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VMDApp Class Reference

The main VMD application instance, created by the main entry point. More...

#include <VMDApp.h>

List of all members.

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...

UITextuiText
 the text interface JRG: made public for save_state. More...

UIVRuivr
 VR tool interface. More...

IMDMgrimdMgr
 IMD manager class. More...

VideoStreamuivs
 Video streaming UI events. More...

Animationanim
 generates delay-based frame change events. More...

DisplayDevicedisplay
 display in which the images are rendered. More...

Scenescene
 list of all Displayable objects to draw. More...

wkf_cpu_caps_tcpucaps
 CPUID, SIMD vector insn capability bits. More...

wkf_threadpool_tthrpool
 CPU thread pool for low-latency calcs. More...

CUDAAccelcuda
 CUDA acceleration system handle. More...

NVENCMgrnvenc
 GPU hardware H.26[45] video [en|de]coder. More...

QuickSurfqsurf
 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...

PickListpickList
 handles all picking events. More...

PickModeListpickModeList
 list of available picking modes. More...

MaterialListmaterialList
 list of materials. More...

Stagestage
 stage object used in the scene. More...

Axesaxes
 axes object used in the scene. More...

FPSfps
 FPS counter used in the scene. More...

CommandQueuecommandQueue
 the command processor. More...

MoleculeListmoleculeList
 list of all loaded molecules. More...

GeometryListgeometryList
 list of all labels etc. More...

SymbolTableatomSelParser
 symbol table and atom selection parser. More...

VMDCollabvmdcollab
 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...


Detailed Description

The main VMD application instance, created by the main entry point.

Definition at line 130 of file VMDApp.h.


Constructor & Destructor Documentation

VMDApp::VMDApp int    argc,
char **    argv,
int    mpion
 

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.

VMDApp::~VMDApp  
 

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.


Member Function Documentation

int VMDApp::activate_menus  
 

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.

int VMDApp::add_menu VMDMenu  
 

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.

const char * VMDApp::animation_dir_name int   
 

Definition at line 1435 of file VMDApp.C.

References Animation::ANIM_TOTAL_DIRS, and NULL.

int VMDApp::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.

Definition at line 1431 of file VMDApp.C.

References Animation::ANIM_TOTAL_DIRS.

int VMDApp::animation_num_styles  
 

number of animation styles, and their names.

Definition at line 1447 of file VMDApp.C.

References Animation::ANIM_TOTAL_STYLES.

int VMDApp::animation_set_dir int   
 

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.

int VMDApp::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.

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.

int VMDApp::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.

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.

int VMDApp::animation_set_stride int   
 

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.

int VMDApp::animation_set_style int   
 

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.

const char * VMDApp::animation_style_name int   
 

Definition at line 1451 of file VMDApp.C.

References Animation::ANIM_TOTAL_STYLES, and NULL.

void VMDApp::append_text const char *    str [inline, static]
 

Definition at line 1204 of file VMDApp.h.

int VMDApp::axes_set_location const char *   
 

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.

int VMDApp::background_processing   [inline]
 

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.

void VMDApp::background_processing_clear   [inline]
 

Definition at line 263 of file VMDApp.h.

Referenced by VMDApp, and VMDupdate.

void VMDApp::background_processing_set   [inline]
 

Definition at line 264 of file VMDApp.h.

Referenced by VideoStream::check_event, and Molecule::get_new_frames.

void VMDApp::clear_text   [inline, static]
 

Definition at line 1207 of file VMDApp.h.

int VMDApp::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.

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.

const char * VMDApp::color_category int   
 

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.

const char * VMDApp::color_category_item const char *    category,
int   
 

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.

int VMDApp::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().

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.

int VMDApp::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().

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.

int VMDApp::color_change_rgb const char *    color,
float    r,
float    g,
float    b
 

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.

int VMDApp::color_change_rgblist int    numcols,
const char **    colors,
float *    rgb3fv
 

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.

int VMDApp::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.

Definition at line 1623 of file VMDApp.C.

References Scene::color_default_value, color_index, and scene.

Referenced by text_cmd_color.

int VMDApp::color_get_from_name const char *    category,
const char *    colorname,
const char **    color
 

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.

const char * VMDApp::color_get_restype const char *    resname
 

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.

int VMDApp::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.

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.

const char * VMDApp::color_mapping const char *    category,
const char *    item
 

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.

const char * VMDApp::color_name int    n
 

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.

int VMDApp::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.

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.

int VMDApp::color_value const char *    colorname,
float *    r,
float *    g,
float *    b
 

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.

int VMDApp::colorscale_method_current  
 

Definition at line 1675 of file VMDApp.C.

References Scene::colorscale_method, and scene.

Referenced by py_scale_method, and tcl_colorinfo_scale.

int VMDApp::colorscale_method_index const char *   
 

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.

const char * VMDApp::colorscale_method_menuname int   
 

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.

const char * VMDApp::colorscale_method_name int   
 

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.

int VMDApp::colorscale_params float *    midpoint,
float *    min,
float *    max,
int *    rev,
int *    posterize
 

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.

int VMDApp::colorscale_setmethod int    method
 

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.

int VMDApp::colorscale_setparams float    midpoint,
float    min,
float    max,
int    rev,
int    posterize
 

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.

void VMDApp::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.

Definition at line 3974 of file VMDApp.C.

References UIObject::Off, and uiText.

int VMDApp::depthcue_set_density float   
 

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.

int VMDApp::depthcue_set_end float   
 

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.

int VMDApp::depthcue_set_mode const char *   
 

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.

int VMDApp::depthcue_set_start float   
 

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.

float VMDApp::display_get_screen_distance  
 

Definition at line 3645 of file VMDApp.C.

References display, and DisplayDevice::distance_to_screen.

float VMDApp::display_get_screen_height  
 

Definition at line 3636 of file VMDApp.C.

References display, and DisplayDevice::screen_height.

void VMDApp::display_get_size int *    w,
int *    h
 

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.

int VMDApp::display_projection_is_perspective void   
 

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.

int VMDApp::display_set_aa int    onoff
 

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.

int VMDApp::display_set_ao int    onoff
 

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.

int VMDApp::display_set_ao_ambient float    a
 

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.

int VMDApp::display_set_ao_direct float    d
 

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.

int VMDApp::display_set_background_mode int    mode
 

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.

int VMDApp::display_set_cachemode const char *    mode
 

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.

int VMDApp::display_set_culling int    onoff
 

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.

int VMDApp::display_set_depthcue int    onoff
 

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.

int VMDApp::display_set_dof int    onoff
 

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.

int VMDApp::display_set_dof_fnumber float    f
 

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.

int VMDApp::display_set_dof_focal_dist float    d
 

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.

int VMDApp::display_set_eyesep float    sep
 

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.

int VMDApp::display_set_farclip float    amt,
int    isdelta
 

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.

int VMDApp::display_set_focallen float    flen
 

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.

int VMDApp::display_set_fps int    onoff
 

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.

int VMDApp::display_set_nearclip float    amt,
int    isdelta
 

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.

void VMDApp::display_set_position int    x,
int    y
 

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.

int VMDApp::display_set_projection const char *    proj
 

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.

int VMDApp::display_set_rendermode const char *    mode
 

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.

void VMDApp::display_set_screen_distance float   
 

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.

void VMDApp::display_set_screen_height float   
 

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.

int VMDApp::display_set_shadows int    onoff
 

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.

void VMDApp::display_set_size int    w,
int    h
 

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.

int VMDApp::display_set_stereo const char *    mode
 

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.

int VMDApp::display_set_stereo_swap int    onoff
 

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.

void VMDApp::display_titlescreen  
 

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.

void VMDApp::display_update  
 

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.

void VMDApp::display_update_on int   
 

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.

int VMDApp::display_update_status  
 

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.

void VMDApp::display_update_ui  
 

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.

int VMDApp::filerender_aasamples const char *    method,
int    aasamples
 

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.

int VMDApp::filerender_aosamples const char *    method,
int    aosamples
 

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.

int VMDApp::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.

Definition at line 1276 of file VMDApp.C.

References FileRenderList::aspectratio.

Referenced by text_cmd_render.

const char * VMDApp::filerender_cur_format const char *    method
 

Return name of currently selected format.

Definition at line 1286 of file VMDApp.C.

References FileRenderList::format.

Referenced by text_cmd_render.

const char * VMDApp::filerender_default_filename const char *    method
 

get the dafault filename for this render method.

Definition at line 1489 of file VMDApp.C.

References FileRenderer::default_filename, FileRenderList::find, and NULL.

const char * VMDApp::filerender_default_option const char *    method
 

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.

const char * VMDApp::filerender_get_format const char *    method,
int    i
 

Return the ith format. NULL if invalid.

Definition at line 1283 of file VMDApp.C.

References FileRenderList::format.

Referenced by text_cmd_render.

int VMDApp::filerender_has_antialiasing const char *    method
 

Return whether given renderer supports antialiasing.

Definition at line 1260 of file VMDApp.C.

References FileRenderList::has_antialiasing.

Referenced by text_cmd_render.

int VMDApp::filerender_has_imagesize const char *    method
 

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.

int VMDApp::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.

Definition at line 1269 of file VMDApp.C.

References FileRenderList::imagesize.

Referenced by text_cmd_render.

const char * VMDApp::filerender_name int    n
 

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.

int VMDApp::filerender_num  
 

Number of file render methods.

Definition at line 1244 of file VMDApp.C.

References FileRenderList::num.

Referenced by py_listall, and text_cmd_render.

int VMDApp::filerender_numformats const char *    method
 

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.

const char * VMDApp::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.

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.

const char * VMDApp::filerender_prettyname int    n
 

Pretty name of Nth renderer.

Definition at line 1250 of file VMDApp.C.

References n, and FileRenderList::pretty_name.

int VMDApp::filerender_render const char *    method,
const char *    filename,
const char *    extcmd
 

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.

int VMDApp::filerender_set_format const char *    method,
const char *    format
 

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.

const char * VMDApp::filerender_shortname_from_prettyname const char *    pretty
 

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.

int VMDApp::filerender_valid const char *    method
 

Return true if renderer exists.

Definition at line 1253 of file VMDApp.C.

References FileRenderList::find, and NULL.

int VMDApp::get_colorscale_colors int    whichScale,
float    min[3],
float    mid[3],
float    max[3]
 

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.

int VMDApp::get_eofexit   [inline]
 

Definition at line 1220 of file VMDApp.h.

Referenced by TclTextInterp::doEvent.

vmdplugin_t * VMDApp::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.

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.

unsigned long VMDApp::get_repserialnum void    [static]
 

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.

unsigned long VMDApp::get_texserialnum void    [static]
 

Definition at line 1168 of file VMDApp.C.

References texserialnum.

const char* VMDApp::get_text   [inline, static]
 

Definition at line 1210 of file VMDApp.h.

const char * VMDApp::guess_filetype const char *    filename
 

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.

int VMDApp::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.

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.

int VMDApp::imd_connected int    molid
 

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.

int VMDApp::imd_disconnect int    molid
 

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.

int VMDApp::imd_sendforces int   ,
const int *   ,
const float *   
 

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.

int VMDApp::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.

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.

int VMDApp::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.

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.

float VMDApp::label_get_text_size   const
 

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.

float VMDApp::label_get_text_thickness   const
 

Definition at line 4058 of file VMDApp.C.

References geometryList, and GeometryList::getTextThickness.

Referenced by py_label_textthickness, and text_cmd_label.

int VMDApp::label_set_text_size float   
 

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.

int VMDApp::label_set_text_thickness float   
 

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.

int VMDApp::label_set_textformat const char *    nm,
int    n,
const char *    format
 

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.

int VMDApp::label_set_textoffset const char *    nm,
int    n,
float    x,
float    y
 

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.

int VMDApp::label_show const char *    category,
int    n,
int    onoff
 

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.

int VMDApp::light_highlight int    lightnum,
int    onoff
 

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.

int VMDApp::light_move int    lightnum,
const float *    newpos
 

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.

int VMDApp::light_on int    lightnum,
int    onoff
 

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.

int VMDApp::light_rotate int    lightnum,
float    amt,
char    axis
 

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.

int VMDApp::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.

Definition at line 1520 of file VMDApp.C.

References PluginMgr::plugins.

Referenced by SaveTrajectoryFltkMenu::act_on_command, and text_cmd_plugin.

int VMDApp::logfile_read const char *    path
 

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.

const char * VMDApp::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.

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.

int VMDApp::material_change const char *    name,
int    property,
float    val
 

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.

int VMDApp::material_delete const char *    name
 

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.

int VMDApp::material_rename const char *    oldname,
const char *    newname
 

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.

int VMDApp::material_restore_default int   
 

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.

void VMDApp::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.

Definition at line 857 of file VMDApp.C.

References commandQueue, and CommandQueue::runcommand.

Referenced by py_addmenu, py_registermenu, and text_cmd_menu.

int VMDApp::menu_id const char *    name
 

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.

int VMDApp::menu_location const char *    name,
int &    x,
int &    y
 

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.

int VMDApp::menu_move const char *    name,
int    x,
int    y
 

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.

const char * VMDApp::menu_name int   
 

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.

void VMDApp::menu_remove_extension const char *    shortname
 

Definition at line 861 of file VMDApp.C.

References commandQueue, and CommandQueue::runcommand.

Referenced by text_cmd_menu.

int VMDApp::menu_select_mol const char *    name,
int    molno
 

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.

int VMDApp::menu_show const char *    name,
int    on
 

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.

int VMDApp::menu_status const char *    name
 

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.

int VMDApp::mobile_get_APIsupported  
 

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.

void VMDApp::mobile_get_client_list ResizeArray< JString * > *&    nick,
ResizeArray< JString * > *&    ip,
ResizeArray< bool > *&    active
 

Get the list of current clients.

Definition at line 4268 of file VMDApp.C.

References Mobile::get_client_list.

Referenced by text_cmd_mobile.

int VMDApp::mobile_get_mode  
 

Get the mobile interface mode.

Definition at line 4264 of file VMDApp.C.

References Mobile::get_move_mode.

Referenced by text_cmd_mobile.

int VMDApp::mobile_get_network_port  
 

Get the mobile interface network port.

Definition at line 4280 of file VMDApp.C.

References Mobile::get_port.

Referenced by text_cmd_mobile.

void VMDApp::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.

Definition at line 4302 of file VMDApp.C.

References Mobile::get_tracker_status, and NULL.

Referenced by MobileTracker::update, and MobileButtons::update.

int VMDApp::mobile_network_port int    port
 

Change the mobile interface network port.

Definition at line 4274 of file VMDApp.C.

References Mobile::network_port.

Referenced by text_cmd_mobile.

int VMDApp::mobile_sendMsg const char *    nick,
const char *    ip,
const char *    msgType,
const char *    msg
 

Send a message to a specific client.

Definition at line 4294 of file VMDApp.C.

References Mobile::sendMsgToClient.

Referenced by text_cmd_mobile.

int VMDApp::mobile_set_activeClient const char *    nick,
const char *    ip
 

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.

int VMDApp::mobile_set_mode int    mode
 

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.

int VMDApp::molecule_activate int    molid,
int    onoff
 

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.

int VMDApp::molecule_add_instance int    molid,
Matrix4   inst
 

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.

int VMDApp::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
 

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.

int VMDApp::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.

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.

int VMDApp::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.

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.

int VMDApp::molecule_bondsrecalc int    molid
 

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.

int VMDApp::molecule_cancel_io int    molid
 

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.

int VMDApp::molecule_delete int    molid
 

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.

int VMDApp::molecule_delete_all void   
 

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.

int VMDApp::molecule_delete_all_instances int    molid
 

Delete all instances in a molecule.

Definition at line 3168 of file VMDApp.C.

References BaseMolecule::clear_instances, MoleculeList::mol_from_id, and moleculeList.

int VMDApp::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).

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.

int VMDApp::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.

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.

int VMDApp::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.

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.

int VMDApp::molecule_fix int    molid,
int    onoff
 

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.

int VMDApp::molecule_frame int    molid
 

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.

int VMDApp::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.

Definition at line 1928 of file VMDApp.C.

References Timestep::a_length, BaseMolecule::add_angle, BaseMolecule::add_atoms, BaseMolecule::add_bond, Scene::add_color_item, BaseMolecule::add_cterm, BaseMolecule::add_dihedral, BaseMolecule::add_improper, MoleculeList::add_molecule, Timestep::alpha, MolAtom::altlocindex, BaseMolecule::altlocNames, BaseMolecule::analyze, BaseMolecule::angles, DrawMolecule::append_frame, BaseMolecule::atom, MolAtom::atomicnumber, BaseMolecule::atomNames, BaseMolecule::atomTypes, Timestep::b_length, Timestep::beta, BaseMolecule::beta, MolAtom::bonds, MolAtom::bondTo, Timestep::c_length, MolAtom::chainindex, BaseMolecule::chainNames, BaseMolecule::charge, MoleculeList::colorCatIndex, commandQueue, AtomSel::coordinates, BaseMolecule::cterms, BaseMolecule::datasetflags, BaseMolecule::dihedrals, AtomSel::firstsel, Timestep::gamma, BaseMolecule::id, BaseMolecule::impropers, BaseMolecule::init_atoms, MolAtom::insertionstr, AtomSel::lastsel, BaseMolecule::mass, MLCAT_MOLECULES, MoleculeList::mol_from_id, MoleculeEvent::MOL_NEW, molecule_rename, moleculeList, AtomSel::molid, BaseMolecule::molname, NameList< int >::name, MolAtom::nameindex, BaseMolecule::nAtoms, BaseMolecule::nFragments, BaseMolecule::nNucleicFragments, BaseMolecule::nProteinFragments, BaseMolecule::nResidues, NULL, BaseMolecule::num_angles, BaseMolecule::num_cterms, BaseMolecule::num_dihedrals, BaseMolecule::num_impropers, BaseMolecule::occupancy, AtomSel::on, Timestep::pos, PROFILE_POP_RANGE, PROFILE_PUSH_RANGE, BaseMolecule::radius, Molecule::rename, MolAtom::resid, MolAtom::resnameindex, BaseMolecule::resNames, Scene::root, CommandQueue::runcommand, scene, MolAtom::segnameindex, BaseMolecule::segNames, AtomSel::selected, AtomSel::timestep, MolAtom::typeindex, and VISCLRS.

Referenced by py_mol_fromsel, and text_cmd_mol.

const char * VMDApp::molecule_get_color  
 

Definition at line 3026 of file VMDApp.C.

References MoleculeList::color, and moleculeList.

Referenced by text_cmd_mol.

const char * VMDApp::molecule_get_material  
 

Definition at line 3044 of file VMDApp.C.

References MoleculeList::material, and moleculeList.

Referenced by text_cmd_mol.

const char * VMDApp::molecule_get_selection  
 

Definition at line 3035 of file VMDApp.C.

References moleculeList, and MoleculeList::selection.

Referenced by text_cmd_mol.

const char * VMDApp::molecule_get_style  
 

Definition at line 3017 of file VMDApp.C.

References moleculeList, and MoleculeList::representation.

Referenced by text_cmd_mol.

int VMDApp::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.

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.

int VMDApp::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.

Definition at line 2817 of file VMDApp.C.

References MoleculeList::mol_index_from_id, and moleculeList.

int VMDApp::molecule_is_active int    molid
 

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.

int VMDApp::molecule_is_displayed int    molid
 

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.

int VMDApp::molecule_is_fixed int    molid
 

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.

int VMDApp::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.

Definition at line 2289 of file VMDApp.C.

References MoleculeList::add_color_names, Molecule::add_coor_file, BaseMolecule::analyze, FileSpec::autobonds, MolFilePlugin::can_read_graphics, MolFilePlugin::can_read_metadata, MolFilePlugin::can_read_pagealigned_timesteps, MolFilePlugin::can_read_qm, MolFilePlugin::can_read_qm_timestep, MolFilePlugin::can_read_structure, MolFilePlugin::can_read_timesteps, MolFilePlugin::can_read_volumetric, DrawMolItem::COL_REGEN, commandQueue, DrawMolecule::components, data, MoleculeList::default_color, MoleculeList::default_material, MoleculeList::default_representation, MoleculeList::default_selection, FileSpec::filebonds, FileSpec::first, DrawMolecule::force_recalc, get_plugin, guess_filetype, BaseMolecule::has_structure, BaseMolecule::id, BaseMolecule::init_atoms, MolFilePlugin::init_read, FileSpec::last, MoleculeList::mol_from_id, MoleculeList::mol_index_from_id, molecule_addrep, molecule_new, molecule_set_style, moleculeList, BaseMolecule::nAtoms, MolFilePlugin::natoms, Molecule::next_frame, NULL, BaseMolecule::num_volume_data, FileSpec::nvolsets, PROFILE_POP_RANGE, PROFILE_PUSH_RANGE, MolFilePlugin::read_metadata, MolFilePlugin::read_optional_structure, MolFilePlugin::read_qm_data, MolFilePlugin::read_rawgraphics, MolFilePlugin::read_structure, MolFilePlugin::read_timestep_pagealign_size, MolFilePlugin::read_volumetric, Molecule::record_database, Molecule::record_file, Molecule::record_remarks, CommandQueue::runcommand, scene, scene_resetview_newmoldata, DrawMolItem::SEL_REGEN, MoleculeList::set_color, MoleculeList::set_material, MoleculeList::set_representation, MoleculeList::set_selection, FileSpec::setids, FileSpec::stride, VMD_FS_IS_REMOTE, vmd_fstype_locality, and FileSpec::waitfor.

