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DrawMolItem Class Reference

Displayable subclass for creating geometric representations of molecules. More...

#include <DrawMolItem.h>

Inheritance diagram for DrawMolItem:

List of all members.

Public Types
enum	RegenChoices { NO_REGEN = 0, MOL_REGEN = 1, SEL_REGEN = 2, REP_REGEN = 4, COL_REGEN = 8 }
	Keep track of whether and why we have to regenerate rendering lists In particular, MOL_REGEN means molecular data has changed, whereas if all we did was change from one timestep to another, and nothing in the timestep has changed, then the update_ts flag is changed instead. The idea is that when we implement cached geometry for multiple frames, or a draw all frames option, we don't want to recreate the geometry unnecessarily. More...
Public Methods
	DrawMolItem (const char , DrawMolecule , AtomColor , AtomRep , AtomSel *)
virtual	~DrawMolItem (void)
int	change_color (AtomColor *)
	change coloring method. More...
int	change_rep (AtomRep *)
	change representation method. More...
int	change_sel (const char *)
	change atom selection. More...
void	force_recalc (int)
	force a recalculation of everything. More...
int	atom_displayed (int)
	if Nth atom is displayed in ANY rep. More...
int	representation_index (void)
	which representation this is. More...
int	set_smoothing (int n)
int	get_smoothing () const
void	set_drawframes (const char *frames)
	Controls for drawing a subset of the molecule's frames. Pass a list of frames to be drawn, or "now" to draw just the current frame (the default). Always succeeds, invalid or out of range frames are ignored. More...
const char *	get_drawframes () const
void	set_pbc (int)
	Controls for display of periodic boundary conditions. Uses the PBC_x defines in VMDDisplayList. More...
int	get_pbc () const
void	set_pbc_images (int)
	Set the number of of periodic image replicas. Must be 1 or higher. More...
int	get_pbc_images () const
void	change_pbc ()
	the pbc parameters in Timestep have changed; update the transformation matrices accordingly (but no need to regenerate display lists). More...
void	change_ss ()
	the secondary structure for the molecule has changed. More...
void	change_ts ()
	the currently displayed timestep has changed. More...
void	change_traj ()
	timesteps have been added or removed from the parent molecule. More...
virtual void	prepare ()
	prepare for drawing, do updates. More...
virtual int	pickable_on ()
	override pickable_on so that it returns true only when both the rep and the molecule are on. More...

virtual void	pick_start (PickMode p, DisplayDevice d, int btn, int tag, const int cell, int dim, const float pos)
	When picked, pass my parent molecule to the pick mode. More...
virtual void	pick_move (PickMode p, DisplayDevice d, int tag, int dim, const float *pos)
	When picked, pass my parent molecule to the pick mode. More...
virtual void	pick_end (PickMode p, DisplayDevice d)
	When picked, pass my parent molecule to the pick mode. More...
Public Attributes
AtomColor *	atomColor
	atom coloring method to use. More...
AtomRep *	atomRep
	atom representation to use. More...
AtomSel *	atomSel
	atom selection to use. More...
int	repNumber
	current representation ID. More...
char	commentBuffer [1024]
	buffer for comments. More...
char *	name
	name of rep, used to identify uniquely. More...
Protected Methods
virtual void	do_color_changed (int)
virtual void	do_color_rgb_changed (int)
virtual void	do_color_scale_changed ()
Protected Attributes
float	spline_basis [4][4]
	spline basis used for ribbons/tubes. More...

Detailed Description

Displayable subclass for creating geometric representations of molecules.

Definition at line 51 of file DrawMolItem.h.

Member Enumeration Documentation

enum DrawMolItem::RegenChoices

Keep track of whether and why we have to regenerate rendering lists In particular, MOL_REGEN means molecular data has changed, whereas if all we did was change from one timestep to another, and nothing in the timestep has changed, then the update_ts flag is changed instead. The idea is that when we implement cached geometry for multiple frames, or a draw all frames option, we don't want to recreate the geometry unnecessarily.

Enumeration values:

NO_REGEN

MOL_REGEN

SEL_REGEN

REP_REGEN

COL_REGEN

Definition at line 314 of file DrawMolItem.h.

Constructor & Destructor Documentation

DrawMolItem::DrawMolItem ( const char * ,

DrawMolecule * ,

AtomColor * ,

AtomRep * ,

AtomSel *

)

Definition at line 50 of file DrawMolItem.C.
References atomColor, atomRep, atomSel, COL_REGEN, create_modified_CR_spline_basis, Displayable::isOn, MAXCOLORS, MOL_REGEN, name, BaseMolecule::nAtoms, NULL, SEL_REGEN, spline_basis, and stringdup.

DrawMolItem::~DrawMolItem ( void ) [virtual]

Definition at line 97 of file DrawMolItem.C.
References atomColor, atomRep, atomSel, name, NULL, and ResizeArray< TubeIndexList * >::num.

Member Function Documentation

int DrawMolItem::atom_displayed ( int )

if Nth atom is displayed in ANY rep.

Definition at line 1016 of file DrawMolItem.C.
References atomSel, BaseMolecule::nAtoms, NULL, and AtomSel::on.

int DrawMolItem::change_color ( AtomColor * )

change coloring method.

Definition at line 841 of file DrawMolItem.C.
References atomColor, and COL_REGEN.
Referenced by DrawMolecule::change_rep, do_color_changed, and do_color_rgb_changed.

void DrawMolItem::change_pbc ( ) [inline]

the pbc parameters in Timestep have changed; update the transformation matrices accordingly (but no need to regenerate display lists).

Definition at line 370 of file DrawMolItem.h.
Referenced by DrawMolecule::change_pbc, and set_pbc.

int DrawMolItem::change_rep ( AtomRep * )

change representation method.

Definition at line 952 of file DrawMolItem.C.
References atomRep, Surf::clear, MSMSInterface::clear, AtomRep::method, AtomRep::MSMS, NULL, ResizeArray< TubeIndexList * >::num, AtomRep::ORBITAL, REP_REGEN, AtomRep::STRUCTURE, AtomRep::SURF, and AtomRep::TUBE.
Referenced by DrawMolecule::change_rep.

int DrawMolItem::change_sel ( const char * )

change atom selection.

Definition at line 1000 of file DrawMolItem.C.
References atomSel, AtomSel::change, AtomSel::NO_PARSE, DrawMolecule::notify, and SEL_REGEN.
Referenced by DrawMolecule::change_rep.

void DrawMolItem::change_ss ( ) [inline]

the secondary structure for the molecule has changed.

Definition at line 373 of file DrawMolItem.h.
Referenced by DrawMolecule::recalc_ss.

void DrawMolItem::change_traj ( ) [inline]

timesteps have been added or removed from the parent molecule.

Definition at line 379 of file DrawMolItem.h.

void DrawMolItem::change_ts ( ) [inline]

the currently displayed timestep has changed.

Definition at line 376 of file DrawMolItem.h.
Referenced by DrawMolecule::change_ts.

void DrawMolItem::do_color_changed ( int ) [protected, virtual]

Reimplemented from Displayable.
Definition at line 789 of file DrawMolItem.C.
References atomColor, Scene::category_index, change_color, COL_REGEN, AtomColor::current_color_use, and Displayable::scene.

void DrawMolItem::do_color_rgb_changed ( int ) [protected, virtual]

Reimplemented from Displayable.
Definition at line 803 of file DrawMolItem.C.
References atomColor, Scene::category_index, Scene::category_item_value, change_color, COL_REGEN, AtomColor::color, BaseMolecule::nAtoms, and Displayable::scene.

void DrawMolItem::do_color_scale_changed ( ) [protected, virtual]

Reimplemented from Displayable.
Definition at line 831 of file DrawMolItem.C.
References atomColor, COL_REGEN, AtomColor::find, and AtomColor::uses_colorscale.

void DrawMolItem::force_recalc ( int )

force a recalculation of everything.

Definition at line 1011 of file DrawMolItem.C.
Referenced by DrawMolecule::force_recalc, VMDApp::molrep_reset_scaleminmax, VMDApp::molrep_set_colorupdate, VMDApp::molrep_set_scaleminmax, and VMDApp::molrep_set_smoothing.

const char* DrawMolItem::get_drawframes ( ) const [inline]

Definition at line 357 of file DrawMolItem.h.
Referenced by VMDApp::molrep_get_drawframes, and GraphicsFltkMenu::update_rep.

int DrawMolItem::get_pbc ( ) const

Definition at line 155 of file DrawMolItem.C.
References Displayable::cmdList, and VMDDisplayList::pbc.
Referenced by VMDApp::molrep_get_pbc, and GraphicsFltkMenu::update_pbc.

int DrawMolItem::get_pbc_images ( ) const

Definition at line 165 of file DrawMolItem.C.
References Displayable::cmdList, and VMDDisplayList::npbc.
Referenced by VMDApp::molrep_get_pbc_images, and GraphicsFltkMenu::update_pbc.

int DrawMolItem::get_smoothing ( ) const [inline]

Definition at line 349 of file DrawMolItem.h.
Referenced by VMDApp::molrep_get_smoothing, VMDApp::molrep_set_smoothing, and GraphicsFltkMenu::update_rep.

virtual void DrawMolItem::pick_end ( PickMode * p,

DisplayDevice * d

) [inline, virtual]

When picked, pass my parent molecule to the pick mode.

Reimplemented from Pickable.
Definition at line 403 of file DrawMolItem.h.
References PickMode::pick_molecule_end.

virtual void DrawMolItem::pick_move ( PickMode * p,

DisplayDevice * d,

int tag,

int dim,

const float * pos

) [inline, virtual]

When picked, pass my parent molecule to the pick mode.

Reimplemented from Pickable.
Definition at line 398 of file DrawMolItem.h.
References PickMode::pick_molecule_move.

virtual void DrawMolItem::pick_start ( PickMode * p,

DisplayDevice * d,

int btn,

int tag,

const int * cell,

int dim,

const float * pos

) [inline, virtual]

When picked, pass my parent molecule to the pick mode.

Reimplemented from Pickable.
Definition at line 392 of file DrawMolItem.h.
References PickMode::pick_molecule_start.

int DrawMolItem::pickable_on ( ) [virtual]

override pickable_on so that it returns true only when both the rep and the molecule are on.

Reimplemented from Displayable.
Definition at line 3101 of file DrawMolItem.C.
References Displayable::displayed.

void DrawMolItem::prepare ( ) [virtual]

prepare for drawing, do updates.

Reimplemented from Displayable.
Definition at line 862 of file DrawMolItem.C.
References atomColor, atomRep, Displayable::cmdList, COL_REGEN, Displayable::displayed, Molecule::file_in_progress, AtomRep::method, AtomColor::method, MOL_REGEN, Displayable::need_matrix_recalc, AtomRep::NEWCARTOON, VMDDisplayList::pbc, AtomColor::PHYSICALTIME, AtomColor::STRUCTURE, AtomRep::STRUCTURE, AtomColor::THROB, AtomColor::TIMESTEP, AtomColor::USER, AtomColor::USER2, AtomColor::USER3, AtomColor::USER4, and AtomColor::VELOCITY.

int DrawMolItem::representation_index ( void )

which representation this is.

Definition at line 851 of file DrawMolItem.C.
References DrawMolecule::component, and DrawMolecule::components.

void DrawMolItem::set_drawframes ( const char * frames )

Controls for drawing a subset of the molecule's frames. Pass a list of frames to be drawn, or "now" to draw just the current frame (the default). Always succeeds, invalid or out of range frames are ignored.

Definition at line 239 of file DrawMolItem.C.
References MOL_REGEN, and stringdup.
Referenced by VMDApp::molrep_set_drawframes.

void DrawMolItem::set_pbc ( int )

Controls for display of periodic boundary conditions. Uses the PBC_x defines in VMDDisplayList.

Definition at line 145 of file DrawMolItem.C.
References change_pbc, Displayable::cmdList, DrawMolecule::notify, and VMDDisplayList::pbc.
Referenced by VMDApp::molrep_set_pbc.

void DrawMolItem::set_pbc_images ( int )

Set the number of of periodic image replicas. Must be 1 or higher.

Definition at line 159 of file DrawMolItem.C.
References Displayable::cmdList, Displayable::need_matrix_recalc, DrawMolecule::notify, and VMDDisplayList::npbc.
Referenced by VMDApp::molrep_set_pbc_images.

int DrawMolItem::set_smoothing ( int n ) [inline]

Definition at line 342 of file DrawMolItem.h.
Referenced by VMDApp::molrep_set_smoothing.

Member Data Documentation

AtomColor* DrawMolItem::atomColor

atom coloring method to use.

Definition at line 53 of file DrawMolItem.h.
Referenced by add_rep_to_browser, change_color, do_color_changed, do_color_rgb_changed, do_color_scale_changed, DrawMolItem, molinfo_get, VMDApp::molrep_get_color, VMDApp::molrep_get_colorupdate, VMDApp::molrep_get_scaleminmax, VMDApp::molrep_reset_scaleminmax, VMDApp::molrep_set_colorupdate, VMDApp::molrep_set_scaleminmax, prepare, GraphicsFltkMenu::update_rep, and ~DrawMolItem.

AtomRep* DrawMolItem::atomRep

atom representation to use.

Definition at line 54 of file DrawMolItem.h.
Referenced by add_rep_to_browser, change_rep, DrawMolItem, molinfo_get, VMDApp::molrep_get_style, prepare, GraphicsFltkMenu::update_rep, and ~DrawMolItem.

AtomSel* DrawMolItem::atomSel

atom selection to use.

Definition at line 55 of file DrawMolItem.h.
Referenced by add_rep_to_browser, Tool::assign_rep, atom_displayed, change_sel, DrawMolItem, molinfo_get, VMDApp::molrep_get_selection, VMDApp::molrep_get_selupdate, VMDApp::molrep_numselected, VMDApp::molrep_set_selupdate, PickModeMoveRep::rotate, Tool::target, PickModeMoveRep::translate, Tool::tug, GraphicsFltkMenu::update_rep, and ~DrawMolItem.

char DrawMolItem::commentBuffer[1024]

buffer for comments.

Definition at line 57 of file DrawMolItem.h.

char* DrawMolItem::name

name of rep, used to identify uniquely.

Definition at line 59 of file DrawMolItem.h.
Referenced by Tool::assign_rep, DrawMolItem, DrawMolecule::get_component_name, and ~DrawMolItem.

int DrawMolItem::repNumber

current representation ID.

Definition at line 56 of file DrawMolItem.h.

float DrawMolItem::spline_basis[4][4] [protected]

spline basis used for ribbons/tubes.

Definition at line 409 of file DrawMolItem.h.
Referenced by DrawMolItem.

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

Generated on Mon May 20 01:46:59 2013 for VMD (current) by

DrawMolItem Class Reference

Public Types

Public Methods

Public Attributes

Protected Methods

Protected Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation