ObjCryst::Molecule Class Reference

Molecule : class for complex scatterer descriptions using cartesian coordinates with bond length/angle restraints, and moves either of individual atoms or using torsion bonds. More...

Inheritance diagram for ObjCryst::Molecule:

Collaboration diagram for ObjCryst::Molecule:

Classes
struct	FlipGroup
	When 3(A1..1n) or more atoms are connected to a same atom A, it defines a 'flip' group, where it is possible to rotate bonds to their symmetric with respect to one plane defined by atoms Ai-A-Aj. More...
struct	RotorGroup
	Defines a group of atoms which can be rotated around an axis defined by two other atoms. More...
struct	StretchModeGroup
	Group of concurrent StretchModes (affecting common restraints) A given stretch mode can only belong to one group. More...

Public Member Functions
	Molecule (Crystal &cryst, const string &name="")
	Constructor. More...
	Molecule (const Molecule &old)
	Copy constructor. More...
	~Molecule ()
	Destructor. More...
virtual Molecule *	CreateCopy () const
virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",...). More...
virtual void	SetName (const string &name)
	Name of the object.
std::string	GetFormula () const
	Formula with atoms in alphabetic order.
virtual void	Print () const
	Print some info about the scatterer (ideally this should be one line...).
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	UpdateDisplay () const
	If there is an interface, this should be automatically be called each time there is a 'new, significant' configuration to report. More...
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	EndOptimization ()
	This should be called by any optimization class at the end of an optimization. More...
virtual void	RandomizeConfiguration ()
	Randomize Configuration (before a global optimization). More...
virtual void	GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type)
	Make a random move of the current configuration. 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 n, RefinablePar &par)
	Get the first derivative values for the LSQ function, for a given parameter. More...
virtual void	TagNewBestConfig () const
	During a global optimization, tells the object that the current config is the latest "best" config. 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...
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
void	AddAtom (const REAL x, const REAL y, const REAL z, const ScatteringPower *pPow, const string &name, const bool updateDisplay=true)
	Add an atom. More...
vector< MolAtom * >::iterator	RemoveAtom (MolAtom &, const bool del=true)
	Remove an atom. More...
void	AddNonFlipAtom (MolAtom &atom)
void	removeNonFlipAtom (MolAtom &atom)
vector< MolAtom * >	getNonFlipAtomList ()
void	AddBond (MolAtom &atom1, MolAtom &atom2, const REAL length, const REAL sigma, const REAL delta, const REAL bondOrder=1., const bool updateDisplay=true)
	Add a bond. More...
vector< MolBond * >::iterator	RemoveBond (const MolBond &, const bool del=true)
	Remove a bond. More...
vector< MolBond * >::const_iterator	FindBond (const MolAtom &, const MolAtom &) const
	Searches whether a bond between two atoms already exists. More...
vector< MolBond * >::iterator	FindBond (const MolAtom &, const MolAtom &)
	Searches whether a bond between two atoms already exists. More...
void	AddBondAngle (MolAtom &atom1, MolAtom &atom2, MolAtom &atom3, const REAL angle, const REAL sigma, const REAL delta, const bool updateDisplay=true)
	Add a bond angle restraint. More...
vector< MolBondAngle * >::iterator	RemoveBondAngle (const MolBondAngle &, const bool del=true)
	Remove a BondAngle. More...
vector< MolBondAngle * > ::const_iterator	FindBondAngle (const MolAtom &at1, const MolAtom &at0, const MolAtom &at2) const
	Searches whether a bond between three atoms already exists, searching for either (at1,at2,at3) and (at3,at2,at1), as these are equivalent. More...
void	AddDihedralAngle (MolAtom &atom1, MolAtom &atom2, MolAtom &atom3, MolAtom &atom4, const REAL angle, const REAL sigma, const REAL delta, const bool updateDisplay=true)
	Add a dihedral angle restraint. More...
vector< MolDihedralAngle * > ::iterator	RemoveDihedralAngle (const MolDihedralAngle &, const bool del=true)
	Remove a dihedral angle. More...
vector< MolDihedralAngle * > ::const_iterator	FindDihedralAngle (const MolAtom &at1, const MolAtom &at2, const MolAtom &at3, const MolAtom &at4) const
	Searches whether a dihedral between four atoms already exists, searching for either (at1,at2,at3,at4) and (at4,at3,at2,at1), as these are equivalent. More...
void	AddRigidGroup (const RigidGroup &, const bool updateDisplay=true)
	Add a rigid group of atoms. More...
std::vector< RigidGroup * > ::iterator	RemoveRigidGroup (const RigidGroup &group, const bool updateDisplay=true, const bool del=true)
	Remove a rigid group of atoms. More...
MolAtom &	GetAtom (unsigned int i)
const MolAtom &	GetAtom (unsigned int i) const
MolAtom &	GetAtom (const string &name)
const MolAtom &	GetAtom (const string &name) const
vector< MolAtom * > ::reverse_iterator	FindAtom (const string &name)
	Search a MolAtom from its name. More...
vector< MolAtom * > ::const_reverse_iterator	FindAtom (const string &name) const
	Search a MolAtom from its name. More...
void	OptimizeConformation (const long nbTrial=10000, const REAL stopCost=0.)
	Minimize configuration from internal restraints (bond lengths, angles and dihedral angles). More...
void	OptimizeConformationSteepestDescent (const REAL maxStep=0.1, const unsigned nbStep=1)
	Optimize the conformation from internal restraints (bond lengths, angles and dihedral angles), using a steepest descent algorithm. More...
void	MolecularDynamicsEvolve (std::map< MolAtom *, XYZ > &v0, const unsigned nbStep, const REAL dt, const std::vector< MolBond * > &vb, const std::vector< MolBondAngle * > &va, const std::vector< MolDihedralAngle * > &vd, std::map< RigidGroup *, std::pair< XYZ, XYZ > > &vr, REAL nrj0=0)
	Change the conformation of the molecule using molecular dynamics principles. More...
const std::vector< MolAtom * > &	GetAtomList () const
const std::vector< MolBond * > &	GetBondList () const
const std::vector < MolBondAngle * > &	GetBondAngleList () const
const std::vector < MolDihedralAngle * > &	GetDihedralAngleList () const
std::vector< MolAtom * > &	GetAtomList ()
std::vector< MolBond * > &	GetBondList ()
std::vector< MolBondAngle * > &	GetBondAngleList ()
std::vector< MolDihedralAngle * > &	GetDihedralAngleList ()
std::list < StretchModeBondLength > &	GetStretchModeBondLengthList ()
std::list< StretchModeBondAngle > &	GetStretchModeBondAngleList ()
std::list< StretchModeTorsion > &	GetStretchModeTorsionList ()
const std::list < StretchModeBondLength > &	GetStretchModeBondLengthList () const
const std::list < StretchModeBondAngle > &	GetStretchModeBondAngleList () const
const std::list < StretchModeTorsion > &	GetStretchModeTorsionList () const
const std::vector< RigidGroup * > &	GetRigidGroupList () const
	List of rigid group of atoms. More...
std::vector< RigidGroup * > &	GetRigidGroupList ()
	List of rigid group of atoms. More...
void	RotateAtomGroup (const MolAtom &at1, const MolAtom &at2, const set< MolAtom * > &atoms, const REAL angle, const bool keepCenter=true)
	Rotate a group of atoms around an axis defined by two atoms. More...
void	RotateAtomGroup (const MolAtom &at, const REAL vx, const REAL vy, const REAL vz, const set< MolAtom * > &atoms, const REAL angle, const bool keepCenter=true)
	Rotate a group of atoms around an axis defined by one atom and a vector. More...
void	TranslateAtomGroup (const set< MolAtom * > &atoms, const REAL dx, const REAL dy, const REAL dz, const bool keepCenter=true)
	Translate a group of atoms in a given direction. More...
void	RestraintStatus (ostream &os) const
	Print the status of all restraints (bond length, angles...)
void	RestraintExport (ostream &os) const
	Print the restraints (bond length, angles...) as whole labels and number in column text format which accessible to other programs.
const map< MolAtom *, set < MolAtom * > > &	GetConnectivityTable ()
	Get the connectivity table.
RefinableObjClock &	GetBondListClock ()
	get the clock associated to the list of bonds
const RefinableObjClock &	GetBondListClock () const
	get the clock associated to the list of bonds
RefinableObjClock &	GetAtomPositionClock ()
	Get the clock associated to the atomic positions.
const RefinableObjClock &	GetAtomPositionClock () const
	Get the clock associated to the atomic positions.
RefinableObjClock &	GetRigidGroupClock ()
	Get the clock associated to the list of rigid groups (clicked also whenever a rigid group is modified)
const RefinableObjClock &	GetRigidGroupClock () const
	Get the clock associated to the list of rigid groups (clicked also whenever a rigid group is modified)
void	RigidifyWithDihedralAngles ()
	Add dihedral angles so as to rigidify the Molecule. More...
REAL	BondLengthRandomChange (const StretchModeBondLength &mode, const REAL amplitude, const bool respectRestraint=true)
	Stretch a bond, while respecting the Restraint (if any). More...
REAL	BondAngleRandomChange (const StretchModeBondAngle &mode, const REAL amplitude, const bool respectRestraint=true)
	change a bond angle, while respecting the Restraint (if any). More...
REAL	DihedralAngleRandomChange (const StretchModeTorsion &mode, const REAL amplitude, const bool respectRestraint=true)
	Change a dihedral angle, while respecting the Restraint (if any). More...
const MolAtom *	GetCenterAtom () const
	Get the atom defining the origin of the Molecule Equal to 0 if no atom as been set. More...
void	SetCenterAtom (const MolAtom &at)
	Get the atom defining the origin of the Molecule Equal to 0 if no atom as been set. More...
const std::vector< MolZAtom > &	AsZMatrix (const bool keeporder) const
	Molecule as Z-matrix. More...
void	SetDeleteSubObjInDestructor (const bool b)
	Set whether to delete the MolAtoms, MolBonds, MolBondAngles and MolDihedralAngles in the destructor. More...
virtual void	InitRefParList ()
void	BuildRingList ()
	Build the list of rings in the molecule. More...
void	BuildConnectivityTable () const
	Build the Connectivity table. More...
void	BuildRotorGroup ()
	Build the groups of atoms that will be rotated during global optimization. More...
void	TuneGlobalOptimRotationAmplitude ()
	Tune the rotation amplitude for free torsions and for the overall Molecule Rotation. More...
void	BuildFlipGroup ()
	Build the groups of atoms that can be flipped. More...
void	BuildStretchModeBondLength ()
	Build the groups of atoms moved when stretching a bond length, while respecting the Molecule restraints.
void	BuildStretchModeBondAngle ()
	Build the groups of atoms moved when changing a bond angle, while respecting the Molecule restraints.
void	BuildStretchModeTorsion ()
	Build the groups of atoms moved when changing a dihedral angle, while respecting the Molecule restraints.
void	BuildStretchModeTwist ()
	Build the groups of atoms used to twist internally the Molecule, e.g. More...
void	BuildStretchModeGroups ()
	Separate StretchMode that break more than their assigned restraint from others. More...
void	BuildMDAtomGroups ()
	Find groups of atoms that cannot be moved relatively to each other using the free or non-free stretch modes. More...
void	UpdateScattCompList () const
	Update the Molecule::mScattCompList from the cartesian coordinates of all atoms, and the orientation parameters.
void	InitOptions ()
	Build options for this object.
void	ResetRigidGroupsPar () const
	Set the orientation & translation parameters of all rigid groups to 0, after correcting the atomic positions. More...
void	FlipAtomGroup (const FlipGroup &, const bool keepCenter=true)
	Flip a group of atom. See Molecule::FlipGroup.
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.
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	SetApproximationFlag (const bool allow)
	Enable or disable numerical approximations. More...
void	BeginGlobalOptRandomMove ()
	Raise a flag, to be sure not to make a random change more than once in each RefinableObj. 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...
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
virtual void	GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
	Get the gene group assigned to each parameter. More...
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...
const RefinableObjClock &	GetClockMaster () const
	This clocks records any change in the object. See refinableObj::mClockMaster.

Public Attributes
ScatteringComponentList	mScattCompList
	The list of scattering components. More...
vector< MolAtom * >	mvNonFlipAtom
vector< MolAtom * >	mvpAtom
	The list of atoms. More...
vector< MolBond * >	mvpBond
	The list of bonds. More...
vector< MolBondAngle * >	mvpBondAngle
	The list of bond angles. More...
vector< MolDihedralAngle * >	mvpDihedralAngle
	The list of dihedral angles. More...
map< MolAtom *, std::vector < MolBond * > >	mvAtomBond
	List of Bonds for each atom. More...
std::vector< RigidGroup * >	mvRigidGroup
	Rigid groups of atoms. More...
list< MolRing >	mvRing
	The list of rings. More...
Quaternion	mQuat
	The unit quaternion defining the orientation. More...
bool	mDeleteSubObjInDestructor
	Base Rotation amplitude (in radians) for the Molecule, so that the average atomic displacement is equal to 0.1 A. More...
REAL	mBaseRotationAmplitude
RefinableObjClock	mClockAtomList
RefinableObjClock	mClockBondList
RefinableObjClock	mClockBondAngleList
RefinableObjClock	mClockDihedralAngleList
RefinableObjClock	mClockRigidGroup
RefinableObjClock	mClockAtomPosition
RefinableObjClock	mClockAtomScattPow
RefinableObjClock	mClockOrientation
RefinableObjClock	mClockLogLikelihood
RefinableObjClock	mClockConnectivityTable
RefinableObjClock	mClockRingList
RefinableObjClock	mClockRotorGroup
RefinableObjClock	mClockFlipGroup
RefinableObjClock	mClockStretchModeBondLength
RefinableObjClock	mClockStretchModeBondAngle
RefinableObjClock	mClockStretchModeTorsion
RefinableObjClock	mClockStretchModeTwist
RefinableObjClock	mClockMDAtomGroup
unsigned long	mLocalParamSet
unsigned long	mRandomConformChangeNbTest
unsigned long	mRandomConformChangeNbAccept
REAL	mRandomConformChangeTemp
REAL	mLastLogLike
bool	mIsSelfOptimizing
RefObjOpt	mFlexModel
	OPtion for the different types of flexibility possible for this molecule: rigid body, free atoms + restraints, torsion angles... More...
RefObjOpt	mFlipModel
RefObjOpt	mAutoOptimizeConformation
	Option to automatically optimize the starting conformation, if the total restraint cost is too high. More...
RefObjOpt	mOptimizeOrientation
	Option to optimize the Molecule's orientation. More...
RefObjOpt	mMoleculeCenter
	Option to choose the center of rotation of the Molecule for the global orientation either as the geometrical center, or as a given atom.
const MolAtom *	mpCenterAtom
	Atom chosen as center of rotation, if mRotationCenter is set to use an atom rather than the geometrical center.
map< MolAtom *, set< MolAtom * > >	mConnectivityTable
	Connectivity table: for each atom, keep the list of atoms bonded to it. More...
list< RotorGroup >	mvRotorGroupTorsion
	List of RotorGroups corresponding to free torsion bonds. More...
list< RotorGroup >	mvRotorGroupTorsionSingleChain
	List of RotorGroups corresponding to free torsion bonds, but with only one chain of atoms listed. More...
list< RotorGroup >	mvRotorGroupInternal
	List of RotorGroups for internal rotations. More...
list< FlipGroup >	mvFlipGroup
	The list of FlipGroups.
list< StretchModeBondLength >	mvStretchModeBondLength
	List of StretchModeBondLength.
list< StretchModeBondAngle >	mvStretchModeBondAngle
	List of StretchModeBondLength.
list< StretchModeTorsion >	mvStretchModeTorsion
	List of StretchModeBondLength.
list< StretchModeTwist >	mvStretchModeTwist
	List of StretchModeTwist.
std::list< StretchMode * >	mvpStretchModeFree
	Groups of StretchMode not breaking any restraint (unless the one they are associated to)
std::list< StretchMode * >	mvpStretchModeNotFree
	Groups of StretchMode breaking restraints (beyond the one they are associated to)
list< MDAtomGroup >	mvMDAtomGroup
	Groups of atoms that should be moved according to molecular dynamics principles.
std::set< MolAtom * >	mvMDFullAtomGroup
	Full list of atoms that can be moved using molecular dynamics This excludes any atom part of a rigid group.
REAL	mMDMoveFreq
	Frequency of using molecular dynamics move during GlobalOptRandomMove()
REAL	mMDMoveEnergy
	Relative energy of molecule during molecular dynamics move Default: 40, 10 (slow conformation change), 200 (large changes)
std::vector< MolZAtom >	mAsZMatrix
	The Molecule, as a lightweight ZMatrix, for export purposes.
REAL	mLogLikelihood
	The current log(likelihood)
REAL	mLogLikelihoodScale
	Scale (multiplier) for the log(likelihood) More...
CrystVector_REAL	mLSQCalc
	Current LSQ Calc - one value for each restraint (bond distance, angle or dihedral angle)
CrystVector_REAL	mLSQObs
	Current LSQ Calc - one value for each restraint (bond distance, angle or dihedral angle ideal values)
CrystVector_REAL	mLSQWeight
	Current LSQ Calc - one value for each restraint(bond distance, angle or dihedral angle sigmas)

Additional Inherited Members
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::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

Molecule : class for complex scatterer descriptions using cartesian coordinates with bond length/angle restraints, and moves either of individual atoms or using torsion bonds.

This can also be used for non-organic compounds (polyhedras etc...)

Note

the parametrization is very different from ZScatterer: we keep a list of x,y,z which do not use limits (they must not), but the coordinates must be restrained or constrained from the expected bond lengths, angles and dihedral angles. The list of parameters is re-created in BeginOptimization() (except for the global x y z parameters for the global position of the Molecule, in fractionnal coordinates).

: all atoms must be somehow connected

Definition at line 731 of file Molecule.h.

Constructor & Destructor Documentation

ObjCryst::Molecule::Molecule	(	Crystal &	cryst,
		const string &	name = ""
	)

Constructor.

Definition at line 1894 of file Molecule.cpp.

ObjCryst::Molecule::Molecule

(

const Molecule &

old

)

Copy constructor.

Definition at line 1982 of file Molecule.cpp.

ObjCryst::Molecule::~Molecule

(

)

Destructor.

Definition at line 2075 of file Molecule.cpp.

Member Function Documentation

void ObjCryst::Molecule::AddAtom	(	const REAL	x,
		const REAL	y,
		const REAL	z,
		const ScatteringPower *	pPow,
		const string &	name,
		const bool	updateDisplay = true
	)

Add an atom.

Definition at line 3786 of file Molecule.cpp.

void ObjCryst::Molecule::AddBond	(	MolAtom &	atom1,
		MolAtom &	atom2,
		const REAL	length,
		const REAL	sigma,
		const REAL	delta,
		const REAL	bondOrder = 1.,
		const bool	updateDisplay = true
	)

Add a bond.

Definition at line 3923 of file Molecule.cpp.

void ObjCryst::Molecule::AddBondAngle	(	MolAtom &	atom1,
		MolAtom &	atom2,
		MolAtom &	atom3,
		const REAL	angle,
		const REAL	sigma,
		const REAL	delta,
		const bool	updateDisplay = true
	)

Add a bond angle restraint.

Definition at line 3976 of file Molecule.cpp.

void ObjCryst::Molecule::AddDihedralAngle	(	MolAtom &	atom1,
		MolAtom &	atom2,
		MolAtom &	atom3,
		MolAtom &	atom4,
		const REAL	angle,
		const REAL	sigma,
		const REAL	delta,
		const bool	updateDisplay = true
	)

Add a dihedral angle restraint.

Definition at line 4022 of file Molecule.cpp.

void ObjCryst::Molecule::AddRigidGroup	(	const RigidGroup &	group,
		const bool	updateDisplay = true
	)

Add a rigid group of atoms.

See Molecule::mvRigidGroup

Definition at line 4073 of file Molecule.cpp.

const vector< MolZAtom > & ObjCryst::Molecule::AsZMatrix

(

const bool

keeporder

)

const

Molecule as Z-matrix.

Parameters

keeporder

if true, the order of the atoms is exactly the same as in the Molecule.

Definition at line 5116 of file Molecule.cpp.

void ObjCryst::Molecule::BeginOptimization ( const bool  allowApproximations = false, const bool  enableRestraints = false  )

virtual

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

This will also check that everything is ready, eg call the RefinableObj::Prepare() function. This also affects all sub-objects.

Note

this may be called several time for some objects which are used by several other objects, or for nested optimizations (e.g. least-squares optimizations inside a global one).

EndOptimization() must be called at the end of the optimization, the same number of time BeginOptimization() was called !

Parameters

allowApproximations	if true, then the object can use faster but less precise functions during the optimization. This is useful for global optimization not using derivatives.
enableRestraints	xrefitem deprecated 28.

Reimplemented from ObjCryst::RefinableObj.

Definition at line 2385 of file Molecule.cpp.

REAL ObjCryst::Molecule::BondAngleRandomChange	(	const StretchModeBondAngle &	mode,
		const REAL	amplitude,
		const bool	respectRestraint = true
	)

change a bond angle, while respecting the Restraint (if any).

Returns

the actual change in bond angle.

Parameters

the desired angular change. This will be the actual change if there is no restraint or if the restraint is constant in this range.

Definition at line 4931 of file Molecule.cpp.

REAL ObjCryst::Molecule::BondLengthRandomChange	(	const StretchModeBondLength &	mode,
		const REAL	amplitude,
		const bool	respectRestraint = true
	)

Stretch a bond, while respecting the Restraint (if any).

Returns

the actual change in bond length.

Parameters

the desired change in bond length. This will be the actual change if there is no restraint or if the restraint is constant in this range.

Definition at line 4887 of file Molecule.cpp.

void ObjCryst::Molecule::BuildConnectivityTable

(

)

const

Build the Connectivity table.

Definition at line 5299 of file Molecule.cpp.

void ObjCryst::Molecule::BuildFlipGroup

(

)

Build the groups of atoms that can be flipped.

This is not const because we temporarily modify the molecule conformation to test which FlipGroups are forbidden by restraints (but it should be const).

Definition at line 7040 of file Molecule.cpp.

void ObjCryst::Molecule::BuildMDAtomGroups

(

)

Find groups of atoms that cannot be moved relatively to each other using the free or non-free stretch modes.

Usually these will correspond to atoms inside a flexible ring.

These atoms (if they are not in a rigid group) are stored in a MDAtomGroup so that they can still move using molecular dynamics.

this should be called after BuildStretchModeGroups(), to make sure the list of free/non-free stretch mode has been built.

Definition at line 7368 of file Molecule.cpp.

void ObjCryst::Molecule::BuildRingList

(

)

Build the list of rings in the molecule.

The list is only rebuilt if the bond or atom list has changed,so it should be safe to call again this function.

Note

So far this is a const method as the ring list just reflects the bond list and therefore is mutable (see Molecule::mvRing)... but maybe this could change...

Definition at line 5259 of file Molecule.cpp.

void ObjCryst::Molecule::BuildRotorGroup

(

)

Build the groups of atoms that will be rotated during global optimization.

This is not const because we temporarily modify the molecule conformation to test which RotorGroups are forbidden by restraints (but it should be const).

Definition at line 5337 of file Molecule.cpp.

void ObjCryst::Molecule::BuildStretchModeGroups

(

)

Separate StretchMode that break more than their assigned restraint from others.

See Molecule::mvpStretchModeFree and Molecule::mvpStretchModeNotFree

Definition at line 7213 of file Molecule.cpp.

void ObjCryst::Molecule::BuildStretchModeTwist

(

)

Build the groups of atoms used to twist internally the Molecule, e.g.

by rotating one chain of atoms between 2 given atoms.

Definition at line 6595 of file Molecule.cpp.

Molecule * ObjCryst::Molecule::CreateCopy ( ) const

virtual

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

Implements ObjCryst::Scatterer.

Definition at line 2100 of file Molecule.cpp.

REAL ObjCryst::Molecule::DihedralAngleRandomChange	(	const StretchModeTorsion &	mode,
		const REAL	amplitude,
		const bool	respectRestraint = true
	)

Change a dihedral angle, while respecting the Restraint (if any).

Returns

the actual change in bond angle.

Parameters

the desired angular change. This will be the actual change if there is no restraint or if the restraint is constant in this range.

Definition at line 4988 of file Molecule.cpp.

void ObjCryst::Molecule::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 2512 of file Molecule.cpp.

vector< MolAtom * >::reverse_iterator ObjCryst::Molecule::FindAtom

(

const string &

name

)

Search a MolAtom from its name.

Search begins at the end, and the first match is returned. returns mvAtom.rend() if no atom matches

Definition at line 7630 of file Molecule.cpp.

vector< MolAtom * >::const_reverse_iterator ObjCryst::Molecule::FindAtom

(

const string &

name

)

const

Search a MolAtom from its name.

Search begins at the end, and the first match is returned. returns mvAtom.rend() if no atom matches

Definition at line 7643 of file Molecule.cpp.

vector< MolBond * >::const_iterator ObjCryst::Molecule::FindBond	(	const MolAtom &	at1,
		const MolAtom &	at2
	)		const

Searches whether a bond between two atoms already exists.

If no bond is found, returns Molecule::mvpAtom.end().

Definition at line 3955 of file Molecule.cpp.

vector< MolBond * >::iterator ObjCryst::Molecule::FindBond	(	const MolAtom &	at1,
		const MolAtom &	at2
	)

Searches whether a bond between two atoms already exists.

If no bond is found, returns Molecule::mvpAtom.end().

Definition at line 3965 of file Molecule.cpp.

vector< MolBondAngle * >::const_iterator ObjCryst::Molecule::FindBondAngle	(	const MolAtom &	at1,
		const MolAtom &	at0,
		const MolAtom &	at2
	)		const

Searches whether a bond between three atoms already exists, searching for either (at1,at2,at3) and (at3,at2,at1), as these are equivalent.

If no bond angle is found, returns Molecule::mvpBondAngle.end().

Definition at line 4007 of file Molecule.cpp.

vector< MolDihedralAngle * >::const_iterator ObjCryst::Molecule::FindDihedralAngle	(	const MolAtom &	at1,
		const MolAtom &	at2,
		const MolAtom &	at3,
		const MolAtom &	at4
	)		const

Searches whether a dihedral between four atoms already exists, searching for either (at1,at2,at3,at4) and (at4,at3,at2,at1), as these are equivalent.

If no dihedral angle is found, returns Molecule::mvpDihedralAngle.end().

Definition at line 4056 of file Molecule.cpp.

const MolAtom * ObjCryst::Molecule::GetCenterAtom

(

)

const

Get the atom defining the origin of the Molecule Equal to 0 if no atom as been set.

Definition at line 5029 of file Molecule.cpp.

const string & ObjCryst::Molecule::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 2106 of file Molecule.cpp.

string ObjCryst::Molecule::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 3183 of file Molecule.cpp.

REAL ObjCryst::Molecule::GetLogLikelihood ( ) const

virtual

Get -log(likelihood) of the current configuration for the object.

By default (no likelihood evaluation available), this is equal to 0.

This call should not be recursive, it is the task of the algorithm to get the sum of likelihoods for all objects invlolved.

Note

contrary to the old "Cost Function" approach, with log(Likelihood) there is no 'choice' of cost function, so that it is the task of the object to give the optimized likelihood (possibly with user options).

Reimplemented from ObjCryst::RefinableObj.

Definition at line 3058 of file Molecule.cpp.

const CrystVector_REAL & ObjCryst::Molecule::GetLSQDeriv ( const unsigned int  n, RefinablePar &  par  )

virtual

Get the first derivative values for the LSQ function, for a given parameter.

Note that the default method in the base RefinableObj class is to use numerical derivatives, so it should be overridden for better precision.

Todo:

This should be a const method, and the given RefPar should be const too...

Reimplemented from ObjCryst::RefinableObj.

Definition at line 3118 of file Molecule.cpp.

const std::vector< RigidGroup * > & ObjCryst::Molecule::GetRigidGroupList

(

)

const

List of rigid group of atoms.

See Molecule::mvRigidGroup

Definition at line 4394 of file Molecule.cpp.

std::vector< RigidGroup * > & ObjCryst::Molecule::GetRigidGroupList

(

)

List of rigid group of atoms.

See Molecule::mvRigidGroup

Definition at line 4395 of file Molecule.cpp.

const ScatteringComponentList & ObjCryst::Molecule::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 3175 of file Molecule.cpp.

void ObjCryst::Molecule::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 3398 of file Molecule.cpp.

void ObjCryst::Molecule::GlobalOptRandomMove ( const REAL  mutationAmplitude, const RefParType *  type  )

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 2652 of file Molecule.cpp.

void ObjCryst::Molecule::InitRefParList ( )

virtual

Prepare refinable parameters for the scatterer object

Implements ObjCryst::Scatterer.

Definition at line 5208 of file Molecule.cpp.

void ObjCryst::Molecule::MolecularDynamicsEvolve	(	std::map< MolAtom *, XYZ > &	v0,
		const unsigned	nbStep,
		const REAL	dt,
		const std::vector< MolBond * > &	vb,
		const std::vector< MolBondAngle * > &	va,
		const std::vector< MolDihedralAngle * > &	vd,
		std::map< RigidGroup *, std::pair< XYZ, XYZ > > &	vr,
		REAL	nrj0 = 0
	)

Change the conformation of the molecule using molecular dynamics principles.

Optionnally, move only a subgroup of atoms and only take into account some restraints.

The atoms actually moved are those included as keys in v0, and those part of the rigid bodies in vr.

Parameters

v0	initial speed of all atoms. On return, includes the new speed coordinates. Only the atoms used as keys in v0 will be moved, so this should be used to work only on a subgroup of atoms.
nbStep	number of steps to perform.
dt	time step. Recommended value are such that v0[].xyz * dt = 0.001
vb,va,vd	vector of bond, bond angle and dihedral angle restraints to be taken into account. If these are empty, the full list of restraints of the Molecule are taken into account, including rigid groups. If they are not empty, then it is assumed that no atom moved belongs to a rigid group.
vr	initial speed for the angular and translation parameters of rigid groups included in the evolution. For each entry of the map the first XYZ coordinates are the speed for RigidGroup::mX,mY,mZ, and the second are the speed for the angular coordinates of the quaternion Q1,Q2,Q3
nrj0	the total energy the system should try to maintain. If equal to 0, the initial energy will be used. The speed will be de/increased to compensate any energy change.

Definition at line 4278 of file Molecule.cpp.

void ObjCryst::Molecule::OptimizeConformation	(	const long	nbTrial = 10000,
		const REAL	stopCost = 0.
	)

Minimize configuration from internal restraints (bond lengths, angles and dihedral angles).

Useful when adding manually atoms to get an initial reasonable configuration.

Definition at line 4184 of file Molecule.cpp.

void ObjCryst::Molecule::OptimizeConformationSteepestDescent	(	const REAL	maxStep = 0.1,
		const unsigned	nbStep = 1
	)

Optimize the conformation from internal restraints (bond lengths, angles and dihedral angles), using a steepest descent algorithm.

Parameters

maxStep	maximum displacement allowed along any coordinate for all atoms.
nbStep	number of steps - the gradient is re-calculated after each step.

Definition at line 4202 of file Molecule.cpp.

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

virtual

Output a description of the scatterer for POVRay. This should only be called by the Crystal Object to which belongs this scatterer.

Implements ObjCryst::Scatterer.

Definition at line 3189 of file Molecule.cpp.

void ObjCryst::Molecule::RandomizeConfiguration ( )

virtual

Randomize Configuration (before a global optimization).

This Affects only parameters which are limited and not fixed. The randomization also affects all sub-objects (recursive).

Reimplemented from ObjCryst::RefinableObj.

Definition at line 2539 of file Molecule.cpp.

vector< MolAtom * >::iterator ObjCryst::Molecule::RemoveAtom	(	MolAtom &	atom,
		const bool	del = true
	)

Remove an atom.

Returns the iterator to the next atom in the list.

This also removes all corresponding bonds, bond angles, etc... If del is true (default), then the MolAtom object is deleted. The del flag gets sent to the RemoveXXX functions for the corresponding objects.

Definition at line 3842 of file Molecule.cpp.

vector< MolBond * >::iterator ObjCryst::Molecule::RemoveBond	(	const MolBond &	bond,
		const bool	del = true
	)

Remove a bond.

Returns the iterator to the next bond in the list.

If del is true (default), then the MolBond object is deleted.

Definition at line 3936 of file Molecule.cpp.

vector< MolBondAngle * >::iterator ObjCryst::Molecule::RemoveBondAngle	(	const MolBondAngle &	angle,
		const bool	del = true
	)

Remove a BondAngle.

If del is true (default), then the MolBondAngle object is deleted.

Definition at line 3988 of file Molecule.cpp.

vector< MolDihedralAngle * >::iterator ObjCryst::Molecule::RemoveDihedralAngle	(	const MolDihedralAngle &	angle,
		const bool	del = true
	)

Remove a dihedral angle.

If del is true (default), then the MolDihedralAngle object is deleted.

Definition at line 4036 of file Molecule.cpp.

vector< RigidGroup * >::iterator ObjCryst::Molecule::RemoveRigidGroup	(	const RigidGroup &	group,
		const bool	updateDisplay = true,
		const bool	del = true
	)

Remove a rigid group of atoms.

See Molecule::mvRigidGroup

If del is true (default), then the RigidGroup object is deleted.

Definition at line 4153 of file Molecule.cpp.

void ObjCryst::Molecule::ResetRigidGroupsPar

(

)

const

Set the orientation & translation parameters of all rigid groups to 0, after correcting the atomic positions.

This is required before saving the structure, as these parameters are not saved.

Definition at line 7806 of file Molecule.cpp.

void ObjCryst::Molecule::RigidifyWithDihedralAngles

(

)

Add dihedral angles so as to rigidify the Molecule.

In practice, for every sequence of atoms A-B-C-D, add the dihedral angle defined by these 4 atoms, unless either ABC or BCD are aligned (angle below 10�).

No duplicate dihedral angle is generated.

Definition at line 4589 of file Molecule.cpp.

void ObjCryst::Molecule::RotateAtomGroup	(	const MolAtom &	at1,
		const MolAtom &	at2,
		const set< MolAtom * > &	atoms,
		const REAL	angle,
		const bool	keepCenter = true
	)

Rotate a group of atoms around an axis defined by two atoms.

Parameters

keepCenter

if true, the coordinates of the molecule are modified so that only the rotated atoms are moved.

Definition at line 4397 of file Molecule.cpp.

void ObjCryst::Molecule::RotateAtomGroup	(	const MolAtom &	at,
		const REAL	vx,
		const REAL	vy,
		const REAL	vz,
		const set< MolAtom * > &	atoms,
		const REAL	angle,
		const bool	keepCenter = true
	)

Rotate a group of atoms around an axis defined by one atom and a vector.

Parameters

keepCenter

if true, the coordinates of the molecule are modified so that only the rotated atoms are moved.

Definition at line 4406 of file Molecule.cpp.

void ObjCryst::Molecule::SetCenterAtom

(

const MolAtom &

at

)

Get the atom defining the origin of the Molecule Equal to 0 if no atom as been set.

Definition at line 5034 of file Molecule.cpp.

void ObjCryst::Molecule::SetDeleteSubObjInDestructor

(

const bool

b

)

Set whether to delete the MolAtoms, MolBonds, MolBondAngles and MolDihedralAngles in the destructor.

By default these sub-objects are deleted.

Definition at line 7802 of file Molecule.cpp.

void ObjCryst::Molecule::TagNewBestConfig ( ) const

virtual

During a global optimization, tells the object that the current config is the latest "best" config.

This can be used by the object to make more intellingent random moves (use with caution: highly experimental !).

Reimplemented from ObjCryst::RefinableObj.

Definition at line 3124 of file Molecule.cpp.

void ObjCryst::Molecule::TranslateAtomGroup	(	const set< MolAtom * > &	atoms,
		const REAL	dx,
		const REAL	dy,
		const REAL	dz,
		const bool	keepCenter = true
	)

Translate a group of atoms in a given direction.

Parameters

keepCenter

if true, the coordinates of the molecule are modified so that only the translated atoms are moved.

Definition at line 4499 of file Molecule.cpp.

void ObjCryst::Molecule::TuneGlobalOptimRotationAmplitude

(

)

Tune the rotation amplitude for free torsions and for the overall Molecule Rotation.

This should be done after Molecule::BuildRotorGroup();

Definition at line 6861 of file Molecule.cpp.

void ObjCryst::Molecule::UpdateDisplay ( ) const

virtual

If there is an interface, this should be automatically be called each time there is a 'new, significant' configuration to report.

Reimplemented from ObjCryst::RefinableObj.

Definition at line 2379 of file Molecule.cpp.

void ObjCryst::Molecule::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 2267 of file Molecule.cpp.

void ObjCryst::Molecule::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 2167 of file Molecule.cpp.

Member Data Documentation

RefObjOpt ObjCryst::Molecule::mAutoOptimizeConformation

Option to automatically optimize the starting conformation, if the total restraint cost is too high.

This is done in BeginOptimization().

This is enabled by default, and should be disabled by people who already supply a good starting conformation for their molecule.

Definition at line 1211 of file Molecule.h.

map<MolAtom *,set<MolAtom *> > ObjCryst::Molecule::mConnectivityTable

mutable

Connectivity table: for each atom, keep the list of atoms bonded to it.

All atoms are referenced from their index.

Definition at line 1230 of file Molecule.h.

bool ObjCryst::Molecule::mDeleteSubObjInDestructor

Base Rotation amplitude (in radians) for the Molecule, so that the average atomic displacement is equal to 0.1 A.

Default=0.02*pi

Definition at line 1169 of file Molecule.h.

RefObjOpt ObjCryst::Molecule::mFlexModel

OPtion for the different types of flexibility possible for this molecule: rigid body, free atoms + restraints, torsion angles...

Warning

still EXPERIMENTAL !

Definition at line 1201 of file Molecule.h.

REAL ObjCryst::Molecule::mLogLikelihoodScale

Scale (multiplier) for the log(likelihood)

Changing this scale is equivalent to changing the sigma values of all bonds, bond angles and dihedral angles - but it allows a simple global scaling for the user.

Definition at line 1366 of file Molecule.h.

RefObjOpt ObjCryst::Molecule::mOptimizeOrientation

Option to optimize the Molecule's orientation.

Useful to completely fix the Molecule.

Definition at line 1216 of file Molecule.h.

Quaternion ObjCryst::Molecule::mQuat

The unit quaternion defining the orientation.

Definition at line 1160 of file Molecule.h.

ScatteringComponentList ObjCryst::Molecule::mScattCompList

mutable

The list of scattering components.

this is mutable since it only reflects the list of atoms.

Definition at line 1123 of file Molecule.h.

map<MolAtom* , std::vector<MolBond*> > ObjCryst::Molecule::mvAtomBond

List of Bonds for each atom.

This duplicates the information in Molecule::mvBond

Definition at line 1146 of file Molecule.h.

vector<MolAtom*> ObjCryst::Molecule::mvpAtom

The list of atoms.

Definition at line 1129 of file Molecule.h.

vector<MolBond*> ObjCryst::Molecule::mvpBond

The list of bonds.

Definition at line 1133 of file Molecule.h.

vector<MolBondAngle*> ObjCryst::Molecule::mvpBondAngle

The list of bond angles.

Definition at line 1137 of file Molecule.h.

vector<MolDihedralAngle*> ObjCryst::Molecule::mvpDihedralAngle

The list of dihedral angles.

Definition at line 1141 of file Molecule.h.

std::vector<RigidGroup*> ObjCryst::Molecule::mvRigidGroup

Rigid groups of atoms.

This group will be kept strictly rigid, preventing the use of any stretch mode altering their relative position. The entire group of atoms can however be rotated or translated.

Definition at line 1151 of file Molecule.h.

list<MolRing> ObjCryst::Molecule::mvRing

mutable

The list of rings.

Note

this only reflects the bond list, so it is mutable.

Definition at line 1156 of file Molecule.h.

list<RotorGroup> ObjCryst::Molecule::mvRotorGroupInternal

mutable

List of RotorGroups for internal rotations.

This lists groups of atoms that can be rotated between two given atoms. This is useful to alter the conformation of large rings, where no free torsion bonds exists, and also for long flexible chains.

Definition at line 1276 of file Molecule.h.

list<RotorGroup> ObjCryst::Molecule::mvRotorGroupTorsion

mutable

List of RotorGroups corresponding to free torsion bonds.

In this list are list of atoms on one side of a bond, that can be rotated freely around this bond. Each bond is listed only once, with the side which has the smallest number of atoms.

Definition at line 1261 of file Molecule.h.

list<RotorGroup> ObjCryst::Molecule::mvRotorGroupTorsionSingleChain

mutable

List of RotorGroups corresponding to free torsion bonds, but with only one chain of atoms listed.

The difference with Molecule::mRotorGroupTorsion is that if the bond is A-B, with atom A linked with atoms A1,A2,A3, in this list only one chain (starting either from A1, A2 or A3) will be rotated, instead of the 3 chains. This is useful when searching for the absolute configuration of atoms.

Definition at line 1270 of file Molecule.h.

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

• Molecule.h
• Molecule.cpp