ZScatterer: the basic type of complex scatterers, where atom positions are defined using a standard "Z-Matrix" description. More...

Inheritance diagram for ObjCryst::ZScatterer:

Collaboration diagram for ObjCryst::ZScatterer:

Public Member Functions
	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 ZScatterer *	CreateCopy () const

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.

Protected Member Functions
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
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...

Private Member Functions
virtual void	InitRefParList ()
	Prepare refinable parameters for the scatterer object.

Private Attributes
long	mNbDummyAtom
	Number of "dummy" atoms in the structure.

CrystVector_int	mComponentIndex
	Index of atoms in the ScatteringComponentList. More...

REAL	mPhi
	Angles giving the orientation of the ZScatterer (stored in radian) More...

REAL	mChi

REAL	mPsi

ObjRegistry< ZAtom >	mZAtomRegistry
	Registry for ZAtoms in this Scatterer.

long	mCenterAtomIndex
	Index of the atom used as a pivot (the scatterer is rotated around this atom). More...

CrystMatrix_REAL	mPhiChiPsiMatrix
	Rotation matrix for the orientation of the scatterer.

bool	mUseGlobalScattPow
	Does the ZScatterer use a global scattering power ? More...

GlobalScatteringPower *	mpGlobalScattPow
	the global scattering power used, if mUseGlobalScattPow=true More...

CrystVector_REAL	mXCoord
	Storage for Cartesian coordinates. More...

CrystVector_REAL	mYCoord

CrystVector_REAL	mZCoord

RefinableObjClock	mClockCoord
	Last time the cartesian coordinates were computed.

ZMoveMinimizer *	mpZMoveMinimizer

Detailed Description

ZScatterer: the basic type of complex scatterers, where atom positions are defined using a standard "Z-Matrix" description.

This is used to describe inorganic polyhedras, as well as molecules.

Definition at line 190 of file ZScatterer.h.

Constructor & Destructor Documentation

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.

Parameters

name	the name of the scatterer
cryst	the crystal in which the scatterer is (needed to convert from cartesian to fractionnal coordinates).
x,y,z	fractionnal coordinates of the scatterer
phi,chi	angles defining the orientation of the scatterer

Definition at line 214 of file ZScatterer.cpp.

ObjCryst::ZScatterer::ZScatterer ( const ZScatterer & old )

Copy constructor.

Definition at line 238 of file ZScatterer.cpp.

Member Function Documentation

void ObjCryst::ZScatterer::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.

If &ScatteringPower=0, then it is a 'dummy' atom and will be ignored for any scattering analysis. The 'name' supplied may not be respected, and can be replaced by 'ZScatterer_name'+'AtomNum'+'ScattPowName'

Definition at line 317 of file ZScatterer.cpp.

ZScatterer * ObjCryst::ZScatterer::CreateCopy ( ) const

virtual

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

Implements ObjCryst::Scatterer.

Reimplemented in ObjCryst::ZPolyhedron.

Definition at line 306 of file ZScatterer.cpp.

void ObjCryst::ZScatterer::EndOptimization ( )

virtual

This should be called by any optimization class at the end of an optimization.

This also affects all sub-objects.

Note: this may be called several time for some objects which are used by several other objects.

Reimplemented from ObjCryst::RefinableObj.

Definition at line 1144 of file ZScatterer.cpp.

void ObjCryst::ZScatterer::ExportFenskeHallZMatrix ( ostream & os )

Export to Fenske-Hall ZMatrix file.

Todo:: USe more strict formatting than space-delimited.

Definition at line 1505 of file ZScatterer.cpp.

const string & ObjCryst::ZScatterer::GetClassName ( ) const

virtual

Name for this class ("RefinableObj", "Crystal",...).

This is only useful to distinguish different classes when picking up objects from the RefinableObj Global Registry

Reimplemented from ObjCryst::Scatterer.

Definition at line 311 of file ZScatterer.cpp.

string ObjCryst::ZScatterer::GetComponentName ( const int i ) const

virtual

Name for the i-th component of this scatterer.

If the component is an Atom, Then the name is that of the atom. Else, it is the name of the scatterer plus the component number in the scatterer plus the name of the ScatteringPower.

Note: It would be better to return a reference, but we don't want to keep a name for all components... Weeelll, needs some more thinking... see what performance hit results (if any).

Bug:: does not take into account dummy atoms !!

Implements ObjCryst::Scatterer.

Definition at line 417 of file ZScatterer.cpp.

void ObjCryst::ZScatterer::GetGeneGroup	(	const RefinableObj &	obj,
		CrystVector_uint &	groupIndex,
		unsigned int &	firstGroup
	)		const

virtual

Get the gene group assigned to each parameter.

Each parameter (a gene in terms of genetic algorithms) can be assigned to a gene group. Thus when mating two configurations, genes will be exchanged by groups. By default (in the base RefinabeObj class), each parameter is alone in its group. Derived classes can group genes for a better s** life.

The number identifying a gene group only has a meaning in a given object. It can also change on subsequent calls, and thus is not unique.

Parameters

obj	the , supplied by an algorithm class (OptimizationObj,..), which contains a list of parameters, some of which (but possibly all or none) are parameters belonging to this object.
groupIndex	a vector of unsigned integers, one for each parameter in the input object, giving an unsigned integer value as gene group index. At the beginning this vector should contain only zeros (no group assigned).
firstGroup	this is the number of groups which have already been assigned, plus one. The gene groups returned by this object will start from this value, and increment firstGroup for each gene group used, so that different RefinableObj cannot share a gene group.

Note: this function is not optimized, and should only be called at the beginning of a refinement.

Reimplemented from ObjCryst::RefinableObj.

Definition at line 1101 of file ZScatterer.cpp.

const ScatteringComponentList & ObjCryst::ZScatterer::GetScatteringComponentList ( ) const

virtual

Get the list of all scattering components for this scatterer.

This is the most important function of this class, giving the list of scattering positions along with the associated ScatteringPower.

Implements ObjCryst::Scatterer.

Definition at line 410 of file ZScatterer.cpp.

void ObjCryst::ZScatterer::GLInitDisplayList	(	const bool	noSymmetrics = `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

Create an OpenGL Display List of the scatterer. This should only be called by a Crystal object.

Parameters

noSymmetrics	if false (the default), then all symmetrics are shown in the 3D display, within the limits defined by the min/max parameters \ param xMin,xMax,yMin,yMax,zMin,zMax: in fractionnal coordinates, the region in which we want scaterrer to be displayed. The test is made on the center of the scatterer (eg a ZScatterer (molecule) will not be 'cut' on the border).
displayNames	if true, only the names of the scatterers will be displayed, at the position of the scatterers (to actually see them, they will have to be translated with respect to the drawing of the scatterers).
hideHydrogens	if true, do not display hydrogens/deuterium and their bonds

Implements ObjCryst::Scatterer.

Definition at line 646 of file ZScatterer.cpp.

void ObjCryst::ZScatterer::GlobalOptRandomMove	(	const REAL	mutationAmplitude,
		const RefParType *	type = `gpRefParTypeObjCryst`
	)

virtual

Make a random move of the current configuration.

This is for global optimization algorithms. the moves for each parameter are less than their global optimization step, multiplied by the mutation amplitude.

Warning: : this makes a random move for the parameter declared for this object, and it is the duty of the object to decide whether the included objects should be moved and how. (eg an algorithm should only call for a move with the top object, and this object decides how he and his sub-objects moves). By default (RefinableObj implementation) all included objects are moved recursively.

RefinableObj::

Parameters

mutationAmplitude	multiplier for the maximum move amplitude, for all parameters
type	restrain the change exclusively to parameters of a given type (same type or descendant from this RefParType).

Reimplemented from ObjCryst::RefinableObj.

Definition at line 1531 of file ZScatterer.cpp.

void ObjCryst::ZScatterer::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)

Parameters

is	the input stream from which to read the z-matrix
names	if true, instead of reading a standard Fenske-Hall z-matrix, the file will be read with names, i.e. with an added first column with the names of the atoms, and the number used to reference the bond, bond angle and dihedral angle atoms are replaced by the names of the atoms.

Warning: : this should be called before any atom has been added (if there are already atoms, they should be removed but this has not been tested...)

Note: : this will search in the Crystal associated with this ZScatterer the relevant ScatteringPowerAtom, which should have the name of the corresponding symbol (eg 'H', 'C',...) if these are not found then they will be added to the Crystal with a default isotropic B-factor equal to 1.; : this also sets relative limits of +/-.03 Angstroems for all bond distances, and +/-3.6 degress for bond and dihedral angles.

Todo:: : identify which dihedral angles should not be limited, by analysing a coordination table.

Definition at line 1267 of file ZScatterer.cpp.

ostream & ObjCryst::ZScatterer::POVRayDescription	(	ostream &	os,
		const CrystalPOVRayOptions &	options
	)		const

virtual

Warning: Not implemented for ZScatterer

Implements ObjCryst::Scatterer.

Definition at line 469 of file ZScatterer.cpp.

void ObjCryst::ZScatterer::SetUseGlobalScatteringPower ( const bool useIt )

virtual

use a Global scattering power for this scatterer ?

If true, then the overall scattering power of this ZScatterer will be approximated to an isotropic scattering power computed for this scatterer. Of course, only use this if the "isotropic" approximation is reasonable for this scatterer (typically true for 'large' polyhedra). See GlobalScatteringPower.

Warning: EXPERIMENTAL

Definition at line 1070 of file ZScatterer.cpp.

void ObjCryst::ZScatterer::UpdateCoordinates ( ) const

protected

Update the atom coordinates (in real units, in Angstroems).

This takes into account the translation and global rotation of the scatterer (ie this does not generate 'internal coordinates).

Definition at line 1811 of file ZScatterer.cpp.

void ObjCryst::ZScatterer::XMLInput	(	istream &	is,
		const XMLCrystTag &	tag
	)

virtual

Input From stream.

Todo:: Add an bool XMLInputTag(is,tag) function to recognize all the tags from the stream. So that each inherited class can use the XMLInputTag function from its parent (ie take advantage of inheritance). The children class would first try to interpret the tag, then if unsuccessful would pass it to its parent (thus allowing overloading), etc...

Reimplemented from ObjCryst::RefinableObj.

Definition at line 685 of file ObjCryst/IO.cpp.

void ObjCryst::ZScatterer::XMLOutput	(	ostream &	os,
		int	indent = `0`
	)		const

virtual

Output to stream in well-formed XML.

Todo:: Use inheritance.. as for XMLInputTag()...

Reimplemented from ObjCryst::RefinableObj.

Definition at line 638 of file ObjCryst/IO.cpp.

Member Data Documentation

CrystMatrix_long ObjCryst::ZScatterer::m3DDisplayIndex

protected

For 3D display of the structure, bonds, triangular and quadric faces can be displayed.

This matrix determines what is drawn. This is a 5-column matrix. The first column indicates the type of drawing (0: : nothing, 1: display the atom (a sphere), 2: bond, 3: triangular face, 4: quadric face) the other columns indicate the index of the atoms involved in the drawing (2 atoms for a bond, 3 for....)

If the matrix is empty only the individual atoms are displayed.

Todo:: This is still experimental. This is only used for the display of ZPolyhedron, and should be more developped (and it should also be saved in XML files !)

Definition at line 377 of file ZScatterer.h.

long ObjCryst::ZScatterer::mCenterAtomIndex

private

Index of the atom used as a pivot (the scatterer is rotated around this atom).

This should more or less be at the center of the Scatterer.

Definition at line 426 of file ZScatterer.h.

CrystVector_int ObjCryst::ZScatterer::mComponentIndex

private

Index of atoms in the ScatteringComponentList.

We need this list because Dummy atoms are not included in it. So this is an integer array with [ 0 1 2 4 5 6].. where the missing '3' marks a Dummy atom. Thus to get the name of component 'i' in the component list, you must take the mComponentIndex(i) atom in the ZAtom Registry.

Definition at line 394 of file ZScatterer.h.

GlobalScatteringPower* ObjCryst::ZScatterer::mpGlobalScattPow

private

the global scattering power used, if mUseGlobalScattPow=true

Warning: EXPERIMENTAL.

Definition at line 437 of file ZScatterer.h.

REAL ObjCryst::ZScatterer::mPhi

private

Angles giving the orientation of the ZScatterer (stored in radian)

The position of any atom can be transformed from internal coordinates (orthonormal coordinates derived from the ZMatrix, with first atom at (0,0,0), second atom at (x,0,0), third atom at (x,y,0),...) to orthonormal coordinates in the crystal reference frame (ie with orientation of the ZScatterer) using :

$\left[ \begin{array}{c} x(i) \\ y(i) \\ z(i) \end{array} \right]_{orthonormal} = \left[ \begin{array}{ccc} \cos(\chi) & 0 & -\sin(\chi) \\ 0 & 1 & 0 \\ \sin(\chi) & 0 & \cos(\chi) \end{array} \right] \times \left[ \begin{array}{ccc} \cos(\phi) & -\sin(\phi) & 0 \\ \sin(\phi) & \cos(\phi) & 0 \\ 0 & 0 & 1 \end{array} \right] \times \left[ \begin{array}{ccc} 1 & 0 & 0 \\ 0 & \cos(\psi) & -\sin(\psi) \\ 0 & \sin(\psi) & \cos(\psi) \end{array} \right] \times \left[ \begin{array}{c} x_0(i) \\ y_0(i) \\ z_0(i) \end{array} \right]$

, where x0(i), y0(i) and z0(i) describe the position for atom (i) in internal coordinates, and x(i), y(i), z(i) are coordinates of the rotated ZScatterer.

The rotation is performed around a 'pivot' atom (see ZScatterer::mPivotAtom)

Definition at line 420 of file ZScatterer.h.

bool ObjCryst::ZScatterer::mUseGlobalScattPow

private

Does the ZScatterer use a global scattering power ?

Warning: EXPERIMENTAL.

Definition at line 433 of file ZScatterer.h.

CrystVector_REAL ObjCryst::ZScatterer::mXCoord

mutableprivate

Storage for Cartesian coordinates.

The (0,0,0) is on the central atom. This includes Dummy atoms.

Definition at line 441 of file ZScatterer.h.

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

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation