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MoleculeList Class Reference

Manages a list of the molecules being displayed. More...

#include <MoleculeList.h>

List of all members.

Public Methods
void	add_color_names (int)
	put new names from given molecule into color lists. More...
	MoleculeList (VMDApp *, Scene *)
virtual	~MoleculeList (void)
int	num (void)
	return the number of molecules in this list. More...
Molecule *	molecule (int n)
	return the Nth molecule (index runs 0 ... (count-1)). More...
int	mol_index_from_id (int id)
	return the index of the molecule with given ID (-1 if error). More...
Molecule *	mol_from_id (int id)
	return the molecule with given ID (NULL if error). More...
void	add_molecule (Molecule *)
	add a new molecule; return it's position in molList. More...
int	del_molecule (int)
	remove the molecule from the list with given ID. Return success. More...
int	del_all_molecules (void)
	delete all molecules (linear time in worst case). More...
int	set_color (char *)
	get/set current atom coloring method. More...
char *	color (void)
int	set_representation (char *)
	get/set current atom representation method. More...
char *	representation (void)
int	set_selection (const char *)
	get/set current atom selection command. Return success. More...
const char *	selection () const
int	set_material (char *)
	get/set current atom material method. More...
const char *	material (void)
int	set_default_color (const char *)
	default values for new reps. More...
int	set_default_representation (const char *)
int	set_default_selection (const char *)
int	set_default_material (const char *)
const char *	default_color () const
const char *	default_representation () const
const char *	default_selection () const
const char *	default_material () const
int	add_rep (int n)
	add a new graphics representation to the specified molecule. uses the 'current' coloring, representation, and selection settings. More...
int	change_rep (int m, int n)
	change the graphics representation m, for the specified molecule n. uses the 'current' coloring, representation, and selection settings. More...
int	change_repcolor (int m, int n, char *)
	change just the coloring method for the mth rep in the nth molecule. More...
int	change_repmethod (int m, int n, char *)
	change just the representation for the mth rep in the nth molecule. More...
int	change_repsel (int m, int n, const char *)
	change just the selection for the mth rep in the nth molecule. Return success. More...
int	change_repmat (int m, int n, const char *)
	change just the material for the mth rep in the nth molecule. More...
int	del_rep (int m, int n)
	delete a graphics representation m, for the specified molecule n. return success. More...
Molecule *	top (void)
	query or set the top molecule. More...
int	is_top (int n)
int	is_top (Molecule *m)
void	make_top (int n)
void	make_top (Molecule *m)
int	active (int n)
	query/set active status of Nth molecule. More...
int	active (Molecule *m)
void	activate (int n)
void	inactivate (int n)
int	displayed (int n)
	query/set displayed status of Nth molecule. More...
int	displayed (Molecule *m)
void	show (int n)
void	hide (int n)
int	fixed (int n)
	query/set fixed status of Nth molecule. More...
int	fixed (Molecule *m)
void	fix (int n)
void	unfix (int n)
void	center_from_top_molecule_reps (void)
	Sets molecules' tranformations to center and scale properly. More...
void	center_top_molecule (void)
void	center_all_molecules (void)
Molecule *	check_pickable (Pickable *pobj)
	given a pickable, find it and return the Molecule*, or NULL. More...
Public Attributes
NameList< const char * >	resTypes
	mapping of residue names <--> residue types (hydrophobic, neutral, etc.). More...
int	colorCatIndex [NUM_MLCAT]
	color category indices. More...
Protected Methods
void	init_colors ()
	do action when a new color list is provided. More...

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Detailed Description

Manages a list of the molecules being displayed.

Definition at line 47 of file MoleculeList.h.

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Constructor & Destructor Documentation

MoleculeList::MoleculeList (  VMDApp *   , Scene *    )

Definition at line 41 of file MoleculeList.C. References DEFAULT_ATOMCOLOR, DEFAULT_ATOMREP, DEFAULT_ATOMSEL, init_colors, inthash_init, MaterialList::material_name, VMDApp::materialList, NULL, and stringdup.

MoleculeList::~MoleculeList (  void    )  [virtual]

Definition at line 67 of file MoleculeList.C. References inthash_destroy, molecule, and num.

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Member Function Documentation

void MoleculeList::activate (  int    n )  [inline]

Definition at line 222 of file MoleculeList.h. References DrawMolecule::active, molecule, and n. Referenced by VMDApp::molecule_activate.

int MoleculeList::active (  Molecule *    m )  [inline]

Definition at line 221 of file MoleculeList.h. References active.

int MoleculeList::active (  int    n )  [inline]

query/set active status of Nth molecule. Definition at line 220 of file MoleculeList.h. References DrawMolecule::active, molecule, and n. Referenced by active, VMDApp::molecule_is_active, and MolBrowser::update.

void MoleculeList::add_color_names (  int    )

put new names from given molecule into color lists. Definition at line 114 of file MoleculeList.C. References Scene::add_color_item, NameList< const char * >::add_name, BaseMolecule::altlocNames, BaseMolecule::atomNames, BaseMolecule::atomTypes, BaseMolecule::chainNames, colorCatIndex, BaseMolecule::id, MLCAT_CHAINS, MLCAT_CONFORMATIONS, MLCAT_MOLECULES, MLCAT_NAMES, MLCAT_RESNAMES, MLCAT_SEGNAMES, MLCAT_TYPES, molecule, NameList::name, NameList::num, Scene::num_category_items, BaseMolecule::resNames, resTypes, BaseMolecule::segNames, NameList::set_data, NameList< const char * >::typecode, and VISCLRS. Referenced by atomsel_set, and VMDApp::molecule_load.

void MoleculeList::add_molecule (  Molecule *    )

add a new molecule; return it's position in molList. Definition at line 238 of file MoleculeList.C. References ResizeArray< Molecule * >::append, BaseMolecule::id, inthash_insert, make_top, and ResizeArray< Molecule * >::num. Referenced by VMDApp::molecule_from_selection_list, and VMDApp::molecule_new.

int MoleculeList::add_rep (  int    n )

add a new graphics representation to the specified molecule. uses the 'current' coloring, representation, and selection settings. Definition at line 414 of file MoleculeList.C. References DrawMolecule::add_rep, DrawMolecule::app, VMDApp::atomSelParser, AtomSel::change, AtomColor::find, BaseMolecule::id, mat, MaterialList::material, VMDApp::materialList, molecule, and n. Referenced by VMDApp::molecule_addrep.

void MoleculeList::center_all_molecules (  void    )

Definition at line 521 of file MoleculeList.C. References Displayable::add_cent_trans, molecule, Displayable::mult_scale, n, num, and Displayable::reset_transformation. Referenced by VMDApp::scene_resetview.

void MoleculeList::center_from_top_molecule_reps (  void    )

Sets molecules' tranformations to center and scale properly. Definition at line 500 of file MoleculeList.C. References DrawMolecule::cov, DrawMolecule::scale_factor, and z. Referenced by VMDApp::scene_resetview.

void MoleculeList::center_top_molecule (  void    )

Definition at line 512 of file MoleculeList.C. References Displayable::add_cent_trans, Displayable::mult_scale, and Displayable::reset_transformation. Referenced by VMDApp::scene_resetview_newmoldata.

int MoleculeList::change_rep (  int    m, int    n )

change the graphics representation m, for the specified molecule n. uses the 'current' coloring, representation, and selection settings. Definition at line 430 of file MoleculeList.C. References DrawMolecule::change_rep, change_repmat, material, molecule, and n. Referenced by VMDApp::molecule_modrep.

int MoleculeList::change_repcolor (  int    m, int    n, char *    )

change just the coloring method for the mth rep in the nth molecule. Definition at line 439 of file MoleculeList.C. References AtomColor::change, DrawMolecule::change_rep, molecule, n, and NULL. Referenced by VMDApp::molrep_set_color.

int MoleculeList::change_repmat (  int    m, int    n, const char *    )

change just the material for the mth rep in the nth molecule. Definition at line 474 of file MoleculeList.C. References Displayable::change_material, DrawMolecule::component, MaterialList::material, MaterialList::material_index, VMDApp::materialList, molecule, and n. Referenced by change_rep, and VMDApp::molrep_set_material.

int MoleculeList::change_repmethod (  int    m, int    n, char *    )

change just the representation for the mth rep in the nth molecule. Definition at line 451 of file MoleculeList.C. References AtomRep::change, DrawMolecule::change_rep, molecule, n, and NULL. Referenced by VMDApp::molrep_set_style.

int MoleculeList::change_repsel (  int    m, int    n, const char *    )

change just the selection for the mth rep in the nth molecule. Return success. Definition at line 463 of file MoleculeList.C. References VMDApp::atomSelParser, DrawMolecule::change_rep, molecule, n, NULL, and SymbolTable::parse. Referenced by VMDApp::molrep_set_selection.

Molecule * MoleculeList::check_pickable (  Pickable *    pobj )

given a pickable, find it and return the Molecule*, or NULL. Definition at line 534 of file MoleculeList.C. References DrawMolecule::component, DrawMolecule::components, molecule, DrawMolecule::moleculeGraphics, NULL, and num. Referenced by GeometryFltkMenu::act_on_command, get_nearby_atom, PickList::pick_check, print_atom_info, and Tool::target.

char* MoleculeList::color (  void    )  [inline]

Definition at line 150 of file MoleculeList.h. References AtomColor::cmdStr. Referenced by VMDApp::molecule_get_color.

const char* MoleculeList::default_color (    )  const [inline]

Definition at line 169 of file MoleculeList.h. Referenced by VMDApp::molecule_load, and text_cmd_mol.

const char* MoleculeList::default_material (    )  const [inline]

Definition at line 178 of file MoleculeList.h. Referenced by VMDApp::molecule_load, and text_cmd_mol.

const char* MoleculeList::default_representation (    )  const [inline]

Definition at line 172 of file MoleculeList.h. Referenced by VMDApp::molecule_load, and text_cmd_mol.

const char* MoleculeList::default_selection (    )  const [inline]

Definition at line 175 of file MoleculeList.h. Referenced by VMDApp::molecule_load, and text_cmd_mol.

int MoleculeList::del_all_molecules (  void    )

delete all molecules (linear time in worst case). Definition at line 321 of file MoleculeList.C. References inthash_destroy, inthash_init, make_top, molecule, n, NULL, num, and ResizeArray< Molecule * >::remove. Referenced by VMDApp::molecule_delete_all.

int MoleculeList::del_molecule (  int    )

remove the molecule from the list with given ID. Return success. Definition at line 272 of file MoleculeList.C. References BaseMolecule::id, inthash_destroy, inthash_init, inthash_insert, is_top, make_top, mol_from_id, mol_index_from_id, molecule, n, NULL, num, and ResizeArray< Molecule * >::remove. Referenced by VMDApp::molecule_delete.

int MoleculeList::del_rep (  int    m, int    n )

delete a graphics representation m, for the specified molecule n. return success. Definition at line 491 of file MoleculeList.C. References DrawMolecule::del_rep, molecule, n, and NULL. Referenced by VMDApp::molrep_delete.

int MoleculeList::displayed (  Molecule *    m )  [inline]

Definition at line 227 of file MoleculeList.h. References Displayable::displayed.

int MoleculeList::displayed (  int    n )  [inline]

query/set displayed status of Nth molecule. Definition at line 226 of file MoleculeList.h. References Displayable::displayed, displayed, molecule, and n. Referenced by displayed, VMDApp::molecule_is_displayed, and MolBrowser::update.

void MoleculeList::fix (  int    n )  [inline]

Definition at line 234 of file MoleculeList.h. References Displayable::fix, molecule, and n. Referenced by VMDApp::molecule_fix.

int MoleculeList::fixed (  Molecule *    m )  [inline]

Definition at line 233 of file MoleculeList.h. References Displayable::fixed.

int MoleculeList::fixed (  int    n )  [inline]

query/set fixed status of Nth molecule. Definition at line 232 of file MoleculeList.h. References Displayable::fixed, molecule, and n. Referenced by VMDApp::molecule_is_fixed, and MolBrowser::update.

void MoleculeList::hide (  int    n )  [inline]

Definition at line 229 of file MoleculeList.h. References molecule, n, and Displayable::off. Referenced by VMDApp::molecule_display.

void MoleculeList::inactivate (  int    n )  [inline]

Definition at line 223 of file MoleculeList.h. References DrawMolecule::active, inactivate, molecule, and n. Referenced by inactivate, and VMDApp::molecule_activate.

void MoleculeList::init_colors (    )  [protected]

do action when a new color list is provided. Definition at line 85 of file MoleculeList.C. References Scene::add_color_category, Scene::add_color_item, Scene::color_index, colorCatIndex, MLCAT_CHAINS, MLCAT_CONFORMATIONS, MLCAT_ELEMENTS, MLCAT_MOLECULES, MLCAT_NAMES, MLCAT_RESNAMES, MLCAT_RESTYPES, MLCAT_SEGNAMES, MLCAT_SPECIAL, MLCAT_SSTRUCT, MLCAT_SURFACES, and MLCAT_TYPES. Referenced by MoleculeList.

int MoleculeList::is_top (  Molecule *    m )  [inline]

Definition at line 215 of file MoleculeList.h.

int MoleculeList::is_top (  int    n )  [inline]

Definition at line 214 of file MoleculeList.h. References molecule, and n. Referenced by del_molecule, molinfo_get, and MolBrowser::update.

void MoleculeList::make_top (  Molecule *    m )

Definition at line 256 of file MoleculeList.C. References VMDApp::commandQueue, BaseMolecule::id, mol_index_from_id, MoleculeEvent::MOL_TOP, and CommandQueue::runcommand.

void MoleculeList::make_top (  int    n )  [inline]

Definition at line 216 of file MoleculeList.h. References molecule, and n. Referenced by add_molecule, del_all_molecules, del_molecule, VMDApp::molecule_make_top, and py_resetview.

const char * MoleculeList::material (  void    )

Definition at line 408 of file MoleculeList.C. References MaterialList::material_name, and VMDApp::materialList. Referenced by change_rep, and VMDApp::molecule_get_material.

Molecule* MoleculeList::mol_from_id (  int    id )  [inline]

return the molecule with given ID (NULL if error). Definition at line 130 of file MoleculeList.h. References mol_index_from_id, and molecule. Referenced by access_tcl_atomsel, VolMapCreateILS::add_map_to_molecule, assign_atoms, Tool::assign_rep, atomsel_new, atomsel_set, atomselect_move, atomselect_moveby, build_xyzr_from_sel, calc_cc, calc_density_bounds, GeometryMol::calculate_all, calculate_angle, calculate_bond, calculate_dihed, VolMapCreate::calculate_max_radius, VolMapCreate::calculate_minmax, center_of_mass, GeometryMol::check_mol, cmd_gettimestep, cmd_rawtimestep, compute_elect_energy, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, compute_pbcminmax, del_molecule, density_add, density_average, density_binmask, density_clamp, density_com, density_correlate, density_crop, density_downsample, density_histogram, density_info, density_mdff_potential, density_move, density_moveto, density_multiply, density_range, density_sadd, density_save, density_sigma, density_smooth, density_smult, density_subtract, density_supersample, density_trim, SaveTrajectoryFltkMenu::do_save, Tool::dograb, fit, fpbc_join, fpbc_recenter, fpbc_unwrap, fpbc_wrap, GeometryMol::GeometryMol, get_molecule, get_weights_from_attribute, getmolid, Tool::getTargetScale, VMDApp::imd_connect, colvarproxy_vmd::load_atoms, colvarproxy_vmd::load_coords, mask, mdff_cc, mdff_sim, measure_avpos, measure_avpos_perresidue, measure_center_perresidue, measure_cluster, measure_dipole, measure_energy, measure_geom, measure_gofr, measure_inertia, measure_pbc2onc, measure_pbc_neighbors, measure_rdf, measure_rmsd_perresidue, measure_rmsdmat_qcp, measure_rmsdmat_qcp_ooc, measure_rmsf, measure_rmsf_perresidue, measure_sasa_perresidue, measure_sasa_thread, mol_from_id, SaveTrajectoryFltkMenu::molchooser_activate_selection, VMDApp::molecule_add_instance, VMDApp::molecule_add_volumetric, VMDApp::molecule_bondsrecalc, VMDApp::molecule_cancel_io, VMDApp::molecule_delete_all_instances, VMDApp::molecule_deleteframes, VMDApp::molecule_dupframe, VMDApp::molecule_frame, VMDApp::molecule_from_selection_list, VMDApp::molecule_load, VMDApp::molecule_name, VMDApp::molecule_num_instances, VMDApp::molecule_numatoms, VMDApp::molecule_numframes, VMDApp::molecule_orblocalize, VMDApp::molecule_reanalyze, VMDApp::molecule_rename, VMDApp::molecule_savetrajectory, VMDApp::molecule_set_dataset_flag, VMDApp::molecule_ssrecalc, VMDApp::molecule_valid_id, VMDApp::molrep_get_by_name, VMDApp::molrep_get_clipplane, VMDApp::molrep_get_color, VMDApp::molrep_get_colorupdate, VMDApp::molrep_get_drawframes, VMDApp::molrep_get_instances, VMDApp::molrep_get_material, VMDApp::molrep_get_name, 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_instances, VMDApp::molrep_set_pbc, VMDApp::molrep_set_pbc_images, VMDApp::molrep_set_scaleminmax, VMDApp::molrep_set_selupdate, VMDApp::molrep_set_smoothing, VMDApp::molrep_show, VMDApp::num_molreps, parse_timestep, GeometrySpring::prepare, py_activate, py_atomselect, py_fix, py_get_accessions, py_get_center, py_get_databases, py_get_filenames, py_get_filetypes, py_get_remarks, py_get_rotation, py_get_scale, py_get_trans, py_is_active, py_is_fixed, py_is_shown, py_label_add, py_mol_del_volumetric, py_mol_get_volumetric, py_mol_num_volumetric, py_mol_write, py_resetview, py_set_center, py_set_frame, py_set_rotation, py_set_scale, py_set_trans, py_show, segment_volume, colvarproxy_vmd::setup, Tool::target, tcl_get_weights, tcl_graphics, text_cmd_mol, AtomSel::timestep, topo_add_angle, topo_add_bond, topo_add_dihed, topo_add_improp, topo_angletypes, topo_bondtypes, topo_del_all_angles, topo_del_all_bonds, topo_del_all_dihed, topo_del_all_impropers, topo_del_angle, topo_del_bond, topo_del_dihed, topo_del_improper, topo_dihetypes, topo_get_angle, topo_get_bond, topo_get_dihed, topo_get_impro, topo_imptypes, Tool::tug, colvarproxy_vmd::update_input, vmd_measure_cluster, vmd_measure_clustsize, vmd_measure_contacts, vmd_measure_hbonds, vmd_measure_minmax, vmd_measure_sasa, vmd_measure_sasaperresidue, vmd_measure_volinterior, vmd_volmap_compare, vmd_volmap_ils, VolMapCreateILS::write_map, and GeometryMol::~GeometryMol.

int MoleculeList::mol_index_from_id (  int    id )  [inline]

return the index of the molecule with given ID (-1 if error). Definition at line 113 of file MoleculeList.h. References inthash_lookup, and num. Referenced by GraphicsFltkMenu::act_on_command, del_molecule, make_top, mol_from_id, VMDApp::molecule_activate, VMDApp::molecule_addrep, VMDApp::molecule_display, VMDApp::molecule_fix, VMDApp::molecule_index_from_id, VMDApp::molecule_is_active, VMDApp::molecule_is_displayed, VMDApp::molecule_is_fixed, VMDApp::molecule_load, VMDApp::molecule_make_top, VMDApp::molecule_modrep, molinfo_get, molinfo_set, VMDApp::molrep_delete, VMDApp::molrep_set_color, VMDApp::molrep_set_material, VMDApp::molrep_set_selection, and VMDApp::molrep_set_style.

Molecule* MoleculeList::molecule (  int    n )  [inline]

return the Nth molecule (index runs 0 ... (count-1)). Definition at line 105 of file MoleculeList.h. References n, NULL, and num. Referenced by GraphicsFltkMenu::act_on_command, activate, active, add_color_names, add_rep, center_all_molecules, change_rep, change_repcolor, change_repmat, change_repmethod, change_repsel, check_pickable, del_all_molecules, del_molecule, del_rep, displayed, Tool::dograb, fix, fixed, Animation::goto_frame, hide, inactivate, is_top, make_top, mol_from_id, VMDApp::molecule_delete_all, VMDApp::molecule_id, molecule_tcl, molinfo_get, molinfo_set, PickModeCenter::pick_molecule_end, GraphicsFltkRepOrbital::regen_excitationlist, GraphicsFltkRepOrbital::regen_orbitallist, GraphicsFltkRepOrbital::regen_wavefunctypes, GraphicsFltkMenu::set_pbc, show, unfix, Tool::ungrab, MolBrowser::update, GraphicsFltkMenu::update_molchooser, GraphicsFltkMenu::update_pbc, GraphicsFltkMenu::update_rep, GraphicsFltkMenu::update_repbrowser, GraphicsFltkMenu::update_repindex, VMDApp::VMDupdate, GraphicsFltkMenu::volindex_update, and ~MoleculeList.

int MoleculeList::num (  void    )  [inline]

return the number of molecules in this list. Definition at line 102 of file MoleculeList.h. References ResizeArray::num. Referenced by center_all_molecules, check_pickable, del_all_molecules, del_molecule, Tool::dograb, Animation::goto_frame, mol_index_from_id, molecule, molecule_tcl, VMDApp::num_molecules, PickModeCenter::pick_molecule_end, VMDApp::scene_resetview_newmoldata, Tool::ungrab, MolBrowser::update, VMDApp::VMDupdate, and ~MoleculeList.

char* MoleculeList::representation (  void    )  [inline]

Definition at line 154 of file MoleculeList.h. References AtomRep::cmdStr. Referenced by VMDApp::molecule_get_style.

const char* MoleculeList::selection (    )  const [inline]

Definition at line 158 of file MoleculeList.h. Referenced by VMDApp::molecule_get_selection.

int MoleculeList::set_color (  char *    )

get/set current atom coloring method. Definition at line 370 of file MoleculeList.C. References AtomColor::change. Referenced by VMDApp::molecule_load, and VMDApp::molecule_set_color.

int MoleculeList::set_default_color (  const char *    )

default values for new reps. Definition at line 336 of file MoleculeList.C. References AtomColor::change. Referenced by text_cmd_mol.

int MoleculeList::set_default_material (  const char *    )

Definition at line 362 of file MoleculeList.C. References MaterialList::material_index, and VMDApp::materialList. Referenced by text_cmd_mol.

int MoleculeList::set_default_representation (  const char *    )

Definition at line 345 of file MoleculeList.C. References AtomRep::change. Referenced by text_cmd_mol.

int MoleculeList::set_default_selection (  const char *    )

Definition at line 354 of file MoleculeList.C. References VMDApp::atomSelParser, and SymbolTable::parse. Referenced by text_cmd_mol.

int MoleculeList::set_material (  char *    )

get/set current atom material method. Definition at line 394 of file MoleculeList.C. References MaterialList::material_index, MaterialList::material_name, and VMDApp::materialList. Referenced by VMDApp::molecule_load, and VMDApp::molecule_set_material.

int MoleculeList::set_representation (  char *    )

get/set current atom representation method. Definition at line 376 of file MoleculeList.C. References AtomRep::change. Referenced by VMDApp::molecule_load, and VMDApp::molecule_set_style.

int MoleculeList::set_selection (  const char *    )

get/set current atom selection command. Return success. Definition at line 382 of file MoleculeList.C. References VMDApp::atomSelParser, SymbolTable::parse, and stringdup. Referenced by VMDApp::molecule_load, and VMDApp::molecule_set_selection.

void MoleculeList::show (  int    n )  [inline]

Definition at line 228 of file MoleculeList.h. References molecule, n, and Displayable::on. Referenced by VMDApp::molecule_display.

Molecule* MoleculeList::top (  void    )  [inline]

query or set the top molecule. Definition at line 213 of file MoleculeList.h. Referenced by GraphicsFltkMenu::act_on_command, find_molecule, Animation::frame, graphics_tcl, molecule_tcl, VMDApp::molecule_top, Animation::num, py_imdconnect, py_resetview, and text_cmd_imd.

void MoleculeList::unfix (  int    n )  [inline]

Definition at line 235 of file MoleculeList.h. References molecule, n, and Displayable::unfix. Referenced by VMDApp::molecule_fix.

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Member Data Documentation

int MoleculeList::colorCatIndex[NUM_MLCAT]

color category indices. Definition at line 92 of file MoleculeList.h. Referenced by add_color_names, VMDApp::color_set_restype, AtomColor::current_color_use, AtomColor::find, init_colors, VMDApp::molecule_from_selection_list, VMDApp::molecule_new, and VMDApp::molecule_rename.

NameList<const char *> MoleculeList::resTypes

mapping of residue names <--> residue types (hydrophobic, neutral, etc.). Definition at line 89 of file MoleculeList.h. Referenced by add_color_names, VMDApp::color_get_restype, VMDApp::color_set_restype, and AtomColor::find.

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

• MoleculeList.h
• MoleculeList.C

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