kalzium

Avogadro::BondCentricTool

Avogadro::BondCentricTool Class Reference

#include <bondcentrictool.h>

Inheritance diagram for Avogadro::BondCentricTool:

[legend]

List of all members.

Detailed Description

Bond Centric Molecule Manipulation Tool.

Author:: Shahzad Ali, Ross Braithwaite, James Bunt

This class is a molecule manipulation system based on bond-centric design as apposed to points in free space design. It is based off the NavigationTool class by Marcus D. Hanwell.

Definition at line 63 of file bondcentrictool.h.


Public Slots
void	showAnglesChanged (int state)
void	snapToAngleChanged (int newAngle)
void	snapToCheckBoxChanged (int state)
Public Member Functions
	BondCentricTool (QObject *parent=0)
virtual bool	paint (GLWidget *widget)
virtual void	readSettings (QSettings &settings)
void	setMolecule (Molecule *molecule)
virtual QWidget *	settingsWidget ()
virtual int	usefulness () const
virtual void	writeSettings (QSettings &settings) const
virtual	~BondCentricTool ()
Description methods
virtual QString	description () const
virtual QString	name () const
Tool Methods
virtual QUndoCommand *	mouseMove (GLWidget widget, const QMouseEvent event)
virtual QUndoCommand *	mousePress (GLWidget widget, const QMouseEvent event)
virtual QUndoCommand *	mouseRelease (GLWidget widget, const QMouseEvent event)
virtual QUndoCommand *	wheel (GLWidget widget, const QWheelEvent event)
Protected Member Functions
void	clearData ()
Eigen::Vector3d	performRotation (double angle, Eigen::Vector3d rotationVector, Eigen::Vector3d centerVector, Eigen::Vector3d positionVector)
Construction Plane/Angles Methods
Eigen::Vector3d *	calculateSnapTo (Bond bond, Eigen::Vector3d referencePoint, double maximumAngle)
void	drawAngles (GLWidget widget, Atom atom, Bond *bond)
void	drawAngleSector (GLWidget *widget, Eigen::Vector3d origin, Eigen::Vector3d direction1, Eigen::Vector3d direction2, bool alternateAngle=false)
void	drawAtomAngles (GLWidget widget, Atom atom)
void	drawDihedralAngle (GLWidget widget, Atom A, Atom D, Bond BC, bool alternateAngle=false)
void	drawDihedralAngles (GLWidget widget, Atom A, Bond *BC)
void	drawDihedralRectangle (GLWidget widget, Bond bond, Atom *atom, double rgb[3])
void	drawDihedralRectanglesOfAtom (GLWidget widget, Bond bond, Atom *atom, double rgb[3])
void	drawManipulationRectangle (GLWidget widget, Bond bond, Eigen::Vector3d *referencePoint, double rgb[3])
void	drawSingleDihedralAngles (GLWidget widget, Atom A, Bond *BC)
void	drawSkeletonAngles (GLWidget widget, SkeletonTree skeleton)
void	drawSphere (GLWidget *widget, const Eigen::Vector3d &center, double radius, float alpha)
bool	isAtomInBond (Atom atom, Bond bond)
Protected Attributes
Atom *	m_clickedAtom
Bond *	m_clickedBond
Eigen::Vector3d *	m_currentReference
Eigen::Vector3d *	m_directionVector
QPoint	m_lastDraggingPosition
QGridLayout *	m_layout
bool	m_leftButtonPressed
bool	m_midButtonPressed
Molecule *	m_molecule
bool	m_movedSinceButtonPressed
Eigen::Vector3d *	m_referencePoint
bool	m_rightButtonPressed
Bond *	m_selectedBond
QWidget *	m_settingsWidget
bool	m_showAngles
QCheckBox *	m_showAnglesBox
SkeletonTree *	m_skeleton
bool	m_snapped
int	m_snapToAngle
QSpinBox *	m_snapToAngleBox
QLabel *	m_snapToAngleLabel
QCheckBox *	m_snapToCheckBox
bool	m_snapToEnabled
QLabel *	m_spacer
ToolGroup *	m_toolGroup
QUndoCommand *	m_undo

Constructor & Destructor Documentation

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

Constructor.

Definition at line 65 of file bondcentrictool.cpp.

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

Deconstructor.

Definition at line 100 of file bondcentrictool.cpp.

Member Function Documentation

Eigen::Vector3d * Avogadro::BondCentricTool::calculateSnapTo	(	Bond *	bond,
		Eigen::Vector3d *	referencePoint,
		double	maximumAngle
	)			`[protected]`

Calculates whether the manipulation plane is close enough to any atoms (that are 1 bond away from either of the atoms attached to the given bond) to 'snap-to' them.

NOTE: Any atoms that lie along the same line as the bond are disregarded in the calculations otherwise the plane would always try snap-to them as their angle is 0.

Parameters:

	bond	The bond through which the manipulation plane lies.
	referencePoint	The current reference point that defines the manipulation plane.
	maximumAngle	The maximum angle between the current reference point and any atom that determines whether or not the plane is close enough to snap-to the atom.

Returns:: A vector representing the closest Atom to the manipulation plane, to be used as the reference point for drawing the plane, if any atom is close enough. If no atom is close enough to 'snap-to', NULL is returned.

Definition at line 1430 of file bondcentrictool.cpp.

void Avogadro::BondCentricTool::clearData ( ) [protected]

Clears any data and frees up any memory that is used by the tool.

This procedure should be used when the tool is changed, the molecule cleared, or the program exits etc.

Definition at line 124 of file bondcentrictool.cpp.

virtual QString Avogadro::BondCentricTool::description ( ) const [inline, virtual]

Tool Description (ie. Draws atoms and bonds).

Reimplemented from Avogadro::Tool.

Definition at line 78 of file bondcentrictool.h.

void Avogadro::BondCentricTool::drawAngles	(	GLWidget *	widget,
		Atom *	atom,
		Bond *	bond
	)			`[protected]`

Draws sectors around a given atom representing the angles between neighbouring atoms bonded with this atom and an atom bonded to this atom by a given bond.

Parameters:

	widget	The widget the angle-sectors will be drawn on.
	atom	The atom whose angles are being drawn.
	bond	The bond attached to the given atom that will be used as a reference point for all the angles.

Precondition:: The given atom must be either the begin or end atom of the given bond.

Definition at line 1052 of file bondcentrictool.cpp.

void Avogadro::BondCentricTool::drawAngleSector	(	GLWidget *	widget,
		Eigen::Vector3d	origin,
		Eigen::Vector3d	direction1,
		Eigen::Vector3d	direction2,
		bool	alternateAngle = `false`
	)			`[protected]`

Draws a sector that shows the angle between two lines from a given origin.

Parameters:

	widget	The widget this angle-sector will be drawn on.
	origin	The origin around which this angle is being calculated.
	direction1	A vector that defines the line from the given origin through this point.
	direction2	A vector that defines the line from the given origin through this second point.

Definition at line 959 of file bondcentrictool.cpp.

void Avogadro::BondCentricTool::drawAtomAngles	(	GLWidget *	widget,
		Atom *	atom
	)			`[protected]`

Draws sectors around a given atom representing the angles between neighbouring atoms bonded with this atom.

Parameters:

	widget	The widget the angle-sectors will be drawn on.
	atom	The atom whose angles are being drawn.

Definition at line 1025 of file bondcentrictool.cpp.

void Avogadro::BondCentricTool::drawDihedralAngle	(	GLWidget *	widget,
		Atom *	A,
		Atom *	D,
		Bond *	BC,
		bool	alternateAngle = `false`
	)			`[protected]`

Definition at line 1130 of file bondcentrictool.cpp.

void Avogadro::BondCentricTool::drawDihedralAngles	(	GLWidget *	widget,
		Atom *	A,
		Bond *	BC
	)			`[protected]`

Definition at line 1175 of file bondcentrictool.cpp.

void Avogadro::BondCentricTool::drawDihedralRectangle	(	GLWidget *	widget,
		Bond *	bond,
		Atom *	atom,
		double	rgb[3]
	)			`[protected]`

Definition at line 1586 of file bondcentrictool.cpp.

void Avogadro::BondCentricTool::drawDihedralRectanglesOfAtom	(	GLWidget *	widget,
		Bond *	bond,
		Atom *	atom,
		double	rgb[3]
	)			`[protected]`

Definition at line 1674 of file bondcentrictool.cpp.

void Avogadro::BondCentricTool::drawManipulationRectangle	(	GLWidget *	widget,
		Bond *	bond,
		Eigen::Vector3d *	referencePoint,
		double	rgb[3]
	)			`[protected]`

Draws a rectangle through a bond that can be used as a construction plane to manipulate the bond itself, or the atoms at either end of the bond.

Parameters:

	widget	The widget the rectangle will be drawn on.
	bond	The bond through which the rectangle will be drawn.
	referencePoint	A point orthagonal to the bond that defines the plane the rectangle will be drawn on.
	rgb	An array of doubles representing the red/green/blue values of the color for the rectangle.

Definition at line 1544 of file bondcentrictool.cpp.

void Avogadro::BondCentricTool::drawSingleDihedralAngles	(	GLWidget *	widget,
		Atom *	A,
		Bond *	BC
	)			`[protected]`

Definition at line 1289 of file bondcentrictool.cpp.

void Avogadro::BondCentricTool::drawSkeletonAngles	(	GLWidget *	widget,
		SkeletonTree *	skeleton
	)			`[protected]`

Draws sectors around the root Atom of a given SkeletonTree based on the root Bond of the tree and whether or not adjacent Atoms form a part of the skeleton or not.

Parameters:

	widget	The widget the angle-sectors will be drawn on.
	skeleton	The SkeletonTree whose root Atom's angles are to be drawn.

Definition at line 1088 of file bondcentrictool.cpp.

void Avogadro::BondCentricTool::drawSphere	(	GLWidget *	widget,
		const Eigen::Vector3d &	center,
		double	radius,
		float	alpha
	)			`[protected]`

Draws a sphere of a given radius around a given vector.

Parameters:

	widget	The widget the sphere will be drawn on.
	center	The center of the sphere.
	radius	The radius of the sphere.
	alpha	The alpha value that determines the opacity of the sphere.

Definition at line 1709 of file bondcentrictool.cpp.

bool Avogadro::BondCentricTool::isAtomInBond	(	Atom *	atom,
		Bond *	bond
	)			`[protected]`

Methods used to construct and draw the angle-sectors, the construction plane, and the rotation-sphere.

Checks whether a given atom is at either end of a given bond.

Parameters:

	atom	The atom that is being examined for membership of the given bond.
	bond	The bond that is being examined to see if the given atom is attached to it.

Returns:: True if the given atom is the begin or end atom of the given bond, false otherwise, or if either of the pointers point to NULL.

Definition at line 944 of file bondcentrictool.cpp.

QUndoCommand * Avogadro::BondCentricTool::mouseMove	(	GLWidget *	widget,
		const QMouseEvent *	event
	)			`[virtual]`

Response to mouse movement.

Parameters:

	widget	the GLWidget where the even occurred
	event	the mouse event information

Implements Avogadro::Tool.

Definition at line 432 of file bondcentrictool.cpp.

QUndoCommand * Avogadro::BondCentricTool::mousePress	(	GLWidget *	widget,
		const QMouseEvent *	event
	)			`[virtual]`

Callback methods for ui.actions on the canvas.

Implements Avogadro::Tool.

Definition at line 190 of file bondcentrictool.cpp.

QUndoCommand * Avogadro::BondCentricTool::mouseRelease	(	GLWidget *	widget,
		const QMouseEvent *	event
	)			`[virtual]`

Response to mouse release.

Parameters:

	widget	the GLWidget where the even occurred
	event	the mouse event information

Implements Avogadro::Tool.

Definition at line 396 of file bondcentrictool.cpp.

virtual QString Avogadro::BondCentricTool::name ( ) const [inline, virtual]

Tool Name (ie Draw).

Implements Avogadro::Tool.

Definition at line 76 of file bondcentrictool.h.

bool Avogadro::BondCentricTool::paint ( GLWidget * widget ) [virtual]

Called by the GLWidget allowing overlay painting by the tool.

Tools get painted last in the overall scheme.

Parameters:

widget

the GLWidget to paint to

Reimplemented from Avogadro::Tool.

Definition at line 829 of file bondcentrictool.cpp.

Eigen::Vector3d Avogadro::BondCentricTool::performRotation	(	double	angle,
		Eigen::Vector3d	rotationVector,
		Eigen::Vector3d	centerVector,
		Eigen::Vector3d	positionVector
	)			`[protected]`

Performs a rotation on a vector.

Parameters:

	angle	The angle to rotate by in radians.
	rotationVector	The Vector3d to rotate around, must be a unit vector.
	centerVector	The Vector3d postion around which to rotate.
	postionVector	The Vector3d postion of the vector to rotate.