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ObjCryst::Molecule Member List

This is the complete list of members for ObjCryst::Molecule, including all inherited members.
AddAtom(const REAL x, const REAL y, const REAL z, const ScatteringPower *pPow, const string &name)ObjCryst::Molecule
AddBond(MolAtom &atom1, MolAtom &atom2, const REAL length, const REAL sigma, const REAL delta, const REAL bondOrder=1.)ObjCryst::Molecule
AddBondAngle(MolAtom &atom1, MolAtom &atom2, MolAtom &atom3, const REAL angle, const REAL sigma, const REAL delta)ObjCryst::Molecule
AddDihedralAngle(MolAtom &atom1, MolAtom &atom2, MolAtom &atom3, MolAtom &atom4, const REAL angle, const REAL sigma, const REAL delta)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
AddSubRefObj(RefinableObj &)ObjCryst::RefinableObj [protected]
BeginGlobalOptRandomMove()ObjCryst::RefinableObj
BeginOptimization(const bool allowApproximations=false, const bool enableRestraints=false)ObjCryst::Molecule [virtual]
BuildConnectivityTable() constObjCryst::Molecule [private]
BuildFlipGroup()ObjCryst::Molecule [private]
BuildRingList() constObjCryst::Molecule [private]
BuildRotorGroup()ObjCryst::Molecule [private]
ClearParamSet(const unsigned long id) constObjCryst::RefinableObj
CreateCopy() constObjCryst::Molecule [virtual]
CreateParamSet(const string name="") constObjCryst::RefinableObj
DeRegisterClient(RefinableObj &) constObjCryst::RefinableObj [virtual]
EndOptimization()ObjCryst::RefinableObj [virtual]
EraseAllParamSet()ObjCryst::RefinableObj
FindAtom(const string &name)ObjCryst::Molecule [private]
FindAtom(const string &name) constObjCryst::Molecule [private]
FindBond(const MolAtom &, const MolAtom &) constObjCryst::Molecule
FindBondAngle(const MolAtom &at1, const MolAtom &at0, const MolAtom &at2) constObjCryst::Molecule
FindPar(const string &name) constObjCryst::RefinableObj [protected]
FindPar(const REAL *) constObjCryst::RefinableObj [protected]
FindParamSet(unsigned long id) constObjCryst::RefinableObj [protected]
FixAllPar()ObjCryst::RefinableObj
FlipAtomGroup(const FlipGroup &)ObjCryst::Molecule [private]
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
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
GetClassName() constObjCryst::Molecule [virtual]
GetClockScattCompList() constObjCryst::Scatterer [protected]
GetClockScatterer() constObjCryst::Scatterer
GetClockScatterer()ObjCryst::Scatterer
GetColour() constObjCryst::Scatterer [virtual]
GetColourRGB() constObjCryst::Scatterer [virtual]
GetComponentName(const int i) constObjCryst::Molecule [virtual]
GetConnectivityTable() constObjCryst::Molecule
GetCrystal() constObjCryst::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) constObjCryst::RefinableObj [virtual]
GetLogLikelihood() constObjCryst::Molecule [virtual]
GetLSQCalc(const unsigned int) constObjCryst::RefinableObj [virtual]
GetLSQDeriv(const unsigned int, RefinablePar &)ObjCryst::RefinableObj [virtual]
GetLSQObs(const unsigned int) constObjCryst::RefinableObj [virtual]
GetLSQWeight(const unsigned int) constObjCryst::RefinableObj [virtual]
GetName() constObjCryst::RefinableObj [virtual]
GetNbComponent() constObjCryst::Molecule [virtual]
GetNbLSQFunction() constObjCryst::RefinableObj [virtual]
GetNbOption() constObjCryst::RefinableObj
GetNbPar() constObjCryst::RefinableObj
GetNbParNotFixed() constObjCryst::RefinableObj
GetOccupancy() constObjCryst::Scatterer
GetOption(const unsigned int i)ObjCryst::RefinableObj
GetOption(const unsigned int i) constObjCryst::RefinableObj
GetPar(const long i)ObjCryst::RefinableObj
GetPar(const long i) constObjCryst::RefinableObj
GetPar(const string &name)ObjCryst::RefinableObj
GetPar(const string &name) constObjCryst::RefinableObj
GetPar(const REAL *)ObjCryst::RefinableObj
GetPar(const REAL *) constObjCryst::RefinableObj
GetParamSet(const unsigned long setId) constObjCryst::RefinableObj
GetParamSet(const unsigned long setId)ObjCryst::RefinableObj
GetParamSet_ParNotFixedHumanValue(const unsigned long setId, const long parNumber) constObjCryst::RefinableObj
GetParNotFixed(const long i)ObjCryst::RefinableObj
GetParNotFixed(const long i) constObjCryst::RefinableObj
GetRefParListClock() constObjCryst::RefinableObj
GetRestraintCost() constObjCryst::RefinableObj [virtual]
GetScatteringComponentList() constObjCryst::Molecule [virtual]
GetSubObjRegistry()ObjCryst::RefinableObj
GetSubObjRegistry() constObjCryst::RefinableObj
GetX() constObjCryst::Scatterer
GetY() constObjCryst::Scatterer
GetZ() constObjCryst::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) constObjCryst::Molecule [virtual]
GlobalOptRandomMove(const REAL mutationAmplitude, const RefParType *type)ObjCryst::Molecule [virtual]
InitOptions()ObjCryst::Molecule [private]
InitRandomSeedFromTime() constObjCryst::RefinableObj [protected]
InitRefParList()ObjCryst::Molecule [private, virtual]
InitRGBColour()ObjCryst::Scatterer [protected, virtual]
IsBeingRefined() constObjCryst::RefinableObj
mClientObjRegistryObjCryst::RefinableObj [protected]
mClockAtomList (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mClockAtomPosition (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mClockAtomScattPow (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mClockBondAngleList (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mClockBondList (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mClockConnectivityTable (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mClockDihedralAngleList (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mClockFlipGroup (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mClockLogLikelihood (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mClockOrientation (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mClockRingList (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mClockRotorGroup (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mClockScattCompListObjCryst::Scatterer [protected]
mClockScattererObjCryst::Scatterer [protected]
mColourNameObjCryst::Scatterer [protected]
mColourRGBObjCryst::Scatterer [protected]
mConnectivityTableObjCryst::Molecule [private]
mDeleteRefParInDestructorObjCryst::RefinableObj [protected]
mFlexModelObjCryst::Molecule [private]
mIsbeingRefinedObjCryst::RefinableObj [protected]
mIsSelfOptimizing (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mLastLogLike (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mLocalParamSet (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mLogLikelihoodObjCryst::Molecule [private]
mLSQDerivObjCryst::RefinableObj [protected]
mNameObjCryst::RefinableObj [protected]
mNbRefParNotFixedObjCryst::RefinableObj [protected]
mOccupancyObjCryst::Scatterer [protected]
Molecule(Crystal &cryst, const string &name="")ObjCryst::Molecule
Molecule(const Molecule &old)ObjCryst::Molecule
mOptionRegistryObjCryst::RefinableObj [protected]
mpCrystObjCryst::Scatterer [protected]
mQuatObjCryst::Molecule [private]
mRandomConformChangeNbAccept (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mRandomConformChangeNbTest (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mRandomConformChangeTemp (defined in ObjCryst::Molecule)ObjCryst::Molecule [private]
mRandomMoveIsDoneObjCryst::RefinableObj [protected]
mRefParListClockObjCryst::RefinableObj [protected]
mRefparNotFixedIndexObjCryst::RefinableObj [protected]
mScattCompListObjCryst::Molecule [private]
mSubObjRegistryObjCryst::RefinableObj [protected]
mvAtomBondObjCryst::Molecule [private]
mvFlipGroupObjCryst::Molecule [private]
mvpAtomObjCryst::Molecule [private]
mvpBondObjCryst::Molecule [private]
mvpBondAngleObjCryst::Molecule [private]
mvpDihedralAngleObjCryst::Molecule [private]
mvpRefParObjCryst::RefinableObj [protected]
mvpRestraintObjCryst::RefinableObj [protected]
mvpSavedValuesSetObjCryst::RefinableObj [protected]
mvRingObjCryst::Molecule [private]
mvRotorGroupInternalObjCryst::Molecule [private]
mvRotorGroupTorsionObjCryst::Molecule [private]
mvRotorGroupTorsionSingleChainObjCryst::Molecule [private]
mXYZObjCryst::Scatterer [protected]
operator string() constObjCryst::Scatterer
operator=(const RefinableObj &old)ObjCryst::RefinableObj
OptimizeConformation(const long nbTrial=10000, const REAL stopCost=0.)ObjCryst::Molecule
POVRayDescription(ostream &os, const bool noSymmetrics=false) constObjCryst::Molecule [virtual]
Prepare()ObjCryst::RefinableObj [protected, virtual]
PrepareForRefinement() constObjCryst::RefinableObj
Print() constObjCryst::Molecule [virtual]
RandomizeConfiguration()ObjCryst::Molecule [virtual]
RefinableObj()ObjCryst::RefinableObj
RefinableObj(const bool internalUseOnly)ObjCryst::RefinableObj
RefinableObj(const RefinableObj &old)ObjCryst::RefinableObj
RegisterClient(RefinableObj &) constObjCryst::RefinableObj [virtual]
RemoveAtom(const 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
RemoveSubRefObj(RefinableObj &)ObjCryst::RefinableObj [protected]
ResetParList()ObjCryst::RefinableObj
RestoreParamSet(const unsigned long id)ObjCryst::RefinableObj
RestraintStatus(ostream &os) constObjCryst::Molecule
RotateAtomGroup(const MolAtom &at1, const MolAtom &at2, const set< unsigned long > &atoms, const REAL angle)ObjCryst::Molecule
RotateAtomGroup(const MolAtom &at, const REAL vx, const REAL vy, const REAL vz, const set< unsigned long > &atoms, const REAL angle)ObjCryst::Molecule
SaveParamSet(const unsigned long id) constObjCryst::RefinableObj
Scatterer()ObjCryst::Scatterer
Scatterer(const Scatterer &old)ObjCryst::Scatterer
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() constObjCryst::Molecule [virtual]
UnFixAllPar()ObjCryst::RefinableObj
UpdateDisplay() constObjCryst::RefinableObj [virtual]
UpdateScattCompList() constObjCryst::Molecule [private]
XMLInput(istream &is, const XMLCrystTag &tag)ObjCryst::Molecule [virtual]
XMLOutput(ostream &os, int indent=0) constObjCryst::Molecule [virtual]
~Molecule()ObjCryst::Molecule
~RefinableObj()ObjCryst::RefinableObj [virtual]
~Scatterer()ObjCryst::Scatterer [virtual]

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