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, 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
AddNonFlipAtom(MolAtom &atom) (defined in ObjCryst::Molecule)	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 &, const bool keepCenter=true)	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
GetFormula() const	ObjCryst::Molecule
GetGeneGroup(const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const	ObjCryst::RefinableObj	virtual
GetLogLikelihood() const	ObjCryst::Molecule	virtual
GetLSQ_FullDeriv(const unsigned int, std::set< RefinablePar * > &vPar)	ObjCryst::RefinableObj	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
getNonFlipAtomList() (defined in ObjCryst::Molecule)	ObjCryst::Molecule
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() (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 bool hideHydrogens=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
mFlipModel (defined in ObjCryst::Molecule)	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
mLSQ_FullDeriv	ObjCryst::RefinableObj	mutableprotected
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
mvNonFlipAtom (defined in ObjCryst::Molecule)	ObjCryst::Molecule
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
removeNonFlipAtom(MolAtom &atom) (defined in ObjCryst::Molecule)	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
RestraintExport(ostream &os) const	ObjCryst::Molecule
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::Molecule	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