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GeometryMol Class Reference

Base class for objects that make atomic measurements in a molecule. More...

#include <GeometryMol.h>

Inheritance diagram for GeometryMol:

List of all members.

Public Methods
int	items (void)
	number of items in this object. More...
int	com_index (int i)
	direct access to the component ids. More...
int	obj_index (int i)
	direct access to the object ids. More...
float	value (void)
	most recent value. More...
int	has_value (void)
	do we have a useful value to print? More...
virtual float	calculate (void)
	recalculate the value of this geometry, and return it. More...
virtual void	set_pick (void)
	if so, call this command to set the variable(s). More...
	GeometryMol (int, int , int , const int cells, MoleculeList mlist, CommandQueue , Displayable )
	constructor: # items, molecule list to use, command queue for events. More...
virtual	~GeometryMol (void)
const char *	name (void)
	return the name of this geometry marker; by default, just blank. More...
const char *	unique_name (void)
	return 'unique' name of the marker, which should be different than other names for different markers of this same type. More...
int	ok (void)
	check whether the geometry value can still be calculated. More...
int	calculate_all (ResizeArray< float > &)
	calculate a list of items, if this object can do so. Return success. More...
void	update ()
	redraw the label due to molecule rotations or changes in coordinates. More...
void	set_color (int c)
	set the color used to draw the label. More...
void	set_text_size (float size)
	set the size used for text labels. More...
void	set_text_thickness (float thick)
	set the line thickness used for text labels. More...
const float *	text_offset () const
void	set_text_offset (const float offset[2])
const char *	text_format () const
	text format: the string to be printed for atom labels, with the following substitutions: R = resname r = resname in "camel case" (i.e. only first letter capitalized) d = resid a = atom name q = atom charge i = zero-based atom index. More...
void	set_text_format (const char *aFormat)
Protected Methods
void	geom_set_name (void)
	set the name of this item. More...
void	sort_items (void)
	sort the elements in the list, so that the lowest atom index is first (but preserve the relative order, i.e. a-b-c or c-b-a). More...
Molecule *	check_mol (int m, int a)
	check whether the given molecule m & atom index a is OK if OK, return Molecule pointer; otherwise, return NULL. More...
Molecule *	transformed_atom_coord (int ind, float *)
	for the given pick point, find the TRANSFORMED coords for the given atom. return Molecule pointer if successful, NULL otherwise. More...
Molecule *	normal_atom_coord (int ind, float *)
	for the given Molecule, find the UNTRANSFORMED coords for the given atom. return Molecule pointer if successful, NULL otherwise. Also applies current periodic image for this coordinate. More...
void	display_line (float , float , VMDDisplayList *)
	draws a line between the two given points. More...
void	display_string (const char , VMDDisplayList )
	print given text at current valuePos position. More...
void	atom_full_name (char buf, Molecule mol, int ind)
void	atom_short_name (char buf, Molecule mol, int ind)
void	atom_formatted_name (JString &str, Molecule *mol, int ind)
void	set_pick_selection (int, int, int *)
	methods for setting Tcl variables. More...
void	set_pick_selection ()
void	set_pick_value (double)
virtual void	create_cmd_list ()=0
Protected Attributes
MoleculeList *	molList
CommandQueue *	cmdqueue
int	numItems
	number of components used to calculate geometry value. More...
int *	objIndex
	indices of objects containing the components. More...
int *	comIndex
	indices of the components. More...
int *	cellIndex
	unit cell IDs for the components. More...
float	geomValue
	most recent value. More...
int	hasValue
	do we have a useful value to print? More...
float	valuePos [3]
	location where to print value in the scene. More...
char *	gmName
	name of the molecule geometry monitor. More...
char *	uniquegmName
	unique name of the geometry monitor. More...
ResizeArray< GeometryMonitor * >	monitors
int	my_color

Detailed Description

Base class for objects that make atomic measurements in a molecule.

Definition at line 41 of file GeometryMol.h.

Constructor & Destructor Documentation

GeometryMol::GeometryMol ( int ,

int * ,

int * ,

const int * cells,

MoleculeList * mlist,

CommandQueue * ,

Displayable *

)

constructor: # items, molecule list to use, command queue for events.

Definition at line 52 of file GeometryMol.C.
References ResizeArray< GeometryMonitor * >::append, cellIndex, cmdqueue, comIndex, geom_set_name, geomValue, gmName, hasValue, MoleculeList::mol_from_id, molList, monitors, my_color, n, NULL, numItems, objIndex, DrawMolecule::register_monitor, sort_items, and uniquegmName.

GeometryMol::~GeometryMol ( void ) [virtual]

Definition at line 108 of file GeometryMol.C.
References cellIndex, comIndex, gmName, MoleculeList::mol_from_id, GeometryMonitor::molid, molList, monitors, ResizeArray< GeometryMonitor * >::num, objIndex, uniquegmName, and DrawMolecule::unregister_monitor.

Member Function Documentation

void GeometryMol::atom_formatted_name ( JString & str,

Molecule * mol,

int ind

) [protected]

Definition at line 140 of file GeometryMol.C.
References MolAtom::altlocindex, BaseMolecule::altlocNames, BaseMolecule::atom, MolAtom::atomicnumber, BaseMolecule::atomNames, BaseMolecule::atomTypes, BaseMolecule::beta, MolAtom::chainindex, BaseMolecule::chainNames, BaseMolecule::charge, DrawMolecule::current, Timestep::force, DrawMolecule::frame, get_pte_label, JString::gsub, BaseMolecule::id, BaseMolecule::mass, BaseMolecule::molname, NameList< int >::name, MolAtom::nameindex, NULL, BaseMolecule::occupancy, Timestep::physical_time, Timestep::pos, MolAtom::resid, MolAtom::resnameindex, BaseMolecule::resNames, MolAtom::segnameindex, BaseMolecule::segNames, JString::to_camel, and MolAtom::typeindex.
Referenced by GeometryAtom::create_cmd_list.

void GeometryMol::atom_full_name ( char * buf,

Molecule * mol,

int ind

) [protected]

Definition at line 128 of file GeometryMol.C.
References BaseMolecule::id.
Referenced by geom_set_name.

void GeometryMol::atom_short_name ( char * buf,

Molecule * mol,

int ind

) [protected]

Definition at line 132 of file GeometryMol.C.
References BaseMolecule::atom, BaseMolecule::atomNames, NameList< int >::name, MolAtom::nameindex, MolAtom::resid, MolAtom::resnameindex, and BaseMolecule::resNames.
Referenced by geom_set_name.

virtual float GeometryMol::calculate ( void ) [inline, virtual]

recalculate the value of this geometry, and return it.

Reimplemented in GeometryAngle.
Definition at line 63 of file GeometryMol.h.
Referenced by GeometryList::add_geometry, calculate_all, geom2dict, GeometryMonitor::notify, and text_cmd_label.

int GeometryMol::calculate_all ( ResizeArray< float > & )

calculate a list of items, if this object can do so. Return success.

Definition at line 426 of file GeometryMol.C.
References ResizeArray::append, calculate, DrawMolecule::frame, has_value, items, MoleculeList::mol_from_id, molList, n, DrawMolecule::numframes, objIndex, and DrawMolecule::override_current_frame.
Referenced by getvalues, and text_cmd_label.

Molecule * GeometryMol::check_mol ( int m,

int a

) [protected]

check whether the given molecule m & atom index a is OK if OK, return Molecule pointer; otherwise, return NULL.

Definition at line 322 of file GeometryMol.C.
References MoleculeList::mol_from_id, molList, BaseMolecule::nAtoms, and NULL.
Referenced by geom_set_name, normal_atom_coord, and ok.

int GeometryMol::com_index ( int i ) [inline]

direct access to the component ids.

Definition at line 47 of file GeometryMol.h.
References comIndex.
Referenced by dict2geom, and geom2dict.

virtual void GeometryMol::create_cmd_list ( ) [protected, pure virtual]

Implemented in GeometryAngle.
Referenced by update.

void GeometryMol::display_line ( float * ,

float * ,

VMDDisplayList *

) [protected]

draws a line between the two given points.

Definition at line 382 of file GeometryMol.C.
References DispCmdLine::putdata.
Referenced by GeometrySpring::create_cmd_list, GeometryDihedral::create_cmd_list, GeometryBond::create_cmd_list, and GeometryAngle::create_cmd_list.

void GeometryMol::display_string ( const char * ,

VMDDisplayList *

) [protected]

print given text at current valuePos position.

Definition at line 389 of file GeometryMol.C.
References DispCmdText::putdata, and valuePos.
Referenced by GeometrySpring::create_cmd_list, GeometryDihedral::create_cmd_list, GeometryBond::create_cmd_list, GeometryAtom::create_cmd_list, and GeometryAngle::create_cmd_list.

void GeometryMol::geom_set_name ( void ) [protected]

set the name of this item.

Definition at line 250 of file GeometryMol.C.
References atom_full_name, atom_short_name, cellIndex, check_mol, comIndex, gmName, items, objIndex, stringdup, and uniquegmName.
Referenced by GeometryMol.

int GeometryMol::has_value ( void ) [inline]

do we have a useful value to print?

Definition at line 60 of file GeometryMol.h.
References hasValue.
Referenced by GeometryList::add_geometry, calculate_all, getvalues, and text_cmd_label.

int GeometryMol::items ( void ) [inline]

number of items in this object.

Definition at line 44 of file GeometryMol.h.
References numItems.
Referenced by calculate_all, dict2geom, geom2dict, geom_set_name, sort_items, and text_cmd_label.

const char * GeometryMol::name ( void )

return the name of this geometry marker; by default, just blank.

Definition at line 398 of file GeometryMol.C.
References gmName.
Referenced by GeometryList::add_geometry, and unique_name.

Molecule * GeometryMol::normal_atom_coord ( int ind,

float *

) [protected]

for the given Molecule, find the UNTRANSFORMED coords for the given atom. return Molecule pointer if successful, NULL otherwise. Also applies current periodic image for this coordinate.

Definition at line 356 of file GeometryMol.C.
References cellIndex, check_mol, comIndex, DrawMolecule::current, Timestep::get_transform_from_cell, mat, Matrix4::multpoint3d, NULL, objIndex, and Timestep::pos.
Referenced by GeometrySpring::calculate, GeometryDihedral::calculate, GeometryBond::calculate, GeometryAngle::calculate, and transformed_atom_coord.

int GeometryMol::obj_index ( int i ) [inline]

direct access to the object ids.

Definition at line 52 of file GeometryMol.h.
References objIndex.
Referenced by dict2geom, and geom2dict.

int GeometryMol::ok ( void )

check whether the geometry value can still be calculated.

Definition at line 411 of file GeometryMol.C.
References check_mol, comIndex, numItems, and objIndex.
Referenced by GeometryList::add_geometry, geom2dict, GeometryList::prepare, and text_cmd_label.

void GeometryMol::set_color ( int c ) [inline]

set the color used to draw the label.

Definition at line 145 of file GeometryMol.h.
References my_color, and update.
Referenced by GeometryList::add_geometry.

virtual void GeometryMol::set_pick ( void ) [inline, virtual]

if so, call this command to set the variable(s).

Reimplemented in GeometryAngle.
Definition at line 66 of file GeometryMol.h.
Referenced by GeometryList::add_geometry.

void GeometryMol::set_pick_selection ( ) [protected]

Definition at line 480 of file GeometryMol.C.
References cmdqueue, and CommandQueue::runcommand.
Referenced by GeometrySpring::set_pick, GeometryDihedral::set_pick, GeometryBond::set_pick, GeometryAtom::set_pick, and GeometryAngle::set_pick.

void GeometryMol::set_pick_selection ( int ,

int ,

int *

) [protected]

methods for setting Tcl variables.

Definition at line 476 of file GeometryMol.C.
References atoms, cmdqueue, num, and CommandQueue::runcommand.

void GeometryMol::set_pick_value ( double ) [protected]

Definition at line 484 of file GeometryMol.C.
References cmdqueue, and CommandQueue::runcommand.
Referenced by GeometrySpring::set_pick, GeometryDihedral::set_pick, GeometryBond::set_pick, and GeometryAngle::set_pick.

void GeometryMol::set_text_format ( const char * aFormat ) [inline]

Definition at line 171 of file GeometryMol.h.
References update.
Referenced by GeometryList::setTextFormat.

void GeometryMol::set_text_offset ( const float offset[2] ) [inline]

Definition at line 155 of file GeometryMol.h.
References update.
Referenced by GeometryList::setTextOffset.

void GeometryMol::set_text_size ( float size ) [inline]

set the size used for text labels.

Definition at line 148 of file GeometryMol.h.
References size, and update.
Referenced by GeometryList::add_geometry, and GeometryList::setTextSize.

void GeometryMol::set_text_thickness ( float thick ) [inline]

set the line thickness used for text labels.

Definition at line 151 of file GeometryMol.h.
References update.
Referenced by GeometryList::add_geometry, and GeometryList::setTextThickness.

void GeometryMol::sort_items ( void ) [protected]

sort the elements in the list, so that the lowest atom index is first (but preserve the relative order, i.e. a-b-c or c-b-a).

Definition at line 297 of file GeometryMol.C.
References cellIndex, comIndex, items, and objIndex.
Referenced by GeometryMol.

const char* GeometryMol::text_format ( ) const [inline]

text format: the string to be printed for atom labels, with the following substitutions: R = resname r = resname in "camel case" (i.e. only first letter capitalized) d = resid a = atom name q = atom charge i = zero-based atom index.

Definition at line 170 of file GeometryMol.h.
Referenced by GeometryList::getTextFormat.

const float* GeometryMol::text_offset ( ) const [inline]

Definition at line 153 of file GeometryMol.h.
Referenced by GeometryList::getTextOffset.

Molecule * GeometryMol::transformed_atom_coord ( int ind,

float *

) [protected]

for the given pick point, find the TRANSFORMED coords for the given atom. return Molecule pointer if successful, NULL otherwise.

Definition at line 335 of file GeometryMol.C.
References DrawMolecule::atom_displayed, comIndex, normal_atom_coord, NULL, and Displayable::tm.
Referenced by GeometrySpring::create_cmd_list, GeometryDihedral::create_cmd_list, GeometryBond::create_cmd_list, GeometryAtom::create_cmd_list, and GeometryAngle::create_cmd_list.

const char * GeometryMol::unique_name ( void )

return 'unique' name of the marker, which should be different than other names for different markers of this same type.

Definition at line 405 of file GeometryMol.C.
References name, and uniquegmName.
Referenced by GeometryList::add_geometry.

void GeometryMol::update ( ) [inline]

redraw the label due to molecule rotations or changes in coordinates.

Definition at line 142 of file GeometryMol.h.
References create_cmd_list.
Referenced by GeometryMonitor::notify, set_color, set_text_format, set_text_offset, set_text_size, and set_text_thickness.

float GeometryMol::value ( void ) [inline]

most recent value.

Definition at line 57 of file GeometryMol.h.
References geomValue.

Member Data Documentation

int* GeometryMol::cellIndex [protected]

unit cell IDs for the components.

Definition at line 75 of file GeometryMol.h.
Referenced by geom_set_name, GeometryMol, normal_atom_coord, sort_items, and ~GeometryMol.

CommandQueue* GeometryMol::cmdqueue [protected]

Definition at line 70 of file GeometryMol.h.
Referenced by GeometryMol, set_pick_selection, and set_pick_value.

int* GeometryMol::comIndex [protected]

indices of the components.

Definition at line 74 of file GeometryMol.h.
Referenced by com_index, GeometryAtom::create_cmd_list, geom_set_name, GeometryMol, normal_atom_coord, ok, GeometrySpring::prepare, GeometrySpring::set_pick, GeometryDihedral::set_pick, GeometryBond::set_pick, GeometryAtom::set_pick, GeometryAngle::set_pick, sort_items, transformed_atom_coord, and ~GeometryMol.

float GeometryMol::geomValue [protected]

most recent value.

Definition at line 76 of file GeometryMol.h.
Referenced by GeometrySpring::calculate, GeometryDihedral::calculate, GeometryBond::calculate, GeometryAngle::calculate, GeometrySpring::create_cmd_list, GeometryDihedral::create_cmd_list, GeometryBond::create_cmd_list, GeometryAngle::create_cmd_list, GeometryMol, GeometrySpring::set_pick, GeometryDihedral::set_pick, GeometryBond::set_pick, GeometryAngle::set_pick, and value.

char* GeometryMol::gmName [protected]

name of the molecule geometry monitor.

Definition at line 79 of file GeometryMol.h.
Referenced by geom_set_name, GeometryMol, name, and ~GeometryMol.

int GeometryMol::hasValue [protected]

do we have a useful value to print?

Definition at line 77 of file GeometryMol.h.
Referenced by GeometryAtom::GeometryAtom, GeometryMol, and has_value.

MoleculeList* GeometryMol::molList [protected]

Definition at line 69 of file GeometryMol.h.
Referenced by calculate_all, check_mol, GeometryMol, GeometrySpring::prepare, and ~GeometryMol.

ResizeArray<GeometryMonitor *> GeometryMol::monitors [protected]

Definition at line 178 of file GeometryMol.h.
Referenced by GeometryMol, and ~GeometryMol.

int GeometryMol::my_color [protected]

Definition at line 179 of file GeometryMol.h.
Referenced by GeometryDihedral::create_cmd_list, GeometryBond::create_cmd_list, GeometryAtom::create_cmd_list, GeometryAngle::create_cmd_list, GeometryMol, and set_color.

int GeometryMol::numItems [protected]

number of components used to calculate geometry value.

Definition at line 72 of file GeometryMol.h.
Referenced by GeometryMol, items, and ok.

int* GeometryMol::objIndex [protected]

indices of objects containing the components.

Definition at line 73 of file GeometryMol.h.
Referenced by calculate_all, geom_set_name, GeometryMol, normal_atom_coord, obj_index, ok, GeometrySpring::prepare, GeometrySpring::set_pick, GeometryDihedral::set_pick, GeometryBond::set_pick, GeometryAtom::set_pick, GeometryAngle::set_pick, sort_items, and ~GeometryMol.

char* GeometryMol::uniquegmName [protected]

unique name of the geometry monitor.

Definition at line 80 of file GeometryMol.h.
Referenced by geom_set_name, GeometryMol, unique_name, and ~GeometryMol.

float GeometryMol::valuePos[3] [protected]

location where to print value in the scene.

Definition at line 78 of file GeometryMol.h.
Referenced by GeometrySpring::create_cmd_list, GeometryDihedral::create_cmd_list, GeometryBond::create_cmd_list, GeometryAtom::create_cmd_list, GeometryAngle::create_cmd_list, and display_string.

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

Generated on Wed Apr 24 02:44:54 2024 for VMD (current) by

GeometryMol Class Reference

Public Methods

Protected Methods

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation