HaMolView Class Reference

Class for 3D representation of a set of molecules. More...

#include <hamolview.h>

Inheritance diagram for HaMolView:

List of all members.

Labels manipulation functions
void	FormatLabel (HaChain *chain, HaResidue *group, HaAtom *aptr, const char *label, char *ptr)
int	DeleteLabels ()
void	DefineLabels (const char *label)
void	DefaultLabels (int enable)
void	DisplayLabels ()
int	LabelOptFlag
Monitors functions:
void	DeleteMonitors ()
void	AddMonitors (HaAtom *src, HaAtom *dst)
void	CreateMonitor (Long src, Long dst)
void	DisplayMonitors ()
list< Monitor >	MonitList
Image Output related functions:
void	WriteImageFile (const char *name, int type)
int	WritePPMFile (const char *name, int raw)
int	WriteGIFFile (const char *name)
int	WriteRastFile (const char *name, int encode)
int	WriteEPSFFile (const char *name, int col, int compr)
int	WriteBMPFile (const char *name)
int	WriteVectPSFile (const char *name)
int	WritePICTFile (const char *name)
int	WriteIRISFile (const char *name)
int	WriteScriptFile (const char *name)
int	WriteKinemageFile (const char *name)
int	WriteMolScriptFile (const char *name)
int	WritePOVRayFile (const char *name)
int	WriteVRMLFile (const char *name)
void	WriteVRMLDots ()
void	WriteVRMLColour (int indent, int shade)
	Write VRML specification for colour.
void	WriteVRMLTriple (double x, double y, double z)
	Write coordinate in VRML format.
void	WriteVRMLAtoms ()
	Write atoms in VRML format.
void	WriteVRMLLine (int src, int dst, int shade, int *flag)
void	WriteVRMLWireframe ()
void	DisplaySpaceFill ()
	Plot atoms as spheres in the buffer.
void	DisplayWireframe ()
	function to plot wireframe molecular representation
void	DisplayCylinder (int x1, int y1, int z1, int x2, int y2, int z2, int c1, int c2, int rad)
void	DisplayDoubleBonds ()
void	DisplayBackbone ()
	Plot the molecule backbone.
void	DisplayHBonds (int mode)
	Display H-bonds(mode = HBondMode) or SS-bonds(mode = SSBondMode).
void	DisplayBoxes ()
	Plot boundary box in the buffer.
void	DisplayOnScreenInfo ()
	Print info on the display screen.
void	DisplayPickedAtoms ()
	Display circles around picked atoms.
void	RenderFrame ()
	The Main function to plot object in the buffer pixelmap before output to the display.
void	TestAtomProximity (HaAtom *ptr, int xpos, int ypos)
	Set Atom as the Picked atom if it is closest so far to the (xpos,ypos) point.
void	IdentifyAtom (int xpos, int ypos)
	Find the atom the mouse points to.
void	InitializeTables ()
void	InitializeRenderer ()
Canvas3D *	pCanv
	Pointer to the canvas object that contains the PixelMap buffer to plot different objects.
void	WriteByte (int)
void	WriteLSBShort (int)
void	WriteMSBShort (int)
void	WriteLSBLong (unsigned int)
void	WriteMSBLong (unsigned int)
void	WriteGIFCode (int code)
void	WritePPMWord (int i)
void	FlushRastRLE ()
void	WriteRastRLECode (int val)
void	WriteRastRLEPad ()
void	WriteRastData (int output)
void	OutputEPSFByte (int val)
void	EncodeEPSFPixel (int val, int col)
void	FlushBMPBuffer ()
void	FlushBMPPackets ()
void	ProcessBMPPacket ()
void	WriteBMPCode (int val)
void	WriteBMPData (int output)
int	FindDepth (PSItemPtr item, int type)
void	DepthSort (PSItemPtr *data, char *type, int count)
int	ClipVectSphere (HaAtom *)
int	ClipVectBond (HaAtom *, HaAtom *)
void	WriteVectColour (int col)
void	WriteVectSphere (PSItemPtr *data, char *type, int index)
void	WriteVectWire (HaAtom *src, HaAtom *dst, int col, int dash)
void	WriteVectStick (HaAtom *src, HaAtom *dst, int col, int rad)
Long	CountPSItems ()
void	FetchPSItems (PSItemPtr *, char *)
void	WritePSItems (PSItemPtr *, char *, int)
void	WriteVectDots ()
void	WriteVectLabels ()
void	WriteVectMonitors ()
void	FlushPICTBuffer ()
void	FlushPICTPacket ()
void	WritePICTCode (int val)
void	WritePICTData ()
void	FlushIRISBuffer ()
void	FlushIRISPacket ()
void	WriteIRISCode (int val)
void	DetermineIRISSizes (Long *rowstart, short *rowsize, int *min, int *max)
void	WriteIRISHeader (Long *rowstart, short *rowsize, int min, int max)
void	WriteIRISData ()
void	WriteKinemageDots ()
void	WriteKinemageData ()
int	CheckKinemageChain (HaAtom *src, HaAtom *dst, HaChain *chain)
void	WriteKinemageLabels (HaChain *chain)
void	WriteKinemageRibbons (HaChain *chain)
void	WriteKinemageSpheres (HaChain *chain)
void	OutputKinemageVector (HaAtom *src, HaAtom *dst, int col)
void	WriteKinemageBonds (HaChain *chain)
void	WriteScriptAtoms ()
void	WriteScriptBonds ()
void	WriteScriptBackbone ()
void	WriteScriptRibbons ()
void	WriteScriptLabels ()
void	WriteScriptMonitors ()
void	WriteScriptHBonds (char *obj)
Public Member Functions
HaMolSet *	GetMolSet ()
	Get Molecular Set that the view displays.
void	ResetView ()
virtual int	ExecuteCommand (CmdParser &cmd_pr)
int	ExecuteSetCommand (CmdParser &cmd_pr)
int	ExecuteColourCommand (CmdParser &cmd_pr)
void	ConnectObject (Object3D *pObj)
int	BroadcastCurrAtom ()
int	FillCurrAtomRef (char *buf)
bool	SetImageSize (int new_ImageSize)
int	GetImageSize ()
int	GetImageRadius ()
void	SetUseSlabPlane (int new_UseSlabPlane)
int	UseSlabPlane ()
void	SetSlabMode (int new_SlabMode)
int	SlabMode ()
void	SetSlabValue (int new_SlabValue)
int	SlabValue ()
void	SetSlabInten (int new_SlabInten)
void	SetSliceValue (int new_SliceValue)
int	SliceValue ()
void	SetZOffset (int new_ZOffset)
int	ZOffset ()
virtual void	UpdateThisView (long lHint=0)
virtual void	RefreshScreen ()
int	CreateImage ()
virtual void	ClearImage ()
void	ClearBuffers ()
virtual void	TransferImage ()
virtual int	PrintImage ()
virtual int	ClipboardImage ()
void	ReSizeScreen ()
void	ReAllocBuffers ()
void	BuildHashTable ()
	Build HashTable - partion of selected atoms to grid bins.
void	DrawFrame ()
	Fill FBuffer and DBuffer which determine the image call RenderFrame.
void	ResetRenderer ()
void	SetStereoMode (int)
void	SetPickMode (int)
void	PickAtom (int, int, int)
void	SetRefreshScreen ()
void	InitialTransform ()
	Arrange the molecular set within the window in standard orientation, and set rotation matrix to unity.
void	PrepareTransform ()
void	ApplyTransform ()
void	ResetTransform ()
void	CalcRotCenter (int sel_atoms=FALSE)
	Compute center of rotation of connected molecules ( or selected atoms).
void	CenterSelected ()
	Center Selected portion of the molecular set.
void	GetTransfCoord (const double x_abs, const double y_abs, const double z_abs, double &x_tr, double &y_tr, double &z_tr)
	Get tranformed coordinates (to get screen coordinates multiply by Scale and + ixadd(iyadd).
void	SetAtomScreenRadVal (double rad)
	Set radii of atoms as they seen on the screen.
void	SetRadiusTemperature ()
void	SetAtomScreenRadVdW ()
	Set image atom radii to van der Waals radii.
void	DefaultRepresentation ()
void	DisableSpacefill ()
void	EnableWireframe (int mask, double rad)
void	DisableWireframe ()
void	EnableBackbone (int mask, double rad)
void	DisableBackbone ()
void	SetHBondStatus (int hbonds, int enable, double rad)
void	SetRibbonCartoons ()
void	SetRibbonStatus (int enable, int flag, double width)
void	SetTraceTemperature ()
int	ComputeRevColourMap ()
void	ScaleColourMap (int count)
	Prepare array of shade references Scale to display properties by colors.
void	ColourBackNone ()
void	ColourBondNone ()
void	ColourHBondType ()
void	ColourHBondNone (int hbonds)
void	ColourMonitNone ()
void	ColourBackAttrib (int r, int g, int b)
void	ColourBondAttrib (int r, int g, int b)
void	ColourHBondAttrib (int hbonds, int r, int g, int b)
void	ColourMonitAttrib (int r, int g, int b)
void	ColourDotsAttrib (int r, int g, int b)
void	ColourDotsPotential ()
void	ColourRibbonNone (int flag)
void	ColourRibbonAttrib (int flag, int r, int g, int b)
void	ScaleColourAttrib (int attr)
	Colour Atoms according to attributes(properties).
void	MonoColourAttrib (int r, int g, int b)
void	CPKColourAttrib ()
void	GroupsColourAttrib ()
void	ShapelyColourAttrib ()
void	AminoColourAttrib ()
void	StructColourAttrib ()
int	IsCPKColour (HaAtom *aptr)
Display ET related quantities:
void	DisplayETBestPath ()
Display Electrostatic Related quantities:
void	DisplayContourSurf ()
Atom Selection Functions:
void	RestrictSelected ()
	Restrict view to only selected portion of the molecular set.
Dot Surface functions:
int	TestDot (double x, double y, double z, bool solvent_access)
void	InitElemDots ()
void	AddElemDots (int elem, int density)
void	FreeElemDots ()
void	DeleteDotSurfaces ()
void	CalculateDotSurface (int density)
void	DisplayDotSurfaces ()
Ribbons and Cartoons functions:
void	DisplayRibbon (HaChain *)
	Function called in RenderFrame to display secondary structure elements as ribbons.
Static Public Member Functions
int	Colour2Shade (const int x)
	Given a color index in Lut[] array get corresponding shade index.
int	Shade2Colour (const int x)
	For a given shade get a position of the color in Lut array.
int	OpenDisplay (int, int)
void	SetMouseMode (int)
void	DefineColourMap ()
	Reset color array Lut using array of shades Shade[].
int	IsShadeDefined (unsigned char r, unsigned char g, unsigned char b)
	check if the shade (basic color) defined
int	DefineShade (unsigned char r, unsigned char g, unsigned char b)
	set a new basic color(shade) to the Shade array
int	SetShadeLutEntries (int shade_idx)
	Set intermediate colors (in Lut array) for a shade with index shade_idx (in Shade array).
int	GetColorIdx (unsigned char r, unsigned char g, unsigned char b)
	Get index of the basic color from r,g,b allocating shade if necessary.
Public Attributes
int	debug_level
int	UseDepthCue
int	UseStereo
int	UseClipping
int	SSBondMode
int	HBondMode
int	UseTransparent
int	UseOutLine
int	KinemageFlag
double	StereoAngle
int	DrawBoundBox
int	DrawAxes
int	DrawDoubleBonds
int	DrawUnitCell
double	CartoonHeight
int	SolventDots
double	ProbeRadius
	Probe Radius in atomic units.
int	DrawDots
int	DrawLabels
int	DrawMonitDistance
int	DrawBetaArrows
HaMolSet *	host_mol_set
Partition	HashTable
int	XOffset
int	YOffset
int	ideltx
int	idelty
	Current translation values along X and Y axis.
double	CenX
double	CenY
double	CenZ
	Coordinates of the Center of the Zone.
double	CurRX
	Current value of rotation of the view around X axis ( in [-1.1] interval).
double	CurRY
	Current value of rotation of the view around Y axis ( in [-1.1] interval).
double	CurRZ
	Current value of rotation of the view around Z axis ( in [-1.1] interval).
double	CurTX
	Current translation value of the view along X axis ( in [-1.1] interval).
double	CurTY
	Current translation value of the view along Y axis ( in [-1.1] interval).
double	CurZoom
	Current Zoom value ( in [-1.1] interval).
double	CurSlabValue
	Current slab value ( in [-1.1] interval).
double	LastRX
double	LastRY
double	LastRZ
double	LastTX
double	LastTY
int	PointX
	X screen coordinate of the point of mouse click or release.
int	PointY
	Y screen coordinate of the point of mouse click or release.
int	InitX
	reference X screen coordinate of the point of mouse click in mouse motion tracking
int	InitY
	reference Y screen coordinate of the point of mouse click in mouse motion tracking
int	UseLabelCol
HaMat_double	Rot
	Coordinates of x, y, z directional vectors in the screen(transformed) coordinate system.
HaVec_double	Orig
	Coordinates of the origin of the absolute coordinate system in the screen(transformed) c.s.
double	Zoom
	Zoom value.
double	Scale
	coef of transformation from the World Coordinates in Bohr to Screen integer coordinates
double	DScale
	1.0/(Max size of the displayed portion of the molecular set)
int	UseScreenClip
int	m_screen_transform
	flag to set rotations and traslation only on the screen absolute atomic coordinates are not changed
int	ReDrawFlag
int	Hydrogens
int	HetaGroups
int	DrawAtoms
int	DrawBonds
int	DrawRibbon
int	DrawBestPath
int	DrawContourSurf
int	DrawSolidSurfaces
vector< int >	min_color_map
	Array of minimal set of colors to describe the image.
map< int, int, less< int > >	rev_color_map
	Map from colors to indexes in min_color_map.
Static Public Attributes
int	ZoneBoth = True
	Flag to select bond if both atoms of the bond are selected.
ShadeDesc	Shade [LastShade]
	Array of shades(basic colors) every color used to.
ShadeRef	ScaleRef [LastShade]
	Shades intermediate colors from blue to red.
int	ScaleCount = 0
	Number of colors(shades) in ScaleRef.
int	FakeSpecular = False
int	SpecPower = 8
int	BackR = 0
int	BackG = 0
int	BackB = 0
	Background color (rgb).
int	LabR = 255
int	LabG = 255
int	LabB = 255
	Default labels color (rgb).
int	BoxR = 255
int	BoxG = 255
int	BoxB = 255
	Clor used to plot boxes (rgb).
int	UseBackFade = False
double	Ambient = DefaultAmbient
int	MouseMode = MMRasMol
int	UseHourGlass = True
Protected Member Functions
void	MouseMove (int status, int dx, int dy)
void	ClampShiftVal (int ival, double value)
	Shift value of the current translation, zoom or slab with restriction [-1,1].
void	WrapShiftVal (int iaxis, double value)
	Shift current rotation value around X,Y or Z axis, wraping them to [-1,1] interval.
Protected Attributes
int	StereoView
int	FBufX
int	FBufY
	Save previous values of XRange and YRange.

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Detailed Description

Class for 3D representation of a set of molecules.

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Member Function Documentation

int HaMolView::BroadcastCurrAtom (   )

This function send message IDU_ATOM_SELECT to Dialog classes that are able to prosess this info and call AtomEdit::BroadCastPickedAtom(PkAtom) - for atom select edit boxes

void HaMolView::DrawFrame (   )

Fill FBuffer and DBuffer which determine the image call RenderFrame. Fill FBuffer and DBuffer that determine the image Use RenderFrame and changing View Structure to plot Stereo this mechanism may be used to plot multiple molecule on the same screen for the bulder for example?

void HaMolView::DefineColourMap (   )  [static]

Reset color array Lut using array of shades Shade[]. This function is called in HaMolViewMFC::RefreshScreen when RFColour flag in ReDrawFlag is set Management of colors in HARLEM: Array Shade[] - Contain Basic Colors of HARLEM Array Lut[] as first goes basic color and then with increasing intensity colors obtained by darkening of the basic color ColourDepth - the number of intermediate (darkened) colors to interpolate effects of shaded parts of the object Shade2Colour(j) - macro return the position of the basic color specified by shade in palitra Lut

int HaMolView::ComputeRevColourMap (   )

and compute reverse color map rev_color_map < return number of colors in min_color_map

void HaMolView::ScaleColourMap (  int  count  )

Prepare array of shade references Scale to display properties by colors. Prepare for coloring by property value Fill ScaleRef with ScaleCount colors from blue to red

int HaMolView::DefineShade (  unsigned char  r, unsigned char  g, unsigned char  b )  [static]

set a new basic color(shade) to the Shade array If Shade array is full it will return the position of the shade best matching the color

void HaMolView::RenderFrame (   )

The Main function to plot object in the buffer pixelmap before output to the display. Function to create image by filling View Structure Enter plotting of new elements here

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Member Data Documentation

double HaMolView::LastRZ

Previous values of CurRX,CurRY,CurRZ < Rotations around X,Y and Z axis

double HaMolView::LastTY

Previous values of CurTX,CurTY - < Translations along X,Y axis

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

• hamolview.h
• hamolview_mfc.cpp
• win_dialogs_2.cpp
• hamolview.cpp
• outfile.cpp
• repres.cpp
• transfor.cpp
• script.cpp

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