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) | 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 | |
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::RefinableObj | [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) | ObjCryst::Molecule | |
GetAtom(unsigned int i) const | ObjCryst::Molecule | |
GetAtom(const string &name) | ObjCryst::Molecule | |
GetAtom(const string &name) const | ObjCryst::Molecule | |
GetAtomList() const | ObjCryst::Molecule | |
GetAtomList() | ObjCryst::Molecule | |
GetAtomPositionClock() | ObjCryst::Molecule | |
GetAtomPositionClock() const | ObjCryst::Molecule | |
GetBondAngleList() const | ObjCryst::Molecule | |
GetBondAngleList() | ObjCryst::Molecule | |
GetBondList() const | ObjCryst::Molecule | |
GetBondList() | ObjCryst::Molecule | |
GetBondListClock() | ObjCryst::Molecule | |
GetBondListClock() const | ObjCryst::Molecule | |
GetCenterAtom() const | ObjCryst::Molecule | |
GetClassName() const | ObjCryst::Molecule | [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 | ObjCryst::Molecule | |
GetDihedralAngleList() | 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::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] |
GetName() const | ObjCryst::RefinableObj | [virtual] |
GetNbComponent() const | ObjCryst::Molecule | [virtual] |
GetNbLSQFunction() const | ObjCryst::RefinableObj | [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 | |
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() | ObjCryst::Molecule | |
GetStretchModeBondAngleList() const | ObjCryst::Molecule | |
GetStretchModeBondLengthList() | ObjCryst::Molecule | |
GetStretchModeBondLengthList() const | ObjCryst::Molecule | |
GetStretchModeTorsionList() | ObjCryst::Molecule | |
GetStretchModeTorsionList() const | 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 | [protected, virtual] |
IsBeingRefined() const | ObjCryst::RefinableObj | |
mAsZMatrix | ObjCryst::Molecule | [mutable] |
mAutoOptimizeConformation | ObjCryst::Molecule | |
mBaseRotationAmplitude | ObjCryst::Molecule | |
mClientObjRegistry | ObjCryst::RefinableObj | [mutable, protected] |
mClockAtomList | ObjCryst::Molecule | |
mClockAtomPosition | ObjCryst::Molecule | |
mClockAtomScattPow | ObjCryst::Molecule | |
mClockBondAngleList | ObjCryst::Molecule | |
mClockBondList | ObjCryst::Molecule | |
mClockConnectivityTable | ObjCryst::Molecule | [mutable] |
mClockDihedralAngleList | ObjCryst::Molecule | |
mClockFlipGroup | ObjCryst::Molecule | [mutable] |
mClockLogLikelihood | ObjCryst::Molecule | [mutable] |
mClockMaster | ObjCryst::RefinableObj | [protected] |
mClockOrientation | ObjCryst::Molecule | |
mClockRigidGroup | ObjCryst::Molecule | |
mClockRingList | ObjCryst::Molecule | [mutable] |
mClockRotorGroup | ObjCryst::Molecule | [mutable] |
mClockScattCompList | ObjCryst::Scatterer | [mutable, protected] |
mClockScatterer | ObjCryst::Scatterer | [protected] |
mClockStretchModeBondAngle | ObjCryst::Molecule | [mutable] |
mClockStretchModeBondLength | ObjCryst::Molecule | [mutable] |
mClockStretchModeTorsion | ObjCryst::Molecule | [mutable] |
mClockStretchModeTwist | ObjCryst::Molecule | [mutable] |
mColourName | ObjCryst::Scatterer | [protected] |
mColourRGB | ObjCryst::Scatterer | [protected] |
mConnectivityTable | ObjCryst::Molecule | [mutable] |
mDeleteRefParInDestructor | ObjCryst::RefinableObj | [protected] |
mFlexModel | ObjCryst::Molecule | |
mIsbeingRefined | ObjCryst::RefinableObj | [protected] |
mIsSelfOptimizing | ObjCryst::Molecule | |
mLastLogLike | ObjCryst::Molecule | |
mLocalParamSet | ObjCryst::Molecule | |
mLogLikelihood | ObjCryst::Molecule | [mutable] |
mLSQDeriv | ObjCryst::RefinableObj | [mutable, protected] |
mMoleculeCenter | ObjCryst::Molecule | |
mName | ObjCryst::RefinableObj | [protected] |
mNbRefParNotFixed | ObjCryst::RefinableObj | [mutable, protected] |
mOccupancy | ObjCryst::Scatterer | [protected] |
Molecule(Crystal &cryst, const string &name="") | ObjCryst::Molecule | |
Molecule(const Molecule &old) | ObjCryst::Molecule | |
mOptimizeOrientation | ObjCryst::Molecule | |
mOptionRegistry | ObjCryst::RefinableObj | [protected] |
mpCenterAtom | ObjCryst::Molecule | |
mpCryst | ObjCryst::Scatterer | [protected] |
mQuat | ObjCryst::Molecule | |
mRandomConformChangeNbAccept | ObjCryst::Molecule | [mutable] |
mRandomConformChangeNbTest | ObjCryst::Molecule | [mutable] |
mRandomConformChangeTemp | ObjCryst::Molecule | [mutable] |
mRandomMoveIsDone | ObjCryst::RefinableObj | [protected] |
mRefParListClock | ObjCryst::RefinableObj | [protected] |
mRefparNotFixedIndex | ObjCryst::RefinableObj | [mutable, protected] |
mScattCompList | ObjCryst::Molecule | [mutable] |
mSubObjRegistry | ObjCryst::RefinableObj | [protected] |
mvAtomBond | ObjCryst::Molecule | |
mvFlipGroup | 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 | [mutable, protected] |
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 | |
POVRayDescription(ostream &os, const CrystalPOVRayOptions &options) const | ObjCryst::Molecule | [virtual] |
Prepare() | ObjCryst::RefinableObj | [protected, virtual] |
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 &) | ObjCryst::Molecule | |
RemoveBond(const MolBond &) | ObjCryst::Molecule | |
RemoveBondAngle(const MolBondAngle &) | ObjCryst::Molecule | |
RemoveDihedralAngle(const MolDihedralAngle &) | ObjCryst::Molecule | |
RemovePar(RefinablePar *refPar) | ObjCryst::RefinableObj | |
RemoveRestraint(Restraint *pRestraint) | ObjCryst::RefinableObj | |
RemoveRigidGroup(const RigidGroup &group, const bool updateDisplay=true) | ObjCryst::Molecule | |
RemoveSubRefObj(RefinableObj &) | ObjCryst::RefinableObj | [protected] |
ResetParList() | ObjCryst::RefinableObj | |
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 | |
SetCenterAtom(const MolAtom &at) | ObjCryst::Molecule | |
SetCrystal(Crystal &) | ObjCryst::Scatterer | |
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] |
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::RefinableObj | [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] |