#include <VMDApp.h>
Public Methods | |
| VMDApp (int argc, char **argv, int mpion) | |
| set list of command line arguments. More... | |
| int | VMDinit (int, char **, const char *, int *dispLoc, int *dispSize) |
| initialize the global variables and objects for the general library. Must be passed command-line arguments to program. Creates graphics context and all associated objects, and then starts the UI, then adds any commands that should be done at start. When done, flushes command queue and then returns, when the program is ready to start main event loop. Return TRUE on successful initialization, FALSE if anything failed. More... | |
| ~VMDApp () | |
| void | VMDexit (const char *exitmsg, int exitcode, int pauseseconds) |
| Print the given error message and pause for the given number of seconds before setting a flag that willl make VMDupdate return FALSE. More... | |
| int | background_processing () |
| Background processing flag indicating whether the main event loop should throttle the CPU consumption back when there aren't any other display updates, event handling, or other activities to perform This flag is used by Molecule to inform VMD when background trajectory loading is going on, for example. More... | |
| void | background_processing_clear () |
| void | background_processing_set () |
| void | deactivate_uitext_stdin () |
| Turn off event checking for the text interface; if inactive it will still process text from VMD, like hotkey callbacks, but Tk menus will not work. This is experimental code just for the purpose of making it possible to control VMD from a thread in another program. More... | |
| int | activate_menus () |
| Activate Fltk menus; this should be called only once and only after VMDinit. Return success. More... | |
| int | num_menus () |
| Number of menus we know about. More... | |
| const char * | menu_name (int) |
| Name of nth menu; 0 <= n < num_menus(). More... | |
| int | menu_id (const char *name) |
| return index of named menu, or -1 on fail. More... | |
| int | add_menu (VMDMenu *) |
| add menu. Return success. More... | |
| int | remove_menu (const char *) |
| remove menu. Return success. More... | |
| void | menu_add_extension (const char *shortname, const char *menu_path) |
| Announce that the menu of the given name is a menu extension. This lets widgets add the menu to their own pulldown menus if they wish. More... | |
| void | menu_remove_extension (const char *shortname) |
| int | menu_status (const char *name) |
| Return 1 or 0 if the menu is on or off. Return 0 if the menu does not exist. More... | |
| int | menu_location (const char *name, int &x, int &y) |
| Get the location of the specified menu. More... | |
| int | menu_show (const char *name, int on) |
| Turn the specified menu on or off. More... | |
| int | menu_move (const char *name, int x, int y) |
| Move the specified menu to the given location on the screen. More... | |
| int | menu_select_mol (const char *name, int molno) |
| Tells the specified menu to select the "molno"-th molecule internally. More... | |
| int | filerender_num () |
| Number of file render methods. More... | |
| const char * | filerender_name (int n) |
| Name of Nth file renderer. More... | |
| const char * | filerender_prettyname (int n) |
| Pretty name of Nth renderer. More... | |
| int | filerender_valid (const char *method) |
| Return true if renderer exists. More... | |
| const char * | filerender_shortname_from_prettyname (const char *pretty) |
| Find short renderer name from the "pretty" GUI renderer name. More... | |
| int | filerender_has_antialiasing (const char *method) |
| Return whether given renderer supports antialiasing. More... | |
| int | filerender_aasamples (const char *method, int aasamples) |
| Set the antialiasing sample count and return the new value. More... | |
| int | filerender_aosamples (const char *method, int aosamples) |
| Set the ambient occlusion sample count and return the new value. More... | |
| int | filerender_has_imagesize (const char *method) |
| Return whether the given renderer supports arbitrary image size. More... | |
| int | filerender_imagesize (const char *method, int *imgwidth, int *imgheight) |
| Set/get the image size. If *width or *height are zero, then the existing value will be used instead. If aspect ratio is set, then the aspect ratio will be used to determine the other member of the pair. Return success. More... | |
| int | filerender_aspectratio (const char *method, float *aspect) |
| Set/get the aspect ratio for the image. An aspect ratio of zero means the image is free to take on any size. A positive value means the _height_ of the image will be scaled to maintain the given aspect ratio. Negative values fail. Return success, and place the new value of the aspect ratio in the passed-in pointer. More... | |
| int | filerender_numformats (const char *method) |
| Return the number of file formats the file renderer can produce. Returns zero if the renderer method is invalid. More... | |
| const char * | filerender_get_format (const char *method, int i) |
| Return the ith format. NULL if invalid. More... | |
| const char * | filerender_cur_format (const char *method) |
| Return name of currently selected format. More... | |
| int | filerender_set_format (const char *method, const char *format) |
| Set the output format for the renderer. Return success. More... | |
| int | filerender_render (const char *method, const char *filename, const char *extcmd) |
| do the rendering; return success. More... | |
| const char * | filerender_option (const char *method, const char *option) |
| set the command string to execute after producing the scene file Return the new value, or NULL if the method is invalid. Specify option as NULL to fetch the current value. More... | |
| const char * | filerender_default_option (const char *method) |
| get the default render option for the given method. More... | |
| const char * | filerender_default_filename (const char *method) |
| get the dafault filename for this render method. More... | |
| int | scene_rotate_by (float angle, char axis, float incr=0) |
| rotate the scene by or to the given angle, measured in degrees, about the given axis, either 'x', 'y', or 'z'. For rotate_by, If incr is zero, the rotation will be done in one redraw; otherwise the rotation will be performed in steps of incr. More... | |
| int | scene_rotate_to (float angle, char axis) |
| int | scene_rotate_by (const float *) |
| Rotate the scene by the specified matrix. The translation part will be ignored. More... | |
| int | scene_rotate_to (const float *) |
| int | scene_translate_by (float x, float y, float z) |
| Translate everything that isn't fixed by/to the given amount. More... | |
| int | scene_translate_to (float x, float y, float z) |
| int | scene_scale_by (float s) |
| Scale by/to the given positive scale factor. More... | |
| int | scene_scale_to (float s) |
| void | scene_resetview_newmoldata () |
| recenter the scene on the top molecule or on last settings if no-disrupt mode is enabled, unless there's only one molecule. More... | |
| void | scene_resetview () |
| recenter the scene on the top molecule. If there are no molecules, just restores rotation to default value. More... | |
| int | scene_rock (char axis, float step, int nsteps=0) |
| Rock the scene by the given amount per redraw about the given axis. If nsteps is positive, rock for the specified number of steps, then reverse direction. More... | |
| int | scene_rockoff () |
| Stop rocking the scene. More... | |
| int | scene_stoprotation () |
| Stop rocking AND persistent rotations induced by input devices (like the Mouse). More... | |
| int | animation_num_dirs () |
| Methods for affecting the animation. Only _active_ molecules are affected. I consider this a mistake: it would be better to be able to specify the animation settings for a particular molecule by specify a molecule ID. However, this would make it impossible to log Tcl commands using our current syntax because the Tcl commands operate on all active molecules. If we ever create new Tcl commands and/or deprecate the old ones, we can (and should) change thse API's. Note that there are no get-methods here because you would need to query molecules individually. The Tcl commands just return the value for the top molecule; they can continue to do so, but the API should be per molecule. number of animation direction choices, and their names. More... | |
| const char * | animation_dir_name (int) |
| int | animation_set_dir (int) |
| set the animation direction for all active molecules. More... | |
| int | animation_num_styles () |
| number of animation styles, and their names. More... | |
| const char * | animation_style_name (int) |
| int | animation_set_style (int) |
| set the animation style for all active molecules. More... | |
| int | animation_set_frame (int frame) |
| set the animation frame for all active molecules. If the specified frame is out of range for a particular molecule, then its frame will not change. If frame is -1, go to the first frame. If frame is -2, go to the last frame. More... | |
| int | animation_set_stride (int) |
| set the stride for animation. Must be >= 1. More... | |
| int | animation_set_speed (float) |
| set the animation speed. Must be a float between 0 and 1. 1 means animate as fast as possible; 0 means pause at least 0.5 seconds between frames. More... | |
| vmdplugin_t * | get_plugin (const char *type, const char *name) |
| get a plugin of the specified type and name. If none was found, return NULL. The returned plugin should not be deleted. If multiple plugins are found, the one with the highest version number is returned. More... | |
| int | list_plugins (PluginList &, const char *type=NULL) |
| Get alll plugins of the specfied type. If no type is specified or is NULL, all loaded plugins will be returned. Returns the number of plugins added to the list. More... | |
| int | plugin_dlopen (const char *filename) |
| Try to dlopen the specified shared library and access its plugin API. Return the number of plugins found in the given library, or -1 on error. More... | |
| void | plugin_update () |
| Tell VMD to update its lists of plugins based on all the shared libraries it's loaded. Methods listed below will not be updated after a call to plugin_dlopen until this method is called. More... | |
| void | display_update_on (int) |
| turn display updates on (1) or off (0). More... | |
| int | display_update_status () |
| return 1 or 0 if display updates are on or off, respectively. More... | |
| void | display_update () |
| force a screen redraw right now, without checking for UI events. More... | |
| void | display_update_ui () |
| force a screen redraw right now, and also check for UI events. More... | |
| void | display_set_screen_height (float) |
| get/set the height of the screen. Ignored unless positive. More... | |
| float | display_get_screen_height () |
| void | display_set_screen_distance (float) |
| get/set the distance to the screen. More... | |
| float | display_get_screen_distance () |
| void | display_set_position (int x, int y) |
| get/set the position of the graphics window. More... | |
| void | display_set_size (int w, int h) |
| get/set the size of the graphics window. More... | |
| void | display_get_size (int *w, int *h) |
| int | display_set_stereo (const char *mode) |
| change the stereo mode. More... | |
| int | display_set_stereo_swap (int onoff) |
| change the stereo swapped eye mode. More... | |
| int | display_set_cachemode (const char *mode) |
| change the caching mode. More... | |
| int | display_set_rendermode (const char *mode) |
| change the rendering mode. More... | |
| int | display_set_eyesep (float sep) |
| change eye separation. More... | |
| int | display_set_focallen (float flen) |
| change focal length. More... | |
| int | display_set_projection (const char *proj) |
| set the projection (Perspective or Orthographic, case-insensitive). More... | |
| int | display_projection_is_perspective (void) |
| query whether the projection is a perspective projection type. More... | |
| int | display_set_aa (int onoff) |
| int | display_set_depthcue (int onoff) |
| int | display_set_culling (int onoff) |
| int | display_set_fps (int onoff) |
| int | display_set_background_mode (int mode) |
| int | display_set_nearclip (float amt, int isdelta) |
| int | display_set_farclip (float amt, int isdelta) |
| int | stage_set_location (const char *) |
| int | stage_set_numpanels (int) |
| int | stage_set_size (float) |
| int | axes_set_location (const char *) |
| int | light_on (int lightnum, int onoff) |
| int | light_highlight (int lightnum, int onoff) |
| int | light_rotate (int lightnum, float amt, char axis) |
| int | light_move (int lightnum, const float *newpos) |
| int | depthcue_set_mode (const char *) |
| int | depthcue_set_start (float) |
| int | depthcue_set_end (float) |
| int | depthcue_set_density (float) |
| int | display_set_shadows (int onoff) |
| int | display_set_ao (int onoff) |
| int | display_set_ao_ambient (float a) |
| int | display_set_ao_direct (float d) |
| int | display_set_dof (int onoff) |
| int | display_set_dof_fnumber (float f) |
| int | display_set_dof_focal_dist (float d) |
| void | display_titlescreen () |
| turn on the title screen; burns CPU but will be turned off when a molecule is loaded. More... | |
| int | num_color_categories () |
| Number of color categories. More... | |
| const char * | color_category (int) |
| Name of the nth color category, or NULL if invalid index. More... | |
| int | color_add_item (const char *cat, const char *item, const char *defcolor) |
| add a new color item, consisting of a name and a default color, to the given color category. If the color category does not already exist, it is created. Return success. More... | |
| int | num_color_category_items (const char *category) |
| Number of color items in the given category. More... | |
| const char * | color_category_item (const char *category, int) |
| Item for the given category and index. More... | |
| int | num_colors () |
| Number of available colors. More... | |
| int | num_regular_colors () |
| Number of _regular_ colors, i.e., the ones that have actual names. More... | |
| const char * | color_name (int n) |
| Name of nth color, where 0 <= n < num_colors(). If the index is invalid, return NULL. More... | |
| int | color_index (const char *) |
| Index of given color. If the color is invalid, return -1, other return a number in [0, num_colors()). The color must be one of the colors returned by color_name(). Hence, color_name(color_index("string")) returns its input if "string" is a valid color, or NULL if it isn't. More... | |
| int | color_value (const char *colorname, float *r, float *g, float *b) |
| Get RGB value of given color. Return success. More... | |
| int | color_default_value (const char *colorname, float *r, float *g, float *b) |
| Get default RGB value of given color. The colorname must be one of the regular colors, i.e. have an index in [0,num_regular_colors). Return success. More... | |
| const char * | color_mapping (const char *category, const char *item) |
| Color mapped to given color category and item, or NULL if invalid. More... | |
| const char * | color_get_restype (const char *resname) |
| get the restype for the given resname. if the resname, is unknown, returns "Unassigned". More... | |
| int | color_set_restype (const char *resname, const char *newtype) |
| set the residue type for the given residue name. This will determine how the residue is colored when the coloring method is ResType. The type must be one of the color items in the Restype color category. return success. More... | |
| int | colorscale_params (float *midpoint, float *min, float *max, int *rev, int *posterize) |
| Query color scale parameters. More... | |
| int | colorscale_setparams (float midpoint, float min, float max, int rev, int posterize) |
| Change the settings for the color scale. More... | |
| int | num_colorscale_methods () |
| info about color scale methods. More... | |
| int | colorscale_method_current () |
| const char * | colorscale_method_name (int) |
| const char * | colorscale_method_menuname (int) |
| int | colorscale_setmethod (int method) |
| Change the color scale method. More... | |
| int | colorscale_method_index (const char *) |
| index for given method. Return -1 if invalid, otherwise nonnegative. More... | |
| int | get_colorscale_colors (int whichScale, float min[3], float mid[3], float max[3]) |
| Store the color scale colors in the given arrays. More... | |
| int | set_colorscale_colors (int whichScale, const float min[3], const float mid[3], const float max[3]) |
| Set the color scale colors from the given arrays. More... | |
| int | color_change_name (const char *category, const char *colorname, const char *color) |
| Change the color for a particular color category and name. Color must be one of names returned by color_name(). More... | |
| int | color_change_namelist (int numcols, char **category, char **colorname, char **color) |
| Change a list of colors for particular color categories and names. Each color must be one of names returned by color_name(). More... | |
| int | color_get_from_name (const char *category, const char *colorname, const char **color) |
| Returns the color string for a particular color category and name. More... | |
| int | color_change_rgb (const char *color, float r, float g, float b) |
| Change the RGB value for the specified color. More... | |
| int | color_change_rgblist (int numcols, const char **colors, float *rgb3fv) |
| Change the RGB values for an entire list of colors. More... | |
| int | logfile_read (const char *path) |
| Process the commands in the given file. More... | |
| int | save_state () |
| save VMD state to a Tcl script. A filename will be requested from the user. More... | |
| int | textinterp_change (const char *interpname) |
| change to a new text interpreter mode. Currently "tcl" and "python" are supported. More... | |
| int | num_molecules () |
| Number of molecules currently loaded. More... | |
| int | molecule_new (const char *name, int natoms, int docallbacks=1) |
| Create a new "empty" molecule, basically a blank slate for import low-level graphics or other data. Return the molid of the new molecule. we also allow to set the number of atoms. this is particularly useful for topology building scripts. More... | |
| int | molecule_from_selection_list (const char *name, int mergemode, int numsels, AtomSel **, int docallbacks=1) |
| Create a new molecule from a list of atom selections, copying all existing per-atom fields from the original molecules to the new one. More... | |
| const char * | guess_filetype (const char *filename) |
| Guess a molecule file type from the given filename. Return the filetype, or NULL if unsuccesful. More... | |
| int | molecule_load (int molid, const char *filename, const char *filetype, const FileSpec *spec) |
| Load data from the given file of type filetype. If molid is -1, a new molecule will be created if the file is successfully read; otherwise molid must be a valid molecule id. As much information will be loaded from the file as possible, and within the limits prescribed by FileSpec. Returns the molid of the molecule into which the data was read. If the file type is unknown, use guess_filetype to obtain a filetype; don't pass NULL to filetype. More... | |
| int | molecule_add_volumetric (int molid, const char *dataname, const float origin[3], const float xaxis[3], const float yaxis[3], const float zaxis[3], int xsize, int ysize, int zsize, float *datablock) |
| Add volumetric data to a given molecule. The data block will be deleted by VMD. Return success. More... | |
| int | molecule_add_volumetric (int molid, const char *dataname, const double origin[3], const double xaxis[3], const double yaxis[3], const double zaxis[3], int xsize, int ysize, int zsize, float *datablock) |
| int | molecule_savetrajectory (int molid, const char *filename, const char *filetype, const FileSpec *spec) |
| Write trajectory frames to a file. Return number of frames written before returning, as in the addfile method. Filetype should be one of the file types returned by savecoorfile_plugin_name(). selection must be NULL, or point to an array of flags, one for each atom in the molecule, indicating which atoms' coordinates are to be written. More... | |
| int | molecule_deleteframes (int molid, int first, int last, int stride) |
| Delete the specified range of timesteps from the given molecule, keeping every "stride" molecule (unless stride = 0). More... | |
| int | molecule_index_from_id (int molid) |
| Return the array index of the molecule with the specified ID. Returns -1 if the ID does not exist, otherwise a nonnegative array index is returned. More... | |
| int | molecule_id (int) |
| ID of the ith molecule. This ID is used to specify a molecule for all other methods. Return -1 if the ith molecule is not present; otherwise the ID is a nonnegative integer unique to each molecule. More... | |
| int | molecule_valid_id (int molid) |
| Return true or false if the given molid is valid. More... | |
| int | molecule_numatoms (int molid) |
| number of atoms in molecule. Return -1 on invalid molid, otherwise 0 or more. More... | |
| int | molecule_numframes (int molid) |
| number of frames in molecule. Return -1 on invalid molid, otherwise 0 or more. More... | |
| int | molecule_frame (int molid) |
| Current frame in molecule. Return -1 on invalid molid, otherwise [0, numframes()). More... | |
| int | molecule_dupframe (int molid, int frame) |
| Duplicate the given frame. The new fram will be appended at the end. Passing -1 for frame duplicates the current frame. Return success. More... | |
| const char * | molecule_name (int molid) |
| name of molecule. More... | |
| int | molecule_rename (int molid, const char *newname) |
| int | molecule_cancel_io (int molid) |
| cancel any in-progress file I/O associated with a given molecule. More... | |
| int | molecule_delete (int molid) |
| delete the molecule with the given id. More... | |
| int | molecule_delete_all (void) |
| delete all molecules. More... | |
| int | molecule_activate (int molid, int onoff) |
| make the given molecule 'active' or 'inactive'; active molecules respond to animate requests while inactive molecules do not. More... | |
| int | molecule_is_active (int molid) |
| int | molecule_fix (int molid, int onoff) |
| make the given molecule fixed or unfixed. Fixed molecules do not respond to scene transformation operations. More... | |
| int | molecule_is_fixed (int molid) |
| int | molecule_display (int molid, int onoff) |
| Turn the given molecule on or off. Turning a molecule off causes all its reps to not be rendered. More... | |
| int | molecule_is_displayed (int molid) |
| int | molecule_make_top (int molid) |
| Make the given molecule top. There is always exactly one top molecule, if any are loaded. More... | |
| int | molecule_top () |
| return the molid of the top molecule. More... | |
| int | num_molreps (int molid) |
| number of representations for the given molecule. More... | |
| const char * | molrep_get_style (int molid, int repid) |
| Get/set the current representation style. More... | |
| int | molrep_set_style (int molid, int repid, const char *style) |
| const char * | molrep_get_color (int molid, int repid) |
| Get/set the current representation color. More... | |
| int | molrep_set_color (int molid, int repid, const char *color) |
| const char * | molrep_get_selection (int molid, int repid) |
| Get/set the current representation selection. More... | |
| int | molrep_set_selection (int molid, int repid, const char *selection) |
| int | molrep_numselected (int molid, int repid) |
| Get the number of atoms in the rep's selection. If invalid molid or repid, return -1, otherwise 0 or more. More... | |
| const char * | molrep_get_material (int molid, int repid) |
| Get/set the current representation material. More... | |
| int | molrep_set_material (int molid, int repid, const char *material) |
| int | num_clipplanes () |
| Number of clipping planes supported per rep. clipid in the next few methods should be in the range [0,max). More... | |
| int | molrep_get_clipplane (int molid, int repid, int clipid, float *center, float *normal, float *color, int *mode) |
| Get clipping plane info for reps. center and normal should point to space for three floats. More... | |
| int | molrep_set_clipcenter (int molid, int repid, int clipid, const float *center) |
| set clip plane properties. More... | |
| int | molrep_set_clipnormal (int molid, int repid, int clipid, const float *normal) |
| int | molrep_set_clipcolor (int molid, int repid, int clipid, const float *color) |
| int | molrep_set_clipstatus (int molid, int repid, int clipid, int onoff) |
| int | molrep_set_smoothing (int molid, int repid, int n) |
| Set smoothing for reps. Coordinates used for calculating graphics will be smoothed with a boxcar average 2*n+1 in size centered on the current frame. More... | |
| int | molrep_get_smoothing (int molid, int repid) |
| Get smoothing for given rep. Returns -1 for invalid rep, otherwise 0 or higher. More... | |
| const char * | molrep_get_name (int molid, int repid) |
| Get the name of the given rep. Return NULL if the id is invalid. More... | |
| int | molrep_get_by_name (int molid, const char *) |
| Get the repid of the rep with the given name. Return -1 if the name was not found. More... | |
| int | molrep_set_pbc (int molid, int repid, int pbc) |
| Set periodic boundary condition display for this rep. More... | |
| int | molrep_get_pbc (int molid, int repid) |
| Get current pbc for this rep; returns -1 if invalid. More... | |
| int | molrep_set_pbc_images (int molid, int repid, int n) |
| Set the number of images to display; must be 1 or higher. Return success. More... | |
| int | molrep_get_pbc_images (int molid, int repid) |
| Get number of images; returns -1 on error. More... | |
| int | molecule_add_instance (int molid, Matrix4 &inst) |
| Add an instance transform to a given molecule. More... | |
| int | molecule_num_instances (int molid) |
| Report number of instances in a molecule, returns -1 if invalid. More... | |
| int | molecule_delete_all_instances (int molid) |
| Delete all instances in a molecule. More... | |
| int | molrep_set_instances (int molid, int repid, int inst) |
| Set molecule instance display for this rep. More... | |
| int | molrep_get_instances (int molid, int repid) |
| Get current instance display for this rep; returns -1 if invalid. More... | |
| int | molrep_show (int molid, int repid, int onff) |
| Show/hide individual rep; this is done in the graphics menu by double- clicking on the rep. More... | |
| int | molrep_is_shown (int molid, int repid) |
| Return 1 if shown, 0 if hidden or does not exist. More... | |
| const char * | molecule_get_style () |
| int | molecule_set_style (const char *style) |
| const char * | molecule_get_color () |
| int | molecule_set_color (const char *color) |
| const char * | molecule_get_selection () |
| int | molecule_set_selection (const char *selection) |
| const char * | molecule_get_material () |
| int | molecule_set_material (const char *material) |
| int | molecule_addrep (int molid) |
| Add a rep to the given molecule, using parameters specified in the molecule_set methods. molid must be a valid molecule id. More... | |
| int | molecule_modrep (int molid, int repid) |
| Change the specified rep, using the same settings as for addrep. More... | |
| int | molrep_delete (int molid, int repid) |
| Delete the specified rep. More... | |
| int | molrep_set_drawframes (int molid, int repid, const char *framesel) |
| Set drawing of selected frames for a given rep. Syntax is "now" or a whitespace-separated list of terms of the form n, beg:end, or beg:stride:end. More... | |
| const char * | molrep_get_drawframes (int molid, int repid) |
| int | molecule_set_dataset_flag (int molid, const char *dataflagstr, int setval) |
| Set/unset dataset flags, indicating to VMD which fields should be written out when the molecule is saved. More... | |
| int | molecule_reanalyze (int molid) |
| Re-analyze the molecule after atom names, bonds, and other other data have been changed. This can be used to fix unrecognized atom names in non-standard nucleic acid residues, and fix other issues on-the-fly without having to hand-edit the files. More... | |
| int | molecule_bondsrecalc (int molid) |
| Force recalculation of bonds for the given molecule based on the current set of coordinates. More... | |
| int | molecule_ssrecalc (int molid) |
| Force the recalculation of the secondary structure for the given molecule based on the current set of coordinates. Return true if the secondary structure was successfully recalculated, otherwise false. More... | |
| int | molecule_orblocalize (int molid, int waveid) |
| Create a new wavefunction object based on existing wavefunction "waveid" with orbitals localized using the Pipek-Mezey algorithm. More... | |
| int | imd_connect (int molid, const char *host, int port) |
| Establish an IMD connection to the given host over the given port, using the given molecule id. Return success. More... | |
| int | imd_connected (int molid) |
| Return true if an IMD simulation is established with the given molid. More... | |
| int | imd_sendforces (int, const int *, const float *) |
| Send forces, assuming an IMD connection is present. Return success. Format: num, indices, forces (xyzxyzxyz). More... | |
| int | imd_disconnect (int molid) |
| Disconnect IMD. Return success. More... | |
| int | vs_connect (const char *host, int port) |
| Establish an connection to the given host over the given port, using the given molecule id. Return success. More... | |
| int | vs_connected () |
| Return true if a video strem is established. More... | |
| int | vs_disconnect () |
| Disconnect. Return success. More... | |
| const char * | par_name () |
| query current node name. More... | |
| int | par_rank () |
| query current node ID. More... | |
| int | par_size () |
| query total number of nodes. More... | |
| void | par_barrier () |
| perform a barrier synchronization across all nodes. More... | |
| int | tool_create (const char *type, int argc, const char **argv) |
| int | tool_delete (int toolnum) |
| int | tool_change_type (int toolnum, const char *type) |
| int | tool_set_position_scale (int toolnum, float newval) |
| int | tool_set_force_scale (int toolnum, float newval) |
| int | tool_set_spring_scale (int toolnum, float newval) |
| int | label_add (const char *category, int num_ids, const int *molids, const int *atomids, const int *cells, float k, int toggle) |
| add a label of the given category using the given molecule id's and atom id's. Return the index of the label object, or -1 on error. If toggle is true, the on/off status of the label will be toggled if the label already exists; if the label does not already exist, the newly created label will be on regardless of the value of toggle. More... | |
| int | label_show (const char *category, int n, int onoff) |
| turn on/off the nth label of the given category. Return success. More... | |
| int | label_delete (const char *category, int n) |
| delete the nth label of the given category. If n is -1, delete all labels from that category. Return success. More... | |
| float | label_get_text_size () const |
| get/size size and thickness of text labels. This affects all labels. More... | |
| int | label_set_text_size (float) |
| float | label_get_text_thickness () const |
| int | label_set_text_thickness (float) |
| int | label_set_textoffset (const char *nm, int n, float x, float y) |
| int | label_set_textformat (const char *nm, int n, const char *format) |
| int | next_molid () |
| Get current molid and increment counter by 1. More... | |
| const char * | material_add (const char *name, const char *copyfrom) |
| add material with given name, copying settings from given material. If name is NULL a default unique name will be chosen; if copyfrom is NULL the 0th material will be copied. The name of the new material is returned, or NULL on error. More... | |
| int | material_delete (const char *name) |
| delete material with given name. Return success. More... | |
| int | material_change (const char *name, int property, float val) |
| change the given material property. property is from MaterialProperty defined in MaterialList. Return success. More... | |
| int | material_rename (const char *oldname, const char *newname) |
| rename the given material. The new name must contain only alphanumeric characters (no spaces). Return success. More... | |
| int | material_restore_default (int) |
| restore the default value of the material with the given index. Return success. Fails if the material has no default. More... | |
| int | mouse_set_mode (int mode, int setting) |
| Change the mouse mode. More... | |
| int | mobile_set_mode (int mode) |
| Change the mobile interface mode. More... | |
| int | mobile_get_mode () |
| Get the mobile interface mode. More... | |
| void | mobile_get_client_list (ResizeArray< JString * > *&nick, ResizeArray< JString * > *&ip, ResizeArray< bool > *&active) |
| Get the list of current clients. More... | |
| int | mobile_network_port (int port) |
| Change the mobile interface network port. More... | |
| int | mobile_get_network_port () |
| Get the mobile interface network port. More... | |
| int | mobile_get_APIsupported () |
| Get the version of the API that we support. More... | |
| int | mobile_set_activeClient (const char *nick, const char *ip) |
| Set the currently active client, identified by nick and ip. More... | |
| int | mobile_sendMsg (const char *nick, const char *ip, const char *msgType, const char *msg) |
| Send a message to a specific client. More... | |
| void | mobile_get_tracker_status (float &tx, float &ty, float &tz, float &rx, float &ry, float &rz, int &buttons) |
| return the current mobile interface event data, used by the UIVR MobileTracker interface. More... | |
| int | spaceball_set_mode (int mode) |
| Change the spaceball mode. More... | |
| int | spaceball_set_sensitivity (float s) |
| Change the spaceball sensitivity. More... | |
| int | spaceball_set_null_region (int nr) |
| Change the spaceball null region. More... | |
| void | spaceball_get_tracker_status (float &tx, float &ty, float &tz, float &rx, float &ry, float &rz, int &buttons) |
| return the current spaceball event data, used by the UIVR SpaceballTracker interface. More... | |
| void | show_stride_message () |
| show Stride message, if necessary. More... | |
| char * | vmd_choose_file (const char *title, const char *extension, const char *extension_label, int do_save) |
| Show a file dialog. Use the first available of: Tk, Fltk, stdin Returns a new'd filename, or NULL. More... | |
| int | VMDupdate (int) |
| redraw the screen and update all things that need updatin'. Return TRUE until exit has been requested by the user. More... | |
| void | set_mouse_callbacks (int on) |
| void | set_mouse_rocking (int on) |
| void | set_eofexit (int onoff) |
| int | get_eofexit () |
| int | molrep_get_selupdate (int molid, int repid) |
| Turn on/off selection auto-update for the specified rep. When on, the representation will recalculate its selection each time there is change in the coordinate frame of the molecule. More... | |
| int | molrep_set_selupdate (int molid, int repid, int onoff) |
| Turn on/off selection auto-update for the specified rep. When on, the representation will recalculate its selection each time there is change in the coordinate frame of the molecule. More... | |
| int | molrep_get_colorupdate (int molid, int repid) |
| Turn on/off automatic color update for the specified rep. More... | |
| int | molrep_set_colorupdate (int molid, int repid, int onoff) |
| Turn on/off automatic color update for the specified rep. More... | |
| int | molrep_get_scaleminmax (int molid, int repid, float *min, float *max) |
| Get/set data range of color scale. More... | |
| int | molrep_set_scaleminmax (int molid, int repid, float min, float max) |
| Get/set data range of color scale. More... | |
| int | molrep_reset_scaleminmax (int molid, int repid) |
| Get/set data range of color scale. More... | |
Static Public Methods | |
| unsigned long | get_repserialnum (void) |
| Get a unique integer serial number used for identifying display lists. More... | |
| unsigned long | get_texserialnum (void) |
| void | set_text (const char *str) |
| text message access methods. More... | |
| void | append_text (const char *str) |
| void | clear_text () |
| const char * | get_text () |
Public Attributes | |
| int | argc_m |
| used if we want to process unknown args elsewhere. More... | |
| const char ** | argv_m |
| needed by Tcl/Python initialization code. More... | |
| UIText * | uiText |
| the text interface JRG: made public for save_state. More... | |
| UIVR * | uivr |
| VR tool interface. More... | |
| IMDMgr * | imdMgr |
| IMD manager class. More... | |
| VideoStream * | uivs |
| Video streaming UI events. More... | |
| Animation * | anim |
| generates delay-based frame change events. More... | |
| DisplayDevice * | display |
| display in which the images are rendered. More... | |
| Scene * | scene |
| list of all Displayable objects to draw. More... | |
| wkf_cpu_caps_t * | cpucaps |
| CPUID, SIMD vector insn capability bits. More... | |
| wkf_threadpool_t * | thrpool |
| CPU thread pool for low-latency calcs. More... | |
| CUDAAccel * | cuda |
| CUDA acceleration system handle. More... | |
| NVENCMgr * | nvenc |
| GPU hardware H.26[45] video [en|de]coder. More... | |
| QuickSurf * | qsurf |
| QuickSurf object shared by all reps, to help minimize the persistent GPU global memory footprint, and to make it easy to force-dump all persistent QuickSurf GPU global memory data structures on-demand for GPU ray tracing, or other tasks that also need a lot of resources. The default persistence of QuickSurf GPU resources enable fast trajectory playback. More... | |
| PickList * | pickList |
| handles all picking events. More... | |
| PickModeList * | pickModeList |
| list of available picking modes. More... | |
| MaterialList * | materialList |
| list of materials. More... | |
| Stage * | stage |
| stage object used in the scene. More... | |
| Axes * | axes |
| axes object used in the scene. More... | |
| FPS * | fps |
| FPS counter used in the scene. More... | |
| CommandQueue * | commandQueue |
| the command processor. More... | |
| MoleculeList * | moleculeList |
| list of all loaded molecules. More... | |
| GeometryList * | geometryList |
| list of all labels etc. More... | |
| SymbolTable * | atomSelParser |
| symbol table and atom selection parser. More... | |
| VMDCollab * | vmdcollab |
| handles collaborative VMD interaction. More... | |
| NameList< char * > | userKeys |
| lookup table for Tcl scripts. More... | |
| NameList< char * > | userKeyDesc |
| describe what the hotkey does. More... | |
| int | UpdateDisplay |
| flag for whether to update the scene. More... | |
| int | exitFlag |
| flag for whether to quit the display loop. More... | |
| int | ResetViewPending |
| pending resetview needs attention. More... | |
| char | nodename [512] |
| MPI node name. More... | |
| int | noderank |
| MPI node rank. More... | |
| int | nodecount |
| MPI node count. More... | |
| int | highlighted_molid |
| Highlighted molecule id and rep. Set by GraphicsFltkMenu, used by PickModeMoveHighlightedRep. More... | |
| int | highlighted_rep |
| Highlighted molecule id and rep. Set by GraphicsFltkMenu, used by PickModeMoveHighlightedRep. More... | |
Definition at line 130 of file VMDApp.h.
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set list of command line arguments.
Definition at line 169 of file VMDApp.C. References anim, argc_m, argv_m, atomSelParser, axes, background_processing_clear, commandQueue, cuda, display, exitFlag, fps, geometryList, highlighted_molid, highlighted_rep, imdMgr, materialList, moleculeList, nodecount, nodename, noderank, NULL, nvenc, pickList, pickModeList, ResetViewPending, scene, stage, thrpool, uiText, uivr, uivs, UpdateDisplay, and vmdcollab. |
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Definition at line 1066 of file VMDApp.C. References anim, atomSelParser, axes, commandQueue, cpucaps, cuda, NameList< char * >::data, NameList< VMDMenu * >::data, display, fps, geometryList, imdMgr, materialList, moleculeList, NULL, NameList< char * >::num, NameList< VMDMenu * >::num, pickList, pickModeList, qsurf, scene, stage, DisplayDevice::supports_gui, thrpool, uiText, uivr, uivs, userKeyDesc, userKeys, vmdcollab, and wkf_threadpool_destroy. |
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Activate Fltk menus; this should be called only once and only after VMDinit. Return success.
Definition at line 3979 of file VMDApp.C. References NameList< VMDMenu * >::add_name, display, VMDMenu::get_name, UIObject::On, DisplayDevice::supports_gui, and uivr. Referenced by VMDinit. |
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add menu. Return success.
Definition at line 828 of file VMDApp.C. References NameList< VMDMenu * >::add_name, VMDMenu::get_name, and NameList< VMDMenu * >::typecode. Referenced by py_addmenu, py_registermenu, and text_cmd_menu. |
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Definition at line 1435 of file VMDApp.C. References Animation::ANIM_TOTAL_DIRS, and NULL. |
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Methods for affecting the animation. Only _active_ molecules are affected. I consider this a mistake: it would be better to be able to specify the animation settings for a particular molecule by specify a molecule ID. However, this would make it impossible to log Tcl commands using our current syntax because the Tcl commands operate on all active molecules. If we ever create new Tcl commands and/or deprecate the old ones, we can (and should) change thse API's. Note that there are no get-methods here because you would need to query molecules individually. The Tcl commands just return the value for the top molecule; they can continue to do so, but the API should be per molecule. number of animation direction choices, and their names.
Definition at line 1431 of file VMDApp.C. References Animation::ANIM_TOTAL_DIRS. |
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number of animation styles, and their names.
Definition at line 1447 of file VMDApp.C. References Animation::ANIM_TOTAL_STYLES. |
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set the animation direction for all active molecules.
Definition at line 1440 of file VMDApp.C. References anim, Animation::anim_dir, Animation::AnimDir, commandQueue, and CommandQueue::runcommand. Referenced by Spaceball::check_event, Mobile::check_event, forward_cb, next_cb, prev_cb, py_forward, py_next, py_pause, py_prev, py_reverse, reverse_cb, and text_cmd_animate. |
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set the animation frame for all active molecules. If the specified frame is out of range for a particular molecule, then its frame will not change. If frame is -1, go to the first frame. If frame is -2, go to the last frame.
Definition at line 1463 of file VMDApp.C. References anim, Animation::anim_dir, Animation::ANIM_PAUSE, commandQueue, Animation::goto_frame, and CommandQueue::runcommand. Referenced by curframe_cb, py_anim_goto, start_cb, stop_cb, and text_cmd_animate. |
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set the animation speed. Must be a float between 0 and 1. 1 means animate as fast as possible; 0 means pause at least 0.5 seconds between frames.
Definition at line 1476 of file VMDApp.C. References anim, commandQueue, CommandQueue::runcommand, and Animation::speed. Referenced by Spaceball::check_event, Mobile::check_event, py_speed, speed_cb, and text_cmd_animate. |
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set the stride for animation. Must be >= 1.
Definition at line 1470 of file VMDApp.C. References anim, commandQueue, CommandQueue::runcommand, and Animation::skip. Referenced by Spaceball::check_event, Mobile::check_event, py_skip, step_cb, and text_cmd_animate. |
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set the animation style for all active molecules.
Definition at line 1456 of file VMDApp.C. References anim, Animation::anim_style, Animation::AnimStyle, commandQueue, and CommandQueue::runcommand. Referenced by MainFltkMenu::act_on_command, py_loop, py_once, py_rock, style_cb, and text_cmd_animate. |
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Definition at line 1451 of file VMDApp.C. References Animation::ANIM_TOTAL_STYLES, and NULL. |
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Definition at line 3869 of file VMDApp.C. References axes, commandQueue, Axes::loc_description, Axes::location, Axes::locations, CommandQueue::runcommand, and strupcmp. Referenced by axes_cb, py_set_location, and text_cmd_axes. |
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Background processing flag indicating whether the main event loop should throttle the CPU consumption back when there aren't any other display updates, event handling, or other activities to perform This flag is used by Molecule to inform VMD when background trajectory loading is going on, for example.
Definition at line 262 of file VMDApp.h. Referenced by VMDupdate. |
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Definition at line 264 of file VMDApp.h. Referenced by VideoStream::check_event, and Molecule::get_new_frames. |
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add a new color item, consisting of a name and a default color, to the given color category. If the color category does not already exist, it is created. Return success.
Definition at line 1564 of file VMDApp.C. References Scene::add_color_category, Scene::add_color_item, Scene::category_index, Scene::color_index, commandQueue, CommandQueue::runcommand, and scene. Referenced by parseColorDefs, and text_cmd_color. |
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Name of the nth color category, or NULL if invalid index.
Definition at line 1560 of file VMDApp.C. References Scene::category_name, n, and scene. Referenced by py_categories, and tcl_colorinfo_categories. |
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Item for the given category and index.
Definition at line 1586 of file VMDApp.C. References Scene::category_index, Scene::category_item_name, n, and scene. Referenced by py_get_colormap, and tcl_colorinfo_category. |
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Change the color for a particular color category and name. Color must be one of names returned by color_name().
Definition at line 1711 of file VMDApp.C. References Scene::category_index, Scene::category_item_index, color_index, commandQueue, CommandQueue::runcommand, scene, and Scene::set_category_item. Referenced by py_set_colormap, and text_cmd_color. |
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Change a list of colors for particular color categories and names. Each color must be one of names returned by color_name().
Definition at line 1734 of file VMDApp.C. References Scene::category_index, Scene::category_item_index, color_index, scene, and Scene::set_category_item. Referenced by text_cmd_color. |
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Change the RGB value for the specified color.
Definition at line 1781 of file VMDApp.C. References color_index, commandQueue, CommandQueue::runcommand, scene, and Scene::set_color_value. Referenced by py_set_colorid, py_set_colors, and text_cmd_color. |
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Change the RGB values for an entire list of colors.
Definition at line 1791 of file VMDApp.C. References color_index, scene, and Scene::set_color_value. Referenced by text_cmd_color. |
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Get default RGB value of given color. The colorname must be one of the regular colors, i.e. have an index in [0,num_regular_colors). Return success.
Definition at line 1623 of file VMDApp.C. References Scene::color_default_value, color_index, and scene. Referenced by text_cmd_color. |
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Returns the color string for a particular color category and name.
Definition at line 1760 of file VMDApp.C. References Scene::category_index, Scene::category_item_index, color_name, Scene::get_category_item, and scene. Referenced by text_cmd_color. |
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get the restype for the given resname. if the resname, is unknown, returns "Unassigned".
Definition at line 1644 of file VMDApp.C. References NameList< const char * >::data, moleculeList, NULL, MoleculeList::resTypes, and NameList< const char * >::typecode. Referenced by text_cmd_color. |
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Index of given color. If the color is invalid, return -1, other return a number in [0, num_colors()). The color must be one of the colors returned by color_name(). Hence, color_name(color_index("string")) returns its input if "string" is a valid color, or NULL if it isn't.
Definition at line 1600 of file VMDApp.C. References Scene::color_index, MAXCOLORS, and scene. Referenced by color_change_name, color_change_namelist, color_change_rgb, color_change_rgblist, color_default_value, color_value, py_color, py_set_colors, tcl_colorinfo_index, tcl_graphics_color, and text_cmd_color. |
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Color mapped to given color category and item, or NULL if invalid.
Definition at line 1632 of file VMDApp.C. References Scene::category_index, Scene::category_item_index, Scene::category_item_value, Scene::color_name, and scene. Referenced by py_get_colormap, and tcl_colorinfo_category. |
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Name of nth color, where 0 <= n < num_colors(). If the index is invalid, return NULL.
Definition at line 1597 of file VMDApp.C. References Scene::color_name, n, and scene. Referenced by color_get_from_name, py_get_colorlist, py_get_colors, py_set_colorid, tcl_colorinfo_colors, and tcl_colorinfo_rgb. |
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set the residue type for the given residue name. This will determine how the residue is colored when the coloring method is ResType. The type must be one of the color items in the Restype color category. return success.
Definition at line 1650 of file VMDApp.C. References NameList< const char * >::add_name, Scene::category_item_index, Scene::category_item_name, Displayable::color_changed, MoleculeList::colorCatIndex, MLCAT_RESTYPES, moleculeList, MoleculeList::resTypes, Scene::root, scene, and NameList< const char * >::set_data. Referenced by parseRestypes, and text_cmd_color. |
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Get RGB value of given color. Return success.
Definition at line 1614 of file VMDApp.C. References color_index, Scene::color_value, and scene. Referenced by py_get_colorlist, py_get_colors, tcl_colorinfo_rgb, and text_cmd_color. |
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Definition at line 1675 of file VMDApp.C. References Scene::colorscale_method, and scene. Referenced by py_scale_method, and tcl_colorinfo_scale. |
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index for given method. Return -1 if invalid, otherwise nonnegative.
Definition at line 1686 of file VMDApp.C. References Scene::colorscale_method_name, Scene::num_colorscale_methods, scene, and strupncmp. Referenced by py_set_scale, and text_cmd_color. |
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Definition at line 1682 of file VMDApp.C. References Scene::colorscale_method_menuname, n, NULL, Scene::num_colorscale_methods, and scene. Referenced by ColorFltkMenu::ColorFltkMenu. |
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Definition at line 1678 of file VMDApp.C. References Scene::colorscale_method_name, n, NULL, Scene::num_colorscale_methods, and scene. Referenced by py_scale_method, py_scale_methods, and tcl_colorinfo_scale. |
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Query color scale parameters.
Definition at line 1667 of file VMDApp.C. References Scene::colorscale_params, and scene. Referenced by py_scale_max, py_scale_midpoint, py_scale_min, py_scale_posterize, py_scale_reverse, py_set_scale, and tcl_colorinfo_scale. |
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Change the color scale method.
Definition at line 1814 of file VMDApp.C. References Scene::colorscale_method_name, commandQueue, Scene::num_colorscale_methods, CommandQueue::runcommand, scene, and Scene::set_colorscale_method. Referenced by py_set_scale, and text_cmd_color. |
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Change the settings for the color scale.
Definition at line 1807 of file VMDApp.C. References commandQueue, CommandQueue::runcommand, scene, and Scene::set_colorscale_params. Referenced by py_set_scale, and text_cmd_color. |
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Turn off event checking for the text interface; if inactive it will still process text from VMD, like hotkey callbacks, but Tk menus will not work. This is experimental code just for the purpose of making it possible to control VMD from a thread in another program.
Definition at line 3974 of file VMDApp.C. References UIObject::Off, and uiText. |
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Definition at line 3926 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_cue_density. Referenced by cuedensity_cb, and text_cmd_display. |
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Definition at line 3920 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_cue_end. Referenced by cueend_cb, and text_cmd_display. |
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Definition at line 3908 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_cue_mode. Referenced by cuemode_cb, and text_cmd_display. |
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Definition at line 3914 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_cue_start. Referenced by cuestart_cb, and text_cmd_display. |
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Definition at line 3645 of file VMDApp.C. References display, and DisplayDevice::distance_to_screen. |
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Definition at line 3636 of file VMDApp.C. References display, and DisplayDevice::screen_height. |
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Definition at line 3668 of file VMDApp.C. References display, DisplayDevice::xSize, and DisplayDevice::ySize. Referenced by py_get, FileRenderList::render, and text_cmd_display. |
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query whether the projection is a perspective projection type.
Definition at line 3780 of file VMDApp.C. References display, DisplayDevice::ORTHOGRAPHIC, and DisplayDevice::projection. Referenced by Spaceball::check_event. |
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Definition at line 3787 of file VMDApp.C. References DisplayDevice::aa_available, DisplayDevice::aa_off, DisplayDevice::aa_on, commandQueue, display, and CommandQueue::runcommand. Referenced by aa_cb, py_set, and text_cmd_display. |
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Definition at line 3938 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_ao_mode. Referenced by aomode_cb, py_set, and text_cmd_display. |
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Definition at line 3944 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_ao_ambient. Referenced by aoambient_cb, py_set, and text_cmd_display. |
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Definition at line 3950 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_ao_direct. Referenced by aodirect_cb, py_set, and text_cmd_display. |
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Definition at line 3814 of file VMDApp.C. References commandQueue, CommandQueue::runcommand, scene, and Scene::set_background_mode. Referenced by backgroundmode_cb, and text_cmd_display. |
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change the caching mode.
Definition at line 3735 of file VMDApp.C. References DisplayDevice::cache_name, commandQueue, display, DisplayDevice::num_cache_modes, CommandQueue::runcommand, and DisplayDevice::set_cache_mode. Referenced by text_cmd_display. |
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Definition at line 3801 of file VMDApp.C. References commandQueue, DisplayDevice::culling_available, DisplayDevice::culling_off, DisplayDevice::culling_on, display, and CommandQueue::runcommand. Referenced by py_set, and text_cmd_display. |
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Definition at line 3794 of file VMDApp.C. References commandQueue, DisplayDevice::cueing_available, DisplayDevice::cueing_off, DisplayDevice::cueing_on, display, and CommandQueue::runcommand. Referenced by depthcue_cb, py_set, and text_cmd_display. |
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Definition at line 3956 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_dof_mode. Referenced by dofmode_cb, py_set, and text_cmd_display. |
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Definition at line 3962 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_dof_fnumber. Referenced by doffnumber_cb, py_set, and text_cmd_display. |
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Definition at line 3968 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_dof_focal_dist. Referenced by doffocaldist_cb, py_set, and text_cmd_display. |
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change eye separation.
Definition at line 3761 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_eyesep. Referenced by eyesep_cb, py_set, and text_cmd_display. |
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Definition at line 3834 of file VMDApp.C. References DisplayDevice::addto_far_clip, commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_far_clip. Referenced by farclip_cb, py_set, and text_cmd_display. |
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change focal length.
Definition at line 3768 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_eye_dist. Referenced by focal_cb, py_set, and text_cmd_display. |
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Definition at line 3808 of file VMDApp.C. References commandQueue, fps, Displayable::off, Displayable::on, and CommandQueue::runcommand. Referenced by fps_cb, and text_cmd_display. |
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Definition at line 3820 of file VMDApp.C. References DisplayDevice::addto_near_clip, commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_near_clip. Referenced by nearclip_cb, py_set, and text_cmd_display. |
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get/set the position of the graphics window.
Definition at line 3649 of file VMDApp.C. References display, and DisplayDevice::reposition_window. Referenced by text_cmd_display. |
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set the projection (Perspective or Orthographic, case-insensitive).
Definition at line 3774 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_projection. Referenced by proj_cb, py_set, and text_cmd_display. |
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change the rendering mode.
Definition at line 3748 of file VMDApp.C. References commandQueue, display, DisplayDevice::num_render_modes, DisplayDevice::render_name, CommandQueue::runcommand, and DisplayDevice::set_render_mode. Referenced by rendermode_cb, and text_cmd_display. |
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get/set the distance to the screen.
Definition at line 3640 of file VMDApp.C. References commandQueue, display, DisplayDevice::distance_to_screen, and CommandQueue::runcommand. Referenced by py_set, screend_cb, text_cmd_display, and VMDreadStartup. |
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get/set the height of the screen. Ignored unless positive.
Definition at line 3631 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::screen_height. Referenced by py_set, screenh_cb, text_cmd_display, and VMDreadStartup. |
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Definition at line 3932 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_shadow_mode. Referenced by py_set, shadowmode_cb, and text_cmd_display. |
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get/set the size of the graphics window.
Definition at line 3660 of file VMDApp.C. References display, display_update_ui, and DisplayDevice::resize_window. Referenced by py_set, and text_cmd_display. |
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change the stereo mode.
Definition at line 3681 of file VMDApp.C. References commandQueue, display, display_set_stereo_swap, DisplayDevice::num_stereo_modes, CommandQueue::runcommand, DisplayDevice::set_stereo_mode, and DisplayDevice::stereo_name. Referenced by py_set, stereo_cb, and text_cmd_display. |
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change the stereo swapped eye mode.
Definition at line 3723 of file VMDApp.C. References commandQueue, display, CommandQueue::runcommand, and DisplayDevice::set_stereo_swap. Referenced by display_set_stereo, stereoswap_cb, and text_cmd_display. |
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turn on the title screen; burns CPU but will be turned off when a molecule is loaded.
Definition at line 3674 of file VMDApp.C. References display, Scene::root, scene, and DisplayDevice::supports_gui. Referenced by VMDreadStartup. |
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force a screen redraw right now, without checking for UI events.
Definition at line 1546 of file VMDApp.C. References UpdateDisplay, VMD_IGNORE_EVENTS, and VMDupdate. Referenced by TclTextInterp::evalFile, py_update, text_cmd_display, and text_cmd_render. |
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turn display updates on (1) or off (0).
Definition at line 1538 of file VMDApp.C. References UpdateDisplay. Referenced by py_update_off, py_update_on, and text_cmd_display. |
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return 1 or 0 if display updates are on or off, respectively.
Definition at line 1542 of file VMDApp.C. References UpdateDisplay. Referenced by text_cmd_display. |
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force a screen redraw right now, and also check for UI events.
Definition at line 1553 of file VMDApp.C. References VMD_CHECK_EVENTS, and VMDupdate. Referenced by display_set_size, py_update_ui, and text_cmd_display. |
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Set the antialiasing sample count and return the new value.
Definition at line 1263 of file VMDApp.C. References FileRenderList::aasamples. Referenced by text_cmd_render. |
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Set the ambient occlusion sample count and return the new value.
Definition at line 1266 of file VMDApp.C. References FileRenderList::aosamples. Referenced by text_cmd_render. |
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Set/get the aspect ratio for the image. An aspect ratio of zero means the image is free to take on any size. A positive value means the _height_ of the image will be scaled to maintain the given aspect ratio. Negative values fail. Return success, and place the new value of the aspect ratio in the passed-in pointer.
Definition at line 1276 of file VMDApp.C. References FileRenderList::aspectratio. Referenced by text_cmd_render. |
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Return name of currently selected format.
Definition at line 1286 of file VMDApp.C. References FileRenderList::format. Referenced by text_cmd_render. |
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get the dafault filename for this render method.
Definition at line 1489 of file VMDApp.C. References FileRenderer::default_filename, FileRenderList::find, and NULL. |
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get the default render option for the given method.
Definition at line 1482 of file VMDApp.C. References FileRenderer::default_exec_string, FileRenderList::find, and NULL. Referenced by text_cmd_render. |
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Return the ith format. NULL if invalid.
Definition at line 1283 of file VMDApp.C. References FileRenderList::format. Referenced by text_cmd_render. |
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Return whether given renderer supports antialiasing.
Definition at line 1260 of file VMDApp.C. References FileRenderList::has_antialiasing. Referenced by text_cmd_render. |
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Return whether the given renderer supports arbitrary image size.
Definition at line 1273 of file VMDApp.C. References FileRenderList::has_imagesize. Referenced by text_cmd_render. |
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Set/get the image size. If *width or *height are zero, then the existing value will be used instead. If aspect ratio is set, then the aspect ratio will be used to determine the other member of the pair. Return success.
Definition at line 1269 of file VMDApp.C. References FileRenderList::imagesize. Referenced by text_cmd_render. |
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Name of Nth file renderer.
Definition at line 1247 of file VMDApp.C. References n, and FileRenderList::name. Referenced by py_listall, and text_cmd_render. |
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Number of file render methods.
Definition at line 1244 of file VMDApp.C. References FileRenderList::num. Referenced by py_listall, and text_cmd_render. |
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Return the number of file formats the file renderer can produce. Returns zero if the renderer method is invalid.
Definition at line 1280 of file VMDApp.C. References FileRenderList::numformats. Referenced by text_cmd_render. |
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set the command string to execute after producing the scene file Return the new value, or NULL if the method is invalid. Specify option as NULL to fetch the current value.
Definition at line 1300 of file VMDApp.C. References commandQueue, FileRenderList::find, NULL, CommandQueue::runcommand, FileRenderer::saved_exec_string, and FileRenderer::set_exec_string. Referenced by text_cmd_render. |
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Pretty name of Nth renderer.
Definition at line 1250 of file VMDApp.C. References n, and FileRenderList::pretty_name. |
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do the rendering; return success.
Definition at line 1293 of file VMDApp.C. References commandQueue, FileRenderList::render, and CommandQueue::runcommand. Referenced by py_render, and text_cmd_render. |
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Set the output format for the renderer. Return success.
Definition at line 1289 of file VMDApp.C. References FileRenderList::set_format. Referenced by text_cmd_render. |
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Find short renderer name from the "pretty" GUI renderer name.
Definition at line 1257 of file VMDApp.C. References FileRenderList::find_short_name_from_pretty_name. Referenced by RenderFltkMenu::act_on_command. |
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Return true if renderer exists.
Definition at line 1253 of file VMDApp.C. References FileRenderList::find, and NULL. |
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Store the color scale colors in the given arrays.
Definition at line 1695 of file VMDApp.C. References Scene::get_colorscale_colors, and scene. Referenced by text_cmd_color. |
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Definition at line 1220 of file VMDApp.h. Referenced by TclTextInterp::doEvent. |
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get a plugin of the specified type and name. If none was found, return NULL. The returned plugin should not be deleted. If multiple plugins are found, the one with the highest version number is returned.
Definition at line 1500 of file VMDApp.C. References NULL, ResizeArray< vmdplugin_t * >::num, and PluginMgr::plugins. Referenced by molecule_load, molecule_savetrajectory, text_cmd_plugin, and write_file. |
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Get a unique integer serial number used for identifying display lists.
Definition at line 1162 of file VMDApp.C. References repserialnum. Referenced by Displayable::reset_disp_list. |
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Definition at line 1168 of file VMDApp.C. References texserialnum. |
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Guess a molecule file type from the given filename. Return the filetype, or NULL if unsuccesful.
Definition at line 2233 of file VMDApp.C. References MolFilePlugin::extension, MolFilePlugin::name, NULL, ResizeArray< vmdplugin_t * >::num, and PluginMgr::plugins. Referenced by 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, fit, mask, mdff_cc, molecule_load, text_cmd_mol, and VMDreadStartup. |
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Establish an IMD connection to the given host over the given port, using the given molecule id. Return success.
Definition at line 3541 of file VMDApp.C. References commandQueue, IMDMgr::connect, imdMgr, MoleculeList::mol_from_id, moleculeList, and CommandQueue::runcommand. Referenced by py_imdconnect, and text_cmd_imd. |
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Return true if an IMD simulation is established with the given molid.
Definition at line 3555 of file VMDApp.C. References IMDMgr::get_imdmol, BaseMolecule::id, and imdMgr. Referenced by Molecule::get_new_frames. |
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Disconnect IMD. Return success.
Definition at line 3577 of file VMDApp.C. References IMDMgr::detach, IMDMgr::get_imdmol, BaseMolecule::id, and imdMgr. Referenced by Molecule::~Molecule. |
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Send forces, assuming an IMD connection is present. Return success. Format: num, indices, forces (xyzxyzxyz).
Definition at line 3566 of file VMDApp.C. References imdMgr, num, and IMDMgr::send_forces. Referenced by Molecule::get_new_frames, and py_sendforces. |
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add a label of the given category using the given molecule id's and atom id's. Return the index of the label object, or -1 on error. If toggle is true, the on/off status of the label will be toggled if the label already exists; if the label does not already exist, the newly created label will be on regardless of the value of toggle.
Definition at line 4022 of file VMDApp.C. References GeometryList::add_geometry, commandQueue, geometryList, n, and CommandQueue::runcommand. Referenced by SpringTool::do_event, PickModeMolLabel::pick_molecule_end, PickModeAddBond::pick_molecule_end, py_label_add, and text_cmd_label. |
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delete the nth label of the given category. If n is -1, delete all labels from that category. Return success.
Definition at line 4087 of file VMDApp.C. References commandQueue, GeometryList::del_geometry, geometryList, n, and CommandQueue::runcommand. Referenced by py_label_delete, and text_cmd_label. |
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get/size size and thickness of text labels. This affects all labels.
Definition at line 4046 of file VMDApp.C. References geometryList, and GeometryList::getTextSize. Referenced by py_label_textsize, and text_cmd_label. |
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Definition at line 4058 of file VMDApp.C. References geometryList, and GeometryList::getTextThickness. Referenced by py_label_textthickness, and text_cmd_label. |
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Definition at line 4050 of file VMDApp.C. References commandQueue, geometryList, CommandQueue::runcommand, and GeometryList::setTextSize. Referenced by py_label_textsize, text_cmd_label, textsizeinputcb, and textsizeslidercb. |
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Definition at line 4062 of file VMDApp.C. References commandQueue, geometryList, CommandQueue::runcommand, and GeometryList::setTextThickness. Referenced by py_label_textthickness, text_cmd_label, textthicknessinputcb, and textthicknessslidercb. |
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Definition at line 4079 of file VMDApp.C. References commandQueue, geometryList, n, CommandQueue::runcommand, and GeometryList::setTextFormat. Referenced by GeometryFltkMenu::apply_format_to_selected_labels, and text_cmd_label. |
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Definition at line 4070 of file VMDApp.C. References commandQueue, geometryList, n, CommandQueue::runcommand, and GeometryList::setTextOffset. Referenced by GeometryFltkMenu::apply_offset_to_selected_labels, and text_cmd_label. |
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turn on/off the nth label of the given category. Return success.
Definition at line 4037 of file VMDApp.C. References commandQueue, geometryList, n, CommandQueue::runcommand, and GeometryList::show_geometry. Referenced by py_label_visible, and text_cmd_label. |
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Definition at line 3887 of file VMDApp.C. References commandQueue, DISP_LIGHTS, Scene::highlight_light, n, CommandQueue::runcommand, and scene. Referenced by Mouse::move_mode, and text_cmd_light. |
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Definition at line 3901 of file VMDApp.C. References commandQueue, DISP_LIGHTS, Scene::move_light, n, CommandQueue::runcommand, and scene. Referenced by text_cmd_light. |
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Definition at line 3881 of file VMDApp.C. References Scene::activate_light, commandQueue, DISP_LIGHTS, n, CommandQueue::runcommand, and scene. Referenced by light_cb, and text_cmd_light. |
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Definition at line 3894 of file VMDApp.C. References commandQueue, DISP_LIGHTS, n, Scene::rotate_light, CommandQueue::runcommand, and scene. Referenced by Mouse::check_event, text_cmd_light, and text_cmd_point_light. |
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Get alll plugins of the specfied type. If no type is specified or is NULL, all loaded plugins will be returned. Returns the number of plugins added to the list.
Definition at line 1520 of file VMDApp.C. References PluginMgr::plugins. Referenced by SaveTrajectoryFltkMenu::act_on_command, and text_cmd_plugin. |
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Process the commands in the given file.
Definition at line 1823 of file VMDApp.C. References UIText::read_from_file, and uiText. Referenced by text_cmd_gopython, and VMDreadStartup. |
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add material with given name, copying settings from given material. If name is NULL a default unique name will be chosen; if copyfrom is NULL the 0th material will be copied. The name of the new material is returned, or NULL on error.
Definition at line 4146 of file VMDApp.C. References MaterialList::add_material, commandQueue, materialList, and CommandQueue::runcommand. Referenced by parseMaterialDefs, py_add, and text_cmd_material. |
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change the given material property. property is from MaterialProperty defined in MaterialList. Return success.
Definition at line 4197 of file VMDApp.C. References commandQueue, MAT_AMBIENT, MAT_DIFFUSE, MAT_MIRROR, MAT_OPACITY, MAT_OUTLINE, MAT_OUTLINEWIDTH, MAT_SHININESS, MAT_SPECULAR, MAT_TRANSMODE, MaterialList::material_index, materialList, CommandQueue::runcommand, MaterialList::set_ambient, MaterialList::set_diffuse, MaterialList::set_mirror, MaterialList::set_opacity, MaterialList::set_outline, MaterialList::set_outlinewidth, MaterialList::set_shininess, MaterialList::set_specular, and MaterialList::set_transmode. Referenced by parseMaterialDefs, py_change, and text_cmd_material. |
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delete material with given name. Return success.
Definition at line 4154 of file VMDApp.C. References commandQueue, MaterialList::delete_material, MaterialList::material_index, materialList, CommandQueue::runcommand, and stringdup. Referenced by py_matdelete, and text_cmd_material. |
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rename the given material. The new name must contain only alphanumeric characters (no spaces). Return success.
Definition at line 4166 of file VMDApp.C. References commandQueue, MaterialList::material_index, materialList, n, CommandQueue::runcommand, MaterialList::set_name, and stringdup. Referenced by py_rename, and text_cmd_material. |
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restore the default value of the material with the given index. Return success. Fails if the material has no default.
Definition at line 4215 of file VMDApp.C. References commandQueue, materialList, MaterialList::restore_default, and CommandQueue::runcommand. Referenced by py_set_default, and text_cmd_material. |
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Announce that the menu of the given name is a menu extension. This lets widgets add the menu to their own pulldown menus if they wish.
Definition at line 857 of file VMDApp.C. References commandQueue, and CommandQueue::runcommand. Referenced by py_addmenu, py_registermenu, and text_cmd_menu. |
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return index of named menu, or -1 on fail.
Definition at line 869 of file VMDApp.C. References NameList< VMDMenu * >::typecode. Referenced by py_location, and py_menushow. |
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Get the location of the specified menu.
Definition at line 879 of file VMDApp.C. References NameList< VMDMenu * >::data, NameList< VMDMenu * >::typecode, and VMDMenu::where. Referenced by py_location, and text_cmd_menu. |
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Move the specified menu to the given location on the screen.
Definition at line 898 of file VMDApp.C. References NameList< VMDMenu * >::data, VMDMenu::move, and NameList< VMDMenu * >::typecode. Referenced by py_location, and text_cmd_menu. |
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Name of nth menu; 0 <= n < num_menus().
Definition at line 865 of file VMDApp.C. References NameList< VMDMenu * >::name. Referenced by text_cmd_menu. |
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Definition at line 861 of file VMDApp.C. References commandQueue, and CommandQueue::runcommand. Referenced by text_cmd_menu. |
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Tells the specified menu to select the "molno"-th molecule internally.
Definition at line 906 of file VMDApp.C. References NameList< VMDMenu * >::data, VMDMenu::selectmol, and NameList< VMDMenu * >::typecode. Referenced by MolBrowser::handle, loadnew_cb, and text_cmd_menu. |
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Turn the specified menu on or off.
Definition at line 886 of file VMDApp.C. References commandQueue, NameList< VMDMenu * >::data, UIObject::Off, UIObject::On, CommandQueue::runcommand, and NameList< VMDMenu * >::typecode. Referenced by loadnew_cb, menu_cb, py_menushow, render_cb, text_cmd_menu, and VMDinit. |
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Return 1 or 0 if the menu is on or off. Return 0 if the menu does not exist.
Definition at line 873 of file VMDApp.C. References UIObject::active, NameList< VMDMenu * >::data, and NameList< VMDMenu * >::typecode. Referenced by py_menushow, and text_cmd_menu. |
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Get the version of the API that we support.
Definition at line 4284 of file VMDApp.C. References Mobile::get_APIsupported. Referenced by text_cmd_mobile. |
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Get the list of current clients.
Definition at line 4268 of file VMDApp.C. References Mobile::get_client_list. Referenced by text_cmd_mobile. |
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Get the mobile interface mode.
Definition at line 4264 of file VMDApp.C. References Mobile::get_move_mode. Referenced by text_cmd_mobile. |
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Get the mobile interface network port.
Definition at line 4280 of file VMDApp.C. References Mobile::get_port. Referenced by text_cmd_mobile. |
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return the current mobile interface event data, used by the UIVR MobileTracker interface.
Definition at line 4302 of file VMDApp.C. References Mobile::get_tracker_status, and NULL. Referenced by MobileTracker::update, and MobileButtons::update. |
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Change the mobile interface network port.
Definition at line 4274 of file VMDApp.C. References Mobile::network_port. Referenced by text_cmd_mobile. |
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Send a message to a specific client.
Definition at line 4294 of file VMDApp.C. References Mobile::sendMsgToClient. Referenced by text_cmd_mobile. |
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Set the currently active client, identified by nick and ip.
Definition at line 4289 of file VMDApp.C. References Mobile::set_activeClient. Referenced by text_cmd_mobile. |
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Change the mobile interface mode.
Definition at line 4255 of file VMDApp.C. References commandQueue, Mobile::move_mode, Mobile::MoveMode, and CommandQueue::runcommand. Referenced by text_cmd_mobile. |
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make the given molecule 'active' or 'inactive'; active molecules respond to animate requests while inactive molecules do not.
Definition at line 2887 of file VMDApp.C. References MoleculeList::activate, commandQueue, MoleculeList::inactivate, MoleculeList::mol_index_from_id, moleculeList, and CommandQueue::runcommand. Referenced by MolBrowser::handle, mol_active_cb, molinfo_set, py_activate, and text_cmd_mol. |
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Add an instance transform to a given molecule.
Definition at line 3155 of file VMDApp.C. References BaseMolecule::add_instance, MoleculeList::mol_from_id, and moleculeList. Referenced by text_cmd_mol. |
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Definition at line 3386 of file VMDApp.C. References BaseMolecule::add_volume_data, commandQueue, MoleculeList::mol_from_id, moleculeList, PROFILE_POP_RANGE, PROFILE_PUSH_RANGE, CommandQueue::runcommand, and scene_resetview_newmoldata. |
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Add volumetric data to a given molecule. The data block will be deleted by VMD. Return success.
Definition at line 3369 of file VMDApp.C. References BaseMolecule::add_volume_data, commandQueue, MoleculeList::mol_from_id, moleculeList, PROFILE_POP_RANGE, PROFILE_PUSH_RANGE, CommandQueue::runcommand, and scene_resetview_newmoldata. Referenced by VolMapCreateILS::add_map_to_molecule, init_new_volume_molecule, mdff_cc, py_mol_add_volumetric, segment_volume, text_cmd_mol, vmd_measure_volinterior, and vmd_volmap_new_fromtype. |
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Add a rep to the given molecule, using parameters specified in the molecule_set methods. molid must be a valid molecule id.
Definition at line 3053 of file VMDApp.C. References MoleculeList::add_rep, commandQueue, MoleculeList::mol_index_from_id, moleculeList, and CommandQueue::runcommand. Referenced by init_new_volume_molecule, molecule_load, py_addrep, and text_cmd_mol. |
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Force recalculation of bonds for the given molecule based on the current set of coordinates.
Definition at line 3276 of file VMDApp.C. References commandQueue, MoleculeList::mol_from_id, MoleculeEvent::MOL_REGEN, moleculeList, DrawMolecule::recalc_bonds, and CommandQueue::runcommand. Referenced by text_cmd_mol. |
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cancel any in-progress file I/O associated with a given molecule.
Definition at line 2831 of file VMDApp.C. References Molecule::cancel, commandQueue, MoleculeList::mol_from_id, moleculeList, and CommandQueue::runcommand. Referenced by mol_cancel_cb, py_mol_cancel, and text_cmd_mol. |
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delete the molecule with the given id.
Definition at line 2839 of file VMDApp.C. References commandQueue, MoleculeList::del_molecule, MoleculeEvent::MOL_DELETE, moleculeList, and CommandQueue::runcommand. Referenced by colvarproxy_vmd::load_atoms, colvarproxy_vmd::load_coords, mol_delete_cb, py_mol_delete, and text_cmd_mol. |
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delete all molecules.
Definition at line 2853 of file VMDApp.C. References commandQueue, MoleculeList::del_all_molecules, BaseMolecule::id, MoleculeEvent::MOL_DELETE, MoleculeList::molecule, moleculeList, num_molecules, and CommandQueue::runcommand. Referenced by text_cmd_mol. |
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Delete all instances in a molecule.
Definition at line 3168 of file VMDApp.C. References BaseMolecule::clear_instances, MoleculeList::mol_from_id, and moleculeList. |
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Delete the specified range of timesteps from the given molecule, keeping every "stride" molecule (unless stride = 0).
Definition at line 2782 of file VMDApp.C. References commandQueue, DrawMolecule::delete_frame, MoleculeList::mol_from_id, moleculeList, DrawMolecule::numframes, and CommandQueue::runcommand. Referenced by MolBrowser::handle, mol_delete_ts_cb, py_delframe, and text_cmd_animate. |
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Turn the given molecule on or off. Turning a molecule off causes all its reps to not be rendered.
Definition at line 2917 of file VMDApp.C. References commandQueue, MoleculeList::hide, MoleculeList::mol_index_from_id, moleculeList, CommandQueue::runcommand, and MoleculeList::show. Referenced by MolBrowser::handle, mol_displayed_cb, molinfo_set, py_set_visible, py_show, and text_cmd_mol. |
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Duplicate the given frame. The new fram will be appended at the end. Passing -1 for frame duplicates the current frame. Return success.
Definition at line 3306 of file VMDApp.C. References commandQueue, DrawMolecule::current, DrawMolecule::duplicate_frame, DrawMolecule::get_frame, MoleculeList::mol_from_id, moleculeList, DrawMolecule::numframes, and CommandQueue::runcommand. Referenced by py_dupframe, and text_cmd_animate. |
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make the given molecule fixed or unfixed. Fixed molecules do not respond to scene transformation operations.
Definition at line 2902 of file VMDApp.C. References commandQueue, MoleculeList::fix, MoleculeList::mol_index_from_id, moleculeList, CommandQueue::runcommand, and MoleculeList::unfix. Referenced by Tool::dograb, MolBrowser::handle, mol_fixed_cb, molinfo_set, py_fix, text_cmd_mol, and Tool::ungrab. |
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Current frame in molecule. Return -1 on invalid molid, otherwise [0, numframes()).
