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DrawMolecule Class Reference

Subclass of BaseMolecule and Displayable for drawing a molecule. More...

#include <DrawMolecule.h>

Inheritance diagram for DrawMolecule:

List of all members.

Public Methods
	DrawMolecule (VMDApp *, Displayable *)
	constructor ... pass in a VMDApp * and a parent displayable. More...
virtual	~DrawMolecule ()
wkf_threadpool_t *	cuda_devpool (void)
	Query CUDA device pool pointer. More...
int	atom_displayed (int)
	return whether the Nth atom is displayed. This is true if ANY representation is displaying the given atom. More...
int	components (void)
	total number of components. More...
DrawMolItem *	component (int)
	return Nth component ... change to proper return type. More...
DrawMolItem *	component_from_pickable (const Pickable *)
	return the component that matches the given Pickable, or NULL if no match. More...
int	get_component_by_name (const char *)
	retrieve the index of the component with the given name. Returns -1 on failure. More...
const char *	get_component_name (int)
	Get the name of the given component. Names are initially "repN", where N starts at 0 and increases each time a rep is created. Return NULL if the index is invalid. More...
int	del_rep (int)
	delete the Nth representation ... return success. More...
void	add_rep (AtomColor *, AtomRep *, AtomSel *, const Material *)
	Add a new representation (component). This always succeeds, since all parameters must have already been verified as valid. The rep takes over ownership of the parameter objects (except Material). More...
int	change_rep (int, AtomColor *, AtomRep *, const char *sel)
	change the Nth representation ... return success. if any object is NULL, that characteristic is not changed. More...
int	show_rep (int repid, int onoff)
	turn the Nth representation on or off. Return success. More...
void	force_recalc (int)
	force a recalc of all representations For MOL_REGEN, this also invalidates the value of cov and scale_factor,. More...
void	change_pbc ()
	Tell reps that the periodic image parameters have been changed. More...
void	change_ts ()
	Tell reps that the currently displayed timestep has changed. More...
int	highlighted_rep () const
	Return the highlighted rep for this molecule. Returns -1 if there is no such rep. More...
int	numframes () const
	number of frames in the files associatd with the molecule. More...
int	frame () const
	index of current frame. More...
void	override_current_frame (int frame)
	change current frame without firing callbacks. More...
Timestep *	current ()
	get the current frame. More...
Timestep *	get_frame (int n)
	get the specifed frame. More...
Timestep *	get_last_frame ()
	get the last frame. More...
void	delete_frame (int n)
	delete the nth frame. More...
void	append_frame (Timestep *)
	append the given frame. More...
void	duplicate_frame (const Timestep *)
	duplicate the given frame passing NULL adds a 'null' frame (i.e. all zeros). More...
float	scale_factor ()
	scaling factor required to make the molecule fit within (-1 ... 1). More...
int	cov (float &, float &, float &)
	center of volume of this molecule. Return success. Fails if there aren't any coordinates, graphics, or volumetric data sets to compute the cov from. More...
int	recalc_bonds (void)
	recalculate bonds via distance bond search based on current timestep. More...
int	need_secondary_structure (int)
	request ss calculation. Return success. More...
void	invalidate_ss ()
	invalidate current secondary structure when structure is changed. More...
int	recalc_ss ()
	recalculate the secondary structure using current coordinates Return success. More...
MoleculeGraphics *	moleculeGraphics () const
virtual void	prepare ()
	specific preparations, called by draw_prepare, supplied by derived class. More...
void	register_monitor (DrawMoleculeMonitor *)
	register monitors. More...
void	unregister_monitor (DrawMoleculeMonitor *)
	unregister monitors. More...
void	notify ()
Public Attributes
int	active
	is this molecule active? Used by MoleculeList. More...
QuickSurf	qsurf
	QuickSurf object shared by all reps in the same molecule. We may have to do further refactoring of the code that manages the QuickSurf GPU resources since having multiple instances can still put excessive pressure on available GPU memory. One solution would be to have a VMDApp method to access GPU memory buffers that are only needed for very short-term fast-running calculations but that must be completely pre-allocated to support fast trajectory playback, etc. More...
Protected Attributes
VMDApp *	app

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Detailed Description

Subclass of BaseMolecule and Displayable for drawing a molecule.

Definition at line 52 of file DrawMolecule.h.

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Constructor & Destructor Documentation

DrawMolecule::DrawMolecule (  VMDApp *   , Displayable *    )

constructor ... pass in a VMDApp * and a parent displayable. Definition at line 48 of file DrawMolecule.C. References active, PickList::add_pickable, BaseMolecule::need_find_bonds, and VMDApp::pickList.

DrawMolecule::~DrawMolecule (    )  [virtual]

Definition at line 67 of file DrawMolecule.C. References app, component, components, ResizeArray< Timestep * >::num, VMDApp::pickList, ResizeArray< Timestep * >::remove, and PickList::remove_pickable.

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Member Function Documentation

void DrawMolecule::add_rep (  AtomColor *   , AtomRep *   , AtomSel *   , const Material *    )

Add a new representation (component). This always succeeds, since all parameters must have already been verified as valid. The rep takes over ownership of the parameter objects (except Material). Definition at line 138 of file DrawMolecule.C. References PickList::add_pickable, app, ResizeArray< DrawMolItem * >::append, Displayable::change_material, and VMDApp::pickList. Referenced by MoleculeList::add_rep.

void DrawMolecule::append_frame (  Timestep *    )

append the given frame. Definition at line 278 of file DrawMolecule.C. References app, ResizeArray< Timestep * >::append, change_ts, VMDApp::commandQueue, BaseMolecule::need_find_bonds, NULL, ResizeArray< Timestep * >::num, override_current_frame, CommandQueue::runcommand, VMDApp::scene_resetview_newmoldata, and vmd_bond_search. Referenced by IMDMgr::check_event, cmd_rawtimestep, duplicate_frame, and CoorPluginData::next.

int DrawMolecule::atom_displayed (  int    )

return whether the Nth atom is displayed. This is true if ANY representation is displaying the given atom. Definition at line 113 of file DrawMolecule.C. References components, Displayable::displayed, and BaseMolecule::nAtoms. Referenced by GeometryMol::transformed_atom_coord.

void DrawMolecule::change_pbc (    )

Tell reps that the periodic image parameters have been changed. Definition at line 197 of file DrawMolecule.C. References DrawMolItem::change_pbc, component, components, and notify.

int DrawMolecule::change_rep (  int   , AtomColor *   , AtomRep *   , const char *    sel )

change the Nth representation ... return success. if any object is NULL, that characteristic is not changed. Definition at line 163 of file DrawMolecule.C. References DrawMolItem::change_color, DrawMolItem::change_rep, DrawMolItem::change_sel, and component. Referenced by MoleculeList::change_rep, MoleculeList::change_repcolor, MoleculeList::change_repmethod, and MoleculeList::change_repsel.

void DrawMolecule::change_ts (    )

Tell reps that the currently displayed timestep has changed. Definition at line 209 of file DrawMolecule.C. References app, DrawMolItem::change_ts, VMDApp::commandQueue, component, components, BaseMolecule::id, notify, DrawForce::prepare, MoleculeGraphics::prepare, and CommandQueue::runcommand. Referenced by append_frame, delete_frame, Animation::goto_frame, molinfo_set, and set_frame.

DrawMolItem * DrawMolecule::component (  int    )

return Nth component ... change to proper return type. Definition at line 90 of file DrawMolecule.C. References components, and NULL. Referenced by GraphicsFltkMenu::act_on_command, Tool::assign_rep, change_pbc, change_rep, MoleculeList::change_repmat, change_ts, MoleculeList::check_pickable, del_rep, force_recalc, get_component_name, molinfo_get, VMDApp::molrep_get_clipplane, VMDApp::molrep_get_color, VMDApp::molrep_get_colorupdate, VMDApp::molrep_get_drawframes, VMDApp::molrep_get_material, VMDApp::molrep_get_pbc, VMDApp::molrep_get_pbc_images, VMDApp::molrep_get_scaleminmax, VMDApp::molrep_get_selection, VMDApp::molrep_get_selupdate, VMDApp::molrep_get_smoothing, VMDApp::molrep_get_style, VMDApp::molrep_is_shown, VMDApp::molrep_numselected, VMDApp::molrep_reset_scaleminmax, VMDApp::molrep_set_clipcenter, VMDApp::molrep_set_clipcolor, VMDApp::molrep_set_clipnormal, VMDApp::molrep_set_clipstatus, VMDApp::molrep_set_colorupdate, VMDApp::molrep_set_drawframes, VMDApp::molrep_set_pbc, VMDApp::molrep_set_pbc_images, VMDApp::molrep_set_scaleminmax, VMDApp::molrep_set_selupdate, VMDApp::molrep_set_smoothing, recalc_ss, DrawMolItem::representation_index, PickModeMoveRep::rotate, show_rep, Tool::target, PickModeMoveRep::translate, Tool::tug, GraphicsFltkMenu::update_pbc, GraphicsFltkMenu::update_rep, GraphicsFltkMenu::update_repbrowser, and ~DrawMolecule.

DrawMolItem * DrawMolecule::component_from_pickable (  const Pickable *    )

return the component that matches the given Pickable, or NULL if no match. Definition at line 99 of file DrawMolecule.C. References components, and NULL.

int DrawMolecule::components (  void    )  [inline]

total number of components. Definition at line 131 of file DrawMolecule.h. References ResizeArray::num. Referenced by atom_displayed, change_pbc, change_ts, MoleculeList::check_pickable, component, component_from_pickable, force_recalc, VMDApp::molecule_load, molinfo_get, VMDApp::num_molreps, recalc_ss, DrawMolItem::representation_index, PickModeMoveRep::rotate, PickModeMoveRep::translate, GraphicsFltkMenu::update_repbrowser, GraphicsFltkMenu::update_repindex, and ~DrawMolecule.

int DrawMolecule::cov (  float &   , float &   , float &    )

center of volume of this molecule. Return success. Fails if there aren't any coordinates, graphics, or volumetric data sets to compute the cov from. Definition at line 391 of file DrawMolecule.C. References MoleculeGraphics::cov, data, ResizeArray< VolumetricData * >::num, MoleculeGraphics::num_elements, VolumetricData::origin, BaseMolecule::volumeList, VolumetricData::xaxis, VolumetricData::yaxis, and VolumetricData::zaxis. Referenced by MoleculeList::center_from_top_molecule_reps, and AtomColor::find.

wkf_threadpool_t * DrawMolecule::cuda_devpool (  void    )

Query CUDA device pool pointer. Definition at line 107 of file DrawMolecule.C. References app, VMDApp::cuda, CUDAAccel::get_cuda_devpool, and NULL. Referenced by Orbital::calculate_mo.

Timestep* DrawMolecule::current (    )  [inline]

get the current frame. Definition at line 193 of file DrawMolecule.h. References NULL, and ResizeArray::num. Referenced by GeometryMol::atom_formatted_name, AtomColor::find, Molecule::get_new_frames, VMDApp::molecule_dupframe, need_secondary_structure, normal_atom_coord, GeometryMol::normal_atom_coord, parse_timestep, PickModeCenter::pick_molecule_end, PickModeMove::pick_molecule_move, PickModeForceFragment::pick_molecule_move, PickModeForceResidue::pick_molecule_move, PickModeForceAtom::pick_molecule_move, print_atom_info, recalc_bonds, PickModeMoveRep::rotate, PickModeMoveMolecule::rotate, PickModeMoveFragment::rotate, PickModeMoveResidue::rotate, selframe, Tool::target, AtomSel::timestep, PickModeMoveRep::translate, PickModeMoveMolecule::translate, PickModeMoveFragment::translate, PickModeMoveResidue::translate, PickModeMoveAtom::translate, vmd_volmap_ils, and write_stride_record.

int DrawMolecule::del_rep (  int    )

delete the Nth representation ... return success. Definition at line 125 of file DrawMolecule.C. References app, component, NULL, VMDApp::pickList, ResizeArray< DrawMolItem * >::remove, and PickList::remove_pickable. Referenced by MoleculeList::del_rep.

void DrawMolecule::delete_frame (  int    n )

delete the nth frame. Definition at line 332 of file DrawMolecule.C. References app, change_ts, VMDApp::commandQueue, ResizeArray< Timestep * >::num, ResizeArray< Timestep * >::remove, and CommandQueue::runcommand. Referenced by VMDApp::molecule_deleteframes.

void DrawMolecule::duplicate_frame (  const Timestep *    )

duplicate the given frame passing NULL adds a 'null' frame (i.e. all zeros). Definition at line 319 of file DrawMolecule.C. References append_frame, BaseMolecule::nAtoms, NULL, and Timestep::zero_values. Referenced by VMDApp::molecule_dupframe, and vmd_volmap_ils.

void DrawMolecule::force_recalc (  int    )

force a recalc of all representations For MOL_REGEN, this also invalidates the value of cov and scale_factor,. Definition at line 179 of file DrawMolecule.C. References app, VMDApp::commandQueue, component, components, DrawMolItem::force_recalc, DrawMolItem::MOL_REGEN, Displayable::need_matrix_recalc, CommandQueue::runcommand, and DrawMolItem::SEL_REGEN. Referenced by access_tcl_atomsel, atomsel_set, atomselect_move, atomselect_moveby, IMDMgr::check_event, cmd_rawtimestep, VMDApp::molecule_load, VMDApp::molecule_reanalyze, PickModeAddBond::pick_molecule_end, PickModeMove::pick_molecule_move, py_align, py_move, py_moveby, MolFilePlugin::read_optional_structure, set, and setbonds.

int DrawMolecule::frame (    )  const [inline]

index of current frame. Definition at line 187 of file DrawMolecule.h. Referenced by GeometryMol::atom_formatted_name, GeometryMol::calculate_all, cmd_rawtimestep, AtomColor::find, Animation::frame, measure_energy, measure_geom, measure_pbc2onc, measure_pbc_neighbors, VMDApp::molecule_frame, molinfo_get, and py_write.

int DrawMolecule::get_component_by_name (  const char *    )

retrieve the index of the component with the given name. Returns -1 on failure. Definition at line 233 of file DrawMolecule.C. References ResizeArray< DrawMolItem * >::num. Referenced by VMDApp::molrep_get_by_name.

const char * DrawMolecule::get_component_name (  int    )

Get the name of the given component. Names are initially "repN", where N starts at 0 and increases each time a rep is created. Return NULL if the index is invalid. Definition at line 245 of file DrawMolecule.C. References component, and DrawMolItem::name. Referenced by VMDApp::molrep_get_name.

Timestep* DrawMolecule::get_frame (  int    n )  [inline]

get the specifed frame. Definition at line 200 of file DrawMolecule.h. References NULL, and ResizeArray::num. Referenced by cmd_gettimestep, cmd_rawtimestep, compute_pbcminmax, find_cluster_thr, get_last_frame, measure_avpos, measure_gofr, measure_pbc2onc, measure_pbc_neighbors, measure_rdf, measure_rmsf, minmax, VMDApp::molecule_dupframe, VMDApp::molecule_orblocalize, molinfo_get, molinfo_set, MolFilePlugin::next, CoorPluginData::next, parse_timestep, py_rmsd, GraphicsFltkRepOrbital::regen_orbitallist, selframe, AtomSel::timestep, and vmd_volmap_ils.

Timestep* DrawMolecule::get_last_frame (    )  [inline]

get the last frame. Definition at line 208 of file DrawMolecule.h. References get_frame, and ResizeArray::num. Referenced by IMDMgr::check_event, parse_timestep, selframe, and AtomSel::timestep.

int DrawMolecule::highlighted_rep (    )  const

Return the highlighted rep for this molecule. Returns -1 if there is no such rep. Definition at line 225 of file DrawMolecule.C. References app, VMDApp::highlighted_molid, VMDApp::highlighted_rep, and BaseMolecule::id. Referenced by PickModeMoveRep::rotate, and PickModeMoveRep::translate.

void DrawMolecule::invalidate_ss (    )

invalidate current secondary structure when structure is changed. Definition at line 451 of file DrawMolecule.C. Referenced by VMDApp::molecule_reanalyze, and MolFilePlugin::read_optional_structure.

MoleculeGraphics* DrawMolecule::moleculeGraphics (    )  const [inline]

Definition at line 245 of file DrawMolecule.h. Referenced by MoleculeList::check_pickable, mol_from_id, MolFilePlugin::read_rawgraphics, and tcl_graphics.

int DrawMolecule::need_secondary_structure (  int    )

request ss calculation. Return success. Definition at line 433 of file DrawMolecule.C. References app, current, VMDApp::show_stride_message, and ss_from_stride. Referenced by AtomColor::find, and recalc_ss.

void DrawMolecule::notify (    )

Definition at line 269 of file DrawMolecule.C. References BaseMolecule::id, and ResizeArray< DrawMoleculeMonitor * >::num. Referenced by change_pbc, DrawMolItem::change_sel, change_ts, prepare, DrawMolItem::set_pbc, and DrawMolItem::set_pbc_images.

int DrawMolecule::numframes (    )  const [inline]

number of frames in the files associatd with the molecule. Definition at line 184 of file DrawMolecule.h. References ResizeArray::num. Referenced by GeometryMol::calculate_all, IMDMgr::check_event, cmd_gettimestep, cmd_rawtimestep, CoorPluginData::CoorPluginData, AtomColor::find, Animation::goto_frame, measure_avpos, measure_cluster, measure_energy, measure_geom, measure_gofr, measure_pbc2onc, measure_pbc_neighbors, measure_rdf, measure_rmsf, VMDApp::molecule_deleteframes, VMDApp::molecule_dupframe, VMDApp::molecule_numframes, VMDApp::molecule_orblocalize, VMDApp::molecule_savetrajectory, molinfo_get, MolFilePlugin::next, CoorPluginData::next, Animation::num, py_write, setframe, and MolBrowser::update.

void DrawMolecule::override_current_frame (  int    frame )

change current frame without firing callbacks. Definition at line 258 of file DrawMolecule.C. References ResizeArray< Timestep * >::num, and num. Referenced by append_frame, GeometryMol::calculate_all, Animation::goto_frame, measure_energy, measure_geom, molinfo_set, and set_frame.

void DrawMolecule::prepare (    )  [virtual]

specific preparations, called by draw_prepare, supplied by derived class. Reimplemented from Displayable. Reimplemented in Molecule. Definition at line 252 of file DrawMolecule.C. References Displayable::needUpdate, and notify. Referenced by Molecule::prepare.

int DrawMolecule::recalc_bonds (  void    )

recalculate bonds via distance bond search based on current timestep. Definition at line 419 of file DrawMolecule.C. References BaseMolecule::clear_bonds, BaseMolecule::count_bonds, current, and vmd_bond_search. Referenced by VMDApp::molecule_bondsrecalc.

int DrawMolecule::recalc_ss (    )

recalculate the secondary structure using current coordinates Return success. Definition at line 455 of file DrawMolecule.C. References DrawMolItem::change_ss, component, components, and need_secondary_structure. Referenced by VMDApp::molecule_ssrecalc.

void DrawMolecule::register_monitor (  DrawMoleculeMonitor *    )

register monitors. Definition at line 464 of file DrawMolecule.C. References ResizeArray< DrawMoleculeMonitor * >::append. Referenced by GeometryMol::GeometryMol.

float DrawMolecule::scale_factor (    )

scaling factor required to make the molecule fit within (-1 ... 1). Definition at line 367 of file DrawMolecule.C. References data, dnorm, ResizeArray< VolumetricData * >::num, MoleculeGraphics::num_elements, scale_factor, MoleculeGraphics::scale_factor, BaseMolecule::volumeList, VolumetricData::xaxis, VolumetricData::yaxis, and VolumetricData::zaxis. Referenced by MoleculeList::center_from_top_molecule_reps, and scale_factor.

int DrawMolecule::show_rep (  int    repid, int    onoff )

turn the Nth representation on or off. Return success. Definition at line 150 of file DrawMolecule.C. References component, Displayable::off, and Displayable::on. Referenced by VMDApp::molrep_show.

void DrawMolecule::unregister_monitor (  DrawMoleculeMonitor *    )

unregister monitors. Definition at line 467 of file DrawMolecule.C. References ResizeArray< DrawMoleculeMonitor * >::find, and ResizeArray< DrawMoleculeMonitor * >::remove. Referenced by GeometryMol::~GeometryMol.

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Member Data Documentation

int DrawMolecule::active

is this molecule active? Used by MoleculeList. Definition at line 54 of file DrawMolecule.h. Referenced by MoleculeList::activate, MoleculeList::active, DrawMolecule, Animation::goto_frame, MoleculeList::inactivate, is_active, molinfo_get, and PickModeCenter::pick_molecule_end.

VMDApp* DrawMolecule::app [protected]

Definition at line 68 of file DrawMolecule.h. Referenced by add_rep, append_frame, change_ts, Molecule::close_coor_file, cuda_devpool, del_rep, delete_frame, force_recalc, Molecule::get_new_frames, highlighted_rep, need_secondary_structure, ~DrawMolecule, and Molecule::~Molecule.

QuickSurf DrawMolecule::qsurf

QuickSurf object shared by all reps in the same molecule. We may have to do further refactoring of the code that manages the QuickSurf GPU resources since having multiple instances can still put excessive pressure on available GPU memory. One solution would be to have a VMDApp method to access GPU memory buffers that are only needed for very short-term fast-running calculations but that must be completely pre-allocated to support fast trajectory playback, etc. Definition at line 56 of file DrawMolecule.h.

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

• DrawMolecule.h
• DrawMolecule.C

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