dy, const REAL dz, const bool keepCenter=true) | ObjCryst::Molecule | |
| TuneGlobalOptimRotationAmplitude() | ObjCryst::Molecule | |
| UnFixAllPar() | ObjCryst::RefinableObj | |
| UpdateDisplay() const | ObjCryst::Molecule | virtual |
| UpdateScattCompList() const | ObjCryst::Molecule | |
| XMLInput(istream &is, const XMLCrystTag &tag) | ObjCryst::Molecule | virtual |
| XMLOutput(ostream &os, int indent=0) const | ObjCryst::Molecule | virtual |
| ~Molecule() | ObjCryst::Molecule | |
| ~RefinableObj() | ObjCryst::RefinableObj | virtual |
| ~Scatterer() | ObjCryst::Scatterer | virtual |