Definition at line 3301 of file VMDApp.C. References DrawMolecule::frame, MoleculeList::mol_from_id, and moleculeList. Referenced by access_tcl_atomsel, MainFltkMenu::act_on_command, print_atom_info, print_mol_summary, and py_get_frame. |
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Definition at line 3026 of file VMDApp.C. References MoleculeList::color, and moleculeList. Referenced by text_cmd_mol. |
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Definition at line 3044 of file VMDApp.C. References MoleculeList::material, and moleculeList. Referenced by text_cmd_mol. |
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Definition at line 3035 of file VMDApp.C. References moleculeList, and MoleculeList::selection. Referenced by text_cmd_mol. |
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Definition at line 3017 of file VMDApp.C. References moleculeList, and MoleculeList::representation. Referenced by text_cmd_mol. |
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ID of the ith molecule. This ID is used to specify a molecule for all other methods. Return -1 if the ith molecule is not present; otherwise the ID is a nonnegative integer unique to each molecule.
Definition at line 2821 of file VMDApp.C. References BaseMolecule::id, MoleculeList::molecule, moleculeList, NULL, and num_molecules. Referenced by SaveTrajectoryFltkMenu::do_save, fill_fltk_molchooser, IdList::find, MolBrowser::handle, myBrowser::handle, mol_active_cb, mol_cancel_cb, mol_delete_cb, mol_delete_ts_cb, mol_displayed_cb, mol_fixed_cb, mol_rename_cb, mol_top_cb, SaveTrajectoryFltkMenu::molchooser_activate_selection, py_mol_listall, GraphicsFltkMenu::set_autoupdate, GraphicsFltkMenu::set_colorupdate, ToolFltkMenu::set_toolrep, GraphicsFltkMenu::update_molchooser, ToolFltkMenu::update_replist, GraphicsFltkMenu::update_selection, ToolFltkMenu::update_toolrep_choosers, GraphicsFltkMenu::use_colorscale_auto, and GraphicsFltkMenu::use_colorscale_minmax. |
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Return the array index of the molecule with the specified ID. Returns -1 if the ID does not exist, otherwise a nonnegative array index is returned.
Definition at line 2817 of file VMDApp.C. References MoleculeList::mol_index_from_id, and moleculeList. |
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Definition at line 2897 of file VMDApp.C. References MoleculeList::active, MoleculeList::mol_index_from_id, and moleculeList. Referenced by IdList::find, MolBrowser::handle, mol_active_cb, and print_mol_summary. |
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Definition at line 2927 of file VMDApp.C. References MoleculeList::displayed, MoleculeList::mol_index_from_id, and moleculeList. Referenced by fill_fltk_molchooser, IdList::find, MolBrowser::handle, mol_displayed_cb, print_arep_summary, print_mol_summary, and py_get_visible. |
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Definition at line 2912 of file VMDApp.C. References MoleculeList::fixed, MoleculeList::mol_index_from_id, and moleculeList. Referenced by IdList::find, MolBrowser::handle, mol_fixed_cb, and print_mol_summary. |
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Make the given molecule top. There is always exactly one top molecule, if any are loaded.
Definition at line 2932 of file VMDApp.C. References commandQueue, MoleculeList::make_top, MoleculeList::mol_index_from_id, moleculeList, and CommandQueue::runcommand. Referenced by MolBrowser::handle, colvarproxy_vmd::load_atoms, colvarproxy_vmd::load_coords, mol_top_cb, molinfo_set, py_set_top, and text_cmd_mol. |
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Change the specified rep, using the same settings as for addrep.
Definition at line 3060 of file VMDApp.C. References MoleculeList::change_rep, commandQueue, MoleculeList::mol_index_from_id, moleculeList, and CommandQueue::runcommand. |
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name of molecule.
Definition at line 3325 of file VMDApp.C. References MoleculeList::mol_from_id, moleculeList, BaseMolecule::molname, and NULL. Referenced by cmd_mol_list, fill_fltk_molchooser, MolBrowser::handle, mol_delete_ts_cb, mol_rename_cb, print_mol_summary, and py_mol_name. |
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Report number of instances in a molecule, returns -1 if invalid.
Definition at line 3163 of file VMDApp.C. References MoleculeList::mol_from_id, moleculeList, and BaseMolecule::num_instances. Referenced by text_cmd_mol. |
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number of atoms in molecule. Return -1 on invalid molid, otherwise 0 or more.
Definition at line 3291 of file VMDApp.C. References MoleculeList::mol_from_id, moleculeList, and BaseMolecule::nAtoms. Referenced by print_mol_summary, and py_mol_numatoms. |
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number of frames in molecule. Return -1 on invalid molid, otherwise 0 or more.
Definition at line 3296 of file VMDApp.C. References MoleculeList::mol_from_id, moleculeList, and DrawMolecule::numframes. Referenced by access_tcl_atomsel, MainFltkMenu::act_on_command, VolMapCreate::calculate_minmax, VolMapCreateILS::compute, VolMapCreate::compute_all, curframe_cb, SaveTrajectoryFltkMenu::do_save, MolBrowser::handle, mol_delete_ts_cb, SaveTrajectoryFltkMenu::molchooser_activate_selection, print_mol_summary, py_numframes, py_rmsdmat_q, Tool::target, text_cmd_animate, vmd_measure_rmsdmat_qcp, and vmd_volmap_ils. |
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Create a new wavefunction object based on existing wavefunction "waveid" with orbitals localized using the Pipek-Mezey algorithm.
Definition at line 3348 of file VMDApp.C. References QMData::expand_basis_array, DrawMolecule::get_frame, MoleculeList::mol_from_id, moleculeList, NULL, DrawMolecule::numframes, QMData::orblocalize, and BaseMolecule::qm_data. Referenced by text_cmd_mol. |
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Re-analyze the molecule after atom names, bonds, and other other data have been changed. This can be used to fix unrecognized atom names in non-standard nucleic acid residues, and fix other issues on-the-fly without having to hand-edit the files.
Definition at line 3256 of file VMDApp.C. References BaseMolecule::analyze, DrawMolItem::COL_REGEN, commandQueue, DrawMolecule::force_recalc, DrawMolecule::invalidate_ss, MoleculeList::mol_from_id, MoleculeEvent::MOL_REGEN, DrawMolItem::MOL_REGEN, moleculeList, CommandQueue::runcommand, and DrawMolItem::SEL_REGEN. Referenced by text_cmd_mol. |
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Definition at line 3330 of file VMDApp.C. References Scene::add_color_item, MoleculeList::colorCatIndex, commandQueue, BaseMolecule::id, MLCAT_MOLECULES, MoleculeList::mol_from_id, MoleculeEvent::MOL_RENAME, moleculeList, Molecule::rename, CommandQueue::runcommand, scene, and VISCLRS. Referenced by MolBrowser::handle, mol_rename_cb, molecule_from_selection_list, molecule_new, py_mol_rename, and text_cmd_mol. |
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Definition at line 3029 of file VMDApp.C. References commandQueue, moleculeList, CommandQueue::runcommand, and MoleculeList::set_color. Referenced by py_addrep, and text_cmd_mol. |
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Set/unset dataset flags, indicating to VMD which fields should be written out when the molecule is saved.
Definition at line 3189 of file VMDApp.C. References BaseMolecule::ALTLOC, BaseMolecule::ANGLES, BaseMolecule::ANGLETYPES, BaseMolecule::ATOMICNUMBER, BaseMolecule::BFACTOR, BaseMolecule::BONDORDERS, BaseMolecule::BONDS, BaseMolecule::BONDTYPES, BaseMolecule::CHARGE, BaseMolecule::CTERMS, BaseMolecule::INSERTION, BaseMolecule::MASS, MoleculeList::mol_from_id, moleculeList, BaseMolecule::NODATA, BaseMolecule::OCCUPANCY, BaseMolecule::RADIUS, BaseMolecule::set_dataset_flag, and BaseMolecule::unset_dataset_flag. Referenced by text_cmd_mol. |
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Definition at line 3047 of file VMDApp.C. References commandQueue, moleculeList, CommandQueue::runcommand, and MoleculeList::set_material. Referenced by py_addrep, and text_cmd_mol. |
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Definition at line 3038 of file VMDApp.C. References commandQueue, moleculeList, CommandQueue::runcommand, and MoleculeList::set_selection. Referenced by py_addrep, and text_cmd_mol. |
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Definition at line 3020 of file VMDApp.C. References commandQueue, moleculeList, CommandQueue::runcommand, and MoleculeList::set_representation. Referenced by init_new_volume_molecule, molecule_load, py_addrep, and text_cmd_mol. |
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Force the recalculation of the secondary structure for the given molecule based on the current set of coordinates. Return true if the secondary structure was successfully recalculated, otherwise false.
Definition at line 3284 of file VMDApp.C. References commandQueue, MoleculeList::mol_from_id, moleculeList, DrawMolecule::recalc_ss, and CommandQueue::runcommand. Referenced by py_mol_ssrecalc, and text_cmd_mol. |
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Return true or false if the given molid is valid.
Definition at line 2828 of file VMDApp.C. References MoleculeList::mol_from_id, moleculeList, and NULL. Referenced by access_tcl_atomsel, IdList::find, fit, mask, mdff_cc, mdff_sim, print_arep_summary, print_mol_summary, py_mol_exists, tcl_colvars_vmd_init, tcl_get_weights, text_cmd_mol, valid_molid, vmd_measure_cluster, vmd_measure_clustsize, vmd_measure_inertia, vmd_measure_pbc_neighbors, vmd_measure_symmetry, vmd_measure_trans_overlap, vmd_measure_volinterior, vmd_volmap_compare, vmd_volmap_ils, and vmd_volmap_new_fromtype. |
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Delete the specified rep.
Definition at line 3067 of file VMDApp.C. References commandQueue, MoleculeList::del_rep, MoleculeList::mol_index_from_id, moleculeList, and CommandQueue::runcommand. Referenced by py_delrep, and text_cmd_mol. |
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Get the repid of the rep with the given name. Return -1 if the name was not found.
Definition at line 3466 of file VMDApp.C. References DrawMolecule::get_component_by_name, MoleculeList::mol_from_id, and moleculeList. Referenced by py_repindex, Tool::target, text_cmd_mol, Tool::tug, and ToolFltkMenu::update_toolrep_choosers. |
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Get clipping plane info for reps. center and normal should point to space for three floats.
Definition at line 3414 of file VMDApp.C. References VMDClipPlane::center, Displayable::clipplane, VMDClipPlane::color, DrawMolecule::component, VMDClipPlane::mode, MoleculeList::mol_from_id, moleculeList, and VMDClipPlane::normal. Referenced by text_cmd_mol. |
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Get/set the current representation color.
Definition at line 2964 of file VMDApp.C. References DrawMolItem::atomColor, AtomColor::cmdStr, DrawMolecule::component, MoleculeList::mol_from_id, moleculeList, NULL, and num_molreps. Referenced by print_arep_summary, and py_get_color. |
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Turn on/off automatic color update for the specified rep.
Definition at line 3102 of file VMDApp.C. References DrawMolItem::atomColor, DrawMolecule::component, AtomColor::do_update, MoleculeList::mol_from_id, moleculeList, NULL, and num_molreps. Referenced by py_get_colorupdate, and text_cmd_mol. |
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Definition at line 3518 of file VMDApp.C. References DrawMolecule::component, DrawMolItem::get_drawframes, MoleculeList::mol_from_id, moleculeList, NULL, and num_molreps. Referenced by text_cmd_mol. |
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Get current instance display for this rep; returns -1 if invalid.
Definition at line 3183 of file VMDApp.C. References DrawMolecule::component, DrawMolItem::get_instances, MoleculeList::mol_from_id, moleculeList, and num_molreps. Referenced by text_cmd_mol. |
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Get/set the current representation material.
Definition at line 3002 of file VMDApp.C. References DrawMolecule::component, Displayable::curr_material, MaterialList::material_name, materialList, MoleculeList::mol_from_id, moleculeList, NULL, and num_molreps. Referenced by py_get_material. |
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Get the name of the given rep. Return NULL if the id is invalid.
Definition at line 3460 of file VMDApp.C. References DrawMolecule::get_component_name, MoleculeList::mol_from_id, moleculeList, and NULL. Referenced by py_get_repname, and text_cmd_mol. |
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Get current pbc for this rep; returns -1 if invalid.
Definition at line 3134 of file VMDApp.C. References DrawMolecule::component, DrawMolItem::get_pbc, MoleculeList::mol_from_id, moleculeList, and num_molreps. Referenced by text_cmd_mol. |
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Get number of images; returns -1 on error.
Definition at line 3148 of file VMDApp.C. References DrawMolecule::component, DrawMolItem::get_pbc_images, MoleculeList::mol_from_id, moleculeList, and num_molreps. Referenced by text_cmd_mol. |
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Get/set data range of color scale.
Definition at line 3472 of file VMDApp.C. References DrawMolItem::atomColor, DrawMolecule::component, AtomColor::find, AtomColor::get_colorscale_minmax, MoleculeList::mol_from_id, moleculeList, num_molreps, and AtomColor::rescale_colorscale_minmax. Referenced by py_get_scaleminmax, text_cmd_mol, and GraphicsFltkMenu::use_colorscale_auto. |
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Get/set the current representation selection.
Definition at line 2979 of file VMDApp.C. References DrawMolItem::atomSel, AtomSel::cmdStr, DrawMolecule::component, MoleculeList::mol_from_id, moleculeList, NULL, and num_molreps. Referenced by SaveTrajectoryFltkMenu::molchooser_activate_selection, print_arep_summary, py_get_selection, ToolFltkMenu::update_replist, and GraphicsFltkMenu::update_selection. |
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Turn on/off selection auto-update for the specified rep. When on, the representation will recalculate its selection each time there is change in the coordinate frame of the molecule.
Definition at line 3075 of file VMDApp.C. References DrawMolItem::atomSel, DrawMolecule::component, AtomSel::do_update, MoleculeList::mol_from_id, moleculeList, NULL, and num_molreps. Referenced by py_get_autoupdate, and text_cmd_mol. |
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Get smoothing for given rep. Returns -1 for invalid rep, otherwise 0 or higher.
Definition at line 3121 of file VMDApp.C. References DrawMolecule::component, DrawMolItem::get_smoothing, MoleculeList::mol_from_id, moleculeList, and num_molreps. Referenced by py_get_smoothing, and text_cmd_mol. |
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Get/set the current representation style.
Definition at line 2949 of file VMDApp.C. References DrawMolItem::atomRep, AtomRep::cmdStr, DrawMolecule::component, MoleculeList::mol_from_id, moleculeList, NULL, and num_molreps. Referenced by print_arep_summary, and py_get_style. |
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Return 1 if shown, 0 if hidden or does not exist.
Definition at line 3531 of file VMDApp.C. References DrawMolecule::component, Displayable::displayed, MoleculeList::mol_from_id, moleculeList, and num_molreps. Referenced by myBrowser::handle, py_get_visible, and text_cmd_mol. |
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Get the number of atoms in the rep's selection. If invalid molid or repid, return -1, otherwise 0 or more.
Definition at line 2995 of file VMDApp.C. References DrawMolItem::atomSel, DrawMolecule::component, MoleculeList::mol_from_id, moleculeList, NULL, num_molreps, and AtomSel::selected. Referenced by print_arep_summary. |
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Get/set data range of color scale.
Definition at line 3497 of file VMDApp.C. References DrawMolItem::atomColor, DrawMolItem::COL_REGEN, commandQueue, DrawMolecule::component, DrawMolItem::force_recalc, MoleculeList::mol_from_id, moleculeList, num_molreps, AtomColor::rescale_colorscale_minmax, and CommandQueue::runcommand. Referenced by py_reset_scaleminmax, text_cmd_mol, and GraphicsFltkMenu::use_colorscale_auto. |
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set clip plane properties.
Definition at line 3428 of file VMDApp.C. References DrawMolecule::component, MoleculeList::mol_from_id, moleculeList, and Displayable::set_clip_center. Referenced by text_cmd_mol. |
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Definition at line 3444 of file VMDApp.C. References DrawMolecule::component, MoleculeList::mol_from_id, moleculeList, and Displayable::set_clip_color. Referenced by text_cmd_mol. |
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Definition at line 3436 of file VMDApp.C. References DrawMolecule::component, MoleculeList::mol_from_id, moleculeList, and Displayable::set_clip_normal. Referenced by text_cmd_mol. |
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Definition at line 3452 of file VMDApp.C. References DrawMolecule::component, MoleculeList::mol_from_id, moleculeList, and Displayable::set_clip_status. Referenced by text_cmd_mol. |
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Definition at line 2971 of file VMDApp.C. References MoleculeList::change_repcolor, CmdMolChangeRepItem::COLOR, commandQueue, MoleculeList::mol_index_from_id, moleculeList, and CommandQueue::runcommand. Referenced by py_modrep, and text_cmd_mol. |
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Turn on/off automatic color update for the specified rep.
Definition at line 3092 of file VMDApp.C. References DrawMolItem::atomColor, DrawMolItem::COL_REGEN, commandQueue, DrawMolecule::component, AtomColor::do_update, DrawMolItem::force_recalc, MoleculeList::mol_from_id, moleculeList, NULL, num_molreps, and CommandQueue::runcommand. Referenced by py_set_colorupdate, GraphicsFltkMenu::set_colorupdate, and text_cmd_mol. |
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Set drawing of selected frames for a given rep. Syntax is "now" or a whitespace-separated list of terms of the form n, beg:end, or beg:stride:end.
Definition at line 3506 of file VMDApp.C. References commandQueue, DrawMolecule::component, MoleculeList::mol_from_id, moleculeList, num_molreps, CommandQueue::runcommand, and DrawMolItem::set_drawframes. Referenced by text_cmd_mol. |
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Set molecule instance display for this rep.
Definition at line 3176 of file VMDApp.C. References commandQueue, DrawMolecule::component, MoleculeList::mol_from_id, moleculeList, num_molreps, CommandQueue::runcommand, and DrawMolItem::set_instances. Referenced by text_cmd_mol. |
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Definition at line 3009 of file VMDApp.C. References MoleculeList::change_repmat, commandQueue, CmdMolChangeRepItem::MAT, MoleculeList::mol_index_from_id, moleculeList, and CommandQueue::runcommand. Referenced by py_modrep, and text_cmd_mol. |
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Set periodic boundary condition display for this rep.
Definition at line 3127 of file VMDApp.C. References commandQueue, DrawMolecule::component, MoleculeList::mol_from_id, moleculeList, num_molreps, CommandQueue::runcommand, and DrawMolItem::set_pbc. Referenced by GraphicsFltkMenu::set_pbc, and text_cmd_mol. |
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Set the number of images to display; must be 1 or higher. Return success.
Definition at line 3140 of file VMDApp.C. References commandQueue, DrawMolecule::component, MoleculeList::mol_from_id, moleculeList, n, num_molreps, CommandQueue::runcommand, and DrawMolItem::set_pbc_images. Referenced by GraphicsFltkMenu::set_pbc, and text_cmd_mol. |
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Get/set data range of color scale.
Definition at line 3487 of file VMDApp.C. References DrawMolItem::atomColor, DrawMolItem::COL_REGEN, commandQueue, DrawMolecule::component, DrawMolItem::force_recalc, MoleculeList::mol_from_id, moleculeList, num_molreps, CommandQueue::runcommand, and AtomColor::set_colorscale_minmax. Referenced by py_modrep, py_set_scaleminmax, text_cmd_mol, and GraphicsFltkMenu::use_colorscale_minmax. |
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Definition at line 2986 of file VMDApp.C. References MoleculeList::change_repsel, commandQueue, MoleculeList::mol_index_from_id, moleculeList, CommandQueue::runcommand, and CmdMolChangeRepItem::SEL. Referenced by py_modrep, and text_cmd_mol. |
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Turn on/off selection auto-update for the specified rep. When on, the representation will recalculate its selection each time there is change in the coordinate frame of the molecule.
Definition at line 3082 of file VMDApp.C. References DrawMolItem::atomSel, commandQueue, DrawMolecule::component, AtomSel::do_update, MoleculeList::mol_from_id, moleculeList, NULL, num_molreps, and CommandQueue::runcommand. Referenced by py_set_autoupdate, GraphicsFltkMenu::set_autoupdate, and text_cmd_mol. |
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Set smoothing for reps. Coordinates used for calculating graphics will be smoothed with a boxcar average 2*n+1 in size centered on the current frame.
Definition at line 3110 of file VMDApp.C. References commandQueue, DrawMolecule::component, DrawMolItem::force_recalc, DrawMolItem::get_smoothing, MoleculeList::mol_from_id, DrawMolItem::MOL_REGEN, moleculeList, n, num_molreps, CommandQueue::runcommand, and DrawMolItem::set_smoothing. Referenced by py_set_smoothing, and text_cmd_mol. |
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Definition at line 2956 of file VMDApp.C. References MoleculeList::change_repmethod, commandQueue, MoleculeList::mol_index_from_id, moleculeList, CmdMolChangeRepItem::REP, and CommandQueue::runcommand. Referenced by py_modrep, and text_cmd_mol. |
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Show/hide individual rep; this is done in the graphics menu by double- clicking on the rep.
Definition at line 3524 of file VMDApp.C. References commandQueue, MoleculeList::mol_from_id, moleculeList, num_molreps, CommandQueue::runcommand, and DrawMolecule::show_rep. Referenced by myBrowser::handle, py_set_visible, and text_cmd_mol. |
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Get current molid and increment counter by 1.
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Number of clipping planes supported per rep. clipid in the next few methods should be in the range [0,max).
Definition at line 3411 of file VMDApp.C. References VMD_MAX_CLIP_PLANE. Referenced by text_cmd_mol. |
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Number of color categories.
Definition at line 1557 of file VMDApp.C. References Scene::num_categories, and scene. Referenced by py_categories, and tcl_colorinfo_categories. |
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Number of color items in the given category.
Definition at line 1581 of file VMDApp.C. References Scene::category_index, Scene::num_category_items, and scene. Referenced by py_get_colormap, and tcl_colorinfo_category. |
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Number of available colors.
Definition at line 1591 of file VMDApp.C. References MAXCOLORS. Referenced by tcl_colorinfo_max. |
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info about color scale methods.
Definition at line 1672 of file VMDApp.C. References Scene::num_colorscale_methods, and scene. Referenced by py_scale_methods, and tcl_colorinfo_scale. |
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Number of menus we know about.
Definition at line 826 of file VMDApp.C. References NameList< VMDMenu * >::num. Referenced by text_cmd_menu. |
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Number of molecules currently loaded.
Definition at line 1842 of file VMDApp.C. References moleculeList, and MoleculeList::num. Referenced by fill_fltk_molchooser, IdList::find, molecule_delete_all, molecule_id, py_mol_listall, py_mol_num, SaveTrajectoryFltkMenu::selectmol, and ToolFltkMenu::update_toolrep_choosers. |
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number of representations for the given molecule.
Definition at line 2944 of file VMDApp.C. References DrawMolecule::components, MoleculeList::mol_from_id, and moleculeList. Referenced by cmd_mol_list, SaveTrajectoryFltkMenu::molchooser_activate_selection, molrep_get_color, molrep_get_colorupdate, molrep_get_drawframes, molrep_get_instances, molrep_get_material, molrep_get_pbc, molrep_get_pbc_images, molrep_get_scaleminmax, molrep_get_selection, molrep_get_selupdate, molrep_get_smoothing, molrep_get_style, molrep_is_shown, molrep_numselected, molrep_reset_scaleminmax, molrep_set_colorupdate, molrep_set_drawframes, molrep_set_instances, molrep_set_pbc, molrep_set_pbc_images, molrep_set_scaleminmax, molrep_set_selupdate, molrep_set_smoothing, molrep_show, print_arep_summary, py_addrep, py_molrep_num, text_cmd_mol, ToolFltkMenu::update_replist, and valid_rep. |
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Number of _regular_ colors, i.e., the ones that have actual names.
Definition at line 1594 of file VMDApp.C. References REGCLRS. Referenced by py_get_colorlist, py_get_colors, py_set_colorid, tcl_colorinfo_colors, and tcl_colorinfo_num. |
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perform a barrier synchronization across all nodes.
Definition at line 4359 of file VMDApp.C. References vmd_mpi_barrier. Referenced by text_cmd_parallel. |
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query current node name.
Definition at line 1050 of file VMDApp.h. References nodename. Referenced by text_cmd_parallel, and vmdinfo_tcl. |
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query current node ID.
Definition at line 1053 of file VMDApp.h. References noderank. Referenced by text_cmd_parallel, and vmdinfo_tcl. |
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query total number of nodes.
Definition at line 1056 of file VMDApp.h. References nodecount. Referenced by text_cmd_parallel, and vmdinfo_tcl. |
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Try to dlopen the specified shared library and access its plugin API. Return the number of plugins found in the given library, or -1 on error.
Definition at line 1525 of file VMDApp.C. References PluginMgr::load_sharedlibrary_plugins. Referenced by text_cmd_plugin. |
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Tell VMD to update its lists of plugins based on all the shared libraries it's loaded. Methods listed below will not be updated after a call to plugin_dlopen until this method is called.
Definition at line 1534 of file VMDApp.C. References commandQueue, and CommandQueue::runcommand. Referenced by text_cmd_plugin, and VMDinit. |
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remove menu. Return success.
Definition at line 837 of file VMDApp.C. References NameList::add_name, NameList< VMDMenu * >::data, VMDMenu::get_name, NameList< VMDMenu * >::num, and NameList< VMDMenu * >::typecode. Referenced by text_cmd_menu. |
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save VMD state to a Tcl script. A filename will be requested from the user.
Definition at line 1828 of file VMDApp.C. References UIText::save_state, uiText, and vmd_choose_file. Referenced by savestate_cb. |
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recenter the scene on the top molecule. If there are no molecules, just restores rotation to default value.
Definition at line 1407 of file VMDApp.C. References MoleculeList::center_all_molecules, MoleculeList::center_from_top_molecule_reps, commandQueue, moleculeList, Displayable::reset_transformation, Scene::root, CommandQueue::runcommand, and scene. Referenced by Win32Joystick::check_event, Spaceball::check_event, MolBrowser::handle, py_resetview, resetview_cb, scene_resetview_newmoldata, and text_cmd_display. |
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recenter the scene on the top molecule or on last settings if no-disrupt mode is enabled, unless there's only one molecule.
Definition at line 1384 of file VMDApp.C. References MoleculeList::center_top_molecule, moleculeList, MoleculeList::num, ResetViewPending, and scene_resetview. Referenced by DrawMolecule::append_frame, molecule_add_volumetric, molecule_load, and VMDupdate. |
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Rock the scene by the given amount per redraw about the given axis. If nsteps is positive, rock for the specified number of steps, then reverse direction.
Definition at line 1414 of file VMDApp.C. References commandQueue, CommandQueue::runcommand, and DisplayRocker::start_rocking. Referenced by text_cmd_rock. |
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Stop rocking the scene.
Definition at line 1420 of file VMDApp.C. References commandQueue, CommandQueue::runcommand, and DisplayRocker::stop_rocking. Referenced by text_cmd_rock. |
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Rotate the scene by the specified matrix. The translation part will be ignored.
Definition at line 1340 of file VMDApp.C. References Displayable::add_rot, CmdRotMat::BY, commandQueue, mat, Scene::root, CommandQueue::runcommand, and scene. |
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rotate the scene by or to the given angle, measured in degrees, about the given axis, either 'x', 'y', or 'z'. For rotate_by, If incr is zero, the rotation will be done in one redraw; otherwise the rotation will be performed in steps of incr.
Definition at line 1314 of file VMDApp.C. References Displayable::add_rot, CmdRotate::BY, VideoStream::cli_connected, VideoStream::cli_send_rotate_by, commandQueue, Scene::root, CommandQueue::runcommand, scene, DisplayRocker::start_rocking, DisplayRocker::stop_rocking, and uivs. Referenced by Win32Joystick::check_event, VideoStream::check_event, Spaceball::check_event, Mouse::check_event, Mobile::check_event, Tool::dograb, py_rotate, text_cmd_rotate, and text_cmd_rotmat. |
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Definition at line 1346 of file VMDApp.C. References commandQueue, mat, Scene::root, CommandQueue::runcommand, scene, Displayable::set_rot, and CmdRotMat::TO. |
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Definition at line 1333 of file VMDApp.C. References commandQueue, Scene::root, CommandQueue::runcommand, scene, Displayable::set_rot, DisplayRocker::stop_rocking, and CmdRotate::TO. Referenced by text_cmd_rotate, and text_cmd_rotmat. |
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Scale by/to the given positive scale factor.
Definition at line 1367 of file VMDApp.C. References CmdScale::BY, VideoStream::cli_connected, VideoStream::cli_send_scale_by, commandQueue, Displayable::mult_scale, Scene::root, CommandQueue::runcommand, scene, and uivs. Referenced by Win32Joystick::check_event, VideoStream::check_event, Spaceball::check_event, Mobile::check_event, py_scale, and text_cmd_scale. |
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Definition at line 1378 of file VMDApp.C. References commandQueue, Scene::root, CommandQueue::runcommand, scene, Displayable::set_scale, and CmdScale::TO. Referenced by text_cmd_scale. |
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Stop rocking AND persistent rotations induced by input devices (like the Mouse).
Definition at line 1425 of file VMDApp.C. References DisplayRocker::stop_rocking, and Mouse::stop_rotation. Referenced by resetview_cb, stoprotation_cb, text_cmd_mouse, and text_cmd_rotate. |
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Translate everything that isn't fixed by/to the given amount.
Definition at line 1352 of file VMDApp.C. References Displayable::add_glob_trans, CmdTranslate::BY, VideoStream::cli_connected, VideoStream::cli_send_translate_by, commandQueue, Scene::root, CommandQueue::runcommand, scene, uivs, and z. Referenced by Win32Joystick::check_event, VideoStream::check_event, Spaceball::check_event, Mobile::check_event, Tool::dograb, py_translate, and text_cmd_translate. |
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Definition at line 1362 of file VMDApp.C. References commandQueue, Scene::root, CommandQueue::runcommand, scene, Displayable::set_glob_trans, CmdTranslate::TO, and z. Referenced by text_cmd_translate. |
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Set the color scale colors from the given arrays.
Definition at line 1700 of file VMDApp.C. References Scene::colorscale_method_name, commandQueue, CommandQueue::runcommand, scene, and Scene::set_colorscale_colors. Referenced by text_cmd_color. |
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Definition at line 1219 of file VMDApp.h. Referenced by VMDreadStartup. |
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Definition at line 3403 of file VMDApp.C. References UIObject::set_callbacks. Referenced by text_cmd_mouse. |
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Definition at line 3407 of file VMDApp.C. References Mouse::set_rocking. Referenced by text_cmd_mouse. |
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text message access methods.
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show Stride message, if necessary.
Definition at line 1174 of file VMDApp.C. Referenced by DrawMolecule::need_secondary_structure. |
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return the current spaceball event data, used by the UIVR SpaceballTracker interface.
Definition at line 4340 of file VMDApp.C. References Spaceball::get_tracker_status, and NULL. Referenced by SpaceballTracker::update, and SpaceballButtons::update. |
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Change the spaceball mode.
Definition at line 4314 of file VMDApp.C. References commandQueue, Spaceball::move_mode, Spaceball::MoveMode, and CommandQueue::runcommand. Referenced by text_cmd_spaceball. |
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Change the spaceball null region.
Definition at line 4331 of file VMDApp.C. References Spaceball::set_null_region. Referenced by text_cmd_spaceball. |
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Change the spaceball sensitivity.
Definition at line 4324 of file VMDApp.C. References Spaceball::set_sensitivity. Referenced by text_cmd_spaceball. |
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Definition at line 3845 of file VMDApp.C. References commandQueue, Stage::loc_description, Stage::location, Stage::locations, CommandQueue::runcommand, stage, and strupcmp. Referenced by stage_cb, and text_cmd_stage. |
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Definition at line 3857 of file VMDApp.C. References commandQueue, num, Stage::panels, CommandQueue::runcommand, and stage. Referenced by text_cmd_stage. |
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Definition at line 3863 of file VMDApp.C. References commandQueue, CommandQueue::runcommand, Stage::size, and stage. Referenced by text_cmd_stage. |
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change to a new text interpreter mode. Currently "tcl" and "python" are supported.
Definition at line 4352 of file VMDApp.C. References UIText::change_interp, and uiText. Referenced by PythonTextInterp::doEvent, text_cmd_gopython, and VMDreadStartup. |
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Definition at line 4103 of file VMDApp.C. References UIVR::change_type, commandQueue, CommandQueue::runcommand, and uivr. Referenced by ToolFltkMenu::select_tool_type, and text_cmd_tool. |
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Definition at line 4096 of file VMDApp.C. References UIVR::add_tool_with_USL, commandQueue, CommandQueue::runcommand, and uivr. Referenced by ToolFltkMenu::create_tool, and text_cmd_tool. |
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Definition at line 4110 of file VMDApp.C. References commandQueue, UIVR::remove_tool, CommandQueue::runcommand, and uivr. Referenced by ToolFltkMenu::delete_tool. |
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Definition at line 4128 of file VMDApp.C. References commandQueue, CommandQueue::runcommand, UIVR::set_force_scale, and uivr. Referenced by ToolFltkMenu::set_forcescale, and text_cmd_tool. |
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Definition at line 4119 of file VMDApp.C. References commandQueue, CommandQueue::runcommand, UIVR::set_position_scale, and uivr. Referenced by ToolFltkMenu::set_positionscale, and text_cmd_tool. |
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Definition at line 4137 of file VMDApp.C. References commandQueue, CommandQueue::runcommand, UIVR::set_spring_scale, and uivr. Referenced by ToolFltkMenu::set_springscale, and text_cmd_tool. |
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Show a file dialog. Use the first available of: Tk, Fltk, stdin Returns a new'd filename, or NULL.
Definition at line 1193 of file VMDApp.C. References UIText::get_tcl_interp, JString::length, NULL, result, stringdup, strupcmp, and uiText. Referenced by SaveTrajectoryFltkMenu::do_save, loadstate_cb, logfile_cb, and save_state. |
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Print the given error message and pause for the given number of seconds before setting a flag that willl make VMDupdate return FALSE.
Definition at line 1031 of file VMDApp.C. References exitFlag, UIText::get_tcl_interp, noderank, NULL, uiText, vmd_mpi_barrier, vmd_msleep, and vmd_sleep. Referenced by TclTextInterp::doEvent, myglwindow::hide, FreeVRScene::prepare, CaveScene::prepare, py_vmdexit, quit_cb, text_cmd_quit, and VMDinit. |
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redraw the screen and update all things that need updatin'. Return TRUE until exit has been requested by the user.
Definition at line 914 of file VMDApp.C. References background_processing, background_processing_clear, CommandQueue::check_events, VideoStream::cli_connected, commandQueue, display, Scene::draw, Scene::draw_finished, CommandQueue::execute_all, Molecule::get_new_frames, MoleculeList::molecule, moleculeList, DisplayDevice::needRedraw, NULL, MoleculeList::num, Scene::prepare, PROFILE_POP_RANGE, PROFILE_PUSH_RANGE, DisplayDevice::readpixels_rgba4u, scene, scene_resetview_newmoldata, VideoStream::srv_connected, VideoStream::srv_send_frame, DisplayDevice::supports_gui, uivs, UpdateDisplay, VideoStream::video_frame_pending, and vmd_msleep. Referenced by display_update, display_update_ui, myglwindow::draw, main, py_vmdupdate, and VMDinit. |
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Establish an connection to the given host over the given port, using the given molecule id. Return success.
Definition at line 3593 of file VMDApp.C. References VideoStream::cli_connect, and uivs. |
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Return true if a video strem is established.
Definition at line 3606 of file VMDApp.C. References uivs. |
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Disconnect. Return success.
Definition at line 3614 of file VMDApp.C. References VideoStream::cli_disconnect, and uivs. |
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generates delay-based frame change events.
Definition at line 206 of file VMDApp.h. Referenced by animation_set_dir, animation_set_frame, animation_set_speed, animation_set_stride, animation_set_style, py_skip, py_speed, py_style, text_cmd_animate, VMDApp, VMDinit, and ~VMDApp. |
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used if we want to process unknown args elsewhere.
Definition at line 198 of file VMDApp.h. Referenced by PythonTextInterp::PythonTextInterp, TclTextInterp::TclTextInterp, and VMDApp. |
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needed by Tcl/Python initialization code.
Definition at line 199 of file VMDApp.h. Referenced by PythonTextInterp::PythonTextInterp, TclTextInterp::TclTextInterp, and VMDApp. |
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symbol table and atom selection parser.
Definition at line 238 of file VMDApp.h. Referenced by access_tcl_atomsel, MoleculeList::add_rep, atomsel_get, atomsel_new, atomsel_set, MoleculeList::change_repsel, SaveTrajectoryFltkMenu::do_save, get_attribute_index, get_weights_from_attribute, GraphicsFltkMenu::GraphicsFltkMenu, make_tcl_atomsel, parseAtomselMacros, py_addmacro, py_allmacros, py_atomselect, py_delmacro, py_getmacro, py_list_attrs, MoleculeList::set_default_selection, MoleculeList::set_selection, tcl_get_weights, vmd_measure_cluster, vmd_measure_clustsize, VMDApp, VMDinit, and ~VMDApp. |
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axes object used in the scene.
Definition at line 233 of file VMDApp.h. Referenced by axes_set_location, initaxes, MainFltkMenu::MainFltkMenu, py_get_location, text_cmd_axes, VMDApp, VMDinit, and ~VMDApp. |
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CPUID, SIMD vector insn capability bits.
Definition at line 210 of file VMDApp.h. Referenced by QuickSurf::calc_surf, Orbital::calculate_mo, AtomSel::change, same_double, same_int, VMDinit, and ~VMDApp. |
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CUDA acceleration system handle.
Definition at line 214 of file VMDApp.h. Referenced by DrawMolecule::cuda_devpool, measure_rdf, measure_rmsdmat_qcp_ooc, text_cmd_vmdbench, VMDApp, VMDinit, and ~VMDApp. |
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flag for whether to quit the display loop.
Definition at line 243 of file VMDApp.h. Referenced by TclTextInterp::evalFile, text_cmd_quit, VMDApp, VMDexit, and VMDinit. |
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FPS counter used in the scene.
Definition at line 234 of file VMDApp.h. Referenced by display_set_fps, text_cmd_display, VMDApp, VMDinit, and ~VMDApp. |
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list of all labels etc.
Definition at line 237 of file VMDApp.h. Referenced by label_add, label_delete, label_get_text_size, label_get_text_thickness, label_set_text_size, label_set_text_thickness, label_set_textformat, label_set_textoffset, label_show, py_label_add, py_label_delete, py_label_getvalues, py_label_visible, py_listall, text_cmd_label, VMDApp, VMDinit, and ~VMDApp. |
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Highlighted molecule id and rep. Set by GraphicsFltkMenu, used by PickModeMoveHighlightedRep.
Definition at line 251 of file VMDApp.h. Referenced by DrawMolecule::highlighted_rep, GraphicsFltkMenu::update_molchooser, and VMDApp. |
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Highlighted molecule id and rep. Set by GraphicsFltkMenu, used by PickModeMoveHighlightedRep.
Definition at line 251 of file VMDApp.h. Referenced by DrawMolecule::highlighted_rep, GraphicsFltkMenu::update_rep, and VMDApp. |
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IMD manager class.
Definition at line 204 of file VMDApp.h. Referenced by imd_connect, imd_connected, imd_disconnect, imd_sendforces, py_copyunitcell, py_imdconnect, py_imdconnected, py_imddetach, py_imdkeep, py_imdkill, py_imdpause, py_imdtransfer, py_sendforces, text_cmd_imd, VMDApp, VMDinit, and ~VMDApp. |
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MPI node count.
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MPI node name.
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MPI node rank.
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GPU hardware H.26[45] video [en|de]coder.
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handles all picking events.
Definition at line 229 of file VMDApp.h. Referenced by DrawMolecule::add_rep, Tool::assign_rep, DrawMolecule::del_rep, DrawMolecule::DrawMolecule, get_nearby_atom, Tool::target, Tool::tool_location_update, VMDApp, VMDinit, DrawMolecule::~DrawMolecule, and ~VMDApp. |
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list of available picking modes.
Definition at line 230 of file VMDApp.h. Referenced by mouse_set_mode, PickList::pick_end, PickList::pick_move, PickList::pick_start, PickList::PickList, VMDApp, VMDinit, and ~VMDApp. |
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QuickSurf object shared by all reps, to help minimize the persistent GPU global memory footprint, and to make it easy to force-dump all persistent QuickSurf GPU global memory data structures on-demand for GPU ray tracing, or other tasks that also need a lot of resources. The default persistence of QuickSurf GPU resources enable fast trajectory playback.
Definition at line 218 of file VMDApp.h. Referenced by VMDinit, OptiXDisplayDevice::write_header, and ~VMDApp. |
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pending resetview needs attention.
Definition at line 244 of file VMDApp.h. Referenced by scene_resetview_newmoldata, and VMDApp. |
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stage object used in the scene.
Definition at line 232 of file VMDApp.h. Referenced by MainFltkMenu::MainFltkMenu, stage_set_location, stage_set_numpanels, stage_set_size, text_cmd_stage, VMDApp, VMDinit, and ~VMDApp. |
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CPU thread pool for low-latency calcs.
Definition at line 212 of file VMDApp.h. Referenced by DrawMolecule::cpu_threadpool, measure_rmsdmat_qcp, measure_rmsdmat_qcp_ooc, VMDApp, VMDinit, and ~VMDApp. |
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the text interface JRG: made public for save_state.
Definition at line 202 of file VMDApp.h. Referenced by deactivate_uitext_stdin, M_VRJapp::latePreFrame, logfile_read, py_evaltcl, save_state, textinterp_change, vmd_choose_file, VMDApp, VMDexit, VMDinit, and ~VMDApp. |
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VR tool interface.
Definition at line 203 of file VMDApp.h. Referenced by activate_menus, ToolFltkMenu::choose_buttons, ToolFltkMenu::choose_feedback, ToolFltkMenu::choose_tracker, ToolFltkMenu::reset_device_menus, ToolFltkMenu::reset_tool_list, ToolFltkMenu::select_tool, tool_change_type, tool_create, tool_delete, tool_set_force_scale, tool_set_position_scale, tool_set_spring_scale, ToolFltkMenu::ToolFltkMenu, ToolFltkMenu::update_toolrep_choosers, VMDApp, and ~VMDApp. |
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Video streaming UI events.
Definition at line 205 of file VMDApp.h. Referenced by Mouse::check_event, OptiXRenderer::render_to_videostream, scene_rotate_by, scene_scale_by, scene_translate_by, text_cmd_videostream, OpenGLPbufferDisplayDevice::update, OpenGLDisplayDevice::update, VMDApp, VMDinit, VMDupdate, vs_connect, vs_connected, vs_disconnect, OptiXDisplayDevice::write_trailer, and ~VMDApp. |
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flag for whether to update the scene.
Definition at line 242 of file VMDApp.h. Referenced by display_update, display_update_on, display_update_status, VMDApp, and VMDupdate. |
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describe what the hotkey does.
Definition at line 241 of file VMDApp.h. Referenced by text_cmd_user, and ~VMDApp. |
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lookup table for Tcl scripts.
Definition at line 240 of file VMDApp.h. Referenced by text_cmd_user, TclTextInterp::userkey_cb, and ~VMDApp. |
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handles collaborative VMD interaction.
Definition at line 239 of file VMDApp.h. Referenced by text_cmd_collab, VMDApp, VMDinit, and ~VMDApp. |
1.2.14 written by Dimitri van Heesch,
© 1997-2002