Index

A

a (pyobjcryst.unitcell.UnitCell attribute) AddAtom() (pyobjcryst.molecule.Molecule method) (pyobjcryst.molecule.StretchModeBondAngle method) (pyobjcryst.molecule.StretchModeBondLength method) (pyobjcryst.molecule.StretchModeTorsion method) (pyobjcryst.molecule.StretchModeTwist method) (pyobjcryst.zscatterer.ZScatterer method) AddAtoms() (pyobjcryst.molecule.StretchModeBondAngle method) (pyobjcryst.molecule.StretchModeBondLength method) (pyobjcryst.molecule.StretchModeTorsion method) (pyobjcryst.molecule.StretchModeTwist method) AddAttribute() (pyobjcryst.io.XMLCrystTag method) AddBond() (pyobjcryst.molecule.Molecule method) AddBondAngle() (pyobjcryst.molecule.Molecule method) AddBondValenceRo() (pyobjcryst.crystal.Crystal method) AddChild() (pyobjcryst.refinableobj.RefinableObjClock method) AddDihedralAngle() (pyobjcryst.molecule.Molecule method) AddPar() (pyobjcryst.refinableobj.RefinableObj method)

AddParent() (pyobjcryst.refinableobj.RefinableObjClock method) AddRestraint() (pyobjcryst.refinableobj.RefinableObj method) AddRigidGroup() (pyobjcryst.molecule.Molecule method) AddScatterer() (pyobjcryst.crystal.Crystal method) AddScatteringPower() (pyobjcryst.crystal.Crystal method) alpha (pyobjcryst.unitcell.UnitCell attribute) Angle (pyobjcryst.molecule.MolBondAngle attribute) (pyobjcryst.molecule.MolDihedralAngle attribute) Angle0 (pyobjcryst.molecule.MolBondAngle attribute) (pyobjcryst.molecule.MolDihedralAngle attribute) AngleDelta (pyobjcryst.molecule.MolBondAngle attribute) (pyobjcryst.molecule.MolDihedralAngle attribute) AngleSigma (pyobjcryst.molecule.MolBondAngle attribute) (pyobjcryst.molecule.MolDihedralAngle attribute) ANTIPRISM_TETRAGONAL (pyobjcryst.zscatterer.RegularPolyhedraType attribute) AsymmetricUnit (class in pyobjcryst.spacegroup) AsZMatrix() (pyobjcryst.molecule.Molecule method) Atom (class in pyobjcryst.atom)

B

b (pyobjcryst.unitcell.UnitCell attribute) B11 (pyobjcryst.scatteringpower.ScatteringPower attribute) B12 (pyobjcryst.scatteringpower.ScatteringPower attribute) B13 (pyobjcryst.scatteringpower.ScatteringPower attribute) B22 (pyobjcryst.scatteringpower.ScatteringPower attribute) B23 (pyobjcryst.scatteringpower.ScatteringPower attribute) B33 (pyobjcryst.scatteringpower.ScatteringPower attribute) BeginGlobalOptRandomMove() (pyobjcryst.refinableobj.RefinableObj method) BeginOptimization() (pyobjcryst.refinableobj.RefinableObj method) beta (pyobjcryst.unitcell.UnitCell attribute) Biso (pyobjcryst.scatteringpower.ScatteringPower attribute) BondAngleRandomChange() (pyobjcryst.molecule.Molecule method)

BondLengthRandomChange() (pyobjcryst.molecule.Molecule method) BondOrder (pyobjcryst.molecule.MolBond attribute) BuildConnectivityTable() (pyobjcryst.molecule.Molecule method) BuildFlipGroup() (pyobjcryst.molecule.Molecule method) BuildRingList() (pyobjcryst.molecule.Molecule method) BuildRotorGroup() (pyobjcryst.molecule.Molecule method) BuildStretchModeBondAngle() (pyobjcryst.molecule.Molecule method) BuildStretchModeBondLength() (pyobjcryst.molecule.Molecule method) BuildStretchModeGroups() (pyobjcryst.molecule.Molecule method) BuildStretchModeTorsion() (pyobjcryst.molecule.Molecule method) BuildStretchModeTwist() (pyobjcryst.molecule.Molecule method) BumpMergePar (class in pyobjcryst.crystal)

C

c (pyobjcryst.unitcell.UnitCell attribute) CalcDeriv() (pyobjcryst.molecule.StretchMode method) ChangeSpaceGroup() (pyobjcryst.spacegroup.SpaceGroup method) ChangeToAsymmetricUnit() (pyobjcryst.spacegroup.SpaceGroup method) CIFOutput() (pyobjcryst.crystal.Crystal method) ClearParamSet() (pyobjcryst.refinableobj.RefinableObj method)

Click() (pyobjcryst.refinableobj.RefinableObjClock method) ConnectAtoms() (pyobjcryst.crystal.Crystal method) CreateCrystalFromCIF() (in module pyobjcryst.crystal) CreateParamSet() (pyobjcryst.refinableobj.RefinableObj method) Crystal (class in pyobjcryst.crystal) CUBE (pyobjcryst.zscatterer.RegularPolyhedraType attribute)

D

DeRegister() (pyobjcryst.refinableobj.RefinableObjRegistry method) (pyobjcryst.refinableobj.ScattererRegistry method) (pyobjcryst.refinableobj.ScatteringPowerRegistry method) (pyobjcryst.refinableobj.ZAtomRegistry method) DeRegisterAll() (pyobjcryst.refinableobj.RefinableObjRegistry method) (pyobjcryst.refinableobj.ScattererRegistry method) (pyobjcryst.refinableobj.ScatteringPowerRegistry method) (pyobjcryst.refinableobj.ZAtomRegistry method)

DeRegisterClient() (pyobjcryst.refinableobj.RefinableObj method) DihedralAngleRandomChange() (pyobjcryst.molecule.Molecule method)

E

EndOptimization() (pyobjcryst.refinableobj.RefinableObj method)

EraseAllParamSet() (pyobjcryst.refinableobj.RefinableObj method)

F

Find() (pyobjcryst.refinableobj.RefinableObjRegistry method) (pyobjcryst.refinableobj.ScattererRegistry method) (pyobjcryst.refinableobj.ScatteringPowerRegistry method) (pyobjcryst.refinableobj.ZAtomRegistry method) FindAtom() (pyobjcryst.molecule.Molecule method)

FindBond() (pyobjcryst.molecule.Molecule method) FindBondAngle() (pyobjcryst.molecule.Molecule method) FindDihedralAngle() (pyobjcryst.molecule.Molecule method) FixAllPar() (pyobjcryst.refinableobj.RefinableObj method) FractionalToOrthonormalCoords() (pyobjcryst.unitcell.UnitCell method)

G

gamma (pyobjcryst.unitcell.UnitCell attribute) GetAllEquivRefl() (pyobjcryst.spacegroup.SpaceGroup method) GetAllSymmetrics() (pyobjcryst.spacegroup.SpaceGroup method) GetAngle() (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) GetAngle0() (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) GetAngleDelta() (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) GetAngleSigma() (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) GetAsymUnit() (pyobjcryst.spacegroup.SpaceGroup method) GetAtom() (pyobjcryst.molecule.Molecule method) GetAtom1() (pyobjcryst.molecule.MolBond method) (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) GetAtom2() (pyobjcryst.molecule.MolBond method) (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) GetAtom3() (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) GetAtom4() (pyobjcryst.molecule.MolDihedralAngle method) GetAtomicNumber() (pyobjcryst.scatteringpower.ScatteringPowerAtom method) GetAtomList() (pyobjcryst.molecule.Molecule method) GetAtomPositionClock() (pyobjcryst.molecule.Molecule method) GetAtoms() (pyobjcryst.molecule.StretchModeBondAngle method) (pyobjcryst.molecule.StretchModeBondLength method) (pyobjcryst.molecule.StretchModeTorsion method) (pyobjcryst.molecule.StretchModeTwist method) GetAttribute() (pyobjcryst.io.XMLCrystTag method) GetAttributeName() (pyobjcryst.io.XMLCrystTag method) GetAttributeValue() (pyobjcryst.io.XMLCrystTag method) GetBij() (pyobjcryst.scatteringpower.ScatteringPower method) GetBiso() (pyobjcryst.scatteringpower.ScatteringPower method) GetBMatrix() (pyobjcryst.unitcell.UnitCell method) GetBond() (pyobjcryst.molecule.Molecule method) GetBondAngle() (in module pyobjcryst.molecule) (pyobjcryst.molecule.Molecule method) GetBondAngleList() (pyobjcryst.molecule.Molecule method) GetBondLength() (in module pyobjcryst.molecule) GetBondList() (pyobjcryst.molecule.Molecule method) GetBondListClock() (pyobjcryst.molecule.Molecule method) GetBondOrder() (pyobjcryst.molecule.MolBond method) GetBondValenceCost() (pyobjcryst.crystal.Crystal method) GetBondValenceRoList() (pyobjcryst.crystal.Crystal method) GetBumpMergeCost() (pyobjcryst.crystal.Crystal method) GetBumpMergeParList() (pyobjcryst.crystal.Crystal method) GetCenterAtom() (pyobjcryst.molecule.Molecule method) GetCenterAtomIndex() (pyobjcryst.zscatterer.ZScatterer method) GetChi() (pyobjcryst.zscatterer.ZScatterer method) GetChoice() (pyobjcryst.refinableobj.RefObjOpt method) GetChoiceName() (pyobjcryst.refinableobj.RefObjOpt method) GetClassName() (pyobjcryst.io.XMLCrystTag method) (pyobjcryst.refinableobj.RefObjOpt method) (pyobjcryst.refinableobj.RefinableObj method) (pyobjcryst.zscatterer.ZAtom method) (pyobjcryst.zscatterer.ZScatterer method) GetClientRegistry() (pyobjcryst.refinableobj.RefinableObj method) GetClock() (pyobjcryst.refinableobj.RefObjOpt method) GetClockLatticePar() (pyobjcryst.unitcell.UnitCell method) GetClockMaster() (pyobjcryst.refinableobj.RefinableObj method) GetClockMetricMatrix() (pyobjcryst.unitcell.UnitCell method) GetClockScattCompList() (pyobjcryst.crystal.Crystal method) (pyobjcryst.scatterer.Scatterer method) GetClockScatterer() (pyobjcryst.scatterer.Scatterer method) GetClockScattererList() (pyobjcryst.crystal.Crystal method) GetClockSpaceGroup() (pyobjcryst.spacegroup.SpaceGroup method) GetComponentName() (pyobjcryst.scatterer.Scatterer method) GetConjugate() (pyobjcryst.molecule.Quaternion method) GetConnectivityTable() (pyobjcryst.molecule.Molecule method) GetCrystal() (pyobjcryst.scatterer.Scatterer method) GetDihedralAngle() (in module pyobjcryst.molecule) (pyobjcryst.molecule.Molecule method) GetDihedralAngleList() (pyobjcryst.molecule.Molecule method) GetDynPopCorrIndex() (pyobjcryst.scatteringpower.ScatteringPower method) GetElementName() (pyobjcryst.scatteringpower.ScatteringPowerAtom method) GetExpectedIntensityFactor() (pyobjcryst.spacegroup.SpaceGroup method) GetExtension() (pyobjcryst.spacegroup.SpaceGroup method) GetFormalCharge() (pyobjcryst.scatteringpower.ScatteringPower method) GetFormula() (pyobjcryst.molecule.Molecule method) GetForwardScatteringFactor() (pyobjcryst.scatteringpower.ScatteringPower method) GetGeneGroup() (pyobjcryst.refinableobj.RefinableObj method) GetInversionCenter() (pyobjcryst.spacegroup.SpaceGroup method) GetLastChangeClock() (pyobjcryst.scatteringpower.ScatteringPower method) GetLatticePar() (pyobjcryst.unitcell.UnitCell method) GetLength() (pyobjcryst.molecule.MolBond method) GetLength0() (pyobjcryst.molecule.MolBond method) GetLengthDelta() (pyobjcryst.molecule.MolBond method) GetLengthSigma() (pyobjcryst.molecule.MolBond method) GetLogLikelihood() (pyobjcryst.molecule.MolBond method) (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) (pyobjcryst.refinableobj.RefinableObj method) (pyobjcryst.refinableobj.Restraint method) GetLSQCalc() (pyobjcryst.refinableobj.RefinableObj method) GetLSQDeriv() (pyobjcryst.refinableobj.RefinableObj method) GetLSQObs() (pyobjcryst.refinableobj.RefinableObj method) GetLSQWeight() (pyobjcryst.refinableobj.RefinableObj method) GetMass() (pyobjcryst.atom.Atom method) GetMasterClockScatteringPower() (pyobjcryst.crystal.Crystal method) GetMaximumLikelihoodNbGhostAtom() (pyobjcryst.scatteringpower.ScatteringPower method) GetMaximumLikelihoodParClock() (pyobjcryst.scatteringpower.ScatteringPower method) GetMaximumLikelihoodPositionError() (pyobjcryst.scatteringpower.ScatteringPower method) GetMinDistanceTable() (pyobjcryst.crystal.Crystal method) GetMolecule() (pyobjcryst.molecule.MolAtom method) (pyobjcryst.molecule.MolBond method) (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) GetName() (pyobjcryst.io.XMLCrystTag method) (pyobjcryst.molecule.MolAtom method) (pyobjcryst.molecule.MolBond method) (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) (pyobjcryst.molecule.RigidGroup method) (pyobjcryst.refinableobj.RefObjOpt method) (pyobjcryst.refinableobj.RefParType method) (pyobjcryst.refinableobj.RefinableObj method) (pyobjcryst.refinableobj.RefinableObjRegistry method) (pyobjcryst.refinableobj.ScattererRegistry method) (pyobjcryst.refinableobj.ScatteringPowerRegistry method) (pyobjcryst.refinableobj.ZAtomRegistry method) (pyobjcryst.spacegroup.SpaceGroup method) (pyobjcryst.zscatterer.ZAtom method)

GetNb() (pyobjcryst.refinableobj.RefinableObjRegistry method) (pyobjcryst.refinableobj.ScattererRegistry method) (pyobjcryst.refinableobj.ScatteringPowerRegistry method) (pyobjcryst.refinableobj.ZAtomRegistry method) GetNbAtoms() (pyobjcryst.molecule.Molecule method) GetNbAttribute() (pyobjcryst.io.XMLCrystTag method) GetNbBondAngles() (pyobjcryst.molecule.Molecule method) GetNbBonds() (pyobjcryst.molecule.Molecule method) GetNbChoice() (pyobjcryst.refinableobj.RefObjOpt method) GetNbComponent() (pyobjcryst.scatterer.Scatterer method) (pyobjcryst.scatteringpower.ScatteringComponentList method) GetNbDihedralAngles() (pyobjcryst.molecule.Molecule method) GetNbLSQFunction() (pyobjcryst.refinableobj.RefinableObj method) GetNbOption() (pyobjcryst.refinableobj.RefinableObj method) GetNbPar() (pyobjcryst.refinableobj.RefinableObj method) GetNbParNotFixed() (pyobjcryst.refinableobj.RefinableObj method) GetNbRigidGroups() (pyobjcryst.molecule.Molecule method) GetNbScatterer() (pyobjcryst.crystal.Crystal method) GetNbScatteringPower() (pyobjcryst.scatteringpower.ScatteringPower method) GetNbSymmetrics() (pyobjcryst.spacegroup.SpaceGroup method) GetNbTranslationVectors() (pyobjcryst.spacegroup.SpaceGroup method) GetNorm() (pyobjcryst.molecule.Quaternion method) GetObj() (pyobjcryst.refinableobj.RefinableObjRegistry method) (pyobjcryst.refinableobj.ScattererRegistry method) (pyobjcryst.refinableobj.ScatteringPowerRegistry method) (pyobjcryst.refinableobj.ZAtomRegistry method) GetOccupancy() (pyobjcryst.molecule.MolAtom method) (pyobjcryst.scatterer.Scatterer method) (pyobjcryst.zscatterer.ZAtom method) GetOption() (pyobjcryst.refinableobj.RefinableObj method) GetOrthMatrix() (pyobjcryst.unitcell.UnitCell method) GetOrthonormalCoords() (pyobjcryst.unitcell.UnitCell method) GetPar() (pyobjcryst.refinableobj.RefinableObj method) GetParamSet() (pyobjcryst.refinableobj.RefinableObj method) GetParamSet_ParNotFixedHumanValue() (pyobjcryst.refinableobj.RefinableObj method) GetParamSetName() (pyobjcryst.refinableobj.RefinableObj method) GetParNotFixed() (pyobjcryst.refinableobj.RefinableObj method) GetPhi() (pyobjcryst.zscatterer.ZScatterer method) GetPsi() (pyobjcryst.zscatterer.ZScatterer method) GetRadius() (pyobjcryst.atom.Atom method) (pyobjcryst.scatteringpower.ScatteringPower method) (pyobjcryst.scatteringpowersphere.ScatteringPowerSphere method) (pyobjcryst.zscatterer.GlobalScatteringPower method) GetRefParListClock() (pyobjcryst.refinableobj.RefinableObj method) GetRegistryClock() (pyobjcryst.refinableobj.RefinableObjRegistry method) (pyobjcryst.refinableobj.ScattererRegistry method) (pyobjcryst.refinableobj.ScatteringPowerRegistry method) (pyobjcryst.refinableobj.ZAtomRegistry method) GetResonantScattFactImag() (pyobjcryst.scatteringpower.ScatteringPower method) GetResonantScattFactReal() (pyobjcryst.scatteringpower.ScatteringPower method) GetRestraintCost() (pyobjcryst.refinableobj.RefinableObj method) GetRigidGroupClock() (pyobjcryst.molecule.Molecule method) GetRigidGroupList() (pyobjcryst.molecule.Molecule method) GetScatt() (pyobjcryst.crystal.Crystal method) GetScatterer() (pyobjcryst.crystal.Crystal method) GetScattererRegistry() (pyobjcryst.crystal.Crystal method) GetScatteringComponentList() (pyobjcryst.crystal.Crystal method) (pyobjcryst.scatterer.Scatterer method) GetScatteringFactor() (pyobjcryst.scatteringpower.ScatteringPower method) GetScatteringPower() (pyobjcryst.atom.Atom method) (pyobjcryst.crystal.Crystal method) (pyobjcryst.molecule.MolAtom method) (pyobjcryst.zscatterer.ZAtom method) GetScatteringPowerRegistry() (pyobjcryst.crystal.Crystal method) GetSpaceGroup() (pyobjcryst.unitcell.UnitCell method) GetSpaceGroupNumber() (pyobjcryst.spacegroup.SpaceGroup method) GetStretchModeBondAngleList() (pyobjcryst.molecule.Molecule method) GetStretchModeBondLengthList() (pyobjcryst.molecule.Molecule method) GetStretchModeTorsionList() (pyobjcryst.molecule.Molecule method) GetSubObjRegistry() (pyobjcryst.refinableobj.RefinableObj method) GetSymbol() (pyobjcryst.scatteringpower.ScatteringPower method) GetSymmetryOperations() (pyobjcryst.spacegroup.SpaceGroup method) GetTemperatureFactor() (pyobjcryst.scatteringpower.ScatteringPower method) GetTranslationVectors() (pyobjcryst.spacegroup.SpaceGroup method) GetType() (pyobjcryst.refinableobj.Restraint method) GetUniqueAxis() (pyobjcryst.spacegroup.SpaceGroup method) GetUseDynPopCorr() (pyobjcryst.crystal.Crystal method) GetVolume() (pyobjcryst.unitcell.UnitCell method) GetX() (pyobjcryst.molecule.MolAtom method) (pyobjcryst.scatterer.Scatterer method) GetXCoord() (pyobjcryst.zscatterer.ZScatterer method) GetY() (pyobjcryst.molecule.MolAtom method) (pyobjcryst.scatterer.Scatterer method) GetYCoord() (pyobjcryst.zscatterer.ZScatterer method) GetZ() (pyobjcryst.molecule.MolAtom method) (pyobjcryst.scatterer.Scatterer method) GetZAngle() (pyobjcryst.zscatterer.ZAtom method) (pyobjcryst.zscatterer.ZScatterer method) GetZAngleAtom() (pyobjcryst.zscatterer.ZAtom method) (pyobjcryst.zscatterer.ZScatterer method) GetZAtomRegistry() (pyobjcryst.zscatterer.ZScatterer method) GetZAtomX() (pyobjcryst.zscatterer.ZScatterer method) GetZAtomY() (pyobjcryst.zscatterer.ZScatterer method) GetZAtomZ() (pyobjcryst.zscatterer.ZScatterer method) GetZBondAtom() (pyobjcryst.zscatterer.ZAtom method) (pyobjcryst.zscatterer.ZScatterer method) GetZBondLength() (pyobjcryst.zscatterer.ZAtom method) (pyobjcryst.zscatterer.ZScatterer method) GetZCoord() (pyobjcryst.zscatterer.ZScatterer method) GetZDihedralAngle() (pyobjcryst.zscatterer.ZAtom method) (pyobjcryst.zscatterer.ZScatterer method) GetZDihedralAngleAtom() (pyobjcryst.zscatterer.ZAtom method) (pyobjcryst.zscatterer.ZScatterer method) GetZScatterer() (pyobjcryst.zscatterer.ZAtom method) GlobalOptRandomMove() (pyobjcryst.refinableobj.RefinableObj method) GlobalScatteringPower (class in pyobjcryst.zscatterer)

H

HasInversionCenter() (pyobjcryst.spacegroup.SpaceGroup method)

I

Init() (pyobjcryst.atom.Atom method) (pyobjcryst.refinableobj.RefObjOpt method) (pyobjcryst.scatteringpower.ScatteringPowerAtom method) (pyobjcryst.scatteringpowersphere.ScatteringPowerSphere method) (pyobjcryst.zscatterer.GlobalScatteringPower method) InitOptions() (pyobjcryst.molecule.Molecule method) IsBeingRefined() (pyobjcryst.refinableobj.RefinableObj method) IsCentrosymmetric() (pyobjcryst.spacegroup.SpaceGroup method) IsDescendantFromOrSameAs() (pyobjcryst.refinableobj.RefParType method) IsDummy() (pyobjcryst.atom.Atom method) (pyobjcryst.molecule.MolAtom method) IsEmptyTag() (pyobjcryst.io.XMLCrystTag method)

IsEndTag() (pyobjcryst.io.XMLCrystTag method) IsFreeTorsion() (pyobjcryst.molecule.MolBond method) IsInAsymmetricUnit() (pyobjcryst.spacegroup.AsymmetricUnit method) (pyobjcryst.spacegroup.SpaceGroup method) IsInRing() (pyobjcryst.molecule.MolAtom method) IsInversionCenterAtOrigin() (pyobjcryst.spacegroup.SpaceGroup method) IsIsotropic() (pyobjcryst.scatteringpower.ScatteringPower method) IsReflCentric() (pyobjcryst.spacegroup.SpaceGroup method) IsReflSystematicAbsent() (pyobjcryst.spacegroup.SpaceGroup method) IsResonantScatteringAnisotropic() (pyobjcryst.scatteringpower.ScatteringPower method) IsScatteringFactorAnisotropic() (pyobjcryst.scatteringpower.ScatteringPower method) IsTemperatureFactorAnisotropic() (pyobjcryst.scatteringpower.ScatteringPower method)

L

Length (pyobjcryst.molecule.MolBond attribute) Length0 (pyobjcryst.molecule.MolBond attribute)

LengthDelta (pyobjcryst.molecule.MolBond attribute) LengthSigma (pyobjcryst.molecule.MolBond attribute) loadCrystal() (in module pyobjcryst)

M

MakeAntiPrismTetragonal() (in module pyobjcryst.polyhedron) MakeCube() (in module pyobjcryst.polyhedron) MakeIcosahedron() (in module pyobjcryst.polyhedron) MakeOctahedron() (in module pyobjcryst.polyhedron) MakePrismTrigonal() (in module pyobjcryst.polyhedron) MakeSquarePlane() (in module pyobjcryst.polyhedron) MakeTetrahedron() (in module pyobjcryst.polyhedron) MakeTriangle() (in module pyobjcryst.polyhedron) mCanOverlap (pyobjcryst.crystal.BumpMergePar attribute) mDist2 (pyobjcryst.crystal.BumpMergePar attribute) mDynPopCorr (pyobjcryst.scatteringpower.ScatteringComponent attribute) MillerToOrthonormalCoords() (pyobjcryst.unitcell.UnitCell method) mOccupancy (pyobjcryst.scatteringpower.ScatteringComponent attribute) MolAtom (class in pyobjcryst.molecule) MolBond (class in pyobjcryst.molecule)

MolBondAngle (class in pyobjcryst.molecule) MolDihedralAngle (class in pyobjcryst.molecule) Molecule (class in pyobjcryst.molecule) mpAtom0 (pyobjcryst.molecule.StretchModeBondAngle attribute) (pyobjcryst.molecule.StretchModeBondLength attribute) mpAtom1 (pyobjcryst.molecule.StretchModeBondAngle attribute) (pyobjcryst.molecule.StretchModeBondLength attribute) (pyobjcryst.molecule.StretchModeTorsion attribute) (pyobjcryst.molecule.StretchModeTwist attribute) mpAtom2 (pyobjcryst.molecule.StretchModeBondAngle attribute) (pyobjcryst.molecule.StretchModeTorsion attribute) (pyobjcryst.molecule.StretchModeTwist attribute) mpScattPow (pyobjcryst.scatteringpower.ScatteringComponent attribute) mX (pyobjcryst.scatteringpower.ScatteringComponent attribute) mY (pyobjcryst.scatteringpower.ScatteringComponent attribute) mZ (pyobjcryst.scatteringpower.ScatteringComponent attribute)

N

names (pyobjcryst.general.RadiationType attribute) (pyobjcryst.refinableobj.RefParDerivStepModel attribute) (pyobjcryst.zscatterer.RegularPolyhedraType attribute)

Normalize() (pyobjcryst.molecule.Quaternion method)

O

ObjCrystException, [1] Occupancy (pyobjcryst.molecule.MolAtom attribute) (pyobjcryst.scatterer.Scatterer attribute) (pyobjcryst.scatteringpower.ScatteringComponent attribute)

OCTAHEDRON (pyobjcryst.zscatterer.RegularPolyhedraType attribute) OptimizeConformation() (pyobjcryst.molecule.Molecule method) OptimizeConformationSteepestDescent() (pyobjcryst.molecule.Molecule method) OrthonormalToFractionalCoords() (pyobjcryst.unitcell.UnitCell method) OrthonormalToMillerCoords() (pyobjcryst.unitcell.UnitCell method)

P

PrepareForRefinement() (pyobjcryst.refinableobj.RefinableObj method) Print() (pyobjcryst.io.XMLCrystTag method) (pyobjcryst.refinableobj.RefinableObj method) (pyobjcryst.refinableobj.RefinableObjClock method) (pyobjcryst.refinableobj.RefinableObjRegistry method) (pyobjcryst.refinableobj.ScattererRegistry method) (pyobjcryst.refinableobj.ScatteringPowerRegistry method) (pyobjcryst.refinableobj.ZAtomRegistry method) (pyobjcryst.scatterer.Scatterer method) (pyobjcryst.scatteringpower.ScatteringComponent method) (pyobjcryst.scatteringpower.ScatteringComponentList method) (pyobjcryst.spacegroup.SpaceGroup method) PrintMinDistanceTable() (pyobjcryst.crystal.Crystal method) PrintStatic() (pyobjcryst.refinableobj.RefinableObjClock method) printxyz() (in module pyobjcryst.utils) PRISM_TETRAGONAL_MONOCAP (pyobjcryst.zscatterer.RegularPolyhedraType attribute) PRISM_TRIGONAL_TRICAPPED (pyobjcryst.zscatterer.RegularPolyhedraType attribute)

putAtomsInMolecule() (in module pyobjcryst.utils) pyobjcryst (module) pyobjcryst.atom (module) pyobjcryst.crystal (module) pyobjcryst.general (module) pyobjcryst.io (module) pyobjcryst.molecule (module) pyobjcryst.polyhedron (module) pyobjcryst.refinableobj (module) pyobjcryst.scatterer (module) pyobjcryst.scatteringpower (module) pyobjcryst.scatteringpowersphere (module) pyobjcryst.spacegroup (module) pyobjcryst.unitcell (module) pyobjcryst.utils (module) pyobjcryst.version (module) pyobjcryst.zscatterer (module)

Q

Q0 (pyobjcryst.molecule.Molecule attribute) (pyobjcryst.molecule.Quaternion attribute) Q1 (pyobjcryst.molecule.Molecule attribute) (pyobjcryst.molecule.Quaternion attribute)

Q2 (pyobjcryst.molecule.Molecule attribute) (pyobjcryst.molecule.Quaternion attribute) Q3 (pyobjcryst.molecule.Molecule attribute) (pyobjcryst.molecule.Quaternion attribute) Quaternion (class in pyobjcryst.molecule)

R

RAD_ELECTRON (pyobjcryst.general.RadiationType attribute) RAD_NEUTRON (pyobjcryst.general.RadiationType attribute) RAD_XRAY (pyobjcryst.general.RadiationType attribute) RadiationType (class in pyobjcryst.general) RandomizeConfiguration() (pyobjcryst.refinableobj.RefinableObj method) RandomStretch() (pyobjcryst.molecule.StretchMode method) RefinableObj (class in pyobjcryst.refinableobj) RefinableObjClock (class in pyobjcryst.refinableobj) RefinableObjRegistry (class in pyobjcryst.refinableobj) RefinablePar (class in pyobjcryst.refinableobj) RefObjOpt (class in pyobjcryst.refinableobj) REFPAR_DERIV_STEP_ABSOLUTE (pyobjcryst.refinableobj.RefParDerivStepModel attribute) REFPAR_DERIV_STEP_RELATIVE (pyobjcryst.refinableobj.RefParDerivStepModel attribute) RefParDerivStepModel (class in pyobjcryst.refinableobj) RefParType (class in pyobjcryst.refinableobj) Register() (pyobjcryst.refinableobj.RefinableObjRegistry method) (pyobjcryst.refinableobj.ScattererRegistry method) (pyobjcryst.refinableobj.ScatteringPowerRegistry method) (pyobjcryst.refinableobj.ZAtomRegistry method) RegisterClient() (pyobjcryst.refinableobj.RefinableObj method) RegularPolyhedraType (class in pyobjcryst.zscatterer) release notes RemoveAtom() (pyobjcryst.molecule.Molecule method)

RemoveBond() (pyobjcryst.molecule.Molecule method) RemoveBondAngle() (pyobjcryst.molecule.Molecule method) RemoveBondValenceRo() (pyobjcryst.crystal.Crystal method) RemoveBumpMergeDistance() (pyobjcryst.crystal.Crystal method) RemoveChild() (pyobjcryst.refinableobj.RefinableObjClock method) RemoveDihedralAngle() (pyobjcryst.molecule.Molecule method) RemovePar() (pyobjcryst.refinableobj.RefinableObj method) RemoveParent() (pyobjcryst.refinableobj.RefinableObjClock method) RemoveRestraint() (pyobjcryst.refinableobj.RefinableObj method) RemoveRigidGroup() (pyobjcryst.molecule.Molecule method) RemoveScatterer() (pyobjcryst.crystal.Crystal method) RemoveScatteringPower() (pyobjcryst.crystal.Crystal method) Reset() (pyobjcryst.refinableobj.RefinableObjClock method) (pyobjcryst.scatteringpower.ScatteringComponentList method) ResetDynPopCorr() (pyobjcryst.crystal.Crystal method) ResetParList() (pyobjcryst.refinableobj.RefinableObj method) RestoreParamSet() (pyobjcryst.refinableobj.RefinableObj method) Restraint (class in pyobjcryst.refinableobj) RigidGroup (class in pyobjcryst.molecule) RigidifyWithDihedralAngles() (pyobjcryst.molecule.Molecule method) RotateAtomGroup() (pyobjcryst.molecule.Molecule method) RotateVector() (pyobjcryst.molecule.Quaternion method) RotationQuaternion() (pyobjcryst.molecule.Quaternion static method)

S

SaveParamSet() (pyobjcryst.refinableobj.RefinableObj method) Scatterer (class in pyobjcryst.scatterer) ScattererRegistry (class in pyobjcryst.refinableobj) ScatteringComponent (class in pyobjcryst.scatteringpower) ScatteringComponentList (class in pyobjcryst.scatteringpower) ScatteringPower (class in pyobjcryst.scatteringpower) ScatteringPowerAtom (class in pyobjcryst.scatteringpower) ScatteringPowerRegistry (class in pyobjcryst.refinableobj) ScatteringPowerSphere (class in pyobjcryst.scatteringpowersphere) SetAngle0() (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) SetAngleDelta() (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) SetAngleSigma() (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) SetAtom1() (pyobjcryst.molecule.MolBond method) (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) SetAtom2() (pyobjcryst.molecule.MolBond method) (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) SetAtom3() (pyobjcryst.molecule.MolBondAngle method) (pyobjcryst.molecule.MolDihedralAngle method) SetAtom4() (pyobjcryst.molecule.MolDihedralAngle method) SetBij() (pyobjcryst.scatteringpower.ScatteringPower method) SetBiso() (pyobjcryst.scatteringpower.ScatteringPower method) SetBondOrder() (pyobjcryst.molecule.MolBond method) SetBumpMergeDistance() (pyobjcryst.crystal.Crystal method) SetCenterAtom() (pyobjcryst.molecule.Molecule method) SetCenterAtomIndex() (pyobjcryst.zscatterer.ZScatterer method) SetChi() (pyobjcryst.zscatterer.ZScatterer method) SetChoice() (pyobjcryst.refinableobj.RefObjOpt method) SetCrystal() (pyobjcryst.scatterer.Scatterer method) SetEqual() (pyobjcryst.refinableobj.RefinableObjClock method) SetFormalCharge() (pyobjcryst.scatteringpower.ScatteringPower method) SetFreeTorsion() (pyobjcryst.molecule.MolBond method) SetGlobalOptimStep() (pyobjcryst.refinableobj.RefinableObj method) SetIsEmptyTag() (pyobjcryst.io.XMLCrystTag method) SetIsEndTag() (pyobjcryst.io.XMLCrystTag method) SetIsInRing() (pyobjcryst.molecule.MolAtom method) SetLength0() (pyobjcryst.molecule.MolBond method) SetLengthDelta() (pyobjcryst.molecule.MolBond method) SetLengthSigma() (pyobjcryst.molecule.MolBond method)

SetLimitsAbsolute() (pyobjcryst.refinableobj.RefinableObj method) SetLimitsProportional() (pyobjcryst.refinableobj.RefinableObj method) SetLimitsRelative() (pyobjcryst.refinableobj.RefinableObj method) SetMaximumLikelihoodNbGhostAtom() (pyobjcryst.scatteringpower.ScatteringPower method) SetMaximumLikelihoodPositionError() (pyobjcryst.scatteringpower.ScatteringPower method) SetName() (pyobjcryst.molecule.MolAtom method) (pyobjcryst.refinableobj.RefinableObj method) (pyobjcryst.refinableobj.RefinableObjRegistry method) (pyobjcryst.refinableobj.ScattererRegistry method) (pyobjcryst.refinableobj.ScatteringPowerRegistry method) (pyobjcryst.refinableobj.ZAtomRegistry method) (pyobjcryst.zscatterer.ZAtom method) SetOccupancy() (pyobjcryst.molecule.MolAtom method) (pyobjcryst.scatterer.Scatterer method) (pyobjcryst.zscatterer.ZAtom method) SetParIsFixed() (pyobjcryst.refinableobj.RefinableObj method) SetParIsUsed() (pyobjcryst.refinableobj.RefinableObj method) SetPhi() (pyobjcryst.zscatterer.ZScatterer method) SetPsi() (pyobjcryst.zscatterer.ZScatterer method) SetScatteringPower() (pyobjcryst.zscatterer.ZAtom method) SetSpaceGroup() (pyobjcryst.spacegroup.AsymmetricUnit method) SetSymbol() (pyobjcryst.scatteringpower.ScatteringPowerAtom method) SetType() (pyobjcryst.refinableobj.Restraint method) SetUseDynPopCorr() (pyobjcryst.crystal.Crystal method) SetX() (pyobjcryst.molecule.MolAtom method) (pyobjcryst.scatterer.Scatterer method) SetY() (pyobjcryst.molecule.MolAtom method) (pyobjcryst.scatterer.Scatterer method) SetZ() (pyobjcryst.molecule.MolAtom method) (pyobjcryst.scatterer.Scatterer method) SetZAngle() (pyobjcryst.zscatterer.ZAtom method) (pyobjcryst.zscatterer.ZScatterer method) SetZBondLength() (pyobjcryst.zscatterer.ZAtom method) (pyobjcryst.zscatterer.ZScatterer method) SetZDihedralAngle() (pyobjcryst.zscatterer.ZAtom method) (pyobjcryst.zscatterer.ZScatterer method) SpaceGroup (class in pyobjcryst.spacegroup) SQUARE_PLANE (pyobjcryst.zscatterer.RegularPolyhedraType attribute) Stretch() (pyobjcryst.molecule.StretchMode method) StretchMode (class in pyobjcryst.molecule) StretchModeBondAngle (class in pyobjcryst.molecule) StretchModeBondLength (class in pyobjcryst.molecule) StretchModeTorsion (class in pyobjcryst.molecule) StretchModeTwist (class in pyobjcryst.molecule)

T

TagNewBestConfig() (pyobjcryst.refinableobj.RefinableObj method) TETRAHEDRON (pyobjcryst.zscatterer.RegularPolyhedraType attribute)

TranslateAtomGroup() (pyobjcryst.molecule.Molecule method) TuneGlobalOptimRotationAmplitude() (pyobjcryst.molecule.Molecule method)

U

UnFixAllPar() (pyobjcryst.refinableobj.RefinableObj method)

UnitCell (class in pyobjcryst.unitcell) UpdateScattCompList() (pyobjcryst.molecule.Molecule method)

V

values (pyobjcryst.general.RadiationType attribute) (pyobjcryst.refinableobj.RefParDerivStepModel attribute) (pyobjcryst.zscatterer.RegularPolyhedraType attribute)

W

writexyz() (in module pyobjcryst.utils)

X

X (pyobjcryst.molecule.MolAtom attribute) (pyobjcryst.scatterer.Scatterer attribute) (pyobjcryst.scatteringpower.ScatteringComponent attribute) Xmax() (pyobjcryst.spacegroup.AsymmetricUnit method) Xmin() (pyobjcryst.spacegroup.AsymmetricUnit method)

XMLCrystTag (class in pyobjcryst.io) XMLInput() (pyobjcryst.refinableobj.RefinableObj method) (pyobjcryst.refinableobj.RefObjOpt method) XMLOutput() (pyobjcryst.refinableobj.RefinableObj method) (pyobjcryst.refinableobj.RefObjOpt method)

Y

Y (pyobjcryst.molecule.MolAtom attribute) (pyobjcryst.scatterer.Scatterer attribute) (pyobjcryst.scatteringpower.ScatteringComponent attribute)

Ymax() (pyobjcryst.spacegroup.AsymmetricUnit method) Ymin() (pyobjcryst.spacegroup.AsymmetricUnit method)

Z

Z (pyobjcryst.molecule.MolAtom attribute) (pyobjcryst.scatterer.Scatterer attribute) (pyobjcryst.scatteringpower.ScatteringComponent attribute) ZAtom (class in pyobjcryst.zscatterer)

ZAtomRegistry (class in pyobjcryst.refinableobj) Zmax() (pyobjcryst.spacegroup.AsymmetricUnit method) Zmin() (pyobjcryst.spacegroup.AsymmetricUnit method) ZPolyhedron (class in pyobjcryst.zscatterer) ZScatterer (class in pyobjcryst.zscatterer)