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The molecule can be constructed using the AppendAtom() and AppendBond() methods in one of two ways; either by fully specifying the atom/bond in a single call, or by incrementally setting the various attributes using the convience vtkAtom and vtkBond classes: Single call:vtkMolecule *mol = vtkMolecule::New(); vtkAtom h1 = mol->AppendAtom(1, 0.0, 0.0, -0.5); vtkAtom h2 = mol->AppendAtom(1, 0.0, 0.0, 0.5); vtkBond b = mol->AppendBond(h1, h2, 1); Incremental:vtkMolecule *mol = vtkMolecule::New(); vtkAtom h1 = mol->AppendAtom(); h1.SetAtomicNumber(1); h1.SetPosition(0.0, 0.0, -0.5); vtkAtom h2 = mol->AppendAtom(); h2.SetAtomicNumber(1); vtkVector3d displacement (0.0, 0.0, 1.0); h2.SetPosition(h1.GetPositionAsVector3d() + displacement); vtkBond b = mol->AppendBond(h1, h2, 1); Both of the above methods will produce the same molecule, two hydrogens connected with a 1.0 Angstrom single bond, aligned to the z-axis. The second example also demostrates the use of VTK's vtkVector class, which is fully supported by the Chemistry kit. The vtkMolecule object is intended to be used with the vtkMoleculeMapper class for visualizing molecular structure using common rendering techniques. \warning While direct use of the underlying vtkUndirectedGraph structure is possible due to vtkMolecule's public inheritance, this should not be relied upon and may change in the future. @sa vtkAtom vtkBond vtkMoleculeMapper vtkPeriodicTable vtkCommonDataModelPython.vtkMoleculeV.IsTypeOf(string) -> int C++: static vtkTypeBool IsTypeOf(const char *type) Return 1 if this class type is the same type of (or a subclass of) the named class. Returns 0 otherwise. This method works in combination with vtkTypeMacro found in vtkSetGet.h. V.IsA(string) -> int C++: vtkTypeBool IsA(const char *type) override; Return 1 if this class is the same type of (or a subclass of) the named class. Returns 0 otherwise. This method works in combination with vtkTypeMacro found in vtkSetGet.h. V.SafeDownCast(vtkObjectBase) -> vtkMolecule C++: static vtkMolecule *SafeDownCast(vtkObjectBase *o) V.NewInstance() -> vtkMolecule C++: vtkMolecule *NewInstance() V.Initialize() C++: void Initialize() override; Initialize to an empty graph. V.GetDataObjectType() -> int C++: int GetDataObjectType() override; Return what type of dataset this is. V.AppendAtom() -> vtkAtom C++: vtkAtom AppendAtom() V.AppendAtom(int, vtkVector3f) -> vtkAtom C++: vtkAtom AppendAtom(unsigned short atomicNumber, const vtkVector3f &pos) V.AppendAtom(int, float, float, float) -> vtkAtom C++: vtkAtom AppendAtom(unsigned short atomicNumber, double x, double y, double z) Add new atom with atomic number 0 (dummy atom) at origin. Return a vtkAtom that refers to the new atom. V.GetAtom(int) -> vtkAtom C++: vtkAtom GetAtom(vtkIdType atomId) Return a vtkAtom that refers to the atom with the specified id. V.GetNumberOfAtoms() -> int C++: vtkIdType GetNumberOfAtoms() Return the number of atoms in the molecule. V.AppendBond(int, int, int) -> vtkBond C++: vtkBond AppendBond(vtkIdType atom1, vtkIdType atom2, unsigned short order=1) V.AppendBond(vtkAtom, vtkAtom, int) -> vtkBond C++: vtkBond AppendBond(const vtkAtom &atom1, const vtkAtom &atom2, unsigned short order=1) Add a bond between the specified atoms, optionally setting the bond order (default: 1). Return a vtkBond object referring to the new bond. V.GetBond(int) -> vtkBond C++: vtkBond GetBond(vtkIdType bondId) Return a vtkAtom that refers to the bond with the specified id. V.GetNumberOfBonds() -> int C++: vtkIdType GetNumberOfBonds() Return the number of bonds in the molecule. V.GetAtomAtomicNumber(int) -> int C++: unsigned short GetAtomAtomicNumber(vtkIdType atomId) Return the atomic number of the atom with the specified id. V.SetAtomAtomicNumber(int, int) C++: void SetAtomAtomicNumber(vtkIdType atomId, unsigned short atomicNum) Set the atomic number of the atom with the specified id. V.SetAtomPosition(int, vtkVector3f) C++: void SetAtomPosition(vtkIdType atomId, const vtkVector3f &pos) V.SetAtomPosition(int, float, float, float) C++: void SetAtomPosition(vtkIdType atomId, double x, double y, double z) Set the position of the atom with the specified id. V.GetAtomPosition(int) -> vtkVector3f C++: vtkVector3f GetAtomPosition(vtkIdType atomId) V.GetAtomPosition(int, [float, float, float]) C++: void GetAtomPosition(vtkIdType atomId, float pos[3]) Get the position of the atom with the specified id. V.SetBondOrder(int, int) C++: void SetBondOrder(vtkIdType bondId, unsigned short order) Get/Set the bond order of the bond with the specified id V.GetBondOrder(int) -> int C++: unsigned short GetBondOrder(vtkIdType bondId) Get/Set the bond order of the bond with the specified id V.GetBondLength(int) -> float C++: double GetBondLength(vtkIdType bondId) Get the bond length of the bond with the specified id * ote If the associated vtkBond object is already available, * vtkBond::GetBondLength is potentially much faster than this * function, as a list of all bonds may need to be constructed to * locate the appropriate bond. * \sa UpdateBondList() V.GetAtomicPositionArray() -> vtkPoints C++: vtkPoints *GetAtomicPositionArray() Access the raw arrays used in this vtkMolecule instance V.GetAtomicNumberArray() -> vtkUnsignedShortArray C++: vtkUnsignedShortArray *GetAtomicNumberArray() Access the raw arrays used in this vtkMolecule instance V.GetElectronicData() -> vtkAbstractElectronicData C++: virtual vtkAbstractElectronicData *GetElectronicData() Set/Get the AbstractElectronicData-subclassed object for this molecule. V.SetElectronicData(vtkAbstractElectronicData) C++: virtual void SetElectronicData(vtkAbstractElectronicData *) Set/Get the AbstractElectronicData-subclassed object for this molecule. V.CheckedShallowCopy(vtkGraph) -> bool C++: bool CheckedShallowCopy(vtkGraph *g) override; Performs the same operation as ShallowCopy(), but instead of reporting an error for an incompatible graph, returns false. V.CheckedDeepCopy(vtkGraph) -> bool C++: bool CheckedDeepCopy(vtkGraph *g) override; Performs the same operation as DeepCopy(), but instead of reporting an error for an incompatible graph, returns false. V.ShallowCopy(vtkDataObject) C++: void ShallowCopy(vtkDataObject *obj) override; Shallow copies the data object into this molecule. V.DeepCopy(vtkDataObject) C++: void DeepCopy(vtkDataObject *obj) override; Deep copies the data object into this molecule. V.ShallowCopyStructure(vtkMolecule) C++: virtual void ShallowCopyStructure(vtkMolecule *m) Shallow copies the atoms and bonds from m into this. V.DeepCopyStructure(vtkMolecule) C++: virtual void DeepCopyStructure(vtkMolecule *m) Deep copies the atoms and bonds from m into this. V.ShallowCopyAttributes(vtkMolecule) C++: virtual void ShallowCopyAttributes(vtkMolecule *m) Shallow copies attributes (i.e. everything besides atoms and bonds) fromm into this. V.DeepCopyAttributes(vtkMolecule) C++: virtual void DeepCopyAttributes(vtkMolecule *m) Deep copies attributes (i.e. everything besides atoms and bonds) fromm into this. V.GetPlaneFromBond(vtkBond, vtkVector3f, vtkPlane) -> bool C++: static bool GetPlaneFromBond(const vtkBond &bond, const vtkVector3f &normal, vtkPlane *plane) V.GetPlaneFromBond(vtkAtom, vtkAtom, vtkVector3f, vtkPlane) -> bool C++: static bool GetPlaneFromBond(const vtkAtom &atom1, const vtkAtom &atom2, const vtkVector3f &normal, vtkPlane *plane) Obtain the plane that passes through the indicated bond with the given normal. If the plane is set successfully, the function returns true. * If the normal is not orthogonal to the bond, a new normal will be * constructed in such a way that the plane will be orthogonal to * the plane spanned by the bond vector and the input normal vector. * This ensures that the plane passes through the bond, and the * normal is more of a "hint" indicating the orientation of the plane. * The new normal (n) is defined as the input normal vector (n_i) minus * the projection of itself (proj[n_i]_v) onto the bond vector (v): * * v ^ * | n = (n_i - proj[n_j]_v) * proj[n_i]_v ^ |----x * | | / * | | / n_i * | | / * | |/ * * If n_i is parallel to v, a warning will be printed and no plane will be * added. Obviously, n_i must not be parallel to v. V.HasLattice() -> bool C++: bool HasLattice() Return true if a unit cell lattice is defined. V.ClearLattice() C++: void ClearLattice() Remove any unit cell lattice information from the molecule. V.SetLattice(vtkMatrix3x3) C++: void SetLattice(vtkMatrix3x3 *matrix) V.SetLattice(vtkVector3d, vtkVector3d, vtkVector3d) C++: void SetLattice(const vtkVector3d &a, const vtkVector3d &b, const vtkVector3d &c) The unit cell vectors. The matrix is stored using a row-major layout, with the vectors encoded as columns. V.GetLattice() -> vtkMatrix3x3 C++: vtkMatrix3x3 *GetLattice() V.GetLattice(vtkVector3d, vtkVector3d, vtkVector3d) C++: void GetLattice(vtkVector3d &a, vtkVector3d &b, vtkVector3d &c) V.GetLattice(vtkVector3d, vtkVector3d, vtkVector3d, vtkVector3d) C++: void GetLattice(vtkVector3d &a, vtkVector3d &b, vtkVector3d &c, vtkVector3d &origin) Get the unit cell lattice vectors. The matrix is stored using a row-major layout, with the vectors encoded as columns. Will return nullptr if no unit cell information is available. @sa GetLatticeOrigin V.GetLatticeOrigin() -> vtkVector3d C++: virtual vtkVector3d GetLatticeOrigin() Get the unit cell origin (for rendering purposes). V.SetLatticeOrigin(vtkVector3d) C++: virtual void SetLatticeOrigin(vtkVector3d _arg) Get the unit cell origin (for rendering purposes). UH-HH=HHH]HHDGCC: (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0GNUzRx  0 DXbl  EDPa AE O|R8wFBB A(DI (D BBBF  uEY B P(,"EAD`n AAF XH@ I tED@ AG ED@ AG ED@ AG ED@ AG ED@ AG (ED@ AG LED@ AG pHP E EDP AK EDP AK EDP AK ED` AK (FAD ABG (HFAD` ABG (tFAD` ABG (fFAD ABG gFD@ EE 4oEDp AF xCFBFp<(FBA A(D] (D ABBD 0hFAA D`  AABH 8FDA A(Dr (A ABBH (FCDr ABF @)FDB B(A0Dr 0A(B BBBB @HXFDB B(A0Dp{ 0A(B BBBI (FCG~ ABG MFF0OFDD n ABA DDB:Em $EDP AK HEDP AK lEDP AK EDP AK EDP AK EDP AK EDP AK EDP AK DEDP AK hH@ I      KOu`@w"IP  D u   1Xf  g6ofp!)>%Xh`(: ,+-`./012G4y 506 '2CKW` h$**q0~6<BHNTZ` fl%r9xG~OWkx"7@L\o   " 4 " Z "  "b  "  A P     8     "u  % E U       ? 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