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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, 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
mAsZMatrixObjCryst::Molecule [mutable]
mAutoOptimizeConformationObjCryst::Molecule
mBaseRotationAmplitudeObjCryst::Molecule
mClientObjRegistryObjCryst::RefinableObj [mutable, protected]
mClockAtomListObjCryst::Molecule
mClockAtomPositionObjCryst::Molecule
mClockAtomScattPowObjCryst::Molecule
mClockBondAngleListObjCryst::Molecule
mClockBondListObjCryst::Molecule
mClockConnectivityTableObjCryst::Molecule [mutable]
mClockDihedralAngleListObjCryst::Molecule
mClockFlipGroupObjCryst::Molecule [mutable]
mClockLogLikelihoodObjCryst::Molecule [mutable]
mClockMasterObjCryst::RefinableObj [protected]
mClockOrientationObjCryst::Molecule
mClockRigidGroupObjCryst::Molecule
mClockRingListObjCryst::Molecule [mutable]
mClockRotorGroupObjCryst::Molecule [mutable]
mClockScattCompListObjCryst::Scatterer [mutable, protected]
mClockScattererObjCryst::Scatterer [protected]
mClockStretchModeBondAngleObjCryst::Molecule [mutable]
mClockStretchModeBondLengthObjCryst::Molecule [mutable]
mClockStretchModeTorsionObjCryst::Molecule [mutable]
mClockStretchModeTwistObjCryst::Molecule [mutable]
mColourNameObjCryst::Scatterer [protected]
mColourRGBObjCryst::Scatterer [protected]
mConnectivityTableObjCryst::Molecule [mutable]
mDeleteRefParInDestructorObjCryst::RefinableObj [protected]
mFlexModelObjCryst::Molecule
mIsbeingRefinedObjCryst::RefinableObj [protected]
mIsSelfOptimizingObjCryst::Molecule
mLastLogLikeObjCryst::Molecule
mLocalParamSetObjCryst::Molecule
mLogLikelihoodObjCryst::Molecule [mutable]
mLSQDerivObjCryst::RefinableObj [mutable, protected]
mMoleculeCenterObjCryst::Molecule
mNameObjCryst::RefinableObj [protected]
mNbRefParNotFixedObjCryst::RefinableObj [mutable, protected]
mOccupancyObjCryst::Scatterer [protected]
Molecule(Crystal &cryst, const string &name="")ObjCryst::Molecule
Molecule(const Molecule &old)ObjCryst::Molecule
mOptimizeOrientationObjCryst::Molecule
mOptionRegistryObjCryst::RefinableObj [protected]
mpCenterAtomObjCryst::Molecule
mpCrystObjCryst::Scatterer [protected]
mQuatObjCryst::Molecule
mRandomConformChangeNbAcceptObjCryst::Molecule [mutable]
mRandomConformChangeNbTestObjCryst::Molecule [mutable]
mRandomConformChangeTempObjCryst::Molecule [mutable]
mRandomMoveIsDoneObjCryst::RefinableObj [protected]
mRefParListClockObjCryst::RefinableObj [protected]
mRefparNotFixedIndexObjCryst::RefinableObj [mutable, protected]
mScattCompListObjCryst::Molecule [mutable]
mSubObjRegistryObjCryst::RefinableObj [protected]
mvAtomBondObjCryst::Molecule
mvFlipGroupObjCryst::Molecule [mutable]
mvpAtomObjCryst::Molecule
mvpBondObjCryst::Molecule
mvpBondAngleObjCryst::Molecule
mvpDihedralAngleObjCryst::Molecule
mvpRefParObjCryst::RefinableObj [protected]
mvpRestraintObjCryst::RefinableObj [protected]
mvpSavedValuesSetObjCryst::RefinableObj [mutable, protected]
mvpStretchModeFreeObjCryst::Molecule [mutable]
mvpStretchModeNotFreeObjCryst::Molecule [mutable]
mvRigidGroupObjCryst::Molecule
mvRingObjCryst::Molecule [mutable]
mvRotorGroupInternalObjCryst::Molecule [mutable]
mvRotorGroupTorsionObjCryst::Molecule [mutable]
mvRotorGroupTorsionSingleChainObjCryst::Molecule [mutable]
mvStretchModeBondAngleObjCryst::Molecule [mutable]
mvStretchModeBondLengthObjCryst::Molecule [mutable]
mvStretchModeTorsionObjCryst::Molecule [mutable]
mvStretchModeTwistObjCryst::Molecule [mutable]
mXYZObjCryst::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]

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