| Animation | |
| ArtDisplayDevice | FileRenderer subclass to export VMD scenes to ART ray tracer scene format |
| AtomColor | Parse and maintain the data for how a molecule should be colored |
| AtomData | |
| AtomEntry | |
| AtomGrid | |
| AtomGridCell | |
| atomic_int_struct | |
| AtomList | |
| atomparser_node | Each node of the parse tree contains all data needed for that description |
| atomparser_string | Stores an atom parser string with its string type enumeration |
| AtomPosType | |
| AtomRep | Parse and maintain the data for how a molecule should be represented |
| AtomRepDataInfo | Define which slots are used for a rep style, and their default values |
| AtomRepParamStruct | Structure definition for structures used to define what data each rep needs |
| AtomSel | This interacts with the AtomParser |
| atomsel_ctxt | Context which must be passd to xxx_keyword_info functions in SymbolTable |
| AtomSelThr | |
| Axes | A Displayable object which consisting of a set of axes |
| axis | |
| barrier_struct | |
| BaseMolecule | Base class for all molecules, without display-specific information. This portion of a molecule contains the structural data, and all routines to find the structure (backbone, residues, etc). It contains the animation list as well |
| basis_atom_t | Basis set definition for one atom |
| Best | |
| BinOfAtoms | |
| bond | |
| bondlist | |
| bondsearchthrparms | |
| busbwthrparms | |
| Buttons | Buttons is a representation for a set of n boolean inputs. This fairly abstract class should be subclassed to make Buttons objects that actually know how to get their buttons. This is somewhat parallel to the Tracker object, compare them! |
| CaveButtons | Buttons subclass that gets its info from the CAVE wand |
| CaveDisplayDevice | DisplayDevice subclass that runs in the CAVE |
| CaveScene | Scene subclass that allocates from a CAVE shared memory arena, and coordinates multiple rendering slave processes |
| CaveTracker | VMDTracker subclass that interfaces to the CAVE wand |
| clusterparms_t | |
| CmdAddAtomSelMacro | Create a new atom selection macro |
| CmdAnimDelete | Delete frames |
| CmdAnimDir | Set direction of animation |
| CmdAnimDup | Duplicate a given frame at the end of the traj |
| CmdAnimJump | Jump to a new frame |
| CmdAnimNewFrame | Not really a command, but that's how info gets passed to the GUI's |
| CmdAnimNewNumFrames | Signal that a molecule has a new number of frames |
| CmdAnimSkip | Set frame skip value |
| CmdAnimSpeed | Set animation speed |
| CmdAnimStyle | Set style of animation |
| CmdAnimWriteFile | Write frames to a file |
| CmdColorChange | Change the rgb settings for a specified color |
| CmdColorItem | |
| CmdColorName | Change the color index for a specifed name in a specified category |
| CmdColorScaleColors | |
| CmdColorScaleMethod | Change the method used to calculate the color scale |
| CmdColorScaleSettings | Change the settings for the color scale |
| CmdDelAtomSelMacro | Delete the specified atom selection macro |
| CmdDisplayAAOn | Turn on/off antialiasing |
| CmdDisplayAOAmbient | Set ambient occlusion ambient factor |
| CmdDisplayAODirect | Set ambient occlusion direct lighting factor |
| CmdDisplayAOOn | Set ambient occlusion rendering mode |
| CmdDisplayAxes | Change the axes location |
| CmdDisplayBackgroundGradientOn | Turn on/off background gradient |
| CmdDisplayCacheMode | Set caching mode of display |
| CmdDisplayClip | Clipping plane controls This handles the whole range of clipping plane options There are derived classes so you won't have to have the funky flags to change {near,fixed} clipping plane {to a fixed,by a relative} amount or not |
| CmdDisplayClipFar | Change the far clipping plane to a fixed value |
| CmdDisplayClipFarRel | Change the far clipping plane to by a relative value |
| CmdDisplayClipNear | Change the near clipping plane to a fixed value leaving everything else up to the base class :) |
| CmdDisplayClipNearRel | Change the near clipping plane to by a relative value |
| CmdDisplayCueDensity | Set the depth cueing exp/exp2 density parameter |
| CmdDisplayCueEnd | Set the depth cueing end distance |
| CmdDisplayCueMode | Set depth cueing mode |
| CmdDisplayCueStart | Set the depth cueing start distance |
| CmdDisplayCullingOn | Turn on/off culling |
| CmdDisplayDepthcueOn | Turn on/off depth cueing |
| CmdDisplayEyesep | Set eye separation of display |
| CmdDisplayFocallen | Set focal length of display |
| CmdDisplayFPSOn | FPS indicator |
| CmdDisplayLightHL | Highlight the Nth light |
| CmdDisplayLightMove | Set the position of the Nth light |
| CmdDisplayLightOn | Turn on/off the Nth light |
| CmdDisplayLightRot | Rotate the position of the Nth light |
| CmdDisplayProj | Set the projection to either perspective or orthographic |
| CmdDisplayRenderMode | Set rendering mode of display |
| CmdDisplayScreenDistance | Set distance to screen from origin |
| CmdDisplayScreenHeight | Set screen height value |
| CmdDisplayShadowOn | Set shadow rendering mode |
| CmdDisplayStageLocation | Change the stage location |
| CmdDisplayStagePanels | Set the number of stage panels |
| CmdDisplayStageSize | Set the number of stage panels |
| CmdDisplayStereo | Set stereo mode of display |
| CmdDisplayStereoSwap | Turn on/off stereo eye swap |
| CmdIMDConnect | Connect to a running IMD simulation |
| CmdIMDCopyUnitCell | Set the IMD unit cell copy mode |
| CmdIMDRate | Set the IMD transfer rate and storage mode |
| CmdIMDSim | Change IMD connection status (pause, detach, kill) |
| CmdLabelAdd | Add a new label |
| CmdLabelAddspring | Add a new spring |
| CmdLabelDelete | Delete the Nth label in a category |
| CmdLabelShow | Toggle a geometry category on/off |
| CmdLabelTextFormat | |
| CmdLabelTextOffset | |
| CmdLabelTextSize | |
| CmdLabelTextThickness | |
| CmdMaterialAdd | Add a new material |
| CmdMaterialChange | Change a property of an existing material |
| CmdMaterialDefault | Reset a material to defaults |
| CmdMaterialDelete | Delete a material |
| CmdMaterialRename | Rename an existing material |
| CmdMenuExtensionAdd | Add an item to the VMD extension menu |
| CmdMenuExtensionRemove | Remove an item from the VMD extension menu |
| CmdMenuShow | Turn a menu on/off |
| CmdMobileMode | Change the current mouse mode This command doesn't generate an output text command, it is just used to change the VMD internal state |
| CmdMolActive | Make the Nth molecule 'active' or 'inactive' |
| CmdMolAddRep | Add a new representation to the specified molecule |
| CmdMolBondsRecalc | Re-analyze structure after atom names, bonds, etc have been modified |
| CmdMolCancel | Cancel the loading/saving of a coordinate file |
| CmdMolChangeRep | Change the representation to the current defaults |
| CmdMolChangeRepItem | Change 1 representation characteristic for the specified mol |
| CmdMolColor | Set the current atom coloring method in moleculeList |
| CmdMolDelete | Delete the Nth molecule in the molecule List |
| CmdMolDeleteRep | Delete a representation for the specified molecule |
| CmdMolDrawFrames | Set the range of frames to draw for this rep |
| CmdMolFix | Make the Nth molecule 'fixed' or 'free' |
| CmdMolLoad | Notification that a molecule has been created |
| CmdMolMaterial | Set the current atom material method in moleculeList |
| CmdMolNew | Create a new molecule |
| CmdMolNumPeriodic | Set the number of periodic images displayed for the selected representation |
| CmdMolOn | Make the Nth molecule 'on' or 'off' |
| CmdMolReanalyze | Re-analyze structure after atom names, bonds, etc have been modified |
| CmdMolRename | Rename a molecule |
| CmdMolRep | Set the current atom representation in moleculeList |
| CmdMolRepColorUpdate | Change the auto-update for the color of the specified rep |
| CmdMolRepSelUpdate | Change the auto-update for the selection of the specified rep |
| CmdMolScaleMinmax | Set the color scale min/max range for the selected representation |
| CmdMolSelect | Set the current atom selection in moleculeList |
| CmdMolShowPeriodic | Set which periodic images are displayed for the selected representation |
| CmdMolShowRep | Set the "shown" state for the selected representation |
| CmdMolSmoothRep | Set the trajectory smoothing window size for the selected representation |
| CmdMolSSRecalc | Recalculate secondary structure based on current coordinates |
| CmdMolTop | Make the Nth molecule 'top' |
| CmdMolVolume | Add a new volumetric dataset to the selected molecule |
| CmdMouseMode | Change the current mouse mode This command doesn't generate an output text command, it is just used to change the VMD internal state |
| CmdPluginUpdate | Update the GUI plugin list with any newly loaded plugins |
| CmdRender | Render the global scene |
| CmdRenderOption | Set the render execution command |
| CmdResetView | Reset the current view for the current scene |
| CmdRockOff | Stop rocking the current scene |
| CmdRockOn | Rock the current scene |
| CmdRotate | Rotate the current scene |
| CmdRotMat | Apply a matrix transformation to the current scene |
| CmdScale | Scale the current scene |
| CmdSpaceballMode | Change the current mouse mode This command doesn't generate an output text command, it is just used to change the VMD internal state |
| CmdToolAddDevice | Add a device to a tool |
| CmdToolCallback | Register a callback with a tool |
| CmdToolChange | Change the type of tool, keeping the sensor |
| CmdToolCreate | Create a new tool, attaching a sensor |
| CmdToolDelete | Delete a tool |
| CmdToolDeleteDevice | Delete a device from a tool |
| CmdToolOffset | Change the position offset for a tool |
| CmdToolRep | Attach a tool to a particular representation (instead of picking) |
| CmdToolScale | Change the position scaling factor for a tool |
| CmdToolScaleForce | Change the force scaling factor for a tool |
| CmdToolScaleSpring | Change the force feedback spring constant for a tool |
| CmdTranslate | Translate the current scene |
| ColorFltkMenu | VMDFltkMenu subclass providing a GUI to change color settings |
| ColorScale | Color gradient/ramp used by value-based coloring methods |
| ColorscaleImage | Class to maintain a GUI-usable image of a ColorScale |
| Combinations | |
| Command | Command base class from which all other commands are derived Derived classes must provide a unique constructor, destructor, and optionally provide a 'create_text' routine if the command has a text equivalent which should be echoed to a log file |
| CommandQueue | Stores Commands to be run in a queue, notifies UIs when they are run |
| compile_data | |
| ComputeOccupancyMap_t | |
| CoorData | Abstract base class for objects that periodically read/write timesteps |
| CoorPluginData | CoorPluginData: Uses a MolFilePlugin to load a coordinate file |
| ctxt | XXX old-style context structure; from when we used a SymbolTable instance to loop up functions for molinfo |
| CUDAAccel | Manages enumeration and initialization of OpenGL programmable shaders |
| cudadevprops | |
| CUDAMarchingCubes | |
| CUDAQuickSurf | |
| densitythrparms | |
| DepthSortObject | Class for storage and re-ordering of depth-sorted geometry as needed for PSDisplayDevice |
| DispCmdBeginRepGeomGroup | Mark the beginning of a new representation This should only be called once per rep, or weird things can happen when exporting to external renderers, where we track unique rep group IDs, names, etc. Group names cannot contain spaces, but can allow underscores and all normal alphanumeric characters |
| DispCmdColorIndex | Set the current drawing color to the specified index |
| DispCmdComment | Add a comment to the display list, to make token output etc. meaningful. these are free-form and can occur anywhere |
| DispCmdCone | Plot a cone at the given position |
| DispCmdCylinder | Draw a cylinder between two endpoints |
| DispCmdLine | Plot a line at the given position |
| DispCmdLineArray | Plot a series of lines, all with the same color the array should be of the form v1 v2 v1 v2 ... Note that the data is not stored in the struct; we copy directly into the display list. That way you don't have to keep this struct around after calling putdata. Kinda like DispCmdDataBlock |
| DispCmdLineType | Set the current line type |
| DispCmdLineWidth | Set the current line width |
| DispCmdLitPointArray | Draw points from the specified position, and color arrays, with given size |
| DispCmdPickPoint | Indicate a point which may be picked, and the associated 'tag' |
| DispCmdPickPointArray | Create an array of indexed points which may be picked and their associated tags |
| DispCmdPoint | Plot a point at the given position |
| DispCmdPointArray | Draw points from the specified position, and color arrays, with given size |
| DispCmdPolyLineArray | Plot a series of connected polylines, all with the same color the array should be of the form v1 v2 v3 v4 ... Note that the data is not stored in the struct; we copy directly into the display list. That way you don't have to keep this struct around after calling putdata. Kinda like DispCmdDataBlock |
| DispCmdSphere | Draw a sphere of specified radius at the given position |
| DispCmdSphereArray | Draw spheres from the specified position, radii, and color arrays |
| DispCmdSphereRes | Set the current sphere resolution |
| DispCmdSphereType | Set the current sphere type |
| DispCmdSquare | Draw a square, given 3 of four points |
| DispCmdText | Display 3-D text at the given text coordinates |
| DispCmdTextOffset | Add an offset to rendered text |
| DispCmdTextSize | Change the current text size |
| DispCmdTriangle | Draw a triangle, given the three points (computes the normals from the cross product) and all normals are the same -or- draw the triangle, given the three points and the three normals |
| DispCmdTriMesh | Draw a mesh consisting of vertices, facets, colors, normals etc |
| DispCmdTriStrips | Draw a set of triangle strips |
| DispCmdVolSlice | Apply a 3-D texture to a slice through the current volume texture |
| DispCmdVolumeTexture | Tell OpenGL to cache a 3D texture with the given unique ID. Memory for the texture is retained by the caller, not copied into the display list |
| DispCmdWireMesh | Draw a wire mesh consisting of vertices, facets, colors, normals etc |
| Displayable | Base class for all objects which are drawn by a DisplayDevice |
| DisplayColor | Displayable subclass containing the background color information |
| DisplayDevice | Abstract base class for objects which can process a list of drawing commands and render the drawing to some device (screen, file, preprocessing script, etc.), and provide mouse and keyboard events |
| DisplayFltkMenu | VMDFltkMenu subclass providing a GUI for setting display options |
| DisplayRocker | |
| DrawForce | A Displayable subclass for drawing forces applied by IMD |
| DrawMolecule | Subclass of BaseMolecule and Displayable for drawing a molecule |
| DrawMoleculeMonitor | A monitor class that acts as a proxy for things like labels that have to be notified when molecules change their state |
| DrawMolItem | Displayable subclass for creating geometric representations of molecules |
| DrawTool | Displayable used to render a tool on the screen |
| elementsummary | |
| enthrparms | |
| Feedback | A Feedback is a representation for force-feedback. Subclass this for specific haptic devices |
| FileChooserFltkMenu | VMDFltkMenu subclass providing a GUI for loading files into VMD |
| FileRenderer | This is the base class for all the renderers that go to a file and are on the render list. There are five operations available to the outside world |
| FileRenderer::AdvancedLightState | AdvancedLight state data |
| FileRenderer::LightState | Light state, passed to renderer before render commands are executed |
| FileRenderList | Manage a list of FileRenderer objects that can be used to render a scene |
| FileSpec | File loading parameter specification, what frames, volume sets, etc to load |
| FindWithinData | |
| flint_t | |
| FltkOpenGLDisplayDevice | OpenGLRenderer subclass, displays to an FLTK window |
| FPS | Displayable subclass to display the current display update rate onscreen |
| Fragment | A Fragment contains a list of residues which are connected each other, and to no one else. This is at the residue level, and not the atom level. The residue numbers are the unique_resid as assigned in BaseMolecule |
| FrameEvent | Indicates that the frame of a certain molecule has changed |
| FrameSelector | Fltk dialog for selecting/deleting ranges of frames |
| FreeVRButtons | Buttons subclass that gets its info from the FreeVR wand |
| FreeVRDisplayDevice | OpenGLRenderer subclass for FreeVR displays |
| FreeVRScene | Scene subclass that allocates from a FreeVR shared memory arena, and coordinates multiple rendering slave processes |
| FreeVRTracker | VMDTracker subclass that interfaces to the FreeVR wand |
| GelatoDisplayDevice | FileRenderer subclass to exports VMD scenes to Gelato PYG scene format |
| GeometryAngle | GeometryMol subclass to measure and display the angle between three atoms |
| GeometryAtom | GeometryMol subclass to label an atom |
| GeometryBond | GeometryMol subclass to measure and display bond lengths and distances |
| GeometryDihedral | GeometryMol subclass to measure and display dihedral angle between 4 atoms |
| GeometryFltkMenu | VMDFltkMenu subclass to manage geometry data, labels, and picked atoms |
| GeometryList | Displayable subclass to maintain geometry monitors, and draw them to a scene |
| GeometryMol | Base class for objects that make atomic measurements in a molecule |
| GeometryMonitor | A monitor class that watches GeometryMol objects for updates |
| GeometrySpring | GeometryMol subclass to simulate and draw a spring between two atoms in IMD |
| GeomListStruct | Structure used to store data about each category |
| globmembwthrparms | |
| glxdata | GLX-specific low-level handles and window IDs |
| glxpbufferdata | GLX-specific low-level handles and window IDs |
| gofrparms_t | |
| GrabTool | The grab tool allows users to move molecules around |
| GraphicsFltkMenu | VMDFltkMenu subclass implementing a GUI for controlling graphical representations of molecules |
| GraphicsFltkRep | GUI controls for each draw style, creates rep commands for CmdMolChangeRepItem or CmdMolRep, and sets its valuators correctly given an AtomRep |
| GraphicsFltkRepBeads | 'Beads' representation controls |
| GraphicsFltkRepBonds | 'Bonds' representation controls |
| GraphicsFltkRepCartoon | 'Cartoon' representation controls |
| GraphicsFltkRepCPK | 'CPK' representation controls |
| GraphicsFltkRepDotted | 'Dotted' representation controls |
| GraphicsFltkRepDynamicBonds | 'DynamicBonds' representation controls |
| GraphicsFltkRepFieldLines | 'FieldLines' representation controls |
| GraphicsFltkRepHBonds | 'HBonds' representation controls |
| GraphicsFltkRepIsosurface | 'Isosurface' representation controls |
| GraphicsFltkRepLicorice | 'Licorice' representation controls |
| GraphicsFltkRepLines | 'Lines' representation controls |
| GraphicsFltkRepMSMS | 'MSMS' representation controls |
| GraphicsFltkRepNewCartoon | 'NewCartoon' representation controls |
| GraphicsFltkRepNewRibbons | 'NewRibbons' representation controls |
| GraphicsFltkRepOrbital | 'Orbital' representation controls |
| GraphicsFltkRepOrbital::minmax | Volumetric rep internal class for managing min/max values |
| GraphicsFltkRepPoints | 'Points' representation controls |
| GraphicsFltkRepQuickSurf | 'QuickSurf' representation controls |
| GraphicsFltkRepRibbons | 'Ribbons' representation controls |
| GraphicsFltkRepSolvent | 'Solvent' representation controls |
| GraphicsFltkRepSurf | 'Surf' representation controls |
| GraphicsFltkRepTrace | 'Trace' representation controls |
| GraphicsFltkRepTube | 'Tube' representation controls |
| GraphicsFltkRepVDW | 'VDW' representation controls |
| GraphicsFltkRepVolumeSlice | 'VolumeSlice' representation controls |
| GraphicsFltkRepVolumetric | Base class for reps that use volumetric data XXX We can't get the information we need from AtomRep to fill in the data set names or their min/max ranges. Thus we have to add methods for GraphicsFltkMenu to tell us what this information is |
| GraphicsFltkRepVolumetric::minmax | Volumetric rep internal class for managing min/max values |
| GraphLabelEvent | XXX These are undocumented... The user has requested the given labels to be graphed |
| GRIDCELL | Set of 8 volume samples used for isosurface extraction |
| GridList | |
| GridResCounter | Counter control used set radii |
| GridSearchPair | Linked list of atom index pairs generated by the vmd_gridsearch1 and vmd_gridsearch2 XXX on 64-bit machines the next pointers are as large as the atom index data in each node, so half of the memory is wasted in pointer chasing. Calling malloc/free once per pair when building the linked list is a severe multithreading scalability bottleneck due to OS-level mutex locks in malloc/free and/or the kernel VM. On Linux, it is also problematic due to the threaded version of malloc allocating huge blocks and fragmenting memory tremendously. This implementation should not be used for any threaded code |
| GridSearchPairlist | Linked list of ResizeArrays containing pairlists, optimized for multithreading. Compared with the GridSearchPair linked list, The list of ResizeArrays uses half as much memory per pair, reduces the malloc calls so they are logarithmic rather than linear with the number of bonds, and reduces free call count to one per-thread down from one per-bond. Since the ResizeArray results in a contiguous block of memory, the traversal coherency is also significantly improved. Ultimately we should convert all of the grid search routines to use this type of data structure, or one like it |
| hash_node_t | |
| hash_t | |
| HelpEvent | Indicates that help is desired on the given topic |
| hersheyhandle | |
| IdList | Calculate which molecules to operate upon from the given molecule name; put the data in idList, and return the pointer to the integer list. If NULL is returned, there was an error or no molecules were specified. If an error occurs, this prints out the error message as well. Molecule names are of the form <n1>[|<n2>[.... [|<nN>]...]] where <ni> is either "all", "top", "active", "inactive", "displayed", "on", "off", "fixed", "free", "none", or an ID. There should be no spaces in the name |
| IMDEnergies | |
| IMDheader | IMD communication protocol message header structure |
| IMDMgr | High level interactive MD simulation management and update management |
| IMDSim | Handle the low-level setup and teardown of interactive MD simulations |
| IMDSimBlocking | A single-threaded implementation of the interactive MD coordinate/force update communication loop |
| IMDSimThread | A multithreaded implementation of the interactive MD coordinate/force communication update loop |
| IndexList | |
| Inform | Takes messages and displays them to the given ostream. Also creates 3 global instances: msgInfo, msgWarn, msgErr. A message is sent to an Inform object by treating it as an ostream, then ending the message by sending the 'sendmsg' manipulator |
| InitializeStructureEvent | Set when a molecular structure is created and destroyed |
| InterpEvent | Command subclass that acts as a base class for interpreter events |
| InterpParams_t | |
| inthash_node_t | |
| inthash_t | |
| intstack | |
| IsoContour | Class implementing triangulated isocontour extraction routines |
| IsoSlider | Slider control with text entry box, used to select isovalues, etc |
| IsoSurface | Class implementing triangulated isosurface extraction routines |
| isosurface_cbdata | Isosurface callback data structure containing multiple pointers |
| iterobject | |
| JoystickTool | The 3d analog of a joystick |
| JRegex | Regular expression matching interface |
| JString | A minimalistic string class we use instead of similar classes from the STL or the GNU libraries for better portability and greatly reduced code size. (only implements the functionality we actually need, doesn't balloon the entire VMD binary as some past string class implementations did). Implements regular expression matching methods used by VMD |
| latthrparms | |
| LibGelatoDisplayDevice | FileRenderer subclass to exports VMD scenes to Gelato PYG scene format |
| LibTachyonDisplayDevice | FileRenderer subclass renders via compiled-in Tachyon ray tracing engine |
| LINE | Structure defining a triangle generated by isocontour extraction code |
| LinkageEdge | A Linkage Edge object consists of: - left_atom (smaller atom id), right_atom (larger atom id) - list of linkage paths which include the edge |
| LinkagePath | A Linkage Path object consists of - a list of atoms in the path, contained in the SmallRing - the index of the start and end rings |
| LogfileEvent | Gives the interpreter the text of a command being written to a logfile |
| M_VRJapp | |
| maddthrparms | |
| MainFltkMenu | VMDFltkMenu subclass implementing the main molecule browser GUI, with pulldown menus to change mouse state and bring up other menus |
| match_data | |
| Material | Structure containing material properties used to shade a Displayable |
| MaterialFltkMenu | VMDFltkMenu subclass implementing a GUI for creating and configuring material properties |
| MaterialList | Manages a list of materials that can be applied to Displayable objects |
| Matrix4 | 4x4 matrix class with numerous operators, conversions, etc |
| MayaDisplayDevice | FileRenderer subclass to export VMD scenes to Maya ASCII format |
| Mobile | UIObject subclass for mobile/wireless phone/tablet motion control |
| MobileButtons | Buttons subclass that gets its info from a WiFi SmartMobile |
| MobileClientList | |
| MobileDeviceCommandEvent | Indicates that a mobile device has a specific command to run |
| MobileEvent | Sets the most recent Mobile translation, rotation, and button state |
| mobilehandle | |
| MobileStateChangedEvent | Indicates that the mobile device state has changed |
| MobileTracker | VMDTracker subclass that gets its info from the Mobile driver |
| MolAtom | Structure which holds data for one atom |
| MolBrowser | Fl_Multi_Browser subclass that keeps track of the main VMD menu and a VMDApp context |
| MolData | |
| Molecule | Main Molecule objects, which contains all the capabilities necessary to store, draw, and manipulate a molecule. This adds to the functions of DrawMolecule and BaseMolecule by adding file I/O interfaces etc |
| MoleculeEvent | Set when a molecule is created and destroyed or modified Eventually add codes A/F/D changes, etc |
| MoleculeGraphics | Displayable subclass to generate graphics directly from scripts and plugins |
| MoleculeList | Manages a list of the molecules being displayed |
| MolFilePlugin | VMD interface to 'molfile' plugins. Molfile plugins read coordinate files, structure files, volumetric data, and graphics data. The data is loaded into a new or potentially preexisting molecule in VMD |
| Mouse | UIObject subclass implementing Mouse-based motion control, picking, etc |
| MouseModeEvent | Tell when the mouse mode changes. I hope no one is using this.. |
| MousePositionEvent | Sets the most recent mouse position and button state |
| Msmpot_t | |
| MsmpotCuda_t | |
| MSMSCoord | Structure containing MSMS vertex coordinates |
| MSMSFace | Structure containing MSMS facet information |
| MSMSInterface | Manages communication with the MSMS surface generation program Can only use this class once! |
| My_Fl_Positioner | |
| myBrowser | Fl_Hold_Browser subclass customized to allow double-clicking for toggling graphical representations on and off |
| myFl_Chart | A replacement for Fl_Chart, which has a bug that causes it to sometimes draw outside its bounding box |
| myglwindow | Fl_Gl_Window subclass that implements an OpenGL rendering surface for use by the FltkOpenGLDisplayDevice class |
| NameList< T > | Template class, stores a list of unique names indexed in the order they are added. For each name, which acts as a key, there is an associated integer value. NameList string lookups are accelerated through the use of an internal hash table |
| netint | Structure used to perform byte swapping operations |
| occthrparms_t | |
| OpenGLCache | Class to manage caching of OpenGL-related resources and handles such as display lists, textures, vertex buffer objects, etc. The IDs being stored are sparse unsigned long integer keys |
| OpenGLDisplayDevice | Subclass of OpenGLRenderer, this object has routines used by all the different display devices that are OpenGL-specific. Will render drawing commands into a single X window |
| OpenGLExtensions | Manages the use of OpenGL extensions, provides queries, OS-specific function pointer setup, and some OpenGL state management |
| OpenGLPbufferDisplayDevice | Subclass of OpenGLRenderer, this object has routines used by all the different display devices that are OpenGL-specific. Will render drawing commands into a single X window |
| OpenGLRenderer | DisplayDevice subclass implementing the low-level OpenGL rendering functions used by several derived DisplayDevice subclasses. This class renders drawing commands into a window provided by one of the further subclasses |
| OpenGLShader | Manages enumeration and initialization of OpenGL programmable shaders |
| Orbital | The Orbital class, which stores orbitals, SCF energies, etc. for a single timestep |
| orbital_cbdata | Orbital callback data structure containing multiple pointers |
| orbthrparms | |
| OsgNavigator | |
| ParseTree | An atom selection expression parse tree |
| PBCControls | Fl_Group subclass implementing controls for displaying periodic images for a graphical representation |
| PhoneButtons | Buttons subclass that gets its info from a WiFi SmartPhone |
| PhoneTracker | VMDTracker subclass that gets its info from the Phone driver |
| Pickable | Contains data which may be selected with a pointer in a DisplayDevice |
| PickAtomCallbackEvent | Sets the molid, atomid, and client of the last callback-picked atom |
| PickAtomEvent | Sets the molid and atomid of the last picked atom |
| PickEvent | Command subclass for picking events, used to notify the GUI of updates |
| PickGraphicsEvent | Sets the molid, tag, and button of the last picked user graphics |
| PickList | Maintains a list of Pickable objects, find and deal with items picked by a pointer device |
| PickMode | Pick mode management class |
| PickModeAddBond | PickMode subclass to add bonds between two atoms |
| PickModeAngles | PickMode subclass for angle labels |
| PickModeAtoms | PickMode subclass for labeling atoms |
| PickModeBonds | PickMode subclass for bond/distance labels |
| PickModeCenter | PickMode subclass to define the molecule's centering/global translation |
| PickModeDihedrals | PickMode subclass for dihedral labels |
| PickModeForce | PickMode subclass for applying forces to atoms |
| PickModeForceAtom | PickMode subclass to apply a force to a single atom |
| PickModeForceFragment | PickMode subclass to apply a force to a single fragment |
| PickModeForceResidue | PickMode subclass to apply a force to a single residue |
| PickModeList | List of all available PickMode subclasses |
| PickModeMolLabel | PickMode subclass to add labels to atoms |
| PickModeMove | PickMode subclass for moving atoms (no forces applied) |
| PickModeMoveAtom | PickMode subclass for moving atoms (no forces applied) |
| PickModeMoveFragment | PickMode subclass for moving fragments (no forces applied) |
| PickModeMoveMolecule | PickMode subclass for moving whole molecules (no forces applied) |
| PickModeMoveRep | PickMode subclass for moving a selected rep's atoms (no forces applied) |
| PickModeMoveResidue | PickMode subclass for moving residues (no forces applied) |
| PickModeUser | PickMode subclass to add bonds between two atoms |
| PickSelectionEvent | List the atoms involved in the last geometry object created |
| PickValueEvent | Sets the value of the last created Geometry |
| PinchTool | Tool subclass implementing a function similar to TugTool except that the force is only applied in the direction the tool is oriented |
| PlainTextInterp | TextInterp subclass implementing a last resort text interpreter if no other is available |
| plane | |
| PluginMgr | Scans a specified set of directories looking for shared libraries that implement the vmdplugin interface. Stores a copy of the plugins it finds so that they can be passed to routines that know the specific interface for the plugin |
| PointDistance | |
| PointGroupDefinition | |
| POV3DisplayDevice | FileRenderer subclass exports scenes to POV-Ray 3.x ray tracer scene format |
| prim_t | A Gaussian primitive |
| PrintTool | The print tool allows users to print tracker values on the fly |
| PSDisplayDevice | FileRenderer subclass exports VMD scenes to PostScript files |
| ptrstack | |
| PyAtomSelObject | |
| PythonEvalEvent | This command allows us to evaluate an arbitrary string in the Python interpreter |
| PythonTextInterp | TextInterp subclass implementing the Python-based text command interpreter |
| QMData | QM data management class. Concerns QM related data that are not timestep dependent |
| QMTimestep | Timesteps store coordinates, energies, etc. for one trajectory timestep |
| qsurf_gpuhandle | |
| Quat | Quaternion class |
| QuickSurf | |
| quicksurf_cbdata | QuickSurf callback data structure containing multiple pointers |
| R3dDisplayDevice | FileRenderer subclass exports VMD scene to a file in Raster3D format |
| RadianceDisplayDevice | FileRenderer subclass to export VMD scenes to a Radiance scene file |
| RadiusCounter | Counter control used set radii |
| RayShadeDisplayDevice | FileRenderer subclass to exports VMD scenes to Rayshade scene format |
| rdfthrparms | |
| real_pcre | |
| real_pcre_extra | |
| RenderFltkMenu | VMDFltkMenu subclass implementing a GUI for exporting and rendering VMD scenes via the FileRenderer classes in FileRenderList |
| RenderManDisplayDevice | FileRenderer subclass to exports VMD scenes to Renderman RIB scene format |
| RepChoice | Chooser control used to select from a list of representation settings |
| RepChoiceSmall | Narrow chooser control used to select from a list of representation settings |
| Residue | Based on the uniq_resid assigned in BaseMolecule, a residue knows what other residues it is connected to, and maintains a list of the atoms it contains |
| ResizeArray< T > | A template class which implements a dynamically-growing, automatically resizing array of data of a given type. Elements in the array may be accessed via the [] operator. When new data is added to the end of an array, the size of the array is automatically increased if necessary. XXX Do not parametrize this class with a datatype which cannot be shallow-copied! This class uses memcpy to resize, and therefore classes which contain dynamically-allocated memory blocks will crash and burn if the ResizeArray ever gets resized |
| ResolutionCounter | Counter control used to set tessellation resolution |
| RibbonFrame | |
| RotateTool | Tool subclass implementing a rotational orientation control with haptic feedback which constrains the position of the pointer to the surface of a sphere while it is being manipulated |
| SaveTrajectoryFltkMenu | VMDFltkMenu subclass implementing a GUI for saving trajectory and coordinate frames to files |
| Scene | Contains lists of Displayable objects and draws them to a DisplayDevice |
| SelectionBuilder | Fl_Group subclass implementing a set of controls for browsing atom data fields, editing atom selection macros, and GUI-based atom selection construction |
| SensorConfig | Provides a Sensor with configuration information by parsing one or more configuration files |
| shell_t | A Shell (Gaussian type orbital) |
| ShortSlider | Shorter slider control for use with longer labels |
| SmallRing | A SmallRing contains a list of atoms which are connected to each other to form a loop. The atom numbers are the unique atom numbers as used in BaseMolecule. The ordering of the atoms, in addition to specifying how the atoms in the ring are connected, also gives the orientation (handedness) of the ring if orientated is non-zero |
| SmallRingLinkages | A SmallRingLinkages object contains a list of edges which lie on paths connecting (orientated) SmallRings |
| SnapshotDisplayDevice | FileRenderer subclass to save VMD images in a supported image file format |
| SortableArray< T > | A sort-capable variant of the ResizeArray template class. In addition to the methods provided there, this template also allows either quicksorting or insertion sorting of the elements in the array |
| Spaceball | UIObject subclass for Spaceball-based motion control |
| SpaceballButtons | Buttons subclass that gets its info from the local Spaceball |
| spaceballevent | |
| SpaceballEvent | Sets the most recent Spaceball translation, rotation, and button state |
| spaceballhandle | |
| SpaceballTracker | VMDTracker subclass that gets its info from the Spaceball driver |
| SpringTool | A tool for connecting atoms with springs |
| SQUARECELL | Set of 4 grid samples used for isocontour extraction |
| Stack< T > | A template class which implements a simple stack of arbitrary data. Items are pushed onto and popped off of the stack, or may just be copied from the stack |
| Stage | Displayable subclass implementing a checkered "stage" |
| StepCounter | Counter control used to set volume extraction step size |
| STLDisplayDevice | FileRenderer subclass to export VMD scenes to STL solid model format |
| Surf | Interface to the SURF solvent accessible surface package |
| symbol_data | Simplifies the use of three basic data types in an array situation. It does the conversion as needed and can be told to change size |
| SymbolTable | Tracks names and functions needed to parse a selection for the given class |
| SymbolTableElement | Keeps track of the template-dependent mapping from index to member function |
| Symmetry | |
| TachyonDisplayDevice | FileRenderer subclass to export VMD scenes to the Tachyon scene format |
| TclEvalEvent | Evaluate the given string in the Tcl interpreter |
| TclTextInterp | TextInterp subclass implementing the Tcl-based text command interpreter |
| TextInterp | Base class for all text interpreters |
| Timestep | Timesteps store coordinates, energies, etc. for one trajectory timestep |
| TimestepEvent | Indicates that a new timestep has been received over a remote connection |
| Tool | A Tool represents a virtual device used to manipulate objects on the screen. Tools use input from VMDTracker, Feedback, and Button devices and draw a pointer on the screen. Tools can give up their devices to another tool to effectively allow a tool to change its type on the fly |
| ToolFltkMenu | VMDFltkMenu subclass that implements a GUI for configuring Tool, Sensor, Button, Feedback, and VMDTracker objects |
| TrajectoryReadEvent | Indicates when all the frames of a trajectory have been read |
| TRIANGLE | Structure defining a triangle generated by isosurface extraction code |
| TugTool | A tool for interacting with MD simulations |
| UIObject | User Interface Object base class. All user interface modules are derived from this; it provides methods for registering with the command processor and 'signing up' for which commands it is interested in, as well as generating commands and events |
| UIText | UIObject class providing text based user interfaces for scripting etc |
| UIVR | UIObject subclass implementing a Virtual Reality user interface. I coordinates multiple tools, taking manipulation commands from them and giving them back various messages and flags. UIVR is the thing which has to know about the different kinds of tools |
| UserKeyEvent | Evaluate the given hotkey combination |
| Vector3D | |
| vmd_opencl_orbital_handle | |
| VMDApp | The main VMD application instance, created by the main entry point |
| VMDClipPlane | Data structure describing user specified clipping planes |
| VMDCollab | |
| VMDDIR | Unix directory traversal handle |
| VMDDisplayList | Display list data structure used to hold all of the rendering commands VMD generates and interprets in order to do its 3-D rendering |
| VMDDisplayList::VMDLinkIter | |
| VMDFltkMenu | VMDMenu and FL_Window subclass for managing all FLTK-based menus in VMD |
| VMDMenu | Base class for all GUI menus in VMD |
| VMDTempFile | |
| VMDTitle | Displayable subclass for a flashy title object displayed when VMD starts up, until a molecule is loaded |
| VMDTkinterMenu | VMDMenu subclass to manage Tkinter extension menus added by the user |
| VMDTkMenu | VMDMenu subclass to manage Tk extension menus added by the user |
| VMDTracker | An object representing a connection to a machine that controls 3d input devices (optionally with buttons, force-feedback, etc). One connection may control one or many devices, so there needs to be a global list of trackers which the Sensors peruse when first being initialized. This class is named VMDTracker to avoid name conflicts with the UNC tracker library |
| vmdwinjoystick | Store low-level Win32 joystick status and config info |
| VolMapCreate | Virtual class for dealing with the computation of VolMaps, based on atomic selections and atomic data and coordinates. It provides utilities for computing such maps. Various algorithms and specific calculations are done by child classes. The end result is a VolMap object, which can be passed to VMD (N/A yet) or written to a file |
| VolMapCreateCoulombPotential | |
| VolMapCreateCoulombPotentialMSM | |
| VolMapCreateDensity | |
| VolMapCreateDistance | |
| VolMapCreateILS | Implicit Ligand Sampling (ILS) algorithm. It finds the energy of placing a monoatomic or diatomic ligand at many points in the protein |
| VolMapCreateInterp | |
| VolMapCreateMask | |
| VolMapCreateOccupancy | |
| VolumeTexture | |
| VolumetricData | Volumetric data class for potential maps, electron density maps, etc |
| VRJugglerButtons | Buttons subclass that gets its info from the VRJuggler wand |
| VRJugglerDisplayDevice | DisplayDevice subclass that runs in the VRJuggler |
| VRJugglerScene | |
| VRJugglerSharedData | |
| VRJugglerTracker | VMDTracker subclass that interfaces to the VRJuggler wand |
| Vrml2DisplayDevice | FileRenderer subclass to export VMD scenes to VRML2/VRML97 scene format |
| VrmlDisplayDevice | FileRenderer subclass to export VMD scenes to VRML 1.0 scene format |
| VRPNButtons | Buttons subclass that gets its info over the net from VRPN |
| VRPNFeedback | Feedback subclass for sending haptic forces to VRPN over the net |
| VRPNTracker | VMDTracker subclass the manage VRPN tracker devices |
| VRPNTrackerUserData | VRPN tracker position and orientation data |
| wavef_signa_t | |
| WavefrontDisplayDevice | FileRenderer subclass to export VMD scenes to Wavefront "OBJ" format |
| Wavefunction | |
| Win32Joystick | UIObject subclass to allow joystick-based motion control on MS-Windows |
| wkf_run_barrier_struct | |
| wkf_shared_iterator_struct | |
| wkf_tasktile_struct | |
| wkf_threadlaunch_struct | |
| wkf_threadpool_struct | |
| wkf_threadpool_workerdata_struct | |
| wkf_tilestack_t | |
| wkf_timer | |
| wkfmsgtimer | |
| X3DDisplayDevice | FileRenderer subclass to export VMD scenes to X3D scene format |
| X3DOMDisplayDevice | |
| xidevhandle | |
| xinputhandle | |
| XY | Structure containing xy values for line vertices |
| XYZ | Structure containing xyz values for triangle vertices and normals |
| yy_buffer_state | |
| YYSTYPE | |
| yytoktype | |
