ObjCryst::ZPolyhedron Class Reference

ZPolyhedron: a Scatterer to describe polyhedras such as octahedron, tetrahedron, square plane, etc... More...

Inheritance diagram for ObjCryst::ZPolyhedron:

Collaboration diagram for ObjCryst::ZPolyhedron:

Public Member Functions
	ZPolyhedron (const RegularPolyhedraType type, Crystal &cryst, const REAL x, const REAL y, const REAL z, const string &name, const ScatteringPower *centralAtomPow, const ScatteringPower *periphAtomPow, const REAL centralPeriphDist, const REAL ligandPopu=1, const REAL phi=0., const REAL chi=0., const REAL psi=0.)
	ZPolyhedron constructor. More...
	ZPolyhedron (const ZPolyhedron &)
	Copy Constructor.
virtual ZPolyhedron *	CreateCopy () const
Public Member Functions inherited from ObjCryst::ZScatterer
	ZScatterer (const string &name, Crystal &cryst, const REAL x=0., const REAL y=0., const REAL z=0., const REAL phi=0., const REAL chi=0., const REAL psi=0.)
	ZScatterer constructor. More...
	ZScatterer (const ZScatterer &old)
	Copy constructor. More...
virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",...). More...
void	AddAtom (const string &name, const ScatteringPower *pow, const long atomBond, const REAL bondLength, const long atomAngle, const REAL bondAngle, const long atomDihedral, const REAL dihedralAngle, const REAL popu=1.)
	Add an atom to the Zscatterer. More...
virtual int	GetNbComponent () const
	Number of components in the scatterer (eg number of point scatterers)
virtual const ScatteringComponentList &	GetScatteringComponentList () const
	Get the list of all scattering components for this scatterer. More...
virtual string	GetComponentName (const int i) const
	Name for the i-th component of this scatterer. More...
void	Print () const
	Print a single line of information about this scatterer.
REAL	GetPhi () const
	Access to phi parameter (overall orientation of the scatterer)
REAL	GetChi () const
	Access to chi parameter (overall orientation of the scatterer)
REAL	GetPsi () const
	Access to psi parameter (overall orientation of the scatterer)
void	SetPhi (const REAL)
	Access to phi parameter (overall orientation of the scatterer)
void	SetChi (const REAL)
	Access to chi parameter (overall orientation of the scatterer)
void	SetPsi (const REAL)
	Access to psi parameter (overall orientation of the scatterer)
REAL	GetZAtomX (const int i) const
	Get the X fractionnal coordinate of atom i.
REAL	GetZAtomY (const int i) const
	Get the Y fractionnal coordinate of atom i.
REAL	GetZAtomZ (const int i) const
	Get the Z fractionnal coordinate of atom i.
long	GetZBondAtom (const int i) const
	Index of the 1st atom used to define the i-th atom in the Z-Matrix (the one from which the bondlength is calculated)
long	GetZAngleAtom (const int i) const
	Index of the 2nd atom used to define the i-th atom in the Z-Matrix (the one from which the angle is calculated)
long	GetZDihedralAngleAtom (const int i) const
	Index of the 3rd atom used to define the i-th atom in the Z-Matrix (the one from which the dihedral angle is calculated)
REAL	GetZBondLength (const int i) const
	Const access to bondlength parameter, for the i-th row in the Z-Matrix.
REAL	GetZAngle (const int i) const
	Const access to the angle parameter, for the i-th row in the Z-Matrix.
REAL	GetZDihedralAngle (const int i) const
	Const access to the dihedral angle parameter, for the i-th row in the Z-Matrix.
void	SetZBondLength (const int i, const REAL)
	Access to bondlength parameter, for the i-th row in the Z-Matrix.
void	SetZAngle (const int i, const REAL)
	Access to the angle parameter, for the i-th row in the Z-Matrix.
void	SetZDihedralAngle (const int i, const REAL)
	Access to the dihedral angle parameter, for the i-th row in the Z-Matrix.
const ObjRegistry< ZAtom > &	GetZAtomRegistry () const
	Access to the registry of ZAtoms.
virtual ostream &	POVRayDescription (ostream &os, const CrystalPOVRayOptions &options) const
virtual void	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
virtual void	SetUseGlobalScatteringPower (const bool useIt)
	use a Global scattering power for this scatterer ? More...
virtual void	XMLOutput (ostream &os, int indent=0) const
	Output to stream in well-formed XML. More...
virtual void	XMLInput (istream &is, const XMLCrystTag &tag)
	Input From stream. More...
virtual void	GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
	Get the gene group assigned to each parameter. More...
virtual void	GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst)
	Make a random move of the current configuration. More...
const CrystVector_REAL &	GetXCoord () const
	Get the list of all ZAtom cartesian x coordinates.
const CrystVector_REAL &	GetYCoord () const
	Get the list of all ZAtom cartesian x coordinates.
const CrystVector_REAL &	GetZCoord () const
	Get the list of all ZAtom cartesian x coordinates.
virtual void	EndOptimization ()
	This should be called by any optimization class at the end of an optimization. More...
void	ImportFenskeHallZMatrix (istream &is, bool named=false)
	Import "Fenske-Hall" ZMatrix file (fhz in the babel program http://www.eyesopen.com/babel.html\ example: use "./babel -ipdb foo.pdb -ofhz foo.fhz -d", to convert a pdb file to a Z-Matrix file (the -d removes hydrogen atoms) More...
void	ExportFenskeHallZMatrix (ostream &os)
	Export to Fenske-Hall ZMatrix file. More...
void	SetCenterAtomIndex (const unsigned int)
	Set the index of the central atom (around which the rotation is made)
unsigned int	GetCenterAtomIndex () const
	Get the index of the central atom (around which the rotation is made)
Public Member Functions inherited from ObjCryst::Scatterer
	Scatterer ()
	Constructor.
	Scatterer (const Scatterer &old)
	Copy Constructor.
virtual	~Scatterer ()
	Destructor.
REAL	GetX () const
	X coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More...
REAL	GetY () const
	Y coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More...
REAL	GetZ () const
	Z coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More...
REAL	GetOccupancy () const
	Get the occupancy of the scatterer (0. More...
virtual void	SetX (const REAL x)
	X coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More...
virtual void	SetY (const REAL y)
	Y coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More...
virtual void	SetZ (const REAL z)
	Z coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More...
virtual void	SetOccupancy (const REAL occupancy)
	Change the occupancy of the scatterer (0. More...
	operator string () const
	Conversion function. More...
virtual const string &	GetColour () const
	Colour associated to this scatterer (using POVRay names) More...
virtual const float *	GetColourRGB () const
	Colour associated to this scatterer, 3 RGB Coordinates.
const RefinableObjClock &	GetClockScatterer () const
	Last time anything in the scatterer was changed (atoms, positions, scattering power)
RefinableObjClock &	GetClockScatterer ()
	Last time anything in the scatterer was changed (atoms, positions, scattering power)
void	SetCrystal (Crystal &)
	Set the crystal in which is included this Scatterer.
const Crystal &	GetCrystal () const
	In which crystal is this Scatterer included ?
Crystal &	GetCrystal ()
	In which crystal is this Scatterer included ?
Public Member Functions inherited from ObjCryst::RefinableObj
	RefinableObj ()
	Constructor.
	RefinableObj (const bool internalUseOnly)
	Constructor. More...
	RefinableObj (const RefinableObj &old)
	Defined not implemented... More...
virtual	~RefinableObj ()
	Destructor.
virtual const string &	GetName () const
	Name of the object.
virtual void	SetName (const string &name)
	Name of the object.
void	operator= (const RefinableObj &old)
	Defined not implemented... More...
void	PrepareForRefinement () const
	Find which parameters are used and not fixed, for a refinement /optimization. More...
void	FixAllPar ()
	Fix All parameters.
void	UnFixAllPar ()
	UnFix All parameters.
void	SetParIsFixed (const long parIndex, const bool fix)
	Fix/un-fix one parameter from its #.
void	SetParIsFixed (const string &parName, const bool fix)
	Fix/un-fix one parameter from its name.
void	SetParIsFixed (const RefParType *type, const bool fix)
	Fix/un-fix one family of parameters.
void	SetParIsUsed (const string &parName, const bool use)
	Set whether a parameter is used.
void	SetParIsUsed (const RefParType *type, const bool use)
	Set whether a family of parameters is used.
long	GetNbPar () const
	Total number of refinable parameter in the object. More...
long	GetNbParNotFixed () const
	Total number of non-fixed parameters. Is initialized by PrepareForRefinement()
RefinablePar &	GetPar (const long i)
	Access all parameters in the order they were inputted.
const RefinablePar &	GetPar (const long i) const
	Access all parameters in the order they were inputted.
RefinablePar &	GetPar (const string &name)
	Access all parameters from their name.
const RefinablePar &	GetPar (const string &name) const
	Access all parameters from their name.
RefinablePar &	GetPar (const REAL *)
	Access parameter from its adress.
const RefinablePar &	GetPar (const REAL *) const
	Access parameter from its adress.
RefinablePar &	GetParNotFixed (const long i)
	Access all parameters in the order they were inputted, skipping fixed parameters. More...
const RefinablePar &	GetParNotFixed (const long i) const
	Access all parameters in the order they were inputed, skipping fixed parameters. More...
void	AddPar (const RefinablePar &newRefPar)
	Add a refinable parameter. More...
void	AddPar (RefinablePar *newRefPar)
	Add a refinable parameter. More...
void	AddPar (RefinableObj &newRefParList, const bool copyParam=false)
	Add all the parameters in another RefinableObj. More...
vector< RefinablePar * >::iterator	RemovePar (RefinablePar *refPar)
	Remove a refinable parameter. More...
unsigned long	CreateParamSet (const string name="") const
	Save the current set of refined values in a new set. More...
void	ClearParamSet (const unsigned long id) const
	Erase the param set with the given id, releasing memory.
void	SaveParamSet (const unsigned long id) const
	Save the current set of refined values over a previously-created set of saved values. More...
void	RestoreParamSet (const unsigned long id)
	Restore a saved set of values. More...
const CrystVector_REAL &	GetParamSet (const unsigned long setId) const
	Access one save refpar set. More...
CrystVector_REAL &	GetParamSet (const unsigned long setId)
	Access one save refpar set. More...
REAL	GetParamSet_ParNotFixedHumanValue (const unsigned long setId, const long parNumber) const
	Access the (human) value of one refined parameter in a saved set of parameters. More...
const void	EraseAllParamSet ()
	Erase all saved refpar sets. More...
const string &	GetParamSetName (const unsigned long setId) const
	Get the name associated to a refpar set. More...
void	SetLimitsAbsolute (const string &parName, const REAL min, const REAL max)
	Change the limits for a given parameter, giving absolute new limits.
void	SetLimitsAbsolute (const RefParType *type, const REAL min, const REAL max)
	Change the limits for a category of parameters, giving absolute new limits.
void	SetLimitsRelative (const string &parName, const REAL min, const REAL max)
	Change the limits for a given parameter, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max) Thus min should logically be <0 and max >0. More...
void	SetLimitsRelative (const RefParType *type, const REAL min, const REAL max)
	Change the limits for a category of parameters, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max). More...
void	SetLimitsProportional (const string &parName, const REAL min, const REAL max)
	Change the limits for a given parameter, proportionnaly to the current value. More...
void	SetLimitsProportional (const RefParType *type, const REAL min, const REAL max)
	Change the limits for a category of parameters, proportionnaly to their current value. More...
void	SetGlobalOptimStep (const RefParType *type, const REAL step)
	Change the maximum step to use during Global Optimization algorithms.
ObjRegistry< RefinableObj > &	GetSubObjRegistry ()
	Access to the registry of RefinableObj used by this object.
const ObjRegistry< RefinableObj > &	GetSubObjRegistry () const
	Access to the registry of RefinableObj used by this object.
virtual void	RegisterClient (RefinableObj &) const
	Register a new object using this object. More...
virtual void	DeRegisterClient (RefinableObj &) const
	Deregister an object (which not any more) using this object.
virtual const ObjRegistry < RefinableObj > &	GetClientRegistry () const
	Get the list of clients.
virtual ObjRegistry < RefinableObj > &	GetClientRegistry ()
	Get the list of clients.
bool	IsBeingRefined () const
	Is the object being refined ? (Can be refined by one algorithm at a time only.)
virtual void	BeginOptimization (const bool allowApproximations=false, const bool enableRestraints=false)
	This should be called by any optimization class at the begining of an optimization. More...
virtual void	SetApproximationFlag (const bool allow)
	Enable or disable numerical approximations. More...
virtual void	RandomizeConfiguration ()
	Randomize Configuration (before a global optimization). More...
void	BeginGlobalOptRandomMove ()
	Raise a flag, to be sure not to make a random change more than once in each RefinableObj. More...
virtual REAL	GetLogLikelihood () const
	Get -log(likelihood) of the current configuration for the object. More...
virtual unsigned int	GetNbLSQFunction () const
	Number of LSQ functions.
virtual const CrystVector_REAL &	GetLSQCalc (const unsigned int) const
	Get the current calculated value for the LSQ function.
virtual const CrystVector_REAL &	GetLSQObs (const unsigned int) const
	Get the observed values for the LSQ function.
virtual const CrystVector_REAL &	GetLSQWeight (const unsigned int) const
	Get the weight values for the LSQ function.
virtual const CrystVector_REAL &	GetLSQDeriv (const unsigned int, RefinablePar &)
	Get the first derivative values for the LSQ function, for a given parameter. More...
virtual std::map< RefinablePar *, CrystVector_REAL > &	GetLSQ_FullDeriv (const unsigned int, std::set< RefinablePar * > &vPar)
	Get the first derivative for the LSQ function for each parameter supplied in a list. More...
void	ResetParList ()
	Re-init the list of refinable parameters, removing all parameters. More...
virtual void	UpdateDisplay () const
	If there is an interface, this should be automatically be called each time there is a 'new, significant' configuration to report. More...
unsigned int	GetNbOption () const
	Number of Options for this object.
RefObjOpt &	GetOption (const unsigned int i)
	Access to the options.
const RefObjOpt &	GetOption (const unsigned int i) const
	const access to the options
void	SetDeleteRefParInDestructor (const bool b)
	Set this object not to delete its list of parameters when destroyed. More...
const RefinableObjClock &	GetRefParListClock () const
	What was the last time a RefinablePar was added/removed ? More...
virtual REAL	GetRestraintCost () const
	Get the restraint cost (overall penalty of all restraints) More...
void	AddRestraint (Restraint *pNewRestraint)
	Add a new restraint. More...
vector< Restraint * >::iterator	RemoveRestraint (Restraint *pRestraint)
	Remove a restraint from the list of known restraints. More...
virtual void	TagNewBestConfig () const
	During a global optimization, tells the object that the current config is the latest "best" config. More...
const RefinableObjClock &	GetClockMaster () const
	This clocks records any change in the object. See refinableObj::mClockMaster.

Private Attributes
RegularPolyhedraType	mPolyhedraType

Additional Inherited Members
Protected Member Functions inherited from ObjCryst::ZScatterer
void	UpdateCoordinates () const
	Update the atom coordinates (in real units, in Angstroems). More...
void	UpdateScattCompList () const
	Update the scattering component list, ie compute all atom positions from the bonds/angles/dihedral angles, and convert the coordinates to fractionnal coordinates of the Crystal.
Protected Member Functions inherited from ObjCryst::Scatterer
virtual void	InitRGBColour ()
	Get RGB Colour coordinates from Colour Name. More...
const RefinableObjClock &	GetClockScattCompList () const
	Last time the ScatteringComponentList was generated.
Protected Member Functions inherited from ObjCryst::RefinableObj
long	FindPar (const string &name) const
	Find a refinable parameter with a given name.
long	FindPar (const REAL *) const
	Find a refinable parameter from the adress of its value.
void	AddSubRefObj (RefinableObj &)
void	RemoveSubRefObj (RefinableObj &)
void	AddOption (RefObjOpt *opt)
virtual void	Prepare ()
map< unsigned long, pair < CrystVector_REAL, string > >::iterator	FindParamSet (unsigned long id) const
	Find a parameter set with a given id (and check if it is there)
Protected Attributes inherited from ObjCryst::ZScatterer
CrystMatrix_long	m3DDisplayIndex
	For 3D display of the structure, bonds, triangular and quadric faces can be displayed. More...
ScatteringComponentList	mScattCompList
	The list of scattering components.
long	mNbAtom
	Total number of atoms in the structure.
Protected Attributes inherited from ObjCryst::Scatterer
CrystVector_REAL	mXYZ
	coordinates of the scatterer (or of its center..)
REAL	mOccupancy
	Occupancy : 0 <= occ <= 1 For a multi-atom scatterer (polyhedron,..), this is the overall occupancy of the scatterer (affects all components of the scatterer).
string	mColourName
	Colour for this scatterer (from POVRay)
float	mColourRGB [3]
	Colour for this scatterer using RGB.
RefinableObjClock	mClockScatterer
	Last time anything (number of atoms, positions, scattering power) was changed.
RefinableObjClock	mClockScattCompList
Crystal *	mpCryst
	The crystal in which the Scatterer is This is needed so that we can know which scattering powers are available in the crystal, and also to convert fractionnal to orthonormal coordinates (for some scatterers only). More...
Protected Attributes inherited from ObjCryst::RefinableObj
string	mName
	Name for this RefinableObject. Should be unique, at least in the same scope.+.
vector< RefinablePar * >	mvpRefPar
	Vector of pointers to the refinable parameters.
vector< Restraint * >	mvpRestraint
	Vector of pointers to the restraints for this object. More...
map< unsigned long, pair < CrystVector_REAL, string > >	mvpSavedValuesSet
	Map of (index,pointers to arrays) used to save sets of values for all parameters. More...
long	mNbRefParNotFixed
	Total of not-fixed parameters.
CrystVector_long	mRefparNotFixedIndex
	Index of not-fixed parameters.
int	mOptimizationDepth
	Is the object being refined or optimized ? if mOptimizationDepth=0, no optimization is taking place. More...
ObjRegistry< RefinableObj >	mSubObjRegistry
	Registry of RefinableObject needed for this object (owned by this object or not)
ObjRegistry< RefinableObj >	mClientObjRegistry
	Registry of RefinableObject using this object. More...
ObjRegistry< RefObjOpt >	mOptionRegistry
	List of options for this object. More...
bool	mDeleteRefParInDestructor
	If true (the default), then all RefinablePar will be deleted when the the object is deleted. More...
RefinableObjClock	mRefParListClock
	Last time the RefinableParList was modified (a parameter added or removed).
bool	mRandomMoveIsDone
CrystVector_REAL	mLSQDeriv
	Temporary array used to return derivative values of the LSQ function for given parameters. More...
std::map< unsigned int, std::map< RefinablePar *, CrystVector_REAL > >	mLSQ_FullDeriv
	Temporary map to return the derivative of the LSQ function versus a list of parameters. More...
RefinableObjClock	mClockMaster
	Master clock, which is changed whenever the object has been altered. More...

Detailed Description

ZPolyhedron: a Scatterer to describe polyhedras such as octahedron, tetrahedron, square plane, etc...

These are ZScatterer objects, so that even if they are initialized with constraints, these can be removed to make any configuration.

Definition at line 471 of file ZScatterer.h.

Constructor & Destructor Documentation

ObjCryst::ZPolyhedron::ZPolyhedron	(	const RegularPolyhedraType	type,
		Crystal &	cryst,
		const REAL	x,
		const REAL	y,
		const REAL	z,
		const string &	name,
		const ScatteringPower *	centralAtomPow,
		const ScatteringPower *	periphAtomPow,
		const REAL	centralPeriphDist,
		const REAL	ligandPopu = 1,
		const REAL	phi = 0.,
		const REAL	chi = 0.,
		const REAL	psi = 0.
	)

ZPolyhedron constructor.

Parameters

type	: OCTAHEDRON, TETRAHEDRON,...
cryst	: a crystal is necessary to transform the orthornormal coordinates (in which the relative atom positions are computed) to fractional ones.
x,y,z	: fractional coordinates of the center of the polyhedra
name	: name of the Polyhedra ('WO6','TaSe4_a', 'Tetra01'...). The name can have any format but spaces should be avoided, since it will generate problems when reading the names from a file. And there must not be identical name for two scatterers in a given crystal object.
periphAtomPow,centralAtomPow	the ScatteringPower corresponding to the central and peripheral atoms, respectively.
centralPeriphDist	the distance, in angstroems, from the central to the peripheral atoms
ligandPopu	: the relative population of ligand atoms, equal to 1/n if ligand atoms are shared by n polyhedra. If you are using the 'Dynamical Polpulation Correction', then keep this parameter to 1.
phi,chi,psi	initial angles for this polyhedron

Definition at line 2175 of file ZScatterer.cpp.

Member Function Documentation

ZPolyhedron * ObjCryst::ZPolyhedron::CreateCopy ( ) const

virtual

so-called Virtual copy constructor, needed to make copies of arrays of Scatterers

Reimplemented from ObjCryst::ZScatterer.

Definition at line 2758 of file ZScatterer.cpp.

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The documentation for this class was generated from the following files:

• ZScatterer.h
• ZScatterer.cpp