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, MolBrowser::handle, myglwindow::handle, colvarproxy_vmd::load_atoms, colvarproxy_vmd::load_coords, mask, mdff_cc, py_mol_load, py_mol_read, text_cmd_animate, text_cmd_mol, VMDreadStartup, and vmdWindowProc.

int VMDApp::molecule_make_top int    molid
 

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.

int VMDApp::molecule_modrep int    molid,
int    repid
 

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.

const char * VMDApp::molecule_name int    molid
 

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.

int VMDApp::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.

Definition at line 1848 of file VMDApp.C.

References BaseMolecule::add_atoms, Scene::add_color_item, MoleculeList::add_molecule, BaseMolecule::beta, BaseMolecule::charge, MoleculeList::colorCatIndex, commandQueue, BaseMolecule::default_beta, BaseMolecule::default_charge, BaseMolecule::default_mass, BaseMolecule::default_occup, BaseMolecule::default_radius, BaseMolecule::id, BaseMolecule::init_atoms, BaseMolecule::mass, MLCAT_MOLECULES, MoleculeEvent::MOL_NEW, molecule_rename, moleculeList, NULL, BaseMolecule::occupancy, PROFILE_POP_RANGE, PROFILE_PUSH_RANGE, BaseMolecule::radius, Molecule::rename, Scene::root, CommandQueue::runcommand, scene, and VISCLRS.

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, init_new_volume_molecule, mask, mdff_cc, molecule_load, py_mol_load, py_mol_new, and text_cmd_mol.

int VMDApp::molecule_num_instances int    molid
 

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.

int VMDApp::molecule_numatoms int    molid
 

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.

int VMDApp::molecule_numframes int    molid
 

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.

int VMDApp::molecule_orblocalize int    molid,
int    waveid
 

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.

int VMDApp::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.

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.

int VMDApp::molecule_rename int    molid,
const char *    newname
 

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.

int VMDApp::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.

Definition at line 2639 of file VMDApp.C.

References Molecule::add_coor_file, MolFilePlugin::can_write_volumetric, Molecule::close_coor_file, commandQueue, data, CoorData::DONE, FileSpec::first, get_plugin, MolFilePlugin::init_write, FileSpec::last, MoleculeList::mol_from_id, moleculeList, BaseMolecule::nAtoms, CoorData::next, CoorData::NOTDONE, NULL, BaseMolecule::num_volume_data, DrawMolecule::numframes, FileSpec::nvolsets, PROFILE_POP_RANGE, PROFILE_PUSH_RANGE, CommandQueue::runcommand, FileSpec::selection, FileSpec::setids, FileSpec::stride, FileSpec::waitfor, and MolFilePlugin::write_volumetric.

Referenced by access_tcl_atomsel, SaveTrajectoryFltkMenu::do_save, py_mol_write, py_write, text_cmd_animate, and VolMapCreateILS::write_map.

int VMDApp::molecule_set_color const char *    color
 

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.

int VMDApp::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.

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.

int VMDApp::molecule_set_material const char *    material
 

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.

int VMDApp::molecule_set_selection const char *    selection
 

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.

int VMDApp::molecule_set_style const char *    style
 

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.

int VMDApp::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.

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.

int VMDApp::molecule_top  
 

return the molid of the top molecule.

Definition at line 2939 of file VMDApp.C.

References BaseMolecule::id, moleculeList, and MoleculeList::top.

Referenced by MainFltkMenu::act_on_command, atomsel_new, cmd_gettimestep, cmd_rawtimestep, curframe_cb, IdList::find, parse_timestep, print_mol_summary, py_atomselect, py_get_periodic, py_get_top, py_get_visible, py_measure_angle, py_measure_bond, py_measure_dihed, py_set_periodic, py_timestep, py_velocities, tcl_colvars_vmd_init, text_cmd_animate, text_cmd_mol, topo_add_angle, topo_add_bond, topo_add_dihed, topo_add_improp, topo_angletypes, topo_bondtypes, topo_del_all_angles, topo_del_all_bonds, topo_del_all_dihed, topo_del_all_impropers, topo_del_angle, topo_del_bond, topo_del_dihed, topo_del_improper, topo_dihetypes, topo_get_angle, topo_get_bond, topo_get_dihed, topo_get_impro, topo_imptypes, vmd_measure_angle, vmd_measure_bond, vmd_measure_dihed, vmd_measure_energy, vmd_measure_pbc2onc_transform, vmd_measure_pbc_neighbors, vmd_volmap_compare, vmd_volmap_ils, and vmd_volmap_new_fromtype.

int VMDApp::molecule_valid_id int    molid
 

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.

int VMDApp::molrep_delete int    molid,
int    repid
 

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.

int VMDApp::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.

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.

int VMDApp::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.

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.

const char * VMDApp::molrep_get_color int    molid,
int    repid
 

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.

int VMDApp::molrep_get_colorupdate int    molid,
int    repid
 

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.

const char * VMDApp::molrep_get_drawframes int    molid,
int    repid
 

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.

int VMDApp::molrep_get_instances int    molid,
int    repid
 

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.

const char * VMDApp::molrep_get_material int    molid,
int    repid
 

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.

const char * VMDApp::molrep_get_name int    molid,
int    repid
 

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.

int VMDApp::molrep_get_pbc int    molid,
int    repid
 

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.

int VMDApp::molrep_get_pbc_images int    molid,
int    repid
 

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.

int VMDApp::molrep_get_scaleminmax int    molid,
int    repid,
float *    min,
float *    max
 

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.

const char * VMDApp::molrep_get_selection int    molid,
int    repid
 

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.

int VMDApp::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.

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.

int VMDApp::molrep_get_smoothing int    molid,
int    repid
 

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.

const char * VMDApp::molrep_get_style int    molid,
int    repid
 

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.

int VMDApp::molrep_is_shown int    molid,
int    repid
 

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.

int VMDApp::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.

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.

int VMDApp::molrep_reset_scaleminmax int    molid,
int    repid
 

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.

int VMDApp::molrep_set_clipcenter int    molid,
int    repid,
int    clipid,
const float *    center
 

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.

int VMDApp::molrep_set_clipcolor int    molid,
int    repid,
int    clipid,
const float *    color
 

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.

int VMDApp::molrep_set_clipnormal int    molid,
int    repid,
int    clipid,
const float *    normal
 

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.

int VMDApp::molrep_set_clipstatus int    molid,
int    repid,
int    clipid,
int    onoff
 

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.

int VMDApp::molrep_set_color int    molid,
int    repid,
const char *    color
 

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.

int VMDApp::molrep_set_colorupdate int    molid,
int    repid,
int    onoff
 

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.

int VMDApp::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.

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.

int VMDApp::molrep_set_instances int    molid,
int    repid,
int    inst
 

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.

int VMDApp::molrep_set_material int    molid,
int    repid,
const char *    material
 

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.

int VMDApp::molrep_set_pbc int    molid,
int    repid,
int    pbc
 

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.

int VMDApp::molrep_set_pbc_images int    molid,
int    repid,
int    n
 

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.

int VMDApp::molrep_set_scaleminmax int    molid,
int    repid,
float    min,
float    max
 

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.

int VMDApp::molrep_set_selection int    molid,
int    repid,
const char *    selection
 

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.

int VMDApp::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.

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.

int VMDApp::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.

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.

int VMDApp::molrep_set_style int    molid,
int    repid,
const char *    style
 

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.

int VMDApp::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.

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.

int VMDApp::mouse_set_mode int    mode,
int    setting
 

Change the mouse mode.

Definition at line 4223 of file VMDApp.C.

References PickModeList::ADDBOND, Mouse::ADDBOND, PickModeList::CENTER, Mouse::CENTER, commandQueue, PickModeList::FORCEATOM, Mouse::FORCEATOM, PickModeList::FORCEFRAG, Mouse::FORCEFRAG, PickModeList::FORCERES, Mouse::FORCERES, PickModeList::LABELANGLE, Mouse::LABELANGLE, PickModeList::LABELATOM, Mouse::LABELATOM, PickModeList::LABELBOND, Mouse::LABELBOND, PickModeList::LABELDIHEDRAL, Mouse::LABELDIHEDRAL, Mouse::move_mode, PickModeList::MOVEATOM, Mouse::MOVEATOM, PickModeList::MOVEFRAG, Mouse::MOVEFRAG, Mouse::MoveMode, PickModeList::MOVEMOL, Mouse::MOVEMOL, PickModeList::MOVEREP, Mouse::MOVEREP, PickModeList::MOVERES, Mouse::MOVERES, PickModeList::PICK, Mouse::PICK, pickModeList, PickModeList::QUERY, Mouse::QUERY, CommandQueue::runcommand, and PickModeList::set_pick_mode.

Referenced by mouse_cb, move_light_cb, py_mousemode, and text_cmd_mouse.

int VMDApp::next_molid   [inline]
 

Get current molid and increment counter by 1.

Definition at line 1104 of file VMDApp.h.

int VMDApp::num_clipplanes  
 

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.

int VMDApp::num_color_categories  
 

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.

int VMDApp::num_color_category_items const char *    category
 

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.

int VMDApp::num_colors  
 

Number of available colors.

Definition at line 1591 of file VMDApp.C.

References MAXCOLORS.

Referenced by tcl_colorinfo_max.

int VMDApp::num_colorscale_methods  
 

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.

int VMDApp::num_menus  
 

Number of menus we know about.

Definition at line 826 of file VMDApp.C.

References NameList< VMDMenu * >::num.

Referenced by text_cmd_menu.

int VMDApp::num_molecules  
 

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.

int VMDApp::num_molreps int    molid
 

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.

int VMDApp::num_regular_colors  
 

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.

void VMDApp::par_barrier  
 

perform a barrier synchronization across all nodes.

Definition at line 4359 of file VMDApp.C.

References vmd_mpi_barrier.

Referenced by text_cmd_parallel.

const char* VMDApp::par_name   [inline]
 

query current node name.

Definition at line 1050 of file VMDApp.h.

References nodename.

Referenced by text_cmd_parallel, and vmdinfo_tcl.

int VMDApp::par_rank   [inline]
 

query current node ID.

Definition at line 1053 of file VMDApp.h.

References noderank.

Referenced by text_cmd_parallel, and vmdinfo_tcl.

int VMDApp::par_size   [inline]
 

query total number of nodes.

Definition at line 1056 of file VMDApp.h.

References nodecount.

Referenced by text_cmd_parallel, and vmdinfo_tcl.

int VMDApp::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.

Definition at line 1525 of file VMDApp.C.

References PluginMgr::load_sharedlibrary_plugins.

Referenced by text_cmd_plugin.

void VMDApp::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.

Definition at line 1534 of file VMDApp.C.

References commandQueue, and CommandQueue::runcommand.

Referenced by text_cmd_plugin, and VMDinit.

int VMDApp::remove_menu const char *   
 

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.

int VMDApp::save_state  
 

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.

void VMDApp::scene_resetview  
 

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.

void VMDApp::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.

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.

int VMDApp::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.

Definition at line 1414 of file VMDApp.C.

References commandQueue, CommandQueue::runcommand, and DisplayRocker::start_rocking.

Referenced by text_cmd_rock.

int VMDApp::scene_rockoff  
 

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.

int VMDApp::scene_rotate_by const float *   
 

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.

int VMDApp::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.

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.

int VMDApp::scene_rotate_to const float *   
 

Definition at line 1346 of file VMDApp.C.

References commandQueue, mat, Scene::root, CommandQueue::runcommand, scene, Displayable::set_rot, and CmdRotMat::TO.

int VMDApp::scene_rotate_to float    angle,
char    axis
 

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.

int VMDApp::scene_scale_by float    s
 

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.

int VMDApp::scene_scale_to float    s
 

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.

int VMDApp::scene_stoprotation  
 

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.

int VMDApp::scene_translate_by float    x,
float    y,
float    z
 

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.

int VMDApp::scene_translate_to float    x,
float    y,
float    z
 

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.

int VMDApp::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.

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.

void VMDApp::set_eofexit int    onoff [inline]
 

Definition at line 1219 of file VMDApp.h.

Referenced by VMDreadStartup.

void VMDApp::set_mouse_callbacks int    on
 

Definition at line 3403 of file VMDApp.C.

References UIObject::set_callbacks.

Referenced by text_cmd_mouse.

void VMDApp::set_mouse_rocking int    on
 

Definition at line 3407 of file VMDApp.C.

References Mouse::set_rocking.

Referenced by text_cmd_mouse.

void VMDApp::set_text const char *    str [inline, static]
 

text message access methods.

Definition at line 1201 of file VMDApp.h.

void VMDApp::show_stride_message  
 

show Stride message, if necessary.

Definition at line 1174 of file VMDApp.C.

Referenced by DrawMolecule::need_secondary_structure.

void VMDApp::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.

Definition at line 4340 of file VMDApp.C.

References Spaceball::get_tracker_status, and NULL.

Referenced by SpaceballTracker::update, and SpaceballButtons::update.

int VMDApp::spaceball_set_mode int    mode
 

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.

int VMDApp::spaceball_set_null_region int    nr
 

Change the spaceball null region.

Definition at line 4331 of file VMDApp.C.

References Spaceball::set_null_region.

Referenced by text_cmd_spaceball.

int VMDApp::spaceball_set_sensitivity float    s
 

Change the spaceball sensitivity.

Definition at line 4324 of file VMDApp.C.

References Spaceball::set_sensitivity.

Referenced by text_cmd_spaceball.

int VMDApp::stage_set_location const char *   
 

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.

int VMDApp::stage_set_numpanels int   
 

Definition at line 3857 of file VMDApp.C.

References commandQueue, num, Stage::panels, CommandQueue::runcommand, and stage.

Referenced by text_cmd_stage.

int VMDApp::stage_set_size float   
 

Definition at line 3863 of file VMDApp.C.

References commandQueue, CommandQueue::runcommand, Stage::size, and stage.

Referenced by text_cmd_stage.

int VMDApp::textinterp_change const char *    interpname
 

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.

int VMDApp::tool_change_type int    toolnum,
const char *    type
 

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.

int VMDApp::tool_create const char *    type,
int    argc,
const char **    argv
 

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.

int VMDApp::tool_delete int    toolnum
 

Definition at line 4110 of file VMDApp.C.

References commandQueue, UIVR::remove_tool, CommandQueue::runcommand, and uivr.

Referenced by ToolFltkMenu::delete_tool.

int VMDApp::tool_set_force_scale int    toolnum,
float    newval
 

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.

int VMDApp::tool_set_position_scale int    toolnum,
float    newval
 

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.

int VMDApp::tool_set_spring_scale int    toolnum,
float    newval
 

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.

char * VMDApp::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.

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.

void VMDApp::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.

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.

int VMDApp::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.

Definition at line 336 of file VMDApp.C.

References activate_menus, PickList::add_pickable, affinitize_threads, anim, arm_sve_vecsize_32bits, arm_sve_vecsize_64bits, atomSelParser, atomSelParser_init, axes, commandQueue, CPU_ARM64_AES, CPU_ARM64_ASIMD, CPU_ARM64_ASIMDDP, CPU_ARM64_ASIMDFHM, CPU_ARM64_ASIMDHP, CPU_ARM64_ASIMDRDM, CPU_ARM64_CRC32, CPU_ARM64_FP, CPU_ARM64_SHA1, CPU_ARM64_SHA2, CPU_ARM64_SHA3, CPU_ARM64_SHA512, CPU_ARM64_SVE, CPU_AVX, CPU_AVX2, CPU_AVX512CD, CPU_AVX512ER, CPU_AVX512F, CPU_AVX512PF, CPU_F16C, CPU_FMA, CPU_HT, CPU_HYPERVISOR, CPU_KNL, CPU_SSE2, CPU_SSE4_1, cpucaps, cuda, display, exitFlag, wkf_cpu_caps_struct::flags, fps, geometryList, DisplayDevice::get_num_processes, imdMgr, DisplayDevice::init, NVENCMgr::init, PluginMgr::load_static_plugins, materialList, menu_show, moleculeList, nodecount, nodename, noderank, NULL, CUDAAccel::num_devices, nvenc, NVENCMGR_SUCCESS, Displayable::off, UIObject::On, NVENCMgr::open_session, pickList, pickModeList, plugin_update, CUDAAccel::print_cuda_devices, PROFILE_POP_RANGE, PROFILE_PUSH_RANGE, qsurf, DisplayDevice::queue_events, UIText::read_init, DisplayDevice::renderer_process, repserialnum, Scene::root, CommandQueue::runcommand, scene, set_cave_pointers, set_freevr_pointers, stage, DisplayDevice::supports_gui, texserialnum, thrpool, uiText, uivs, vmd_cl_print_platform_info, vmd_get_avail_physmem_mb, vmd_get_avail_physmem_percent, VMD_IGNORE_EVENTS, vmd_mpi_nodeinfo, vmd_mpi_nodescan, vmd_set_cave_is_initialized, vmdcollab, VMDexit, VMDupdate, wkf_cpu_capability_flags, wkf_thread_numprocessors, wkf_threadpool_create, WKF_THREADPOOL_DEVLIST_CPUSONLY, and wkf_threadpool_launch.

Referenced by initvmd, and main.

int VMDApp::VMDupdate int   
 

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.

int VMDApp::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.

Definition at line 3593 of file VMDApp.C.

References VideoStream::cli_connect, and uivs.

int VMDApp::vs_connected  
 

Return true if a video strem is established.

Definition at line 3606 of file VMDApp.C.

References uivs.

int VMDApp::vs_disconnect  
 

Disconnect. Return success.

Definition at line 3614 of file VMDApp.C.

References VideoStream::cli_disconnect, and uivs.


Member Data Documentation

Animation* VMDApp::anim
 

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.

int VMDApp::argc_m
 

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.

const char** VMDApp::argv_m
 

needed by Tcl/Python initialization code.

Definition at line 199 of file VMDApp.h.

Referenced by PythonTextInterp::PythonTextInterp, TclTextInterp::TclTextInterp, and VMDApp.

SymbolTable* VMDApp::atomSelParser
 

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.

Axes* VMDApp::axes
 

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.

CommandQueue* VMDApp::commandQueue
 

the command processor.

Definition at line 235 of file VMDApp.h.

Referenced by GeometryList::add_geometry, animation_set_dir, animation_set_frame, animation_set_speed, animation_set_stride, animation_set_style, DrawMolecule::append_frame, axes_set_location, DrawMolecule::change_ts, Spaceball::check_event, Molecule::close_coor_file, color_add_item, color_change_name, color_change_rgb, colorscale_setmethod, colorscale_setparams, DrawMolecule::delete_frame, depthcue_set_density, depthcue_set_end, depthcue_set_mode, depthcue_set_start, display_set_aa, display_set_ao, display_set_ao_ambient, display_set_ao_direct, display_set_background_mode, display_set_cachemode, display_set_culling, display_set_depthcue, display_set_dof, display_set_dof_fnumber, display_set_dof_focal_dist, display_set_eyesep, display_set_farclip, display_set_focallen, display_set_fps, display_set_nearclip, display_set_projection, display_set_rendermode, display_set_screen_distance, display_set_screen_height, display_set_shadows, display_set_stereo, display_set_stereo_swap, filerender_option, filerender_render, DrawMolecule::force_recalc, help_cb, imd_connect, label_add, label_delete, label_set_text_size, label_set_text_thickness, label_set_textformat, label_set_textoffset, label_show, light_highlight, light_move, light_on, light_rotate, loadstate_cb, logconsole_cb, logfile_cb, logoff_cb, make_tcl_atomsel, MoleculeList::make_top, material_add, material_change, material_delete, material_rename, material_restore_default, menu_add_extension, menu_remove_extension, menu_show, mobile_set_mode, molecule_activate, molecule_add_volumetric, molecule_addrep, molecule_bondsrecalc, molecule_cancel_io, molecule_delete, molecule_delete_all, molecule_deleteframes, molecule_display, molecule_dupframe, molecule_fix, molecule_from_selection_list, molecule_load, molecule_make_top, molecule_modrep, molecule_new, molecule_reanalyze, molecule_rename, molecule_savetrajectory, molecule_set_color, molecule_set_material, molecule_set_selection, molecule_set_style, molecule_ssrecalc, molrep_delete, molrep_reset_scaleminmax, molrep_set_color, molrep_set_colorupdate, molrep_set_drawframes, molrep_set_instances, molrep_set_material, molrep_set_pbc, molrep_set_pbc_images, molrep_set_scaleminmax, molrep_set_selection, molrep_set_selupdate, molrep_set_smoothing, molrep_set_style, molrep_show, mouse_set_mode, PickList::pick_check, PickModeMolLabel::pick_graphics, PickModeUser::pick_molecule_start, PickModeMolLabel::pick_molecule_start, PickModeAddBond::pick_molecule_start, plugin_update, py_copyunitcell, py_imddetach, py_imdkeep, py_imdkill, py_imdpause, py_imdtransfer, scene_resetview, scene_rock, scene_rockoff, scene_rotate_by, scene_rotate_to, scene_scale_by, scene_scale_to, scene_translate_by, scene_translate_to, set_colorscale_colors, spaceball_set_mode, stage_set_location, stage_set_numpanels, stage_set_size, text_cmd_gopython, text_cmd_imd, text_cmd_tool, text_cmd_videostream, tool_change_type, tool_create, tool_delete, tool_set_force_scale, tool_set_position_scale, tool_set_spring_scale, UIObject::UIObject, FreeVRButtons::update, VMDApp, VMDinit, VMDreadStartup, VMDupdate, and ~VMDApp.

wkf_cpu_caps_t* VMDApp::cpucaps
 

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.

CUDAAccel* VMDApp::cuda
 

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.

DisplayDevice* VMDApp::display
 

display in which the images are rendered.

Definition at line 207 of file VMDApp.h.

Referenced by activate_menus, VideoStream::check_event, Spaceball::check_event, Mouse::check_event, depthcue_set_density, depthcue_set_end, depthcue_set_mode, depthcue_set_start, display_get_screen_distance, display_get_screen_height, display_get_size, display_projection_is_perspective, display_set_aa, display_set_ao, display_set_ao_ambient, display_set_ao_direct, display_set_cachemode, display_set_culling, display_set_depthcue, display_set_dof, display_set_dof_fnumber, display_set_dof_focal_dist, display_set_eyesep, display_set_farclip, display_set_focallen, display_set_nearclip, display_set_position, display_set_projection, display_set_rendermode, display_set_screen_distance, display_set_screen_height, display_set_shadows, display_set_size, display_set_stereo, display_set_stereo_swap, display_titlescreen, FileRenderList::FileRenderList, get_nearby_atom, MainFltkMenu::MainFltkMenu, Mouse::Mouse, Mouse::move_mode, PickList::pick_check, PickList::pick_end, PickList::pick_move, PickList::pick_start, py_get, py_set, py_stereomodes, FileRenderList::render, Mouse::reset, Tool::target, text_cmd_display, VideoStream::VideoStream, VMDApp, VMDinit, VMDupdate, OptiXDisplayDevice::write_trailer, and ~VMDApp.

int VMDApp::exitFlag
 

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.

FPS* VMDApp::fps
 

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.

GeometryList* VMDApp::geometryList
 

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.

int VMDApp::highlighted_molid
 

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.

int VMDApp::highlighted_rep
 

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.

IMDMgr* VMDApp::imdMgr
 

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, text_cmd_imd, VMDApp, VMDinit, and ~VMDApp.

MaterialList* VMDApp::materialList
 

list of materials.

Definition at line 231 of file VMDApp.h.

Referenced by MaterialFltkMenu::act_on_command, GraphicsFltkMenu::act_on_command, MoleculeList::add_rep, MoleculeList::change_repmat, GraphicsFltkMenu::init_materialchooser, MoleculeList::material, material_add, material_change, material_delete, material_rename, material_restore_default, molecule_tcl, MoleculeList::MoleculeList, molrep_get_material, py_add, py_change, py_listall, py_material, py_rename, py_set_default, py_settings, MoleculeList::set_default_material, MoleculeList::set_material, tcl_graphics, text_cmd_material, VMDApp, VMDinit, and ~VMDApp.

MoleculeList* VMDApp::moleculeList
 

list of all loaded molecules.

Definition at line 236 of file VMDApp.h.

Referenced by access_tcl_atomsel, GraphicsFltkMenu::act_on_command, GeometryFltkMenu::act_on_command, GeometryList::add_geometry, VolMapCreateILS::add_map_to_molecule, Tool::assign_rep, atomsel_new, atomsel_set, atomselect_move, atomselect_moveby, VolMapCreate::calculate_max_radius, VolMapCreate::calculate_minmax, center, centerperresidue, cmd_gettimestep, cmd_rawtimestep, color_get_restype, color_set_restype, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, contacts, density_add, density_average, density_binmask, density_clamp, density_com, density_correlate, density_crop, density_downsample, density_histogram, density_info, density_mdff_potential, density_move, density_moveto, density_multiply, density_range, density_sadd, density_save, density_sigma, density_smooth, density_smult, density_subtract, density_supersample, density_trim, SaveTrajectoryFltkMenu::do_save, Tool::dograb, fit, fpbc_join, fpbc_recenter, fpbc_unwrap, fpbc_wrap, get_molecule, get_nearby_atom, get_weights_from_attribute, getmolid, Tool::getTargetScale, graphics_tcl, imd_connect, colvarproxy_vmd::load_atoms, colvarproxy_vmd::load_coords, make_tcl_atomsel, mask, mdff_cc, mdff_sim, measure_hbonds, minmax, mol_from_id, SaveTrajectoryFltkMenu::molchooser_activate_selection, molecule_activate, molecule_add_instance, molecule_add_volumetric, molecule_addrep, molecule_bondsrecalc, molecule_cancel_io, molecule_delete, molecule_delete_all, molecule_delete_all_instances, molecule_deleteframes, molecule_display, molecule_dupframe, molecule_fix, molecule_frame, molecule_from_selection_list, molecule_get_color, molecule_get_material, molecule_get_selection, molecule_get_style, molecule_id, molecule_index_from_id, molecule_is_active, molecule_is_displayed, molecule_is_fixed, molecule_load, molecule_make_top, molecule_modrep, molecule_name, molecule_new, molecule_num_instances, molecule_numatoms, molecule_numframes, molecule_orblocalize, molecule_reanalyze, molecule_rename, molecule_savetrajectory, molecule_set_color, molecule_set_dataset_flag, molecule_set_material, molecule_set_selection, molecule_set_style, molecule_ssrecalc, molecule_tcl, molecule_top, molecule_valid_id, molrep_delete, molrep_get_by_name, molrep_get_clipplane, molrep_get_color, molrep_get_colorupdate, molrep_get_drawframes, molrep_get_instances, molrep_get_material, molrep_get_name, 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_clipcenter, molrep_set_clipcolor, molrep_set_clipnormal, molrep_set_clipstatus, molrep_set_color, molrep_set_colorupdate, molrep_set_drawframes, molrep_set_instances, molrep_set_material, molrep_set_pbc, molrep_set_pbc_images, molrep_set_scaleminmax, molrep_set_selection, molrep_set_selupdate, molrep_set_smoothing, molrep_set_style, molrep_show, num_molecules, num_molreps, parse_timestep, PickList::pick_check, PickModeCenter::pick_molecule_end, print_atom_info, py_activate, py_atomselect, py_fit, py_fix, py_get_accessions, py_get_center, py_get_databases, py_get_filenames, py_get_filetypes, py_get_remarks, py_get_rotation, py_get_scale, py_get_trans, py_hbonds, py_imdconnect, py_is_active, py_is_fixed, py_is_shown, py_label_add, py_measure_angle, py_measure_bond, py_measure_dihed, py_mol_del_volumetric, py_mol_get_volumetric, py_mol_num_volumetric, py_mol_write, py_move, py_moveby, py_resetview, py_rgyr, py_rmsd, py_rmsd_q, py_rmsdmat_q, py_rmsdperresidue, py_rmsf, py_rmsfperresidue, py_set_center, py_set_frame, py_set_rotation, py_set_scale, py_set_trans, py_show, GraphicsFltkRepOrbital::regen_excitationlist, GraphicsFltkRepOrbital::regen_orbitallist, GraphicsFltkRepOrbital::regen_wavefunctypes, sasa, scene_resetview, scene_resetview_newmoldata, segment_volume, GraphicsFltkMenu::set_pbc, colvarproxy_vmd::setup, Tool::target, tcl_get_weights, tcl_graphics, text_cmd_animate, text_cmd_imd, text_cmd_mol, topo_add_angle, topo_add_bond, topo_add_dihed, topo_add_improp, topo_angletypes, topo_bondtypes, topo_del_all_angles, topo_del_all_bonds, topo_del_all_dihed, topo_del_all_impropers, topo_del_angle, topo_del_bond, topo_del_dihed, topo_del_improper, topo_dihetypes, topo_get_angle, topo_get_bond, topo_get_dihed, topo_get_impro, topo_imptypes, Tool::tug, Tool::ungrab, MolBrowser::update, colvarproxy_vmd::update_input, GraphicsFltkMenu::update_molchooser, GraphicsFltkMenu::update_pbc, GraphicsFltkMenu::update_rep, GraphicsFltkMenu::update_repbrowser, GraphicsFltkMenu::update_repindex, vmd_measure_angle, vmd_measure_avpos, vmd_measure_bond, vmd_measure_center, vmd_measure_centerperresidue, vmd_measure_cluster, vmd_measure_clustsize, vmd_measure_contacts, vmd_measure_dihed, vmd_measure_dipole, vmd_measure_energy, vmd_measure_fit, vmd_measure_gofr, vmd_measure_hbonds, vmd_measure_inertia, vmd_measure_minmax, vmd_measure_pbc2onc_transform, vmd_measure_pbc_neighbors, vmd_measure_rdf, vmd_measure_rgyr, vmd_measure_rmsd, vmd_measure_rmsd_qcp, vmd_measure_rmsdmat_qcp, vmd_measure_rmsdmat_qcp_ooc, vmd_measure_rmsdperresidue, vmd_measure_rmsf, vmd_measure_rmsfperresidue, vmd_measure_sasa, vmd_measure_sasalist, vmd_measure_surface, vmd_measure_symmetry, vmd_measure_trans_overlap, vmd_measure_volinterior, vmd_volmap_compare, vmd_volmap_ils, VMDApp, VMDinit, VMDupdate, GraphicsFltkMenu::volindex_update, VolMapCreateILS::write_map, and ~VMDApp.

int VMDApp::nodecount
 

MPI node count.

Definition at line 247 of file VMDApp.h.

Referenced by par_size, VMDApp, and VMDinit.

char VMDApp::nodename[512]
 

MPI node name.

Definition at line 245 of file VMDApp.h.

Referenced by par_name, VMDApp, and VMDinit.

int VMDApp::noderank
 

MPI node rank.

Definition at line 246 of file VMDApp.h.

Referenced by par_rank, VMDApp, VMDexit, and VMDinit.

NVENCMgr* VMDApp::nvenc
 

GPU hardware H.26[45] video [en|de]coder.

Definition at line 216 of file VMDApp.h.

Referenced by VMDApp, and VMDinit.

PickList* VMDApp::pickList
 

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.

PickModeList* VMDApp::pickModeList
 

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.

QuickSurf* VMDApp::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.

Definition at line 218 of file VMDApp.h.

Referenced by VMDinit, OptiXDisplayDevice::write_header, and ~VMDApp.

int VMDApp::ResetViewPending
 

pending resetview needs attention.

Definition at line 244 of file VMDApp.h.

Referenced by scene_resetview_newmoldata, and VMDApp.

Scene* VMDApp::scene
 

list of all Displayable objects to draw.

Definition at line 208 of file VMDApp.h.

Referenced by color_add_item, color_category, color_category_item, color_change_name, color_change_namelist, color_change_rgb, color_change_rgblist, color_default_value, color_get_from_name, color_index, color_mapping, color_name, color_set_restype, color_value, colorscale_method_current, colorscale_method_index, colorscale_method_menuname, colorscale_method_name, colorscale_params, colorscale_setmethod, colorscale_setparams, display_set_background_mode, display_titlescreen, ColorscaleLumaChart::draw, ColorscaleImage::draw, get_colorscale_colors, GraphicsFltkMenu::GraphicsFltkMenu, light_highlight, light_move, light_on, light_rotate, molecule_from_selection_list, molecule_load, molecule_new, molecule_rename, num_color_categories, num_color_category_items, num_colorscale_methods, FileRenderList::render, scene_resetview, scene_rotate_by, scene_rotate_to, scene_scale_by, scene_scale_to, scene_translate_by, scene_translate_to, set_colorscale_colors, text_cmd_display, text_cmd_light, text_cmd_point_light, VMDApp, VMDinit, VMDupdate, and ~VMDApp.

Stage* VMDApp::stage
 

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.

wkf_threadpool_t* VMDApp::thrpool
 

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.

UIText* VMDApp::uiText
 

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.

UIVR* VMDApp::uivr
 

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.

VideoStream* VMDApp::uivs
 

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.

int VMDApp::UpdateDisplay
 

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.

NameList<char *> VMDApp::userKeyDesc
 

describe what the hotkey does.

Definition at line 241 of file VMDApp.h.

Referenced by text_cmd_user, and ~VMDApp.

NameList<char *> VMDApp::userKeys
 

lookup table for Tcl scripts.

Definition at line 240 of file VMDApp.h.

Referenced by text_cmd_user, TclTextInterp::userkey_cb, and ~VMDApp.

VMDCollab* VMDApp::vmdcollab
 

handles collaborative VMD interaction.

Definition at line 239 of file VMDApp.h.

Referenced by text_cmd_collab, VMDApp, VMDinit, and ~VMDApp.


The documentation for this class was generated from the following files:
Generated on Thu Mar 28 02:46:05 2024 for VMD (current) by doxygen1.2.14 written by Dimitri van Heesch, © 1997-2002