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:

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Collaboration diagram for ObjCryst::Molecule:

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List of all members.

Public Member Functions

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

Constructor.

Molecule (const Molecule &old)

Copy constructor.

~Molecule ()

Destructor.

virtual Molecule * CreateCopy () const

virtual const string & GetClassName () const

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

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.

virtual void XMLInput (istream &is, const XMLCrystTag &tag)

Input From stream.

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.

virtual void RandomizeConfiguration ()

Randomize Configuration (before a global optimization).

virtual void GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type)

Make a random move of the current configuration.

virtual REAL GetLogLikelihood () const

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

virtual void TagNewBestConfig () const

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

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.

virtual string GetComponentName (const int i) const

Name for the i-th component of this scatterer.

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

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

Add an atom.

vector< MolAtom * >::iterator RemoveAtom (MolAtom &)

Remove an atom.

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.

vector< MolBond * >::iterator RemoveBond (const MolBond &)

Remove a bond.

vector< MolBond * >::const_iterator FindBond (const MolAtom &, const MolAtom &) const

Searches whether a bond between two atoms already exists.

vector< MolBond * >::iterator FindBond (const MolAtom &, const MolAtom &)

Searches whether a bond between two atoms already exists.

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.

vector< MolBondAngle * >::iterator RemoveBondAngle (const MolBondAngle &)

Remove a BondAngle.

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.

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.

vector< MolDihedralAngle * >
::iterator RemoveDihedralAngle (const MolDihedralAngle &)

Remove a dihedral angle.

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.

void AddRigidGroup (const RigidGroup &, const bool updateDisplay=true)

Add a rigid group of atoms.

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

Remove a rigid group of atoms.

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.

vector< MolAtom * >
::const_reverse_iterator FindAtom (const string &name) const

Search a MolAtom from its name.

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

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

const vector< MolAtom * > & GetAtomList () const

const vector< MolBond * > & GetBondList () const

const vector< MolBondAngle * > & GetBondAngleList () const

const vector< MolDihedralAngle * > & GetDihedralAngleList () const

vector< MolAtom * > & GetAtomList ()

vector< MolBond * > & GetBondList ()

vector< MolBondAngle * > & GetBondAngleList ()

vector< MolDihedralAngle * > & GetDihedralAngleList ()

list< StretchModeBondLength > & GetStretchModeBondLengthList ()

list< StretchModeBondAngle > & GetStretchModeBondAngleList ()

list< StretchModeTorsion > & GetStretchModeTorsionList ()

const list
< StretchModeBondLength > & GetStretchModeBondLengthList () const

const list
< StretchModeBondAngle > & GetStretchModeBondAngleList () const

const list< StretchModeTorsion > & GetStretchModeTorsionList () const

const std::vector< RigidGroup * > & GetRigidGroupList () const

List of rigid group of atoms.

std::vector< RigidGroup * > & GetRigidGroupList ()

List of rigid group of atoms.

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.

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.

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.

void RestraintStatus (ostream &os) const

Print the status of all restraints (bond length, angles...).

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.

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

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

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

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

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

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

const MolAtom * GetCenterAtom () const

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

void SetCenterAtom (const MolAtom &at)

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

const std::vector< MolZAtom > & AsZMatrix (const bool keeporder) const

Molecule as Z-matrix.

virtual void InitRefParList ()

void BuildRingList ()

Build the list of rings in the molecule.

void BuildConnectivityTable () const

Build the Connectivity table.

void BuildRotorGroup ()

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

void TuneGlobalOptimRotationAmplitude ()

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

void BuildFlipGroup ()

Build the groups of atoms that can be flipped.

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.

void BuildStretchModeGroups ()

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

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 FlipAtomGroup (const FlipGroup &)

Flip a group of atom. See Molecule::FlipGroup.

Public Attributes

ScatteringComponentList mScattCompList

The list of scattering components.

vector< MolAtom * > mvpAtom

The list of atoms.

vector< MolBond * > mvpBond

The list of bonds.

vector< MolBondAngle * > mvpBondAngle

The list of bond angles.

vector< MolDihedralAngle * > mvpDihedralAngle

The list of dihedral angles.

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

List of Bonds for each atom.

std::vector< RigidGroup * > mvRigidGroup

Rigid groups of atoms.

list< MolRing > mvRing

The list of rings.

Quaternion mQuat

The unit quaternion defining the orientation.

REAL mBaseRotationAmplitude

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

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

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.

RefObjOpt mAutoOptimizeConformation

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

RefObjOpt mOptimizeOrientation

Option to optimize the Molecule's orientation.

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.

list< RotorGroup > mvRotorGroupTorsion

List of RotorGroups corresponding to free torsion bonds.

list< RotorGroup > mvRotorGroupTorsionSingleChain

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

list< RotorGroup > mvRotorGroupInternal

List of RotorGroups for internal rotations.

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).

std::vector< MolZAtom > mAsZMatrix

The Molecule, as a lightweight ZMatrix, for export purposes.

REAL mLogLikelihood

The current log(likelihood).

Classes

struct FlipGroup

When 3(A1. 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...

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 646 of file Molecule.h.

Constructor & Destructor Documentation

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

Constructor.

Definition at line 1601 of file Molecule.cpp.

ObjCryst::Molecule::Molecule ( const Molecule & old )

Copy constructor.

Definition at line 1680 of file Molecule.cpp.

ObjCryst::Molecule::~Molecule ( )

Destructor.

Definition at line 1765 of file Molecule.cpp.

Member Function Documentation

Molecule * ObjCryst::Molecule::CreateCopy ( ) const [virtual]

For internal use only.

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

Implements ObjCryst::Scatterer.

Definition at line 1787 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 1793 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 1805 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 1882 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.

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,:	if true, then restrained parameters will be allowed to go beyond theur hard limits. This implies that the algorithm will take into account the cost (penalty) related to the restraints. Objects which do not use restraints will simply ignore this. WARNING: this parameter may be removed with the new likelihood scheme.

Reimplemented from ObjCryst::RefinableObj.

Definition at line 1982 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 2021 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 2082 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).

Warning:: : this is in under heavy development, so expect changes...

Reimplemented from ObjCryst::RefinableObj.

Definition at line 2304 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 2317 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 2350 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 2358 of file Molecule.cpp.

ostream & ObjCryst::Molecule::POVRayDescription	(	ostream &	os,
		const CrystalPOVRayOptions &	options
	)			const `[virtual]`

For internal use only.

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 2364 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 `[virtual]`

For internal use only.

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).

Implements ObjCryst::Scatterer.

Definition at line 2534 of file Molecule.cpp.

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 2835 of file Molecule.cpp.

vector< MolAtom * >::iterator ObjCryst::Molecule::RemoveAtom ( MolAtom & atom )

Remove an atom.

Returns the iterator to the next atom in the list.

This also removes all corresponding bonds, bond angles, etc...

Definition at line 2874 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 2926 of file Molecule.cpp.

vector< MolBond * >::iterator ObjCryst::Molecule::RemoveBond ( const MolBond & bond )

Remove a bond.

Returns the iterator to the next bond in the list.

Definition at line 2939 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 2958 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 2968 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 2979 of file Molecule.cpp.

vector< MolBondAngle * >::iterator ObjCryst::Molecule::RemoveBondAngle ( const MolBondAngle & angle )

Remove a BondAngle.

Definition at line 2991 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 3010 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 3025 of file Molecule.cpp.

vector< MolDihedralAngle * >::iterator ObjCryst::Molecule::RemoveDihedralAngle ( const MolDihedralAngle & angle )

Remove a dihedral angle.

Definition at line 3039 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 3059 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 3076 of file Molecule.cpp.

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

Remove a rigid group of atoms.

See Molecule::mvRigidGroup

Definition at line 3085 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 6050 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 6063 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 3103 of file Molecule.cpp.

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

List of rigid group of atoms.

See Molecule::mvRigidGroup

Definition at line 3139 of file Molecule.cpp.

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

List of rigid group of atoms.

See Molecule::mvRigidGroup

Definition at line 3140 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 t


Public Member Functions
	Molecule (Crystal &cryst, const string &name="")
	Constructor.
	Molecule (const Molecule &old)
	Copy constructor.
	~Molecule ()
	Destructor.
virtual Molecule *	CreateCopy () const
virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",.
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.
virtual void	XMLInput (istream &is, const XMLCrystTag &tag)
	Input From stream.
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.
virtual void	RandomizeConfiguration ()
	Randomize Configuration (before a global optimization).
virtual void	GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type)
	Make a random move of the current configuration.
virtual REAL	GetLogLikelihood () const
	Get -log(likelihood) of the current configuration for the object.
virtual void	TagNewBestConfig () const
	During a global optimization, tells the object that the current config is the latest "best" config.
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.
virtual string	GetComponentName (const int i) const
	Name for the i-th component of this scatterer.
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
void	AddAtom (const REAL x, const REAL y, const REAL z, const ScatteringPower *pPow, const string &name, const bool updateDisplay=true)
	Add an atom.
vector< MolAtom * >::iterator	RemoveAtom (MolAtom &)
	Remove an atom.
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.
vector< MolBond * >::iterator	RemoveBond (const MolBond &)
	Remove a bond.
vector< MolBond * >::const_iterator	FindBond (const MolAtom &, const MolAtom &) const
	Searches whether a bond between two atoms already exists.
vector< MolBond * >::iterator	FindBond (const MolAtom &, const MolAtom &)
	Searches whether a bond between two atoms already exists.
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.
vector< MolBondAngle * >::iterator	RemoveBondAngle (const MolBondAngle &)
	Remove a BondAngle.
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.
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.
vector< MolDihedralAngle * > ::iterator	RemoveDihedralAngle (const MolDihedralAngle &)
	Remove a dihedral angle.
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.
void	AddRigidGroup (const RigidGroup &, const bool updateDisplay=true)
	Add a rigid group of atoms.
std::vector< RigidGroup * > ::iterator	RemoveRigidGroup (const RigidGroup &group, const bool updateDisplay=true)
	Remove a rigid group of atoms.
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.
vector< MolAtom * > ::const_reverse_iterator	FindAtom (const string &name) const
	Search a MolAtom from its name.
void	OptimizeConformation (const long nbTrial=10000, const REAL stopCost=0.)
	Minimize configuration from internal restraints (bond lengths, angles and dihedral angles).
const vector< MolAtom * > &	GetAtomList () const
const vector< MolBond * > &	GetBondList () const
const vector< MolBondAngle * > &	GetBondAngleList () const
const vector< MolDihedralAngle * > &	GetDihedralAngleList () const
vector< MolAtom * > &	GetAtomList ()
vector< MolBond * > &	GetBondList ()
vector< MolBondAngle * > &	GetBondAngleList ()
vector< MolDihedralAngle * > &	GetDihedralAngleList ()
list< StretchModeBondLength > &	GetStretchModeBondLengthList ()
list< StretchModeBondAngle > &	GetStretchModeBondAngleList ()
list< StretchModeTorsion > &	GetStretchModeTorsionList ()
const list < StretchModeBondLength > &	GetStretchModeBondLengthList () const
const list < StretchModeBondAngle > &	GetStretchModeBondAngleList () const
const list< StretchModeTorsion > &	GetStretchModeTorsionList () const
const std::vector< RigidGroup * > &	GetRigidGroupList () const
	List of rigid group of atoms.
std::vector< RigidGroup * > &	GetRigidGroupList ()
	List of rigid group of atoms.
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.
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.
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.
void	RestraintStatus (ostream &os) const
	Print the status of all restraints (bond length, angles...).
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.
REAL	BondLengthRandomChange (const StretchModeBondLength &mode, const REAL amplitude, const bool respectRestraint=true)
	Stretch a bond, while respecting the Restraint (if any).
REAL	BondAngleRandomChange (const StretchModeBondAngle &mode, const REAL amplitude, const bool respectRestraint=true)
	change a bond angle, while respecting the Restraint (if any).
REAL	DihedralAngleRandomChange (const StretchModeTorsion &mode, const REAL amplitude, const bool respectRestraint=true)
	Change a dihedral angle, while respecting the Restraint (if any).
const MolAtom *	GetCenterAtom () const
	Get the atom defining the origin of the Molecule Equal to 0 if no atom as been set.
void	SetCenterAtom (const MolAtom &at)
	Get the atom defining the origin of the Molecule Equal to 0 if no atom as been set.
const std::vector< MolZAtom > &	AsZMatrix (const bool keeporder) const
	Molecule as Z-matrix.
virtual void	InitRefParList ()
void	BuildRingList ()
	Build the list of rings in the molecule.
void	BuildConnectivityTable () const
	Build the Connectivity table.
void	BuildRotorGroup ()
	Build the groups of atoms that will be rotated during global optimization.
void	TuneGlobalOptimRotationAmplitude ()
	Tune the rotation amplitude for free torsions and for the overall Molecule Rotation.
void	BuildFlipGroup ()
	Build the groups of atoms that can be flipped.
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.
void	BuildStretchModeGroups ()
	Separate StretchMode that break more than their assigned restraint from others.
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	FlipAtomGroup (const FlipGroup &)
	Flip a group of atom. See Molecule::FlipGroup.
Public Attributes
ScatteringComponentList	mScattCompList
	The list of scattering components.
vector< MolAtom * >	mvpAtom
	The list of atoms.
vector< MolBond * >	mvpBond
	The list of bonds.
vector< MolBondAngle * >	mvpBondAngle
	The list of bond angles.
vector< MolDihedralAngle * >	mvpDihedralAngle
	The list of dihedral angles.
map< MolAtom , std::vector < MolBond > >	mvAtomBond
	List of Bonds for each atom.
std::vector< RigidGroup * >	mvRigidGroup
	Rigid groups of atoms.
list< MolRing >	mvRing
	The list of rings.
Quaternion	mQuat
	The unit quaternion defining the orientation.
REAL	mBaseRotationAmplitude
	Base Rotation amplitude (in radians) for the Molecule, so that the average atomic displacement is equal to 0.1 A.
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
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.
RefObjOpt	mAutoOptimizeConformation
	Option to automatically optimize the starting conformation, if the total restraint cost is too high.
RefObjOpt	mOptimizeOrientation
	Option to optimize the Molecule's orientation.
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.
list< RotorGroup >	mvRotorGroupTorsion
	List of RotorGroups corresponding to free torsion bonds.
list< RotorGroup >	mvRotorGroupTorsionSingleChain
	List of RotorGroups corresponding to free torsion bonds, but with only one chain of atoms listed.
list< RotorGroup >	mvRotorGroupInternal
	List of RotorGroups for internal rotations.
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).
std::vector< MolZAtom >	mAsZMatrix
	The Molecule, as a lightweight ZMatrix, for export purposes.
REAL	mLogLikelihood
	The current log(likelihood).
Classes
struct	FlipGroup
	When 3(A1. 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...