The molecule contains all of the molecular primitives. More...

#include <avogadro/molecule.h>

Inheritance diagram for Avogadro::Molecule:

Public Slots
void	updateMolecule ()
Signals
void	moleculeChanged ()
void	primitiveAdded (Primitive *primitive)
void	primitiveUpdated (Primitive *primitive)
void	primitiveRemoved (Primitive *primitive)
void	atomAdded (Atom *atom)
void	atomUpdated (Atom *atom)
void	atomRemoved (Atom *atom)
void	bondAdded (Bond *bond)
void	bondUpdated (Bond *bond)
void	bondRemoved (Bond *bond)
Public Member Functions
	Molecule (QObject *parent=0)
	Molecule (const Molecule &other)
virtual	~Molecule ()
void	update ()
void	addHydrogens (Atom *atom=0, const QList< unsigned long > &atomIds=QList< unsigned long >(), const QList< unsigned long > &bondIds=QList< unsigned long >())
void	removeHydrogens (Atom *atom=0)
void	setDipoleMoment (const Eigen::Vector3d &moment)
Eigen::Vector3d	dipoleMoment (bool *estimate=0) const
void	calculatePartialCharges () const
void	calculateAromaticity () const
void	calculateGroupIndices () const
Bond *	bond (unsigned long id1, unsigned long id2)
Bond *	bond (const Atom , const Atom )
unsigned long	conformerSize ()
bool	addConformer (const std::vector< Eigen::Vector3d > &conformer, unsigned int index)
std::vector< Eigen::Vector3d > *	addConformer (unsigned int index)
std::vector< Eigen::Vector3d > *	conformer (unsigned int index)
const std::vector< std::vector < Eigen::Vector3d > * > &	conformers () const
bool	setConformer (unsigned int index)
bool	setAllConformers (const std::vector< std::vector< Eigen::Vector3d > * > conformers, bool deleteExisting=true)
void	clearConformers ()
unsigned int	numConformers () const
unsigned int	currentConformer () const
const std::vector< double > &	energies () const
double	energy (int index=-1) const
void	setEnergy (double energy)
void	setEnergy (int index, double energy)
void	setEnergies (const std::vector< double > &energies)
void	clear ()
QReadWriteLock *	lock () const
Molecule parameters
These methods set and get Molecule parameters.
void	setFileName (const QString &name)
QString	fileName () const
Atom properties
These functions are used to change and retrieve the properties of the Atom objects in the Molecule.
Atom *	addAtom ()
Atom *	addAtom (unsigned long id)
Atom *	addAtom (int atomicNum, const Eigen::Vector3d &pos)
Atom *	addAtom (const Atom &other)
void	removeAtom (Atom *atom)
void	removeAtom (unsigned long id)
Atom *	atom (int index) const
Atom *	atomById (unsigned long id) const
QList< Atom * >	atoms () const
void	setAtomPos (unsigned long id, const Eigen::Vector3d &vec)
void	setAtomPos (unsigned long id, const Eigen::Vector3d *vec)
const Eigen::Vector3d *	atomPos (unsigned long id) const
unsigned int	numAtoms () const
Bond properties
These functions are used to change and retrieve the properties of the Bond objects in the Molecule.
Bond *	addBond ()
Bond *	addBond (unsigned long id)
Bond *	addBond (unsigned long beginAtomId, unsigned long endAtomId, short order=1)
Bond *	addBond (Atom beginAtom, Atom endAtom, short order=1)
void	removeBond (Bond *bond)
void	removeBond (unsigned long id)
Bond *	bond (int index) const
Bond *	bondById (unsigned long id) const
QList< Bond * >	bonds () const
unsigned int	numBonds () const
Residue properties
These functions are used to change and retrieve the properties of the Residue objects in the Molecule.
Residue *	addResidue ()
Residue *	addResidue (unsigned long id)
void	removeResidue (Residue *residue)
void	removeResidue (unsigned long id)
Residue *	residue (int index)
const Residue *	residue (int index) const
Residue *	residueById (unsigned long id) const
QList< Residue * >	residues () const
unsigned int	numResidues () const
Ring properties
These functions are used to change and retrieve the properties of the Ring objects in the Molecule. Note: These should probably be generalized to Fragments, but then a convenience function to return a list of just rings would be needed.
Fragment *	addRing ()
Fragment *	addRing (unsigned long id)
void	removeRing (Fragment *ring)
void	removeRing (unsigned long id)
QList< Fragment * >	rings ()
unsigned int	numRings () const
Cube properties
These functions are used to change and retrieve the properties of the Cube objects in the Molecule.
Cube *	addCube ()
Cube *	addCube (unsigned long id)
void	removeCube (Cube *cube)
void	removeCube (unsigned long id)
Cube *	cube (int index) const
Cube *	cubeById (unsigned long id) const
QList< Cube * >	cubes () const
unsigned int	numCubes () const
Mesh properties
These functions are used to change and retrieve the properties of the Mesh objects in the Molecule.
Mesh *	addMesh ()
Mesh *	addMesh (unsigned long id)
void	removeMesh (Mesh *mesh)
void	removeMesh (unsigned long id)
Mesh *	mesh (int index) const
Mesh *	meshById (unsigned long id) const
QList< Mesh * >	meshes () const
unsigned int	numMeshes () const
ZMatrix properties
These functions are used to change and retrieve the properties of the ZMatrix objects in the Molecule.
ZMatrix *	addZMatrix ()
void	removeZMatrix (ZMatrix *zmatrix)
ZMatrix *	zMatrix (int index) const
QList< ZMatrix * >	zMatrices () const
unsigned int	numZMatrices () const
OpenBabel translation functions
These functions are used to exchange information with OpenBabel.
OpenBabel::OBMol	OBMol () const
bool	setOBMol (OpenBabel::OBMol *obmol)
OpenBabel::OBUnitCell *	OBUnitCell () const
bool	setOBUnitCell (OpenBabel::OBUnitCell *obunitcell)
Molecule geometry information and manipulation
These functions can be used to retrieve several aspects of Molecule geometry and to manipulate some aspects.
const Eigen::Vector3d	center () const
const Eigen::Vector3d	normalVector () const
double	radius () const
const Atom *	farthestAtom () const
void	translate (const Eigen::Vector3d &)
Operators
Overloaded operators.
Molecule &	operator= (const Molecule &other)
Molecule &	operator+= (const Molecule &other)
Misc.
Functions that don't neatly fit into the above categories.
PrimitiveList	copyAtomsAndBonds (const QList< Atom * > &atoms, const QList< Bond * > &bonds)
PrimitiveList	copyAtomsAndBonds (const PrimitiveList &atomsAndBonds)
Protected Member Functions
void	computeGeomInfo () const
Protected Attributes
MoleculePrivate *const	d_ptr
QString	m_fileName
std::vector< Eigen::Vector3d > *	m_atomPos
std::vector< std::vector < Eigen::Vector3d > * >	m_atomConformers
unsigned int	m_currentConformer
bool	m_estimatedDipoleMoment
Eigen::Vector3d *	m_dipoleMoment
bool	m_invalidPartialCharges
bool	m_invalidAromaticity
std::vector< Atom * >	m_atoms
std::vector< Bond * >	m_bonds
QList< Atom * >	m_atomList
QList< Bond * >	m_bondList
QReadWriteLock *	m_lock

Detailed Description

The molecule contains all of the molecular primitives.

Author:: Marcus D. Hanwell

The Molecule class contains the core data of the molecule. It is the central model, holding all information displayed by our various views and manipulated by tools and extensions. It typically contains Atom and Bond objects, but may also contain Cube, Mesh, Fragment, Residue and other objects.

Constructor & Destructor Documentation

Avogadro::Molecule::Molecule ( QObject * parent = 0 )

Constructor.

Parameters:

parent The object parent.

References QObject::connect(), QDir::homePath(), QObject::tr(), and Avogadro::Primitive::updated().

Avogadro::Molecule::Molecule ( const Molecule & other )

Copy constructor.

Parameters:

other Molecule to make a copy of.

References QObject::connect(), and Avogadro::Primitive::updated().

Avogadro::Molecule::~Molecule ( ) [virtual]

Destructor.

References QObject::blockSignals(), clear(), and QObject::disconnect().

Member Function Documentation

Atom * Avogadro::Molecule::addAtom ( )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. Create a new Atom object and return a pointer to it.

Note:: Do not delete the object, use removeAtom(Atom*).

Referenced by addAtom(), addHydrogens(), Avogadro::ZMatrix::addRow(), copyAtomsAndBonds(), operator+=(), and setOBMol().

Atom * Avogadro::Molecule::addAtom ( unsigned long id )

Create a new Atom object with the specified id and return a pointer to it. Used when you need to recreate an Atom with the same unique id.

Note:: Do not delete the object, use removeAtom(unsigned long id).

References atom(), atomAdded(), QObject::connect(), Avogadro::Primitive::id(), m_atomConformers, QList::push_back(), Avogadro::Primitive::setId(), Avogadro::Primitive::setIndex(), QList::size(), and Avogadro::Primitive::updated().

Atom * Avogadro::Molecule::addAtom	(	int	atomicNum,
		const Eigen::Vector3d &	pos
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. Create a new Atom object of the specified element at the given position, and return a pointer to it.

Parameters:

atomicNum	Atomic number
pos	Cartesian position

Note:: Do not delete the object, use removeAtom(unsigned long id).

References addAtom(), and Avogadro::Atom::m_atomicNumber.

Atom * Avogadro::Molecule::addAtom ( const Atom & other )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. Create a new Atom object and copy the Atom object other's data into it. A pointer to the new atom in this is returned.

Parameters:

other The atom to copy into the new atom

Note:: Do not delete the new object, use removeAtom(unsigned long id).

References addAtom().

Bond * Avogadro::Molecule::addBond ( )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. Create a new Bond object and return a pointer to it.

Note:: Do not delete the object, use removeBond(Bond*).

Referenced by addBond(), addHydrogens(), Avogadro::ZMatrix::addRow(), copyAtomsAndBonds(), operator+=(), Avogadro::Animation::setFrame(), and setOBMol().

Bond * Avogadro::Molecule::addBond ( unsigned long id )

Create a new Bond object with the specified id and return a pointer to it. Used when you need to recreate a Bond with the same unique id.

Note:: Do not delete the object, use removeBond(unsigned long id).

References bond(), bondAdded(), QObject::connect(), Avogadro::Primitive::id(), QList::push_back(), Avogadro::Primitive::setId(), Avogadro::Primitive::setIndex(), QList::size(), and Avogadro::Primitive::updated().

Bond * Avogadro::Molecule::addBond	(	unsigned long	beginAtomId,
		unsigned long	endAtomId,
		short	order = `1`
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. Create a new bond between two atoms of the specified order. A pointer to the new Bond is returned.

Parameters:

beginAtomId	ID of the beginning atom of the bond
endAtomId	ID of the ending atom of the bond
order	Bond order of the new bond (default 1)

Note:: Do not delete the object, use removeBond(Bond*).

References addBond(), and Avogadro::Bond::setAtoms().

Bond * Avogadro::Molecule::addBond	(	Atom *	beginAtom,
		Atom *	endAtom,
		short	order = `1`
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. Create a new bond between two atoms of the specified order. A pointer to the new Bond is returned.

Parameters:

beginAtom	Pointer to the beginning atom of the bond
endAtom	Pointer to the ending atom of the bond
order	Bond order of the new bond (default 1)

Note:: Do not delete the object, use removeBond(Bond*).; Both beginAtom and endAtom must be owned by this Molecule.

References addBond(), and Avogadro::Bond::setAtoms().

bool Avogadro::Molecule::addConformer	(	const std::vector< Eigen::Vector3d > &	conformer,
		unsigned int	index
	)

Add a new conformer to the Molecule. If the index is an already existing conformer, this conformer will be overwritten. If there is a gap between the currently last index and the new index, new conformers will be created to make sure all indexes have a valid conformer. For example, if there is only one conformer and this method is called with index 9, a total of nine conformers are added (0 existed, 1-9 are created).

Note:: Conformer atom positions are indexed by their unique id (Atom::id()). Use conformerSize() to check the current size needed to accommodate all atoms.

Parameters:

conformer	A vector of Vector3d with all atom positions.
index	The index of the conformer to add.

References conformer(), Avogadro::Primitive::index(), and m_atomConformers.

Referenced by setOBMol().

vector< Vector3d > * Avogadro::Molecule::addConformer ( unsigned int index )

Add a new conformer and return a pointer to it. If the index is an already existing conformer, no new conformer will be created and a pointer to the already existing conformer is returned. If there is a gap between the currently last index and the new index, new conformers will be created to make sure all indexes have a valid conformer. For example, if there is only one conformer and this method is called with index 9, a total of nine conformers are added (0 existed, 1-9 are created) and a pointer to the last one is returned.

Note:: Conformer atom positions are indexed by their unique id (Atom::id()). Use conformerSize() to check the current size needed to accommodate all atoms.

Parameters:

index The index of the new conformer.

Returns:: Pointer to the conformer added.

References Avogadro::Primitive::index(), and m_atomConformers.

Cube * Avogadro::Molecule::addCube ( )

Create a new Cube object and return a pointer to it.

Note:: Do not delete the object, use removeCube(unsigned long id).

Referenced by setOBMol().

Cube * Avogadro::Molecule::addCube ( unsigned long id )

Create a new Cube object with the specified id and return a pointer to it. Used when you need to recreate a Cube with the same unique id.

Note:: Do not delete the object, use removeCube(unsigned long id).

References QObject::connect(), cube(), Avogadro::Primitive::id(), primitiveAdded(), Avogadro::Primitive::setId(), Avogadro::Primitive::setIndex(), and Avogadro::Primitive::updated().

void Avogadro::Molecule::addHydrogens	(	Atom *	atom = `0`,
		const QList< unsigned long > &	atomIds = `QList<unsigned long>()`,
		const QList< unsigned long > &	bondIds = `QList<unsigned long>()`
	)

Add hydrogens to the molecule.

Parameters:

atom	If supplied only add hydrogens to the specified atom.
atomIds	Unique Atom IDs when adding hydrogens in undo/redo.
bondIds	Unique Bond IDs when adding hydrogens in undo/redo.

References addAtom(), addBond(), OpenBabel::OBMol::AddHydrogens(), QList::at(), atom(), OpenBabel::OBAtom::BeginNbrAtom(), bond(), OpenBabel::OBMol::GetAtom(), OpenBabel::OBAtom::GetAtomicNum(), OpenBabel::OBAtom::GetIdx(), OpenBabel::OBAtom::GetPartialCharge(), Avogadro::Primitive::index(), QList::isEmpty(), OpenBabel::OBAtom::IsHydrogen(), OpenBabel::OBMol::NumAtoms(), numAtoms(), OBMol(), Avogadro::Bond::setBegin(), Avogadro::Bond::setEnd(), OpenBabel::OBAtom::SetHyb(), OpenBabel::OBAtom::SetImplicitValence(), OpenBabel::OBMol::SetImplicitValencePerceived(), Avogadro::Atom::setOBAtom(), Avogadro::Atom::setPartialCharge(), and QList::size().

Mesh * Avogadro::Molecule::addMesh ( )

Create a new Mesh object and return a pointer to it.

Note:: Do not delete the object, use removeMesh(unsigned long id).

Mesh * Avogadro::Molecule::addMesh ( unsigned long id )

Create a new Mesh object with the specified id and return a pointer to it. Used when you need to recreate a Mesh with the same unique id.

Note:: Do not delete the object, use removeMesh(unsigned long id).

References QObject::connect(), Avogadro::Primitive::id(), mesh(), primitiveAdded(), Avogadro::Primitive::setId(), Avogadro::Primitive::setIndex(), and Avogadro::Primitive::updated().

Residue * Avogadro::Molecule::addResidue ( )

Create a new Residue object and return a pointer to it.

Note:: Do not delete the object, use removeResidue(Residue *residue).

Referenced by operator+=(), operator=(), and setOBMol().

Residue * Avogadro::Molecule::addResidue ( unsigned long id )

Create a new Residue object with the specified id and return a pointer to it. Used when you need to recreate a Residue with the same unique id.

Note:: Do not delete the object, use removeResidue(unsigned long id).

References QObject::connect(), Avogadro::Primitive::id(), primitiveAdded(), residue(), Avogadro::Primitive::setId(), Avogadro::Primitive::setIndex(), and Avogadro::Primitive::updated().

Fragment * Avogadro::Molecule::addRing ( )

Create a new ring object and return a pointer to it.

Note:: Do not delete the object, use removeRing(Fragment *ring).

Referenced by rings().

Fragment * Avogadro::Molecule::addRing ( unsigned long id )

Create a new Ring object with the specified id and return a pointer to it. Used when you need to recreate a Ring with the same unique id.

Note:: Do not delete the object, use removeRing(unsigned long id).

References QObject::connect(), Avogadro::Primitive::id(), Avogadro::Primitive::setId(), Avogadro::Primitive::setIndex(), and Avogadro::Primitive::updated().

ZMatrix * Avogadro::Molecule::addZMatrix ( )

Create a new ZMatrix object and return a pointer to it.

Note:: Do not delete the object, use removeZMatrix(unsigned long id).

Atom * Avogadro::Molecule::atom ( int index ) const [inline]

Returns:: The Atom at the supplied index.

Note:: Replaces GetAtom.

Referenced by addAtom(), addHydrogens(), calculateGroupIndices(), calculatePartialCharges(), clear(), Avogadro::GLWidget::computeClickedAtom(), Avogadro::GLWidget::computeClickedPrimitive(), computeGeomInfo(), dipoleMoment(), OBMol(), operator+=(), operator=(), rings(), Avogadro::Animation::setFrame(), setOBMol(), and translate().

void Avogadro::Molecule::atomAdded ( Atom * atom ) [signal]

Emitted when an Atom is added.

Parameters:

Atom	pointer to the Atom that was added.

Referenced by addAtom().

Atom * Avogadro::Molecule::atomById ( unsigned long id ) const [inline]

Returns:: The Atom at the supplied unqique id.

Referenced by Avogadro::Residue::addAtom(), Avogadro::Bond::beginAtom(), bond(), Avogadro::Bond::endAtom(), Avogadro::Bond::length(), OBMol(), operator+=(), Avogadro::Residue::removeAtom(), removeAtom(), removeHydrogens(), Avogadro::Bond::setAtoms(), Avogadro::Bond::setBegin(), Avogadro::Bond::setEnd(), and Avogadro::ZMatrix::update().

const Eigen::Vector3d * Avogadro::Molecule::atomPos ( unsigned long id ) const [inline]

Get the position vector of the supplied Atom.

Parameters:

id	Unique id of the Atom.

Returns:: Position vector of the Atom.

Referenced by Avogadro::Bond::beginPos(), Avogadro::Bond::endPos(), Avogadro::Bond::midPos(), Avogadro::Atom::OBAtom(), and Avogadro::Atom::pos().

void Avogadro::Molecule::atomRemoved ( Atom * atom ) [signal]

Emitted when an Atom is removed.

Parameters:

Atom	pointer to the Atom that was removed.

Referenced by removeAtom().

QList< Atom * > Avogadro::Molecule::atoms ( ) const

Returns:: QList of all Atom objects in the Molecule.

Referenced by Avogadro::Engine::atoms(), copyAtomsAndBonds(), dipoleMoment(), Avogadro::NeighborList::NeighborList(), Avogadro::Animation::setFrame(), Avogadro::Cube::setLimits(), and setOBMol().

void Avogadro::Molecule::atomUpdated ( Atom * atom ) [signal]

Emitted when an Atom is updated.

Parameters:

Atom	pointer to the Atom that was updated.

Referenced by translate().

Bond * Avogadro::Molecule::bond ( int index ) const [inline]

Returns:: The Bond at the supplied index.

Note:: Replaces GetBond.

Referenced by addBond(), addHydrogens(), Avogadro::Atom::bond(), bond(), calculateAromaticity(), clear(), Avogadro::GLWidget::computeClickedBond(), Avogadro::GLWidget::computeClickedPrimitive(), OBMol(), operator+=(), operator=(), removeAtom(), removeBond(), Avogadro::ZMatrix::setBond(), and setOBMol().

Bond * Avogadro::Molecule::bond	(	unsigned long	id1,
		unsigned long	id2
	)

Returns:: The bond between the two supplied atom ids if one exists, otherwise 0 is returned.

References atomById(), bond(), bondById(), Avogadro::Atom::bonds(), bonds(), and Avogadro::Bond::otherAtom().

Bond * Avogadro::Molecule::bond	(	const Atom *	a1,
		const Atom *	a2
	)

Returns:: The bond between the two supplied atom pointers if one exists, otherwise 0 is returned.

References bond(), and Avogadro::Primitive::id().

void Avogadro::Molecule::bondAdded ( Bond * bond ) [signal]

Emitted when a Bond is added.

Parameters:

Bond	pointer to the bond that was added.

Referenced by addBond().

Bond * Avogadro::Molecule::bondById ( unsigned long id ) const [inline]

Returns:: The Bond at the supplied unique id.

Referenced by bond(), Avogadro::Atom::formalCharge(), and Avogadro::Atom::neighbors().

void Avogadro::Molecule::bondRemoved ( Bond * bond ) [signal]

Emitted when a Bond is removed.

Parameters:

Bond	pointer to the Bond that was removed.

Referenced by removeBond().

QList< Bond * > Avogadro::Molecule::bonds ( ) const

Returns:: QList of all Bond objects in the Molecule.

Referenced by bond(), Avogadro::Engine::bonds(), copyAtomsAndBonds(), and Avogadro::Animation::setFrame().

void Avogadro::Molecule::bondUpdated ( Bond * bond ) [signal]

Emitted when a Bond is updated.

Parameters:

Bond	pointer to the bond that was updated.

void Avogadro::Molecule::calculateAromaticity ( ) const

Calculate the aromaticity of the bonds.

References bond(), OpenBabel::OBMol::GetBond(), OpenBabel::OBBond::IsAromatic(), OpenBabel::OBMol::NumBonds(), numBonds(), OBMol(), and Avogadro::Bond::setAromaticity().

Referenced by Avogadro::Bond::isAromatic().

void Avogadro::Molecule::calculateGroupIndices ( ) const

Calculate the indices of atoms in groups of atoms of the same element.

References QVector::at(), atom(), numAtoms(), QVector::push_back(), QVector::resize(), Avogadro::Atom::setGroupIndex(), and QVector::size().

Referenced by Avogadro::Atom::groupIndex().

void Avogadro::Molecule::calculatePartialCharges ( ) const

Calculate the partial charges on each atom.

References atom(), OpenBabel::OBMol::GetAtom(), OpenBabel::OBAtom::GetPartialCharge(), numAtoms(), OBMol(), and Avogadro::Atom::setPartialCharge().

Referenced by Avogadro::Atom::partialCharge().

const Eigen::Vector3d Avogadro::Molecule::center ( ) const

Returns:: The position of the center of the Molecule.

References computeGeomInfo().

void Avogadro::Molecule::clear ( )

Remove all elements of the molecule.

References atom(), bond(), QList::clear(), clearConformers(), cube(), QObject::deleteLater(), mesh(), primitiveRemoved(), and residue().

Referenced by operator=(), setOBMol(), and ~Molecule().

void Avogadro::Molecule::clearConformers ( )

Clear all conformers from the molecule, leaving just conformer zero. This conformer will also be set as current conformer.

References m_atomConformers.

Referenced by clear(), and setAllConformers().

void Avogadro::Molecule::computeGeomInfo ( ) const [protected]

Compute all the geometry information for the Molecule. This allows several relatively expensive calculations to be cached by the Molecule instead of being recalculated every time the Molecule is drawn.

FIXME This leads to the dipole moment always getting invalidated as the geometry information must be computed on load

References atom(), Avogadro::Primitive::id(), numAtoms(), and Avogadro::Atom::pos().

Referenced by center(), farthestAtom(), normalVector(), radius(), and setOBMol().

vector< Vector3d > * Avogadro::Molecule::conformer ( unsigned int index )

Note:: Conformer atom positions are indexed by their unique id (Atom::id()). Use conformerSize() to check the current size needed to accommodate all atoms.

Parameters:

index The index of the conformer to retrieve.

Returns:: Pointer to an existing conformer, or NULL if the index doesn't exist.

References m_atomConformers.

Referenced by addConformer(), Avogadro::Animation::setFrames(), Avogadro::Animation::setMolecule(), and setOBMol().

const std::vector< std::vector< Eigen::Vector3d > * > & Avogadro::Molecule::conformers ( ) const

Get const reference to all conformers.

Note:: Conformer atom positions are indexed by their unique id (Atom::id()). Use conformerSize() to check the current size needed to accommodate all atoms.

References m_atomConformers.

Referenced by setAllConformers(), and Avogadro::MoleculeFile::writeConformers().

unsigned long Avogadro::Molecule::conformerSize ( ) [inline]

Get the current conformer size to accommodate all atoms. Since atom positions are indexed by their uniaue id, this is not the same as the number of atoms

     Molecule *molecule;
     ...
     // create a correctly sized conformer and initialize its elements
     std::vector<Eigen::Vector3d> newConformer(molecule->conformerSize(), Eigen::Vector3d::Zero())
     // change the atom posistions in the conformer
     foreach (Atom *atom, molecule->atoms()) {
       newConformer[atom->id()] = ...;
     }
     // add the conformer to the end of the current list (i.e. index = numConformers())
     molecule->addConformer(newConformer, molecule->numConformers())

PrimitiveList Avogadro::Molecule::copyAtomsAndBonds	(	const QList< Atom * > &	atoms,
		const QList< Bond * > &	bonds
	)

Copy the atoms and bonds in the argument lists into new atoms and bonds in this.

Parameters:

atoms	Atoms to copy into this.
bonds	Bonds to copy into this.

Returns:: A PrimitiveList containing new atoms and bonds.

Note:: All atoms and bonds must belong to the same molecule.; All bonds in must be between atoms in .

References addAtom(), addBond(), Avogadro::PrimitiveList::append(), QList::constBegin(), QList::constEnd(), QList::first(), Avogadro::Primitive::id(), QVector::insert(), QList::isEmpty(), QVector::push_back(), QVector::reserve(), and QList::size().

Referenced by copyAtomsAndBonds().

PrimitiveList Avogadro::Molecule::copyAtomsAndBonds ( const PrimitiveList & atomsAndBonds )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. Copy the atoms and bonds in the argument lists into new atoms and bonds in this.

Parameters:

atomsAndBonds Atoms and bonds to copy into this.

Returns:: A PrimitiveList containing the new atoms and bonds.

Note:: All atoms and bonds must belong to the same molecule.; All bonds in the list must be between atoms in the list.; The QList overload of this function is faster.

References QList::append(), atoms(), Avogadro::Primitive::AtomType, bonds(), Avogadro::Primitive::BondType, QList::constBegin(), QList::constEnd(), copyAtomsAndBonds(), QList::reserve(), QList::size(), and Avogadro::PrimitiveList::subList().

Cube * Avogadro::Molecule::cube ( int index ) const

Returns:: The Cube at the supplied index.

Referenced by addCube(), clear(), OBMol(), and setOBMol().

Cube * Avogadro::Molecule::cubeById ( unsigned long id ) const

Returns:: The Cube at the supplied unique id.

References cubes(), and QList::size().

QList< Cube * > Avogadro::Molecule::cubes ( ) const

Returns:: QList of all cubes in the molecule.

Referenced by cubeById(), and removeCube().

unsigned int Avogadro::Molecule::currentConformer ( ) const

Returns:: The current conformer index.

Eigen::Vector3d Avogadro::Molecule::dipoleMoment ( bool * estimate = 0 ) const

Calculate the dipole moment vector for this molecule. If not known, Avogadro will estimate it based on partial charges.

Parameters:

A	boolean to indicate if the dipole is estimated or not

Returns:: The dipole moment of the Molecule.

References atom(), atoms(), OpenBabel::OBForceField::FindForceField(), OpenBabel::OBForceField::GetPartialCharges(), OpenBabel::OBPairData::GetValue(), OBMol(), Avogadro::Atom::partialCharge(), Avogadro::Atom::pos(), and OpenBabel::OBForceField::Setup().

const std::vector< double > & Avogadro::Molecule::energies ( ) const

Returns:: The energies for all conformers (in kJ/mol).

References numConformers().

Referenced by setEnergies(), setEnergy(), and setOBMol().

double Avogadro::Molecule::energy ( int index = -1 ) const

Get the energy of the supplied conformer (in kJ/mol), defaults to returning the energy of the current conformer.

Parameters:

index The conformer, defaults to the current conformer.

Returns:: The energy of the Molecule (or current conformer).

References Avogadro::Primitive::index().

Referenced by OBMol(), and setEnergy().

const Atom * Avogadro::Molecule::farthestAtom ( ) const

Returns:: The Atom furthest away from the center of the Molecule.

References computeGeomInfo().

QString Avogadro::Molecule::fileName ( ) const

Returns:: The full path filename of the molecule.

QReadWriteLock * Avogadro::Molecule::lock ( ) const

Provides locking, should be used before reading/writing to the Molecule.

Referenced by Avogadro::Animation::setFrame(), Avogadro::Animation::start(), and Avogadro::Animation::stop().

Mesh * Avogadro::Molecule::mesh ( int index ) const

Returns:: The Mesh at the supplied index.

Referenced by addMesh(), and clear().

Mesh * Avogadro::Molecule::meshById ( unsigned long id ) const

Returns:: The Mesh at the supplied unique id.

References meshes(), and QList::size().

QList< Mesh * > Avogadro::Molecule::meshes ( ) const

Returns:: QList of all Mesh objects in the Molecule.

Referenced by meshById(), and removeMesh().

void Avogadro::Molecule::moleculeChanged ( ) [signal]

Emitted when the Molecule changes in a big way, e.g. thousands of atoms added/removed. Typically functions should respond by building up their interpretation of the Molecule from the beginning.

Referenced by updateMolecule().

const Eigen::Vector3d Avogadro::Molecule::normalVector ( ) const

Returns:: The normal vector of the Molecule.

References computeGeomInfo().

unsigned int Avogadro::Molecule::numAtoms ( ) const

Returns:: The total number of Atom objects in the molecule.

References QList::size().

Referenced by addHydrogens(), calculateGroupIndices(), calculatePartialCharges(), computeGeomInfo(), and setOBMol().

unsigned int Avogadro::Molecule::numBonds ( ) const

Returns:: The total number of Bond objects in the Mmolecule.

References QList::size().

Referenced by calculateAromaticity().

unsigned int Avogadro::Molecule::numConformers ( ) const

Returns:: The number of conformers.

References m_atomConformers.

Referenced by energies(), Avogadro::Animation::numFrames(), setEnergy(), Avogadro::Animation::setFrame(), Avogadro::Animation::setFrames(), and Avogadro::Animation::setMolecule().

unsigned int Avogadro::Molecule::numCubes ( ) const

Returns:: The total number of Cube objects in the Molecule.

unsigned int Avogadro::Molecule::numMeshes ( ) const

Returns:: The total number of meshes in the molecule.

unsigned int Avogadro::Molecule::numResidues ( ) const

Returns:: The total number of Residue objects in the Molecule.

unsigned int Avogadro::Molecule::numRings ( ) const

Returns:: The total number of rings in the molecule.

unsigned int Avogadro::Molecule::numZMatrices ( ) const

Returns:: The total number of ZMatrix objects in the molecule.

OpenBabel::OBMol Avogadro::Molecule::OBMol ( ) const

Get access to an OpenBabel::OBMol, this is a copy of the internal data structure in OpenBabel form, you must call setOBMol in order to save any changes you make to this object.

Referenced by addHydrogens(), calculateAromaticity(), calculatePartialCharges(), dipoleMoment(), Avogadro::MoleculeFile::replaceMolecule(), rings(), Avogadro::MoleculeFile::writeConformers(), and Avogadro::MoleculeFile::writeMolecule().

OpenBabel::OBUnitCell * Avogadro::Molecule::OBUnitCell ( ) const

Get access to the OpenBabel unit cell, if any

Returns:: the OBUnitCell or NULL if none exists

Referenced by OBMol(), operator=(), and setOBMol().

Molecule & Avogadro::Molecule::operator+= ( const Molecule & other )

Molecule & Avogadro::Molecule::operator= ( const Molecule & other )

void Avogadro::Molecule::primitiveAdded ( Primitive * primitive ) [signal]

Emitted when a child primitive is added.

Parameters:

primitive pointer to the primitive that was added

Referenced by addCube(), addMesh(), addResidue(), operator+=(), and operator=().

void Avogadro::Molecule::primitiveRemoved ( Primitive * primitive ) [signal]

Emitted when a child primitive is removed.

Parameters:

primitive pointer to the primitive that was removed.

Referenced by clear(), removeCube(), removeMesh(), and removeResidue().

void Avogadro::Molecule::primitiveUpdated ( Primitive * primitive ) [signal]

Emitted when a child primitive is updated.

Parameters:

primitive pointer to the primitive that was updated

double Avogadro::Molecule::radius ( ) const

Returns:: The radius of the Molecule.

References computeGeomInfo().

void Avogadro::Molecule::removeAtom ( Atom * atom )

Remove the supplied Atom.

References atomRemoved(), bond(), Avogadro::Atom::bonds(), QObject::deleteLater(), QObject::disconnect(), Avogadro::Primitive::id(), Avogadro::Primitive::index(), QObject::parent(), QList::removeAt(), removeBond(), Avogadro::Primitive::setIndex(), QList::size(), and Avogadro::Primitive::updated().

Referenced by removeAtom(), and removeHydrogens().

void Avogadro::Molecule::removeAtom ( unsigned long id )

Delete the Atom with the unique id specified.

References atomById(), and removeAtom().

void Avogadro::Molecule::removeBond ( Bond * bond )

Remove the supplied Bond.

References Avogadro::Primitive::id(), and QObject::parent().

Referenced by removeAtom(), and Avogadro::Animation::setFrame().

void Avogadro::Molecule::removeBond ( unsigned long id )

Remove the Bond with the unique id specified.

References Avogadro::Bond::beginAtomId(), bond(), bondRemoved(), QObject::deleteLater(), QObject::disconnect(), Avogadro::Bond::endAtomId(), Avogadro::Primitive::id(), Avogadro::Primitive::index(), QList::removeAt(), QList::size(), and Avogadro::Primitive::updated().

void Avogadro::Molecule::removeCube ( Cube * cube )

Remove the supplied Cube.

References QObject::deleteLater(), QObject::disconnect(), Avogadro::Primitive::id(), Avogadro::Primitive::index(), QObject::parent(), primitiveRemoved(), and Avogadro::Primitive::updated().

Referenced by removeCube().

void Avogadro::Molecule::removeCube ( unsigned long id )

Remove the Cube with the unique id specified.

References cubes(), removeCube(), and QList::size().

void Avogadro::Molecule::removeHydrogens ( Atom * atom = 0 )

Remove all hydrogens from the molecule.

Parameters:

atom	If supplied only remove hydrogens connected to the specified atom.

References atomById(), Avogadro::Primitive::id(), Avogadro::Atom::isHydrogen(), Avogadro::Atom::neighbors(), and removeAtom().

void Avogadro::Molecule::removeMesh ( Mesh * mesh )

Remove the supplied Mesh.

References QObject::deleteLater(), QObject::disconnect(), Avogadro::Primitive::id(), Avogadro::Primitive::index(), QObject::parent(), primitiveRemoved(), and Avogadro::Primitive::updated().

Referenced by removeMesh().

void Avogadro::Molecule::removeMesh ( unsigned long id )

Remove the Mesh with the unique id specified.

References meshes(), removeMesh(), and QList::size().

void Avogadro::Molecule::removeResidue ( Residue * residue )

Remove the supplied residue.

References QObject::deleteLater(), QObject::disconnect(), Avogadro::Primitive::id(), Avogadro::Primitive::index(), QObject::parent(), primitiveRemoved(), and Avogadro::Primitive::updated().

Referenced by removeResidue().

void Avogadro::Molecule::removeResidue ( unsigned long id )

Remove the residue with the unique id specified.

References removeResidue(), residues(), and QList::size().

void Avogadro::Molecule::removeRing ( Fragment * ring )

Remove the supplied ring.

References QObject::deleteLater(), QObject::disconnect(), Avogadro::Primitive::id(), Avogadro::Primitive::index(), QObject::parent(), and Avogadro::Primitive::updated().

Referenced by removeRing(), and rings().

void Avogadro::Molecule::removeRing ( unsigned long id )

Remove the ring with the unique id specified.

References removeRing(), rings(), and QList::size().

void Avogadro::Molecule::removeZMatrix ( ZMatrix * zmatrix )

Remove the supplied ZMatrix.

Residue * Avogadro::Molecule::residue ( int index )

Returns:: The residue at the supplied index.

Note:: Replaces GetResidue.

Referenced by addResidue(), clear(), OBMol(), operator+=(), operator=(), and setOBMol().

Residue * Avogadro::Molecule::residueById ( unsigned long id ) const

Returns:: The residue at the supplied unique id.

References residues(), and QList::size().

Referenced by Avogadro::Atom::residue().

QList< Residue * > Avogadro::Molecule::residues ( ) const

Returns:: QList of all Residue objects in the Molecule.

Referenced by operator+=(), operator=(), removeResidue(), residueById(), and setOBMol().

QList< Fragment * > Avogadro::Molecule::rings ( )

Returns:: QList of all rings in the Molecule.

References OpenBabel::OBRing::_path, Avogadro::Fragment::addAtom(), addRing(), atom(), OpenBabel::OBMol::GetSSSR(), OBMol(), and removeRing().

Referenced by removeRing().

bool Avogadro::Molecule::setAllConformers	(	const std::vector< std::vector< Eigen::Vector3d > * >	conformers,
		bool	deleteExisting = `true`
	)

Replace all conformers in the Molecule. This will first clear all conformers. If the number of specified conformers is 0, this method behaves like clearConformers(). In any case, the current conformer is set to the first one (index 0).

Note:: Conformer atom positions are indexed by their unique id (Atom::id()). Use conformerSize() to check the current size needed to accommodate all atoms.

Parameters:

conformer	A vector of conformers (vector of Vector3d)
deleteExisting	Whether to free the memory from the existing conformers

Returns:: True if successful (i.e. all conformers have the correct size: conformerSize()).

References clearConformers(), conformers(), and m_atomConformers.

Referenced by Avogadro::Animation::start(), and Avogadro::Animation::stop().

void Avogadro::Molecule::setAtomPos	(	unsigned long	id,
		const Eigen::Vector3d &	vec
	)

Set the Atom position.

Parameters:

id	Unique id of the Atom to set the position for.
vec	Position vector to set the Atom to.

References Avogadro::Primitive::id().

Referenced by setAtomPos(), Avogadro::Atom::setOBAtom(), and Avogadro::Atom::setPos().

void Avogadro::Molecule::setAtomPos	(	unsigned long	id,
		const Eigen::Vector3d *	vec
	)

Set the Atom position.

Parameters:

id	Unique id of the Atom to set the position for.
vec	Position vector to set the Atom to.

References setAtomPos().

bool Avogadro::Molecule::setConformer ( unsigned int index )

Change the conformer to the one at the specified index. Conformers are indexed from 0 to numConformers() - 1. When the index is invalid (i.e. >= numConformers()), this method returns false.

Returns:: True if the conformer index is valid.

References Avogadro::Primitive::index(), and m_atomConformers.

Referenced by Avogadro::Animation::setFrame(), and setOBMol().

void Avogadro::Molecule::setDipoleMoment ( const Eigen::Vector3d & moment )

Set the dipole moment of the Molecule.

Parameters:

moment The dipole moment of the Molecule.

void Avogadro::Molecule::setEnergies ( const std::vector< double > & energies )

Set the energies for all conformers (in kJ/mol).

Parameters:

energies The vector of all energy values

References energies().

Referenced by setOBMol().

void Avogadro::Molecule::setEnergy ( double energy )

Set the energy for the current conformer (in kJ/mol).

Parameters:

energy The value for this conformer

References energies(), and numConformers().

Referenced by setOBMol().

void Avogadro::Molecule::setEnergy	(	int	index,
		double	energy
	)

Set the energy for the specified conformer (in kJ/mol).

Parameters:

index	the index of the confomer
energy	The energy for this conformer

References energy(), Avogadro::Primitive::index(), and numConformers().

void Avogadro::Molecule::setFileName ( const QString & name )

Set the filename of the molecule.

References QObject::name().

Referenced by Avogadro::MoleculeFile::readMolecule().

bool Avogadro::Molecule::setOBMol ( OpenBabel::OBMol * obmol )

Copy as much data as possible from the supplied OpenBabel::OBMol to the Avogadro Molecule object.

Copy these residues!

Referenced by Avogadro::MoleculeFile::molecule(), and Avogadro::MoleculeFile::readMolecule().

bool Avogadro::Molecule::setOBUnitCell ( OpenBabel::OBUnitCell * obunitcell )

Copy as much data as possible from the supplied OpenBabel::OBUnitCell to this Avogadro Molecule object.

Returns:: True if successful

References OpenBabel::OBGenericDataType::UnitCell.

void Avogadro::Molecule::translate ( const Eigen::Vector3d & offset )

Translate the Molecule using the supplied vector.

References atom(), atomUpdated(), and Avogadro::Primitive::id().

void Avogadro::Molecule::update ( )

Call to trigger an update signal, causing the molecule to be redrawn.

Reimplemented from Avogadro::Primitive.

References Avogadro::Primitive::updated().

Referenced by Avogadro::Animation::setFrame(), and setOBMol().

void Avogadro::Molecule::updateMolecule ( ) [slot]

Signal that the molecule has been changed in some large way, emits the moleculeChanged and updated signals. This indicates that anything listening to this signal should tear town its cache/model and rebuild it.

References moleculeChanged(), and Avogadro::Primitive::updated().

QList< ZMatrix * > Avogadro::Molecule::zMatrices ( ) const

Returns:: QList of all ZMatrix objects in the Molecule.

ZMatrix * Avogadro::Molecule::zMatrix ( int index ) const

Returns:: The ZMatrix at the supplied index.

Member Data Documentation

std::vector< std::vector<Eigen::Vector3d>* > Avogadro::Molecule::m_atomConformers [protected]

Vector containing pointers to various conformers.

Referenced by addAtom(), addConformer(), clearConformers(), conformer(), conformers(), numConformers(), operator=(), setAllConformers(), and setConformer().

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

/home/kitware/dashboards/avogadro/libavogadro/src/molecule.h
/home/kitware/dashboards/avogadro/libavogadro/src/molecule.cpp

Public Slots

Signals

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation