#include <entity.hh>

Inherits GfxObj.

Public Member Functions
	Entity (const String &name, const mol::EntityHandle &eh, const mol::Query &q=mol::Query(), mol::QueryFlags f=0)
	Entity (const String &name, RenderMode::Type m, const mol::EntityHandle &eh, const mol::Query &q=mol::Query(), mol::QueryFlags f=0)
	Entity (const String &name, const mol::EntityView &ev)
	Entity (const String &name, RenderMode::Type m, const mol::EntityView &ev)
virtual geom::AlignedCuboid	GetBoundingBox (bool use_tf=false) const
virtual void	CustomRenderGL (RenderPass pass)
virtual void	RefreshVA ()
virtual bool	OnSelect (const geom::Line3 &l, geom::Vec3 &result, float zlim, bool pick_flag)
mol::AtomHandle	PickAtom (const geom::Line3 &line, Real line_width=0.5)
mol::BondHandle	PickBond (const geom::Line3 &line, Real line_width=0.5)
virtual void	OnRenderModeChange ()
const String	GetRenderModeName (RenderMode::Type mode)
void	SetEnableRenderMode (RenderMode::Type mode, bool enable)
bool	IsRenderModeEnabled (RenderMode::Type mode)
RenderModeTypes	GetNotEmptyRenderModes ()
void	SetRenderMode (RenderMode::Type mode, const mol::EntityView &view, bool keep=false)
void	SetRenderMode (RenderMode::Type mode, const String &selection, bool keep=false)
virtual void	SetRenderMode (RenderMode::Type mode)
mol::EntityView	GetRenderView (RenderMode::Type mode)
virtual void	SetVisible (const mol::EntityView &view, bool visible)
virtual void	SetVisible (const String &sel, bool visible)
virtual void	OptionsChanged (RenderMode::Type mode)
virtual void	SetOpacity (float f)
virtual float	GetOpacity () const
virtual void	SetOutlineWidth (float f)
virtual void	SetOutlineExpandFactor (float f)
virtual void	SetOutlineExpandColor (const Color &c)
void	Reset (const mol::EntityHandle &eh)
void	Reset (const mol::EntityHandle &eh, const mol::Query &q)
void	Reset (const mol::EntityHandle &eh, const mol::Query &q, mol::QueryFlags flags)
void	Reset (const mol::EntityView &ev)
void	Rebuild ()
void	UpdatePositions ()
void	UpdateView ()
void	SetColor (const Color &col, const String &selection=String(""))
void	SetDetailColor (const Color &col, const String &selection=String(""))
void	SetColorForAtom (const Color &col, const mol::AtomHandle &atom)
void	ColorByElement ()
void	ColorByElement (const String &selection)
void	ColorByChain ()
void	ColorByChain (const String &selection)
mol::EntityView	GetView () const
void	SetQuery (const mol::Query &q)
mol::QueryViewWrapper	GetQueryView () const
void	SetQueryView (const mol::QueryViewWrapper &qv)
mol::EntityHandle	GetEntity () const
void	SetBlur (bool f)
void	BlurSnapshot ()
void	SetBlurFactors (float bf1, float bf2)
void	SetSelection (const mol::EntityView &view)
mol::EntityView	GetSelection () const
virtual void	ColorBy (const mol::EntityView &ev, const String &prop, const Gradient &g, float minv, float maxv)
void	ColorBy (const String &prop, const Gradient &gradient, float minv, float maxv, mol::Prop::Level hint=mol::Prop::UNSPECIFIED)
void	ColorBy (const String &prop, const Gradient &gradient, float minv, float maxv, bool clamp)
void	DetailColorBy (const String &prop, const Gradient &gradient, float minv, float maxv, mol::Prop::Level hint=mol::Prop::UNSPECIFIED)
void	ColorBy (const String &prop, const Gradient &gradient, mol::Prop::Level hint=mol::Prop::UNSPECIFIED)
void	ColorBy (const String &prop, const Gradient &gradient, const String &selection)
void	ColorBy (const String &prop, const Color &c1, const Color &c2, float min, float max, mol::Prop::Level hint=mol::Prop::UNSPECIFIED)
void	ColorBy (const String &prop, const Color &c1, const Color &c2, mol::Prop::Level hint=mol::Prop::UNSPECIFIED)
void	RadiusBy (const String &prop, float rmin, float rmax, float vmin, float vmax, mol::Prop::Level hint=mol::Prop::UNSPECIFIED)
void	RadiusBy (const String &prop, float rmin, float rmax, mol::Prop::Level hint=mol::Prop::UNSPECIFIED)
void	ResetRadiusBy ()
void	Apply (const gfx::ByElementColorOp &op, bool store=true)
void	Apply (const gfx::ByChainColorOp &op, bool store=true)
void	Apply (const gfx::UniformColorOp &op, bool store=true)
void	Apply (const gfx::GradientLevelColorOp &op, bool store=true)
void	Apply (const gfx::EntityViewColorOp &op, bool store=true)
void	CleanColorOps ()
void	ReapplyColorOps ()
RenderOptionsPtr	GetOptions (RenderMode::Type render_mode)
void	SetOptions (RenderMode::Type render_mode, RenderOptionsPtr &render_options)
void	ApplyOptions (RenderMode::Type render_mode, RenderOptionsPtr &render_options)
bool	HasSelection () const
void	SetSeqHack (bool b)
bool	GetSeqHack () const
virtual void	Export (Exporter *ex)
Public Member Functions inherited from GfxObj
	GfxObj (const String &name)
virtual GfxNodeP	Copy () const
virtual void	DeepSwap (GfxObj &go)
virtual void	RenderGL (RenderPass pass)
virtual void	RenderPov (PovState &pov)
virtual void	Apply (GfxNodeVisitor &v, GfxNodeVisitor::Stack st)
virtual int	GetType () const
virtual void	SetMatAmb (const Color &c)
virtual void	SetMatDiff (const Color &c)
virtual void	SetMatSpec (const Color &c)
virtual void	SetMatShin (float s)
virtual void	SetMatEmm (const Color &c)
virtual void	ContextSwitch ()
virtual RenderMode::Type	GetRenderMode () const
virtual geom::Vec3	GetCenter () const
virtual void	SetLineWidth (float w)
virtual void	SetPolyMode (unsigned int m)
virtual void	SetAALines (bool f)
virtual void	SetLineHalo (float f)
virtual void	SetOutline (bool f)
virtual bool	GetOutline () const
virtual void	SetOutlineMode (int m)
virtual int	GetOutlineMode () const
virtual float	GetOutlineWidth () const
virtual float	GetOutlineExpandFactor () const
virtual Color	GetOutlineExpandColor () const
virtual void	SetSolid (bool f)
virtual bool	GetSolid () const
virtual void	SetSolidColor (const Color &c)
virtual Color	GetSolidColor () const
virtual void	ProcessLimits (geom::Vec3 &minc, geom::Vec3 &maxc, const geom::Transform &tf) const
virtual void	InitGL ()
virtual void	OnInput (const InputEvent &e)
virtual void	OnGLCleanup ()
void	Clear ()
const geom::Transform &	GetTF () const
void	SetTF (const geom::Transform &tf)
void	AddLabel (const String &s, const geom::Vec3 &pos, const Color &col, float psize)
void	AddLabel (const String &s, const geom::Vec3 &pos, const Color &col)
void	AddLabel (const String &s, const geom::Vec3 &pos, float psize)
void	AddLabel (const String &s, const geom::Vec3 &pos)
void	ClearLabels ()
void	FlagRebuild ()
void	FlagRefresh ()
bool	GetAALines () const
float	GetLineWidth () const
float	GetLineHalo () const
void	SetNormalSmoothFactor (float smoothf)
float	GetNormalSmoothFactor () const
Material	GetMaterial () const
void	SetMaterial (const Material &m)
void	SmoothVertices (float smoothf)
void	GLCleanup ()
void	Debug (unsigned int flags)
Public Member Functions inherited from GfxObjBase
	GfxObjBase (const String &name)
Public Member Functions inherited from GfxNode
	GfxNode (const String &name)
virtual	~GfxNode ()
virtual void	DeepSwap (GfxNode &n)
String	GetName () const
void	RemoveAll ()
void	Rename (const String &name)
void	Add (GfxObjP obj)
bool	IsNameAvailable (const String &name) const
void	Remove (GfxObjP obj)
void	Add (GfxNodeP node)
void	Remove (GfxNodeP node)
void	Remove (const String &name)
size_t	GetChildCount () const
void	Hide ()
void	Show ()
bool	IsVisible () const
bool	IsAttachedToScene () const
gfx::GfxNodeP	GetParent () const
const GfxNodeVector &	GetChildren () const
GfxNodeVector &	GetChildren ()

Protected Member Functions
virtual void	CustomPreRenderGL (bool flag)
virtual void	CustomRenderPov (PovState &pov)
void	UpdateSelection ()
bool	UpdateIfNeeded () const
void	CacheBoundingBox () const
impl::EntityRenderer *	GetOrCreateRenderer (RenderMode::Type)
Protected Member Functions inherited from GfxObj
void	PreRenderGL (bool flag)
void	AppendColorOp (gfx::ColorOp *op)
void	render_labels () const
void	render_depth_only ()

Additional Inherited Members
Static Public Member Functions inherited from GfxObj
static Color	Ele2Color (const String &ele)
Protected Attributes inherited from GfxObj
IndexedVertexArray	va_
RenderMode::Type	render_mode_
unsigned int	debug_flags_
geom::Transform	transform_
bool	rebuild_
bool	refresh_
float	line_width_
unsigned int	poly_mode_
bool	aalines_flag_
float	line_halo_
Material	mat_
unsigned int	mat_dlist_
bool	mat_update_
float	smoothf_
bool	outline_flag_
int	outline_mode_
bool	solid_
Color	solid_color_
boost::ptr_vector< gfx::ColorOp >	c_ops_
TextPrimList	labels_
bool	use_occlusion_

Detailed Description

graphical rendering of mol::EntityHandle entites

Entity is responsible for rendering of molecular entities. A bunch of different RenderMode::Type render modes are supported. To switch the render mode of the full entity, Entity::SetRenderMode(RenderMode::Type) can be used. To only change one part to a different rendering style, use Entity::SetRenderMode(RenderMode::Type, mol::EntityView, bool)

Definition at line 63 of file entity.hh.

Constructor & Destructor Documentation

Entity	(	const String &	name,
		const mol::EntityHandle &	eh,
		const mol::Query &	q = `mol::Query()`,
		mol::QueryFlags	f = `0`
	)

Initialize with an object name, an mol::Entity handle, and optionally with a mol::Query.

If the latter is ommitted, the full view is displayed. A later call to Rebuild() will re-apply the mol::Query to the given mol::EntityHandle

Entity	(	const String &	name,
		RenderMode::Type	m,
		const mol::EntityHandle &	eh,
		const mol::Query &	q = `mol::Query()`,
		mol::QueryFlags	f = `0`
	)

variant with explicit graphics mode instead of the default

Entity	(	const String &	name,
		const mol::EntityView &	ev
	)

Initialize with an object name and an explicit mol::Entity view; later calls to Rebuild always use this mol::Entity view.

Entity	(	const String &	name,
		RenderMode::Type	m,
		const mol::EntityView &	ev
	)

ctor variant with explicit graphics mode instead of the default

Member Function Documentation

void Apply	(	const gfx::ByElementColorOp &	op,
		bool	store = `true`
	)

void Apply	(	const gfx::ByChainColorOp &	op,
		bool	store = `true`
	)

void Apply	(	const gfx::UniformColorOp &	op,
		bool	store = `true`
	)

void Apply	(	const gfx::GradientLevelColorOp &	op,
		bool	store = `true`
	)

void Apply	(	const gfx::EntityViewColorOp &	op,
		bool	store = `true`
	)

void ApplyOptions	(	RenderMode::Type	render_mode,
		RenderOptionsPtr &	render_options
	)

void BlurSnapshot ( )

void CacheBoundingBox ( ) const

protected

void CleanColorOps ( )

Reimplemented from GfxObj.

virtual void ColorBy	(	const mol::EntityView &	ev,
		const String &	prop,
		const Gradient &	g,
		float	minv,
		float	maxv
	)

virtual

color each component based on the gradient-mapped property of the given entity

Reimplemented from GfxObj.

void ColorBy	(	const String &	prop,
		const Gradient &	gradient,
		float	minv,
		float	maxv,
		mol::Prop::Level	hint = `mol::Prop::UNSPECIFIED`
	)

void ColorBy	(	const String &	prop,
		const Gradient &	gradient,
		float	minv,
		float	maxv,
		bool	clamp
	)

void ColorBy	(	const String &	prop,
		const Gradient &	gradient,
		mol::Prop::Level	hint = `mol::Prop::UNSPECIFIED`
	)

void ColorBy	(	const String &	prop,
		const Gradient &	gradient,
		const String &	selection
	)

void ColorBy	(	const String &	prop,
		const Color &	c1,
		const Color &	c2,
		float	min,
		float	max,
		mol::Prop::Level	hint = `mol::Prop::UNSPECIFIED`
	)

void ColorBy	(	const String &	prop,
		const Color &	c1,
		const Color &	c2,
		mol::Prop::Level	hint = `mol::Prop::UNSPECIFIED`
	)

void ColorByChain ( )

color by chain

void ColorByChain ( const String & selection )

color by chain for a specific selection

void ColorByElement ( )

color by element

void ColorByElement ( const String & selection )

color by element for a specific selection

virtual void CustomPreRenderGL ( bool flag )

protectedvirtual

Reimplemented from GfxObj.

virtual void CustomRenderGL ( RenderPass pass )

virtual

internal routine

Reimplemented from GfxObj.

virtual void CustomRenderPov ( PovState & pov )

protectedvirtual

Reimplemented from GfxObj.

void DetailColorBy	(	const String &	prop,
		const Gradient &	gradient,
		float	minv,
		float	maxv,
		mol::Prop::Level	hint = `mol::Prop::UNSPECIFIED`
	)

virtual void Export ( Exporter * ex )

virtual

Reimplemented from GfxObj.

virtual geom::AlignedCuboid GetBoundingBox ( bool use_tf = false ) const

virtual

returns the bounding box of this object

The bounding box, i.e. the left-bottom-front and the right-top-back corner of the object, is obtained with this method. The single boolean parameter denotes whether to return local coordinates or global scene coordinates; global scene coordinates are local coordinates with the object's transformation (if present) applied. The default is false, i.e. return local coordinates.

Reimplemented from GfxObj.

mol::EntityHandle GetEntity ( ) const

return underlying entity

RenderModeTypes GetNotEmptyRenderModes ( )

virtual float GetOpacity ( ) const

inlinevirtual

returns a value smaller than 1.0 if transparency is used in this object

Reimplemented from GfxObj.

Definition at line 147 of file entity.hh.

RenderOptionsPtr GetOptions ( RenderMode::Type render_mode )

Get render options for given render mode.

In Python, also available as the properties:

sline_options
simple_options
tube_options
cartoon_options
cpk_options
trace_options
custom_options

impl::EntityRenderer* GetOrCreateRenderer ( RenderMode::Type )

protected

mol::QueryViewWrapper GetQueryView ( ) const

return internally used query view

const String GetRenderModeName ( RenderMode::Type mode )

mol::EntityView GetRenderView ( RenderMode::Type mode )

mol::EntityView GetSelection ( ) const

get selection

See also:: gfx_ent

bool GetSeqHack ( ) const

mol::EntityView GetView ( ) const

get view

bool HasSelection ( ) const

bool IsRenderModeEnabled ( RenderMode::Type mode )

virtual void OnRenderModeChange ( )

virtual

Reimplemented from GfxObj.

virtual bool OnSelect	(	const geom::Line3 &	l,
		geom::Vec3 &	result,
		float	zlim,
		bool	pick_flag
	)

virtual

Reimplemented from GfxObj.

virtual void OptionsChanged ( RenderMode::Type mode )

virtual

mol::AtomHandle PickAtom	(	const geom::Line3 &	line,
		Real	line_width = `0.5`
	)

pick atom

In case the line intersects several atoms, the atom closest to the near clipping plane is returned. Returns an invalid handle in case no atom was close to the line

Todo:: honour object transformation

mol::BondHandle PickBond	(	const geom::Line3 &	line,
		Real	line_width = `0.5`
	)

pick bond

In case the line intersects several bonds, the bond closest to the near clipping plane is returned. Returns an invalid handle if no bond was close to the line.

Todo:: honour object transformation

void RadiusBy	(	const String &	prop,
		float	rmin,
		float	rmax,
		float	vmin,
		float	vmax,
		mol::Prop::Level	hint = `mol::Prop::UNSPECIFIED`
	)

void RadiusBy	(	const String &	prop,
		float	rmin,
		float	rmax,
		mol::Prop::Level	hint = `mol::Prop::UNSPECIFIED`
	)

void ReapplyColorOps ( )

Reimplemented from GfxObj.

void Rebuild ( )

rebuild graphical object (see ctor comments)

virtual void RefreshVA ( )

virtual

void Reset ( const mol::EntityHandle & eh )

resets used entity handle replaces underlying entity, keeps query and flags intact

void Reset	(	const mol::EntityHandle &	eh,
		const mol::Query &	q
	)

resets used entity handle and query replaces underlying entity and query, keeps flags intact

void Reset	(	const mol::EntityHandle &	eh,
		const mol::Query &	q,
		mol::QueryFlags	flags
	)

resets used entity handle, query and flags this has the same effect as the ctor call with the same parameters

void Reset ( const mol::EntityView & ev )

resets entity view this as the same effect as the ctor call with the same parameters

void ResetRadiusBy ( )

void SetBlur ( bool f )

void SetBlurFactors	(	float	bf1,
		float	bf2
	)

void SetColor	(	const Color &	col,
		const String &	selection = `String("")`
	)

set color for selection

void SetColorForAtom	(	const Color &	col,
		const mol::AtomHandle &	atom
	)

set color for specific atom

void SetDetailColor	(	const Color &	col,
		const String &	selection = `String("")`
	)

void SetEnableRenderMode	(	RenderMode::Type	mode,
		bool	enable
	)

virtual void SetOpacity ( float f )

virtual

set opacity (1 = no transparency)

Reimplemented from GfxObj.

void SetOptions	(	RenderMode::Type	render_mode,
		RenderOptionsPtr &	render_options
	)

virtual void SetOutlineExpandColor ( const Color & c )

virtual

set outline color (mode 3)

Reimplemented from GfxObj.

virtual void SetOutlineExpandFactor ( float f )

virtual

set outline expansion factor (mode 3) this scales with resolution

Reimplemented from GfxObj.

virtual void SetOutlineWidth ( float f )

virtual

set outline width in pixels (modes 1 + 2) this does not scale with resolution

Reimplemented from GfxObj.

void SetQuery ( const mol::Query & q )

set a new query to use (deprecated) this will re-create the object based on the given selection

void SetQueryView ( const mol::QueryViewWrapper & qv )

set new query view, rebuilding object

void SetRenderMode	(	RenderMode::Type	mode,
		const mol::EntityView &	view,
		bool	keep = `false`
	)

void SetRenderMode	(	RenderMode::Type	mode,
		const String &	selection,
		bool	keep = `false`
	)

virtual void SetRenderMode ( RenderMode::Type m )

virtual

change render mode

Reimplemented from GfxObj.

void SetSelection ( const mol::EntityView & view )

set selection

See also:: gfx_ent

void SetSeqHack ( bool b )

virtual void SetVisible	(	const mol::EntityView &	view,
		bool	visible
	)

virtual

virtual void SetVisible	(	const String &	sel,
		bool	visible
	)

virtual

bool UpdateIfNeeded ( ) const

protected

void UpdatePositions ( )

only grab updated positions, dont rebuild the whole thing views won't be regenerated from stored queries

void UpdateSelection ( )

protected

void UpdateView ( )

forces all views to be regenerated from stored queries

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

stage/include/ost/gfx/entity.hh

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation