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VMD (current) Compound Members
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Here is a list of all class members with links to the class documentation for each member:- _ -
- a -
- a
: atomsel_iterobject, Msmpot_t
- a_length
: Timestep
- aa_available()
: DisplayDevice
- aa_enabled()
: DisplayDevice
- aa_off()
: OpenGLRenderer, DisplayDevice
- aa_on()
: OpenGLRenderer, DisplayDevice
- aaAvailable
: DisplayDevice
- aaEnabled
: DisplayDevice
- aaPrevious
: DisplayDevice
- aasamples
: FileRenderList, FileRenderer
- abs_screen_loc_2D()
: OpenGLRenderer, DisplayDevice
- abs_screen_loc_3D()
: OpenGLRenderer, DisplayDevice
- abs_screen_pos()
: DisplayDevice
- acc_force()
: colvar_grid_gradient
- acc_force_weighted()
: colvar_grid_gradient
- acc_value()
: colvar_grid_gradient, colvar_grid_scalar
- acc_work
: colvarbias_restraint_moving
- accelMD_enabled()
: colvarproxy_system
- access_volume_gradient()
: VolumetricData
- acf
: colvar
- acf_colvar_name
: colvar
- acf_coor
: colvar
- acf_length
: colvar
- acf_nframes
: colvar
- acf_normalize
: colvar
- acf_notset
: colvar
- acf_offset
: colvar
- acf_outfile
: colvar
- acf_p2coor
: colvar
- acf_stride
: colvar
- acf_type
: colvar
- acf_type_e
: colvar
- acf_v_history
: colvar
- acf_v_history_p
: colvar
- acf_vel
: colvar
- acf_x_history
: colvar
- acf_x_history_p
: colvar
- acos()
: colvarmodule
- act_on_command()
: Win32Joystick, VMDCollab, VideoStream, UIText, UIObject, ToolFltkMenu, Spaceball, SaveTrajectoryFltkMenu, RenderFltkMenu, UIVR, Mobile, MaterialFltkMenu, MainFltkMenu, IMDMgr, GraphicsFltkMenu, GeometryFltkMenu, FileChooserFltkMenu, DisplayFltkMenu, ColorFltkMenu
- activate()
: MoleculeList
- activate_adv_light()
: Scene
- activate_light()
: Scene
- activate_materials()
: FileRenderer
- activate_menus()
: VMDApp
- active
: UIObject, MoleculeList, DrawMolecule
- active_cvc_square_norm
: colvar
- actual_radius
: MolData
- actual_value()
: colvar
- add
: GridList, AtomList, IndexList, FileRenderList, colvarscript
- add_angle()
: BaseMolecule
- add_atom()
: Residue, atom_group
- add_atom_group_slot()
: colvarproxy_atom_groups
- add_atom_id()
: atom_group
- add_atom_name_residue_range()
: atom_group
- add_atom_numbers()
: atom_group
- add_atom_numbers_range()
: atom_group
- add_atom_slot()
: colvarproxy_atoms
- add_atoms()
: BaseMolecule
- add_atoms_of_group()
: atom_group
- add_bias_force()
: colvar
- add_bias_force_actual_value()
: colvar
- add_bond()
: BaseMolecule, MolAtom
- add_bond_dupcheck()
: BaseMolecule
- add_buttons()
: Tool
- add_cent_trans()
: Displayable
- add_cfunction()
: SymbolTable
- add_child()
: Displayable, colvardeps
- add_color_category()
: Scene
- add_color_item()
: Scene
- add_color_names()
: MoleculeList
- add_colvar()
: colvarbias
- add_cone()
: MoleculeGraphics
- add_config()
: colvarproxy
- add_constant()
: colvar_grid< T >
- add_coor_file()
: Molecule
- add_cterm()
: BaseMolecule
- add_custom_singleword()
: SymbolTable
- add_cylinder()
: MoleculeGraphics
- add_dihedral()
: BaseMolecule
- add_directional_light()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- add_edge()
: GraphLayout
- add_elem()
: colvarvalue
- add_energy()
: colvarproxy_vmd, colvarproxy_system
- add_error_msg()
: colvarscript, colvarproxy
- add_feedback()
: Tool
- add_geometry()
: GeometryList
- add_glob_trans()
: Displayable
- add_grid()
: colvar_grid< T >
- add_hill()
: colvarbias_meta
- add_improper()
: BaseMolecule
- add_index_group()
: atom_group
- add_instance()
: BaseMolecule
- add_keyword()
: SymbolTable, colvarparse
- add_line()
: MoleculeGraphics
- add_map_to_molecule()
: VolMapCreateILS
- add_material()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, MaterialList, ANARIRender
- add_menu()
: VMDApp
- add_molecule()
: MoleculeList
- add_name()
: NameList< T >
- add_pickable()
: PickList
- add_pickpoint()
: MoleculeGraphics
- add_plugin()
: PluginMgr
- add_point()
: MoleculeGraphics
- add_positional_light()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- add_rep()
: MoleculeList, DrawMolecule
- add_rot()
: Displayable
- add_singleword()
: SymbolTable
- add_sphere()
: MoleculeGraphics
- add_spheretube()
: MoleculeGraphics
- add_stringfctn()
: SymbolTable
- add_text()
: MoleculeGraphics
- add_tool_with_USL()
: UIVR
- add_tracker()
: Tool
- add_triangle()
: MoleculeGraphics
- add_tricolor()
: MoleculeGraphics
- add_trinorm()
: MoleculeGraphics
- add_volmap_slot()
: colvarproxy_volmaps
- add_volume_data()
: BaseMolecule
- add_wavefunction()
: QMTimestep
- add_weight_matrix()
: GraphLayout
- ADDBOND
: PickModeList, Mouse
- addconstraint()
: VRPNFeedback, Feedback
- addForce()
: Molecule
- addforcefield()
: VRPNFeedback, Feedback
- addLinkagePath()
: SmallRingLinkages
- addNewClient()
: Mobile
- addPath()
: LinkageEdge
- addPersistentForce()
: Molecule
- addplaneconstraint()
: VRPNFeedback, Tool, Feedback
- address()
: colvar_grid< T >
- addto_far_clip()
: DisplayDevice
- addto_near_clip()
: DisplayDevice
- adv_light_active()
: Scene
- adv_light_attenuation()
: Scene
- adv_light_color()
: Scene
- adv_light_color_default()
: Scene
- adv_light_get_attenuation()
: Scene
- adv_light_get_spotlight()
: Scene
- adv_light_highlighted()
: Scene
- adv_light_pos()
: Scene
- adv_light_pos_default()
: Scene
- adv_light_spotlight()
: Scene
- advLightState
: FileRenderer
- after_restart
: colvar
- ag_features
: atom_group
- alch_Flambda()
: colvar::alch_Flambda
- alch_lambda()
: colvar::alch_lambda
- alignmat
: ComputeOccupancyMap_t
- alive()
: VRJugglerTracker, VRJugglerButtons, SpaceballTracker, SpaceballButtons, PhoneTracker, PhoneButtons, VRPNTracker, VRPNFeedback, VRPNButtons, VMDTracker, Tool, FreeVRTracker, FreeVRButtons, CaveTracker, CaveButtons, MobileTracker, MobileButtons
- allowed_keywords
: colvarparse
- allselected
: DispCmdPickPointArray
- alpha
: Timestep, PerRayData_radiance
- alpha_angles()
: colvar::alpha_angles
- ALT
: DisplayDevice
- alternate_refs
: colvardeps::feature_state
- ALTLOC
: BaseMolecule
- altlocindex
: MolAtom
- altlocNames
: BaseMolecule
- ambient
: VMDDisplayList, osp_material, ort_material, Material, anr_material
- anaface
: NanoShaperFace, MSMSFace
- analyze()
: colvarmodule, colvarbias, colvar, BaseMolecule
- ANARI_AO
: ANARIRender
- ANARI_DEFAULT
: ANARIRender
- ANARI_Global_Init()
: ANARIRender, ANARIDisplayDevice
- ANARI_Global_Shutdown()
: ANARIRender, ANARIDisplayDevice
- ANARI_MATTE
: ANARIRender
- ANARI_NONE
: ANARIRender
- ANARI_NVGL
: ANARIRender
- ANARI_OBJ
: ANARIRender
- ANARI_OSPRAY
: ANARIRender
- ANARI_OTHER
: ANARIRender
- ANARI_OWL
: ANARIRender
- ANARI_PATHTRACER
: ANARIRender
- ANARI_SCIVIS
: ANARIRender
- ANARI_USD
: ANARIRender
- ANARIDisplayDevice()
: ANARIDisplayDevice
- ANARIRender()
: ANARIRender
- angle()
: colvar::angle
- angles
: BaseMolecule
- ANGLES
: BaseMolecule
- angleTypeNames
: BaseMolecule
- angleTypes
: BaseMolecule
- ANGLETYPES
: BaseMolecule
- angstrom_to_internal()
: colvarproxy_system
- angstrom_value_
: colvarproxy_system
- anim
: VMDApp
- ANIM_DELETE
: Command
- anim_dir()
: Animation
- ANIM_DIRECTION
: Command
- ANIM_DUP
: Command
- ANIM_FORWARD
: Animation
- ANIM_FORWARD1
: Animation
- ANIM_JUMP
: Command
- ANIM_LOOP
: Animation
- ANIM_NEW_FRAME
: Command
- ANIM_NEW_NUM_FRAMES
: Command
- ANIM_ONCE
: Animation
- ANIM_PAUSE
: Animation
- ANIM_READ
: Command
- ANIM_REVERSE
: Animation
- ANIM_REVERSE1
: Animation
- ANIM_ROCK
: Animation
- ANIM_SKIP
: Command
- ANIM_SPEED
: Command
- ANIM_STYLE
: Command
- anim_style()
: Animation
- ANIM_TOTAL_DIRS
: Animation
- ANIM_TOTAL_STYLES
: Animation
- ANIM_WRITE
: Command
- ANIMATE
: Spaceball, Mobile
- Animation()
: Animation
- animation_dir_name()
: VMDApp
- animation_num_dirs()
: VMDApp
- animation_num_styles()
: VMDApp
- animation_set_dir()
: VMDApp
- animation_set_frame()
: VMDApp
- animation_set_speed()
: VMDApp
- animation_set_stride()
: VMDApp
- animation_set_style()
: VMDApp
- animation_style_name()
: VMDApp
- AnimDir
: Animation
- AnimStyle
: Animation
- ao_enabled()
: DisplayDevice
- aoAmbient
: DisplayDevice
- aoDirect
: DisplayDevice
- aoEnabled
: DisplayDevice
- aosamples
: FileRenderList, FileRenderer
- apiInit()
: M_VRJapp
- app
: VRJugglerScene, VolMapCreate, UIObject, ctxt, SymbolTable, PyAtomSelObject, PickModeUser, PickModeMolLabel, PickModeAddBond, PickMode, ParseTree, GraphicsFltkMenu, DrawMolecule
- app_win
: spaceballhandle
- append()
: VMDDisplayList, SortableArray< T >, LinkagePath, SmallRing, ResizeArray< T >, Fragment, Displayable, CommandQueue
- append2()
: ResizeArray< T >
- append2x3()
: ResizeArray< T >
- append3()
: ResizeArray< T >
- append3x3()
: ResizeArray< T >
- append4()
: ResizeArray< T >
- append9()
: ResizeArray< T >
- append_frame()
: DrawMolecule
- append_new_config()
: colvarmodule
- append_text()
: VMDApp
- append_trimesh_v3f_n3f_c3f()
: OSPRayRenderer
- appendCommand()
: VRJugglerSharedData, VRJugglerScene, M_VRJapp
- appendList()
: PlainTextInterp
- appendlist()
: ResizeArray< T >
- appendN()
: ResizeArray< T >
- appendString()
: PlainTextInterp
- application
: VRJugglerScene
- applied_force()
: colvar
- apply_atom_force()
: colvarproxy_atoms
- apply_atom_group_force()
: colvarproxy_atom_groups
- apply_colvar_force()
: atom_group
- apply_constraints()
: colvarvalue
- apply_force()
: colvar::map_total, colvar::componentDisabled, colvar::alch_Flambda, colvar::alch_lambda, colvar::cartesian, colvar::rmsd, colvar::euler_theta, colvar::euler_psi, colvar::euler_phi, colvar::spin_angle, colvar::tilt, colvar::orientation_proj, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::groupcoordnum, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::dipole_angle, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::dipole_magnitude, colvar::distance_pairs, colvar::distance_inv, colvar::polar_theta, colvar::polar_phi, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, colvar::distance, colvar::cvc, atom_group, atom
- apply_force_dE_dlambda()
: colvarproxy_system
- apply_format_to_selected_labels()
: GeometryFltkMenu
- apply_offset_to_selected_labels()
: GeometryFltkMenu
- apply_translation()
: atom_group
- apply_volmap_force()
: colvarproxy_volmaps
- arclength
: RibbonFrame
- argc
: CmdToolCreate
- argc_m
: VMDApp
- ARGS
: colvarscript
- argv_m
: VMDApp
- ArithmeticPathBase()
: ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >
- ArtDisplayDevice()
: ArtDisplayDevice
- as_vector()
: colvarvalue, colvarmodule::quaternion, colvarmodule::rvector
- asin()
: colvarmodule
- aspathCV()
: colvar::aspathCV
- aspect()
: DisplayDevice
- Aspect
: DisplayDevice
- aspectratio
: FileRenderList, FileRenderer
- assign_rep()
: Tool
- assign_wavef_id()
: QMData
- asyncenginecount
: cudadevprops
- atan2()
: colvarmodule
- ATI
: OpenGLExtensions
- atimes()
: integrate_potential
- atom
: atom, BaseMolecule, BinOfAtoms, Msmpot_t, colvarmodule
- atom0
: bond
- atom1
: bond
- atom_basis
: orbthrparms
- atom_const_iter
: colvarmodule
- atom_displayed()
: DrawMolItem, DrawMolecule
- atom_formatted_name()
: GeometryMol
- atom_fragment()
: BaseMolecule
- atom_full_name()
: GeometryMol
- atom_group
: atom_group, colvarmodule
- atom_group_by_name()
: colvarmodule
- atom_groups
: colvar::cvc
- atom_groups_charges
: colvarproxy_atom_groups
- atom_groups_coms
: colvarproxy_atom_groups
- atom_groups_ids
: colvarproxy_atom_groups
- atom_groups_masses
: colvarproxy_atom_groups
- atom_groups_max_applied_force_
: colvarproxy_atom_groups
- atom_groups_new_colvar_forces
: colvarproxy_atom_groups
- atom_groups_refcount
: colvarproxy_atom_groups
- atom_groups_rms_applied_force_
: colvarproxy_atom_groups
- atom_groups_total_forces
: colvarproxy_atom_groups
- atom_ids
: colvar
- atom_iter
: colvarmodule
- atom_pos
: colvarmodule
- atom_residue()
: BaseMolecule
- atom_sel_mol
: atomsel_ctxt
- atom_short_name()
: GeometryMol
- atom_weights
: colvar::map_total
- atomColor
: DrawMolItem
- AtomColor()
: AtomColor
- AtomEntry()
: AtomEntry
- ATOMFLAGS
: BaseMolecule
- AtomGrid()
: AtomGrid
- AtomGridCell()
: AtomGridCell
- atomic_gradients
: colvar
- atomicnum
: densitythrparms, basis_atom_t
- atomicnumber
: MolAtom
- ATOMICNUMBER
: BaseMolecule
- atomids
: NanoShaperInterface, MSMSInterface
- AtomList()
: AtomList
- atomNames
: BaseMolecule
- atomparser_node()
: atomparser_node
- atompos
: orbthrparms
- atomRep
: DrawMolItem
- AtomRep()
: AtomRep
- atoms
: enthrparms, SmallRing, Residue, enthrparms, colvar::map_total, colvar::cartesian, colvar::rmsd, colvar::orientation, colvar::eigenvector, colvar::gyration, colvar::dipole_magnitude, colvar::polar_theta, colvar::polar_phi, atom_group
- atoms_charges
: colvarproxy_atoms
- atoms_cog
: colvar::orientation
- atoms_ids
: colvarproxy_atoms, atom_group
- atoms_masses
: colvarproxy_atoms
- atoms_max_applied_force_
: colvarproxy_atoms
- atoms_max_applied_force_id_
: colvarproxy_atoms
- atoms_new_colvar_forces
: colvarproxy_atoms
- atoms_positions
: colvarproxy_atoms
- atoms_refcount
: colvarproxy_atoms
- atoms_rms_applied_force_
: colvarproxy_atoms
- atoms_total_forces
: colvarproxy_atoms
- atomSel
: PyAtomSelObject, DrawMolItem
- AtomSel()
: AtomSel
- ATOMSEL_ADDMACRO
: Command
- atomsel_ctxt()
: atomsel_ctxt
- ATOMSEL_DELMACRO
: Command
- atomSelParser
: VMDApp
- AtomSelThr()
: AtomSelThr
- atomType
: MolAtom
- atomTypes
: BaseMolecule
- attach_cylinder_array()
: OSPRay2Renderer, ANARIRender
- attach_mesh()
: OSPRay2Renderer, ANARIRender
- attach_sphere_array()
: OSPRay2Renderer, ANARIRender
- attenuation
: PerRayData_shadow
- auto_update()
: GraphicsFltkMenu
- autobonds
: FileSpec
- AUX
: DisplayDevice
- avail
: vmdwinjoystick
- available
: colvardeps::feature_state
- average()
: colvar_grid_gradient
- ax
: ComputeOccupancyMap_t
- axes
: VMDApp, Best, colvar::cartesian
- Axes()
: Axes
- AXES_LOWERLEFT
: Axes
- AXES_LOWERRIGHT
: Axes
- AXES_ORIGIN
: Axes
- axes_set_location()
: VMDApp
- AXES_UPPERLEFT
: Axes
- AXES_UPPERRIGHT
: Axes
- AxesPos
: Axes
- AXESPOS_TOTAL
: Axes
- axis
: Symmetry, vmd_cylinder_color, vmd_cylinder, colvar::spin_angle, colvar::tilt, colvar::inertia_z, colvar::distance_z, CmdRockOn, CmdRotate
- axis_norm
: colvar::distance_z
- ay
: ComputeOccupancyMap_t
- az
: ComputeOccupancyMap_t
- azpathCV()
: colvar::azpathCV
- b -
- b
: abuf
- B2_LEFT
: DisplayDevice
- B2_MIDDLE
: DisplayDevice
- B2_RIGHT
: DisplayDevice
- b_1site_force
: colvar::dihedral, colvar::dipole_angle, colvar::angle
- b_anisotropic
: colvar::groupcoordnum, colvar::coordnum
- b_chg_centers
: colvarbias_restraint_moving
- b_chg_force_k
: colvarbias_restraint_moving
- b_debug_gradients
: colvarmodule::rotation
- b_decoupling
: colvarbias_restraint_moving
- b_delete_requested
: colvarproxy
- b_dummy
: atom_group
- b_equilibration
: colvarbias_alb
- B_ESC
: DisplayDevice
- B_F1
: DisplayDevice
- B_F10
: DisplayDevice
- B_F11
: DisplayDevice
- B_F12
: DisplayDevice
- B_F2
: DisplayDevice
- B_F3
: DisplayDevice
- B_F4
: DisplayDevice
- B_F5
: DisplayDevice
- B_F6
: DisplayDevice
- B_F7
: DisplayDevice
- B_F8
: DisplayDevice
- B_F9
: DisplayDevice
- b_group2_center_only
: colvar::coordnum
- b_hard_coupling_range
: colvarbias_alb
- b_hills_traj
: colvarbias_meta
- b_history_files
: colvarbias_reweightaMD
- B_LEFT
: Mouse, DisplayDevice
- b_length
: Timestep
- B_MIDDLE
: Mouse, DisplayDevice
- B_NONE
: Mouse
- b_output_centers
: colvarbias_restraint_centers_moving, colvarbias_alb
- b_output_coupling
: colvarbias_alb
- b_output_energy
: colvarbias
- b_output_grad
: colvarbias_alb
- B_RIGHT
: Mouse, DisplayDevice
- b_simulation_continuing
: colvarproxy
- b_simulation_running
: colvarproxy
- b_smp_active
: colvarproxy_smp
- b_try_scalable
: colvar::cvc
- b_use_cumulant_expansion
: colvarbias_reweightaMD
- b_user_defined_fit
: atom_group
- b_write_gradients
: colvarbias_reweightaMD
- b_write_histogram
: colvarbias_restraint_histogram
- BACKBONE
: AtomColor
- backColor
: FileRenderer
- backgradientbotcolor
: FileRenderer
- backgradientenabled
: FileRenderer
- backgradienttopcolor
: FileRenderer
- background_mode()
: Scene, DisplayDevice
- background_processing()
: VMDApp
- background_processing_clear()
: VMDApp
- background_processing_set()
: VMDApp
- backgroundmode
: DisplayDevice
- backup_file()
: colvarproxy_io, colvarmodule
- BAD_RANGE
: NanoShaperInterface, MSMSInterface
- BaseMolecule()
: BaseMolecule
- basis
: shell_t
- basis_array
: orbthrparms
- basis_string
: QMData
- basisa
: MolData
- basisb
: MolData
- basisc
: MolData
- bcopylatency
: latthrparms
- BEADS
: AtomRep
- begFrame
: CoorPluginData, CmdAnimDelete, CmdAnimWriteFile
- begin()
: atom_group
- beginrepgeomgroup()
: WavefrontDisplayDevice, MayaDisplayDevice, FileRenderer
- best_perm_index
: colvar::rmsd
- BETA
: AtomColor
- beta
: BaseMolecule, Timestep
- BFACTOR
: BaseMolecule
- BGMode
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- bias_by_name()
: colvarmodule
- bias_energy
: colvarbias
- bias_temperature
: colvarbias_meta
- bias_type
: colvarbias
- biases
: colvarmodule, colvar
- biases_active()
: colvarmodule
- biasing_force_scaling_factors
: colvarbias
- biasing_force_scaling_factors_bin
: colvarbias
- bin
: ComputeOccupancyMap_t, Msmpot_t, occthrparms_t, colvarbias_histogram
- bin_count()
: colvarbias
- bin_distance_from_boundaries()
: colvar_grid< T >
- bin_num()
: colvarbias
- bin_offsets
: ComputeOccupancyMap_t
- bin_to_value_scalar()
: colvar_grid< T >
- bin_zero
: ComputeOccupancyMap_t, occthrparms_t
- bincnt
: ComputeOccupancyMap_t
- bincnt_zero
: ComputeOccupancyMap_t
- bincount
: Msmpot_t
- bindepth
: Msmpot_t
- binfill
: Msmpot_t
- binmask()
: VolumetricData
- binoffsets
: occthrparms_t
- block_total
: MsmpotCuda_t
- blur()
: GaussianBlur< IMAGE_T >
- boff
: Msmpot_t
- boltzmann()
: colvarproxy_system
- boltzmann_
: colvarproxy_system
- bonded()
: MolAtom
- BONDORDERS
: BaseMolecule
- bondorders()
: BaseMolecule
- BONDRAD
: AtomRep
- BONDRES
: AtomRep
- BONDS
: BaseMolecule, AtomRep
- bonds
: MolAtom
- bondto
: bondlist
- bondTo
: MolAtom
- bondTypeNames
: BaseMolecule
- BONDTYPES
: BaseMolecule
- bondtypes()
: BaseMolecule
- boundaries_non_periodic
: colvarproxy_system
- boundaries_pbc_ortho
: colvarproxy_system
- boundaries_pbc_triclinic
: colvarproxy_system
- boundaries_type
: colvarproxy_system
- Boundaries_type
: colvarproxy_system
- boundaries_unsupported
: colvarproxy_system
- boxatom
: bondsearchthrparms
- boxby2
: gofrparms_t
- bucket
: inthash_t, hash_t
- buf
: linenoiseState
- buffer
: mobilehandle
- bufferPreDraw()
: M_VRJapp
- buflen
: linenoiseState
- build()
: AtomGrid
- build3Dmipmaps()
: OpenGLRenderer
- build_atom_list()
: colvar
- build_correlation_matrix()
: colvarmodule::rotation
- bus
: wrap_nvmlPciInfo_t
- bus_id_str
: wrap_nvmlPciInfo_t
- buttonchanged
: vmdwinjoystick
- buttonpressevent
: xidevhandle
- buttonpresseventclass
: xidevhandle
- buttonreleaseevent
: xidevhandle
- buttonreleaseeventclass
: xidevhandle
- buttons
: vmdwinjoystick, mobilehandle, spaceballevent
- Buttons()
: DisplayDevice, Buttons
- bx
: ComputeOccupancyMap_t, Msmpot_t
- bx_1
: ComputeOccupancyMap_t, occthrparms_t
- Bxcrds
: glwin_warp_hmd
- BY
: CmdScale, CmdTranslate, CmdRotate, CmdRotMat
- by
: ComputeOccupancyMap_t, Msmpot_t
- by_1
: ComputeOccupancyMap_t, occthrparms_t
- Bycrds
: glwin_warp_hmd
- byOrTo
: CmdScale, CmdTranslate, CmdRotate, CmdRotMat
- bytes
: netint
- bz
: ComputeOccupancyMap_t, Msmpot_t
- bz_1
: ComputeOccupancyMap_t, occthrparms_t
- c -
- C
: elementsummary, colvarmodule::rotation
- c
: flint_t, osp_trimesh_v3f_n3f_c3f, IsoSurface, anr_trimesh_v3f_n3f_c3f
- c0
: vmd_trimesh_c4u_n3b_v3f, vmd_tricolor
- c1
: vmd_trimesh_c4u_n3b_v3f, vmd_tricolor
- c2
: vmd_trimesh_c4u_n3b_v3f, vmd_tricolor
- c_array()
: colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >
- c_length
: Timestep
- cache_mode()
: DisplayDevice
- cache_name()
: DisplayDevice
- cached_alch_lambda
: colvarproxy_system
- cached_alch_lambda_changed
: colvarproxy_system
- cacheMode
: DisplayDevice
- cacheModes
: DisplayDevice
- cacheNames
: DisplayDevice
- cacheskip
: Displayable, VMDDisplayList
- calc()
: colvarmodule, colvar
- calc_1D_pmf()
: UIestimator::UIestimator
- calc_acf()
: colvar
- calc_apply_roto_translation()
: atom_group
- calc_biases()
: colvarmodule
- calc_center_of_geometry()
: atom_group
- calc_center_of_mass()
: atom_group
- calc_colvar_properties()
: colvar
- calc_colvars()
: colvarmodule
- calc_coor_acf()
: colvar
- calc_cvc_gradients()
: colvar
- calc_cvc_Jacobians()
: colvar
- calc_cvc_total_force()
: colvar
- calc_cvc_values()
: colvar
- calc_cvcs()
: colvar
- calc_density_map()
: QuickSurf
- calc_dipole()
: atom_group
- calc_energy()
: colvarbias_meta, colvarbias
- calc_eyedir()
: DisplayDevice
- calc_fit_gradients()
: colvar::cvc, atom_group
- calc_force_invgrads()
: colvar::rmsd, colvar::dihedral, colvar::angle, colvar::eigenvector, colvar::gyration, colvar::distance_xy, colvar::distance_z, colvar::distance, colvar::cvc
- calc_forces()
: colvarbias_meta, colvarbias
- calc_frustum()
: DisplayDevice
- calc_gradients()
: colvar::map_total, colvar::componentDisabled, colvar::alch_Flambda, colvar::alch_lambda, colvar::cartesian, colvar::rmsd, colvar::euler_theta, colvar::euler_psi, colvar::euler_phi, colvar::spin_angle, colvar::tilt, colvar::orientation_proj, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::groupcoordnum, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::dipole_angle, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::dipole_magnitude, colvar::distance_pairs, colvar::distance_inv, colvar::polar_theta, colvar::polar_phi, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, colvar::distance, colvar::cvc
- calc_hills()
: colvarbias_meta
- calc_hills_force()
: colvarbias_meta
- calc_Jacobian_derivative()
: colvar::rmsd, colvar::dihedral, colvar::angle, colvar::eigenvector, colvar::gyration, colvar::distance_xy, colvar::distance_z, colvar::distance, colvar::cvc
- calc_optimal_rotation()
: colvarmodule::rotation
- calc_p2coor_acf()
: colvar
- calc_pmf()
: UIestimator::UIestimator
- calc_required_properties()
: atom_group
- calc_runave()
: colvar
- calc_scripted_forces()
: colvarmodule
- calc_surf()
: QuickSurf, CUDAQuickSurf
- calc_value()
: colvar::map_total, colvar::componentDisabled, colvar::alch_Flambda, colvar::alch_lambda, colvar::cartesian, colvar::rmsd, colvar::euler_theta, colvar::euler_psi, colvar::euler_phi, colvar::spin_angle, colvar::tilt, colvar::orientation_proj, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::groupcoordnum, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::dipole_angle, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::dipole_magnitude, colvar::distance_pairs, colvar::distance_inv, colvar::polar_theta, colvar::polar_phi, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, colvar::distance, colvar::cvc
- calc_vel_acf()
: colvar
- calculate()
: GeometrySpring, GeometryMol, GeometryDihedral, GeometryBond, GeometryAngle
- calculate_all()
: GeometryMol
- calculate_max_radius()
: VolMapCreate
- calculate_minmax()
: VolMapCreate
- calculate_mo()
: Orbital
- calculateTexgenPlanes()
: VolumeTexture
- CameraProjection
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- can_accumulate_data()
: colvarbias
- can_read_angles()
: MolFilePlugin
- can_read_bonds()
: 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_qm_timestep_metadata()
: MolFilePlugin
- can_read_structure()
: MolFilePlugin
- can_read_timestep_metadata()
: MolFilePlugin
- can_read_timesteps()
: MolFilePlugin
- can_read_volumetric()
: MolFilePlugin
- can_write_angles()
: MolFilePlugin
- can_write_bonds()
: MolFilePlugin
- can_write_structure()
: MolFilePlugin
- can_write_timesteps()
: MolFilePlugin
- can_write_volumetric()
: MolFilePlugin
- cancel()
: Molecule
- cancelbutton
: FrameSelector
- canmaphostmem
: cudadevprops
- caps
: vmdwinjoystick
- cartesian()
: colvar::cartesian
- CartesianBasedPath()
: colvar::CartesianBasedPath
- category
: CmdColorItem
- category_index()
: Scene
- category_item_index()
: Scene
- category_item_name()
: Scene
- category_item_value()
: Scene
- category_name()
: Scene
- CaveButtons()
: CaveButtons
- CaveDisplayDevice()
: CaveDisplayDevice
- CaveScene()
: CaveScene
- CaveTracker()
: CaveTracker
- cb()
: PBCControls
- cbits
: compile_data
- cCatStr
: CmdColorName
- cColStr
: CmdColorName
- cell
: rdfthrparms
- cell_axes()
: VolumetricData
- cell_dirs()
: VolumetricData
- cell_lengths()
: VolumetricData
- cell_volume()
: VolumetricData
- cellIndex
: GeometryMol
- cent_trans_off()
: Displayable
- cent_trans_on()
: Displayable
- cent_translating()
: Displayable
- CENTER
: PickModeList, Mouse
- center
: colvarbias_meta::hill, VMDClipPlane, vmd_sphere_color, vmd_sphere, vmd_ring_color
- center_all_molecules()
: MoleculeList
- center_from_top_molecule_reps()
: MoleculeList
- center_of_geometry()
: atom_group
- center_of_mass()
: Symmetry, atom_group
- center_of_mass_scalar_gradient()
: atom_group
- center_ref_pos()
: atom_group
- center_top_molecule()
: MoleculeList
- centers
: colvarbias_meta::hill
- centers_incr
: colvarbias_restraint_centers_moving
- cents
: osp_sphere_array_color, anr_sphere_array_color
- centt
: Displayable
- CHAIN
: AtomColor
- chainindex
: MolAtom
- chainNames
: BaseMolecule
- change()
: AtomSel, AtomRep, AtomColor
- change_center()
: Displayable
- change_color()
: DrawMolItem
- change_configuration()
: colvarmodule, colvarbias_restraint_linear, colvarbias_restraint_harmonic, colvarbias_restraint_k_moving, colvarbias_restraint_centers_moving, colvarbias_restraint_moving, colvarbias_restraint_k, colvarbias_restraint_centers, colvarbias_restraint, colvarbias
- change_instances()
: DrawMolItem
- change_interp()
: UIText
- change_material()
: Displayable
- change_pbc()
: DrawMolItem, DrawMolecule
- change_rep()
: MoleculeList, DrawMolItem, DrawMolecule
- change_repcolor()
: MoleculeList
- change_repmat()
: MoleculeList
- change_repmethod()
: MoleculeList
- change_repsel()
: MoleculeList
- change_sel()
: DrawMolItem
- change_ss()
: DrawMolItem
- change_traj()
: DrawMolItem
- change_ts()
: DrawMolItem, DrawMolecule
- change_type()
: UIVR
- charge
: BaseMolecule, atom
- CHARGE
: BaseMolecule, AtomColor
- check_ascii()
: colvarparse
- check_atom_id()
: colvarproxy_vmd, colvarproxy_atoms
- check_bias_cmd_nargs()
: colvarscript
- check_braces()
: colvarparse
- check_cmd_nargs()
: colvarscript
- check_colvar_cmd_nargs()
: colvarscript
- check_consistency()
: colvar_grid< T >
- check_cvc_range()
: colvar
- check_enabled()
: colvardeps
- check_event()
: Win32Joystick, VMDCollab, VideoStream, UIText, UIObject, Spaceball, UIVR, Tool, Mouse, Mobile, IMDMgr, Animation
- check_events()
: CommandQueue
- check_keywords()
: colvarparse
- check_module_cmd_nargs()
: colvarscript
- check_mol()
: GeometryMol
- check_pickable()
: MoleculeList
- check_plane()
: Orbital
- check_positive_k
: colvarbias_restraint_k
- check_sizes()
: colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >
- check_types()
: colvarvalue
- check_types_assign()
: colvarvalue
- check_verbose_env()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- check_volmap_by_id()
: colvarproxy_volmaps, colvarproxy_vmd
- check_volmap_by_name()
: colvarproxy_volmaps
- checkpoint_freq
: VolMapCreate
- checkpoint_name
: VolMapCreate
- child()
: Displayable
- child_index()
: Displayable
- children
: Displayable
- choose_buttons()
: ToolFltkMenu
- choose_feedback()
: ToolFltkMenu
- choose_tracker()
: ToolFltkMenu
- chop()
: JString
- Cinf
: elementsummary
- cite_feature()
: colvarmodule, usage
- cite_paper()
: usage
- clamp()
: VolumetricData
- Cleanup()
: CUDAMarchingCubes
- clear()
: Surf, Stack< T >, SmallRingLinkages, SmallRing, ResizeArray< T >, OpenGLRenderer, NanoShaperInterface, NameList< T >, MSMSInterface, IsoSurface, IsoContour, myFl_Chart, DisplayDevice, colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >, colvarparse, colvarbias
- clear_all_lights()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- clear_angles()
: BaseMolecule
- clear_atom()
: colvarproxy_atoms
- clear_atom_group()
: colvarproxy_atom_groups
- clear_bonds()
: BaseMolecule
- clear_changed()
: DisplayColor
- clear_cterms()
: BaseMolecule
- clear_dihedrals()
: BaseMolecule
- clear_error()
: colvarmodule
- clear_error_msgs()
: colvarproxy
- clear_impropers()
: BaseMolecule
- clear_instances()
: BaseMolecule
- clear_keyword_registry()
: colvarparse
- clear_rep()
: Tool
- clear_state_data()
: colvarbias_meta, colvarbias_ti, colvarbias
- clear_str_result()
: colvarscript
- clear_text()
: VMDApp
- clear_volmap()
: colvarproxy_volmaps, colvarproxy_vmd
- cli_connect()
: VideoStream
- cli_connected()
: VideoStream
- cli_decode_frame()
: VideoStream
- cli_disconnect()
: VideoStream
- cli_gethost()
: VideoStream
- cli_getport()
: VideoStream
- cli_listen()
: VideoStream
- cli_send_keyboard()
: VideoStream
- cli_send_rotate_by()
: VideoStream
- cli_send_scale_by()
: VideoStream
- cli_send_translate_by()
: VideoStream
- cli_wait_msg()
: VideoStream
- clientdata
: wkf_threadlaunch_struct
- clip_center
: FileRenderer
- clip_color
: FileRenderer
- clip_mode
: FileRenderer
- clip_normal
: FileRenderer
- clip_width()
: DisplayDevice
- ClipMode
: OptiXRenderer
- clipplane()
: VMDDisplayList, Displayable
- clipplanes
: VMDDisplayList
- clockratekhz
: cudadevprops
- clone()
: VRJugglerTracker, VRJugglerButtons, SpaceballTracker, SpaceballButtons, PhoneTracker, PhoneButtons, VRPNTracker, VRPNFeedback, VRPNButtons, VMDTracker, FreeVRTracker, FreeVRButtons, Feedback, CaveTracker, CaveButtons, Buttons, MobileTracker, MobileButtons
- close_coor_file()
: Molecule
- close_file()
: WavefrontDisplayDevice, SnapshotDisplayDevice, MayaDisplayDevice, LibTachyonDisplayDevice, FileRenderer
- close_input_stream()
: colvarproxy_io
- close_input_streams()
: colvarproxy_io
- close_output_stream()
: colvarproxy_io
- close_output_streams()
: colvarproxy_io
- close_traj_file()
: colvarmodule
- closed()
: SmallRing
- cmd_arg_shift()
: colvarscript
- CMD_AXES
: Command
- CMD_STAGE
: Command
- CmdAddAtomSelMacro()
: CmdAddAtomSelMacro
- CmdAnimDelete()
: CmdAnimDelete
- CmdAnimDir()
: CmdAnimDir
- CmdAnimDup()
: CmdAnimDup
- CmdAnimJump()
: CmdAnimJump
- CmdAnimNewFrame()
: CmdAnimNewFrame
- CmdAnimNewNumFrames()
: CmdAnimNewNumFrames
- CmdAnimSkip()
: CmdAnimSkip
- CmdAnimSpeed()
: CmdAnimSpeed
- CmdAnimStyle()
: CmdAnimStyle
- CmdAnimWriteFile()
: CmdAnimWriteFile
- cmdbuf
: GraphicsFltkRep
- CmdColorChange()
: CmdColorChange
- CmdColorItem()
: CmdColorItem
- CmdColorName()
: CmdColorName
- CmdColorScaleColors()
: CmdColorScaleColors
- CmdColorScaleMethod()
: CmdColorScaleMethod
- CmdColorScaleSettings()
: CmdColorScaleSettings
- CmdDelAtomSelMacro()
: CmdDelAtomSelMacro
- CmdDisplayAAOn()
: CmdDisplayAAOn
- CmdDisplayAOAmbient()
: CmdDisplayAOAmbient
- CmdDisplayAODirect()
: CmdDisplayAODirect
- CmdDisplayAOOn()
: CmdDisplayAOOn
- CmdDisplayAxes()
: CmdDisplayAxes
- CmdDisplayBackgroundGradientOn()
: CmdDisplayBackgroundGradientOn
- CmdDisplayCacheMode()
: CmdDisplayCacheMode
- CmdDisplayClip()
: CmdDisplayClip
- CmdDisplayClipFar()
: CmdDisplayClipFar
- CmdDisplayClipFarRel()
: CmdDisplayClipFarRel
- CmdDisplayClipNear()
: CmdDisplayClipNear
- CmdDisplayClipNearRel()
: CmdDisplayClipNearRel
- CmdDisplayCueDensity()
: CmdDisplayCueDensity
- CmdDisplayCueEnd()
: CmdDisplayCueEnd
- CmdDisplayCueMode()
: CmdDisplayCueMode
- CmdDisplayCueStart()
: CmdDisplayCueStart
- CmdDisplayCullingOn()
: CmdDisplayCullingOn
- CmdDisplayDepthcueOn()
: CmdDisplayDepthcueOn
- CmdDisplayDoFFNumber()
: CmdDisplayDoFFNumber
- CmdDisplayDoFFocalDist()
: CmdDisplayDoFFocalDist
- CmdDisplayDoFOn()
: CmdDisplayDoFOn
- CmdDisplayEyesep()
: CmdDisplayEyesep
- CmdDisplayFocallen()
: CmdDisplayFocallen
- CmdDisplayFPSOn()
: CmdDisplayFPSOn
- CmdDisplayLightHL()
: CmdDisplayLightHL
- CmdDisplayLightMove()
: CmdDisplayLightMove
- CmdDisplayLightOn()
: CmdDisplayLightOn
- CmdDisplayLightRot()
: CmdDisplayLightRot
- CmdDisplayProj()
: CmdDisplayProj
- CmdDisplayRenderMode()
: CmdDisplayRenderMode
- CmdDisplayScreenDistance()
: CmdDisplayScreenDistance
- CmdDisplayScreenHeight()
: CmdDisplayScreenHeight
- CmdDisplayShadowOn()
: CmdDisplayShadowOn
- CmdDisplayStageLocation()
: CmdDisplayStageLocation
- CmdDisplayStagePanels()
: CmdDisplayStagePanels
- CmdDisplayStageSize()
: CmdDisplayStageSize
- CmdDisplayStereo()
: CmdDisplayStereo
- CmdDisplayStereoSwap()
: CmdDisplayStereoSwap
- CmdIMDConnect()
: CmdIMDConnect
- CmdIMDCopyUnitCell()
: CmdIMDCopyUnitCell
- CmdIMDCopyUnitCellCommand
: CmdIMDCopyUnitCell
- CmdIMDRate()
: CmdIMDRate
- CmdIMDRateCommand
: CmdIMDRate
- CmdIMDSim()
: CmdIMDSim
- CmdIMDSimCommand
: CmdIMDSim
- CmdLabelAdd()
: CmdLabelAdd
- CmdLabelAddspring()
: CmdLabelAddspring
- CmdLabelDelete()
: CmdLabelDelete
- CmdLabelShow()
: CmdLabelShow
- CmdLabelTextFormat()
: CmdLabelTextFormat
- CmdLabelTextOffset()
: CmdLabelTextOffset
- CmdLabelTextSize()
: CmdLabelTextSize
- CmdLabelTextThickness()
: CmdLabelTextThickness
- cmdList
: Displayable
- CmdMaterialAdd()
: CmdMaterialAdd
- CmdMaterialChange()
: CmdMaterialChange
- CmdMaterialDefault()
: CmdMaterialDefault
- CmdMaterialDelete()
: CmdMaterialDelete
- CmdMaterialRename()
: CmdMaterialRename
- CmdMenuExtensionAdd()
: CmdMenuExtensionAdd
- CmdMenuExtensionRemove()
: CmdMenuExtensionRemove
- CmdMenuShow()
: CmdMenuShow
- CmdMobileMode()
: CmdMobileMode
- CmdMolActive()
: CmdMolActive
- CmdMolAddRep()
: CmdMolAddRep
- CmdMolBondsRecalc()
: CmdMolBondsRecalc
- CmdMolCancel()
: CmdMolCancel
- CmdMolChangeRep()
: CmdMolChangeRep
- CmdMolChangeRepItem()
: CmdMolChangeRepItem
- CmdMolColor()
: CmdMolColor
- CmdMolDelete()
: CmdMolDelete
- CmdMolDeleteRep()
: CmdMolDeleteRep
- CmdMolDrawFrames()
: CmdMolDrawFrames
- CmdMolFix()
: CmdMolFix
- CmdMolLoad()
: CmdMolLoad
- CmdMolMaterial()
: CmdMolMaterial
- CmdMolNew()
: CmdMolNew
- CmdMolNumPeriodic()
: CmdMolNumPeriodic
- CmdMolOn()
: CmdMolOn
- CmdMolReanalyze()
: CmdMolReanalyze
- CmdMolRename()
: CmdMolRename
- CmdMolRep()
: CmdMolRep
- CmdMolRepColorUpdate()
: CmdMolRepColorUpdate
- CmdMolRepSelUpdate()
: CmdMolRepSelUpdate
- CmdMolScaleMinmax()
: CmdMolScaleMinmax
- CmdMolSelect()
: CmdMolSelect
- CmdMolShowInstances()
: CmdMolShowInstances
- CmdMolShowPeriodic()
: CmdMolShowPeriodic
- CmdMolShowRep()
: CmdMolShowRep
- CmdMolSmoothRep()
: CmdMolSmoothRep
- CmdMolSSRecalc()
: CmdMolSSRecalc
- CmdMolTop()
: CmdMolTop
- CmdMolVolume()
: CmdMolVolume
- CmdMouseMode()
: CmdMouseMode
- CmdPluginUpdate()
: CmdPluginUpdate
- cmdq
: vmd_opencl_orbital_handle
- cmdQueue
: M_VRJapp, UIObject
- cmdqueue
: GeometryMol
- CmdRender()
: CmdRender
- CmdRenderOption()
: CmdRenderOption
- CmdResetView()
: CmdResetView
- CmdRockOff()
: CmdRockOff
- CmdRockOn()
: CmdRockOn
- CmdRotate()
: CmdRotate
- CmdRotMat()
: CmdRotMat
- CmdScale()
: CmdScale
- CmdSpaceballMode()
: CmdSpaceballMode
- cmdStr
: AtomSel, AtomRep, AtomColor
- cmdText
: Command
- CmdToolAddDevice()
: CmdToolAddDevice
- CmdToolCallback()
: CmdToolCallback
- CmdToolChange()
: CmdToolChange
- CmdToolCreate()
: CmdToolCreate
- CmdToolDelete()
: CmdToolDelete
- CmdToolDeleteDevice()
: CmdToolDeleteDevice
- CmdToolOffset()
: CmdToolOffset
- CmdToolRep()
: CmdToolRep
- CmdToolScale()
: CmdToolScale
- CmdToolScaleForce()
: CmdToolScaleForce
- CmdToolScaleSpring()
: CmdToolScaleSpring
- CmdTranslate()
: CmdTranslate
- Cmdtype
: Command
- cNameStr
: CmdColorName
- code
: real_pcre
- coeff
: prim_t
- coeffs
: colvar::dihedPC
- COL_REGEN
: DrawMolItem
- colindex_visible()
: GraphicsFltkMenu
- collect_cvc_data()
: colvar
- collect_cvc_gradients()
: colvar
- collect_cvc_Jacobians()
: colvar
- collect_cvc_total_forces()
: colvar
- collect_cvc_values()
: colvar
- collect_gradients()
: colvar::dihedPC, colvar::alpha_angles, colvar::cvc
- collintol
: Symmetry
- color
: MoleculeList, VMDClipPlane, osp_positional_light, osp_directional_light, vmd_sphere_color, vmd_ring_color, vmd_cylinder_color, ort_positional_light, ort_directional_light, FileRenderer::AdvancedLightState, FileRenderer::LightState, DispCmdColorIndex, DepthSortObject, CmdColorChange, AtomColor, anr_positional_light, anr_directional_light
- COLOR
: MoleculeGraphics, CmdMolChangeRepItem
- COLOR_ADD_ITEM
: Command
- color_add_item()
: VMDApp
- color_category()
: VMDApp
- color_category_item()
: VMDApp
- COLOR_CHANGE
: Command
- color_change_name()
: VMDApp
- color_change_namelist()
: VMDApp
- color_change_rgb()
: VMDApp
- color_change_rgblist()
: VMDApp
- color_changed()
: DisplayColor, Displayable
- color_default_value()
: VMDApp, Scene
- color_get_from_name()
: VMDApp
- color_get_restype()
: VMDApp
- color_id()
: DisplayColor
- color_index()
: VMDApp, Scene, AtomColor
- color_mapping()
: VMDApp
- COLOR_NAME
: Command
- color_name()
: VMDApp, Scene
- color_rgb_changed()
: Displayable
- color_scale_changed()
: Displayable
- COLOR_SCALE_COLORS
: Command
- COLOR_SCALE_METHOD
: Command
- COLOR_SCALE_SETTINGS
: Command
- color_set_restype()
: VMDApp
- color_value()
: VMDApp, Scene
- colorCatIndex
: MoleculeList
- colorData
: DisplayDevice
- ColorFltkMenu()
: ColorFltkMenu
- COLORID
: AtomColor
- colorIndex
: FileRenderer
- ColorMethod
: AtomColor
- colors
: densitythrparms, osp_cylinder_array_color, osp_sphere_array_color, osp_cylinder_array_color, osp_sphere_array_color, CmdColorScaleColors, anr_cylinder_array_color, anr_sphere_array_color
- colorscale_method()
: Scene
- colorscale_method_current()
: VMDApp
- colorscale_method_index()
: VMDApp
- colorscale_method_menuname()
: VMDApp, Scene
- colorscale_method_name()
: VMDApp, Scene
- colorscale_params()
: VMDApp, Scene
- colorscale_setmethod()
: VMDApp
- colorscale_setparams()
: VMDApp
- colorscale_type()
: Scene
- ColorscaleImage()
: ColorscaleImage
- ColorscaleLumaChart()
: ColorscaleLumaChart
- colortable
: ColorScaleTypeInfo
- colortabsz
: ColorScaleTypeInfo
- cols
: osp_cylinder_array_color, osp_sphere_array_color, osp_trimesh_v3f_n3f_c3f, linenoiseState, anr_cylinder_array_color, anr_sphere_array_color, anr_trimesh_v3f_n3f_c3f
- colvar()
: colvar
- colvar_array_size
: colvarbias_histogram
- colvar_by_name()
: colvarmodule
- colvar_centers
: colvarbias_restraint_centers, colvarbias_alb
- colvar_distance()
: colvarbias_restraint_harmonic_walls
- colvar_forces
: colvarbias
- colvar_grid()
: colvar_grid< T >
- colvar_grid_count()
: colvar_grid_count
- colvar_grid_gradient()
: colvar_grid_gradient
- colvar_grid_scalar()
: colvar_grid_scalar
- colvar_sigmas
: colvarbias_meta
- colvar_values
: colvarbias
- colvarbias()
: colvarbias
- colvarbias_abf()
: colvarbias_abf
- colvarbias_alb()
: colvarbias_alb
- colvarbias_histogram()
: colvarbias_histogram
- colvarbias_meta
: colvarbias_meta, colvarbias_meta::hill
- colvarbias_restraint()
: colvarbias_restraint
- colvarbias_restraint_centers()
: colvarbias_restraint_centers
- colvarbias_restraint_centers_moving()
: colvarbias_restraint_centers_moving
- colvarbias_restraint_harmonic()
: colvarbias_restraint_harmonic
- colvarbias_restraint_harmonic_walls()
: colvarbias_restraint_harmonic_walls
- colvarbias_restraint_histogram()
: colvarbias_restraint_histogram
- colvarbias_restraint_k()
: colvarbias_restraint_k
- colvarbias_restraint_k_moving()
: colvarbias_restraint_k_moving
- colvarbias_restraint_linear()
: colvarbias_restraint_linear
- colvarbias_restraint_moving()
: colvarbias_restraint_moving
- colvarbias_reweightaMD()
: colvarbias_reweightaMD
- colvarbias_ti()
: colvarbias_ti
- colvardeps()
: colvardeps
- colvarmodule()
: colvarmodule
- colvarparams()
: colvarparams
- colvarparse()
: colvarparse
- colvarproxy
: colvarproxy, colvarscript, colvarmodule
- colvarproxy_atom_groups()
: colvarproxy_atom_groups
- colvarproxy_atoms()
: colvarproxy_atoms
- colvarproxy_io()
: colvarproxy_io
- colvarproxy_replicas()
: colvarproxy_replicas
- colvarproxy_script()
: colvarproxy_script
- colvarproxy_smp()
: colvarproxy_smp
- colvarproxy_system()
: colvarproxy_system
- colvarproxy_tcl()
: colvarproxy_tcl
- colvarproxy_vmd()
: colvarproxy_vmd
- colvarproxy_volmaps()
: colvarproxy_volmaps
- colvars
: colvarproxy, colvarbias
- colvarscript
: colvarscript, colvarmodule
- colvarvalue()
: colvarvalue
- com_index()
: GeometryMol
- Combinations()
: Combinations
- COMBINE_AVG
: VolMapCreate
- COMBINE_MAX
: VolMapCreate
- COMBINE_MIN
: VolMapCreate
- COMBINE_PMF
: VolMapCreate
- COMBINE_STDEV
: VolMapCreate
- CombineType
: VolMapCreate
- combo
: shell_t, Combinations
- combo_addframe()
: VolMapCreate
- combo_begin()
: VolMapCreate
- combo_end()
: VolMapCreate
- combo_export()
: VolMapCreate
- combolist
: Combinations
- comIndex
: GeometryMol
- COMM
: colvarscript
- comm
: colvarbias_meta
- Command()
: Command
- command
: colvarscript
- command_wanted()
: UIObject
- CommandQueue()
: CommandQueue
- commandQueue
: VMDApp
- commandStrings
: VRJugglerSharedData
- comment()
: X3DDisplayDevice, WavefrontDisplayDevice, VrmlDisplayDevice, Vrml2DisplayDevice, TachyonDisplayDevice, RenderManDisplayDevice, RayShadeDisplayDevice, RadianceDisplayDevice, R3dDisplayDevice, PSDisplayDevice, POV3DisplayDevice, MayaDisplayDevice, GelatoDisplayDevice, FileRenderer, ArtDisplayDevice, ANARIRender, ANARIDisplayDevice
- commentBuffer
: DrawMolItem
- commit_rep()
: ANARIRender
- communicate_forces()
: colvarbias, colvar
- Communication
: colvarbias_meta
- compare
: JString
- compare_cvc()
: colvar
- compare_wavef_guitype_to_type()
: QMData
- CompileShaders()
: OpenGLShader
- component
: DrawMolecule, NanoShaperFace, MSMSFace
- component_from_pickable()
: DrawMolecule
- componentDisabled()
: colvar::componentDisabled
- components()
: DrawMolecule
- compute()
: VolMapCreateILS, Surf, IsoSurface, IsoContour, GraphLayout, GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >, ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >
- compute_all()
: VolMapCreate
- compute_coordnum()
: colvar::coordnum
- compute_cumulant_expansion_factor()
: colvarbias_reweightaMD
- compute_frame()
: VolMapCreateCoulombPotentialMSM, VolMapCreateCoulombPotential, VolMapCreateDistance, VolMapCreateOccupancy, VolMapCreateInterp, VolMapCreateDensity, VolMapCreateMask, VolMapCreate
- compute_from_file()
: NanoShaperInterface, MSMSInterface
- compute_from_socket()
: MSMSInterface
- compute_init()
: VolMapCreateCoulombPotentialMSM, VolMapCreateCoulombPotential, VolMapCreateDistance, VolMapCreateOccupancy, VolMapCreateInterp, VolMapCreateDensity, VolMapCreateMask, VolMapCreate
- compute_max_atom_groups_applied_force()
: colvarproxy_atom_groups
- compute_max_atoms_applied_force()
: colvarproxy_atoms
- compute_max_volmaps_applied_force()
: colvarproxy_volmaps
- compute_overlap_integrals()
: QMData
- compute_overlap_matrix()
: colvarmodule::rotation
- compute_rms_atom_groups_applied_force()
: colvarproxy_atom_groups
- compute_rms_atoms_applied_force()
: colvarproxy_atoms
- compute_rms_volmaps_applied_force()
: colvarproxy_volmaps
- compute_selfcoordnum()
: colvar::selfcoordnum
- compute_voldata()
: colvarproxy_vmd
- compute_volmap()
: colvarproxy_volmaps, colvarproxy_vmd
- compute_volume_gradient()
: VolumetricData, BaseMolecule
- COMPUTED
: NanoShaperInterface, MSMSInterface
- computed_frames
: VolMapCreate
- computeDerivatives()
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >, ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >
- computeIsosurface()
: CUDAMarchingCubes
- computemode
: cudadevprops
- computeSurfaceArea()
: CUDAMarchingCubes
- computeValue()
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >, ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >
- CONE
: MoleculeGraphics
- cone()
: X3DDisplayDevice, VrmlDisplayDevice, Vrml2DisplayDevice, RenderManDisplayDevice, RayShadeDisplayDevice, POV3DisplayDevice, FileRenderer, ArtDisplayDevice
- cone_trunc()
: RadianceDisplayDevice, FileRenderer
- config_changed()
: colvarmodule
- config_key
: colvar::cvc
- config_string
: colvarparse
- CONFORMATION
: AtomColor
- conformers
: ComputeOccupancyMap_t, occthrparms_t
- conjugate()
: colvarmodule::quaternion
- connect()
: VMDCollab, IMDMgr
- connected()
: IMDMgr
- constant()
: Matrix4
- constfactor
: FileRenderer::AdvancedLightState
- contextInit()
: M_VRJapp
- CONTROL
: DisplayDevice
- convert()
: symbol_data
- coord
: AtomData
- CoorData()
: CoorData
- CoorDataState
: CoorData
- coordinates()
: AtomSel
- coordnum()
: colvar::coordnum
- coords
: ComputeOccupancyMap_t, NanoShaperInterface, MSMSInterface, MolData
- CoorPluginData()
: CoorPluginData
- copy()
: LinkagePath, SmallRing
- copy_grid()
: colvar_grid< T >
- COPYCELL_OFF
: CmdIMDCopyUnitCell
- COPYCELL_ON
: CmdIMDCopyUnitCell
- cos()
: colvarmodule
- cos_theta()
: colvarmodule::rotation
- cosine()
: colvarmodule::quaternion
- count
: MolData
- count_bonds()
: BaseMolecule
- count_h
: gofrparms_t
- count_i
: gofrparms_t
- count_o_end
: gofrparms_t
- count_o_start
: gofrparms_t
- coupling_accum
: colvarbias_alb
- coupling_rate
: colvarbias_alb
- cov()
: MoleculeGraphics, DrawMolecule
- cpDown
: DisplayDevice
- CPK
: AtomRep
- cpLeft
: DisplayDevice
- cpRight
: DisplayDevice
- cpu_only
: ComputeOccupancyMap_t
- cpu_threadpool()
: DrawMolecule
- cpucaps
: VMDApp, densitythrparms, orbthrparms
- cpUp
: DisplayDevice
- crds
: qcprmsdthreadparms, gpuqcprmsdthreadparms
- create()
: Combinations
- create_cmd_list()
: GeometrySpring, GeometryMol, GeometryDihedral, GeometryBond, GeometryAtom, GeometryAngle
- create_colorcmd()
: GraphicsFltkMenu
- create_context()
: OptiXRenderer
- create_inbufs()
: NVENCMgr
- create_matcmd()
: GraphicsFltkMenu
- create_multiframecmd()
: GraphicsFltkMenu
- create_orbital()
: QMData
- create_repcmd()
: GraphicsFltkMenu
- create_selcmd()
: GraphicsFltkMenu
- create_sorted_ids()
: atom_group
- create_text()
: CmdToolCallback, CmdToolDeleteDevice, CmdToolAddDevice, CmdToolRep, CmdToolOffset, CmdToolScaleSpring, CmdToolScaleForce, CmdToolScale, CmdToolDelete, CmdToolChange, CmdToolCreate, Command, CmdRockOff, CmdRockOn, CmdScale, CmdTranslate, CmdRotate, CmdRotMat, CmdRender, CmdPluginUpdate, CmdMolShowRep, CmdMolSmoothRep, CmdMolDrawFrames, CmdMolScaleMinmax, CmdMolShowInstances, CmdMolNumPeriodic, CmdMolShowPeriodic, CmdMolRename, CmdMolSSRecalc, CmdMolBondsRecalc, CmdMolReanalyze, CmdMolDeleteRep, CmdMolRepColorUpdate, CmdMolRepSelUpdate, CmdMolChangeRepItem, CmdMolChangeRep, CmdMolAddRep, CmdMolMaterial, CmdMolColor, CmdMolRep, CmdMolSelect, CmdMolTop, CmdMolOn, CmdMolFix, CmdMolActive, CmdMolDelete, CmdMolCancel, CmdMolLoad, CmdMenuShow, CmdMaterialDefault, CmdMaterialDelete, CmdMaterialChange, CmdMaterialRename, CmdMaterialAdd, CmdLabelTextFormat, CmdLabelTextOffset, CmdLabelTextThickness, CmdLabelTextSize, CmdLabelDelete, CmdLabelShow, CmdLabelAddspring, CmdLabelAdd, CmdIMDCopyUnitCell, CmdIMDRate, CmdIMDSim, CmdIMDConnect, CmdDisplayLightMove, CmdDisplayLightRot, CmdDisplayLightHL, CmdDisplayLightOn, CmdDisplayStageSize, CmdDisplayStagePanels, CmdDisplayStageLocation, CmdDisplayAxes, CmdDisplayDoFFocalDist, CmdDisplayDoFFNumber, CmdDisplayDoFOn, CmdDisplayAODirect, CmdDisplayAOAmbient, CmdDisplayAOOn, CmdDisplayShadowOn, CmdDisplayCueDensity, CmdDisplayCueEnd, CmdDisplayCueStart, CmdDisplayCueMode, CmdDisplayClip, CmdDisplayFPSOn, CmdDisplayBackgroundGradientOn, CmdDisplayCullingOn, CmdDisplayDepthcueOn, CmdDisplayAAOn, CmdDisplayScreenDistance, CmdDisplayScreenHeight, CmdDisplayFocallen, CmdDisplayEyesep, CmdDisplayProj, CmdDisplayRenderMode, CmdDisplayCacheMode, CmdDisplayStereoSwap, CmdDisplayStereo, CmdResetView, CmdColorItem, CmdColorScaleColors, CmdColorScaleSettings, CmdColorScaleMethod, CmdColorChange, CmdColorName, CmdAnimDup, CmdAnimDelete, CmdAnimWriteFile, CmdAnimSpeed, CmdAnimSkip, CmdAnimJump, CmdAnimStyle, CmdAnimDir
- create_tool()
: ToolFltkMenu
- create_unique_basis()
: QMData
- create_window()
: VMDTkMenu
- crop()
: VolumetricData
- crossing_threshold
: colvarmodule::rotation
- cterms
: BaseMolecule
- CTERMS
: BaseMolecule
- ctx
: vmd_opencl_orbital_handle, oglhandle
- ctxt()
: ctxt
- ctypes
: match_data, compile_data
- cube()
: FileRenderer
- cube_array()
: FileRenderer
- cubeindex
: GRIDCELL, SQUARECELL
- cuda
: VMDApp
- cuda_devpool()
: DrawMolecule
- cuda_gpucount
: wrap_nvml_handle
- cuda_nvml_device_id
: wrap_nvml_handle
- CUDAAccel()
: CUDAAccel
- CUDAMarchingCubes()
: CUDAMarchingCubes
- CUDAQuickSurf()
: CUDAQuickSurf
- CUE_EXP
: DisplayDevice
- CUE_EXP2
: DisplayDevice
- CUE_LINEAR
: DisplayDevice
- cue_mode_name()
: DisplayDevice
- cueDensity
: DisplayDevice
- cueEnd
: DisplayDevice
- cueing_available()
: DisplayDevice
- cueing_enabled()
: DisplayDevice
- cueing_off()
: OpenGLRenderer, DisplayDevice
- cueing_on()
: OpenGLRenderer, DisplayDevice
- cueingAvailable
: DisplayDevice
- cueingEnabled
: DisplayDevice
- cueMode
: DisplayDevice
- CueMode
: DisplayDevice
- cueStart
: DisplayDevice
- culling_available()
: DisplayDevice
- culling_enabled()
: DisplayDevice
- culling_off()
: OpenGLRenderer, DisplayDevice
- culling_on()
: OpenGLRenderer, DisplayDevice
- cullingAvailable
: DisplayDevice
- cullingEnabled
: DisplayDevice
- curColor
: GeomListStruct
- curformat
: FileRenderer
- curframe
: gofrparms_t
- curpath
: PluginMgr
- curr_material()
: Displayable
- current
: DrawMolecule, wkf_shared_iterator_struct
- current_bin()
: colvarbias
- current_bin_scalar()
: colvar_grid< T >
- current_bin_scalar_bound()
: colvar_grid< T >
- current_bin_scalar_fraction()
: colvar_grid< T >
- current_color_use()
: AtomColor
- current_coupling
: colvarbias_alb
- current_pick_mode()
: PickModeList
- current_update_d
: watershed_gpu_state_t< GROUP_T, IMAGE_T >
- current_value_d
: watershed_gpu_state_t< GROUP_T, IMAGE_T >
- cursor
: glxdata
- CursorCodes
: DisplayDevice
- custom_singleword_name()
: SymbolTable
- cutoff
: ComputeOccupancyMap_t, clusterparms_t, occthrparms_t
- cv
: colvar_grid< T >
- cv_addenergy
: colvarscript
- cv_features
: colvar
- cv_prec
: colvarmodule
- cv_traj_freq
: colvarmodule
- cv_traj_name
: colvarmodule
- cv_traj_write_labels
: colvarmodule
- cv_width
: colvarmodule
- cvb_features
: colvarbias
- CVBasedPath()
: colvar::CVBasedPath
- cvc()
: colvar::cvc
- cvc_features
: colvar::cvc
- cvc_flags
: colvar
- cvc_param_exists()
: colvar
- cvcs
: colvar
- cvec
: linenoiseCompletions
- cx
: glxdata
- cycle_x
: Msmpot_t
- cycle_y
: Msmpot_t
- cycle_z
: Msmpot_t
- CYLINDER
: MoleculeGraphics
- cylinder()
: X3DDisplayDevice, VrmlDisplayDevice, Vrml2DisplayDevice, TachyonDisplayDevice, RenderManDisplayDevice, RayShadeDisplayDevice, RadianceDisplayDevice, R3dDisplayDevice, POV3DisplayDevice, OSPRayDisplayDevice, OSPRay2DisplayDevice, OptiXDisplayDevice, OpenGLRenderer, LibTachyonDisplayDevice, GelatoDisplayDevice, FileRenderer, ArtDisplayDevice
- cylinder_array()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- cylinder_array_color()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- cylinderRes
: DisplayDevice
- cylinders
: osp_cylinder_array_color
- cyls
: osp_cylinder_array_color, anr_cylinder_array_color
- d -
- d
: VMDDIR
- d_restraint_potential_dk()
: colvarbias_restraint_linear, colvarbias_restraint_harmonic_walls, colvarbias_restraint_harmonic, colvarbias_restraint
- data
: NameList< T >, VolumetricData, inthash_node_t, hash_node_t, colvarmodule::matrix2d< T >, colvarmodule::matrix2d< T >::row, colvarmodule::vector1d< T >, colvar_grid< T >
- Data
: NameList< T >
- data_array()
: colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >
- data_begin_pos
: colvarparse
- data_end_pos
: colvarparse
- datarange()
: VolumetricData
- dataset
: GraphicsFltkRepVolumetric
- dataset_append()
: GraphicsFltkRepOrbital, GraphicsFltkRepVolumetric
- dataset_clear()
: GraphicsFltkRepOrbital, GraphicsFltkRepVolumetric
- dataset_flag
: BaseMolecule
- datasetflags
: BaseMolecule
- dcos_theta_dq()
: colvarmodule::rotation
- deactivate_materials()
: FileRenderer
- deactivate_uitext_stdin()
: VMDApp
- debug()
: colvarmodule
- debug_gradients()
: colvar::cvc
- debug_gradients_step_size
: colvarmodule
- decr_ref_count()
: colvardeps
- decrease_depth()
: colvarmodule
- default_beta()
: BaseMolecule
- default_charge()
: BaseMolecule
- default_color()
: MoleculeList
- default_exec_string()
: FileRenderer
- default_filename()
: FileRenderer
- default_mass()
: BaseMolecule
- default_material()
: MoleculeList
- default_occup()
: BaseMolecule
- default_radius()
: BaseMolecule
- default_representation()
: MoleculeList
- default_restart_frequency()
: colvarproxy_io
- default_selection()
: MoleculeList
- defaultColor
: GeomListStruct
- defaultCommandLine
: FileRenderer
- defaultFilename
: FileRenderer
- defcolor
: CmdColorItem
- define_adv_light()
: Scene
- define_light()
: Scene
- define_volume_texture()
: TachyonDisplayDevice, LibTachyonDisplayDevice, FileRenderer
- defValue
: AtomRepDataInfo
- deg
: CmdRockOn, CmdRotate
- del_all_molecules()
: MoleculeList
- del_geometry()
: GeometryList
- del_molecule()
: MoleculeList
- del_rep()
: MoleculeList, DrawMolecule
- delete_all()
: MoleculeGraphics
- delete_basis_set()
: QMData
- delete_features()
: colvar::cvc, colvarbias, atom_group, colvar
- delete_frame()
: DrawMolecule
- delete_hill()
: colvarbias_meta
- delete_id()
: MoleculeGraphics
- delete_material()
: MaterialList, Displayable
- delete_requested()
: colvarproxy
- delete_tool()
: ToolFltkMenu
- deleteUnused()
: OpenGLCache
- delr
: rdfthrparms
- delta
: VolMapCreate, gofrparms_t
- delta_grid()
: colvar_grid< T >
- DeltaCounter()
: DeltaCounter
- density
: Msmpot_t, orbthrparms
- density_matrix()
: Wavefunction
- depth
: colvarmodule, watershed_gpu_state_t< GROUP_T, IMAGE_T >, PerRayData_radiance, glwin_fbo_target
- depth_s
: colvarmodule
- depth_v
: colvarmodule
- depthcue_set_density()
: VMDApp
- depthcue_set_end()
: VMDApp
- depthcue_set_mode()
: VMDApp
- depthcue_set_start()
: VMDApp
- DepthSortObject()
: DepthSortObject
- description
: colvardeps::feature, colvardeps
- destroy_context()
: OSPRayRenderer, OptiXRenderer
- destroy_scene()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- detach()
: IMDSimThread, IMDSimBlocking, IMDSim, IMDMgr
- DETACH
: CmdIMDSim
- determinant()
: colvarmodule::rmatrix
- determineClosestFrames()
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- dev
: xidevhandle
- dev_bin
: MsmpotCuda_t
- dev_dialbox
: xinputhandle
- dev_maxpm
: MsmpotCuda_t
- dev_nbins
: MsmpotCuda_t
- dev_padmap
: MsmpotCuda_t
- dev_spaceball
: xinputhandle
- device
: wrap_nvmlPciInfo_t
- device_asyncenginecount()
: CUDAAccel
- device_canmaphostmem()
: CUDAAccel
- device_clock_ghz()
: CUDAAccel
- device_computemode()
: CUDAAccel
- device_count()
: OptiXRenderer, OptiXDisplayDevice, HMDMgr
- device_egrids
: MsmpotCuda_t
- device_index()
: CUDAAccel
- device_integratedgpu()
: CUDAAccel
- device_kerneltimeoutenabled()
: CUDAAccel
- device_list()
: OptiXRenderer
- device_membytes()
: CUDAAccel
- device_name()
: VRJugglerTracker, VRJugglerButtons, SpaceballTracker, SpaceballButtons, PhoneTracker, PhoneButtons, VRPNTracker, VRPNFeedback, VRPNButtons, VMDTracker, FreeVRTracker, FreeVRButtons, Feedback, CaveTracker, CaveButtons, Buttons, MobileTracker, MobileButtons, CUDAAccel
- device_pageablememaccess()
: CUDAAccel
- device_pageablememaccessuseshostpagetables()
: CUDAAccel
- device_qgrids
: MsmpotCuda_t
- device_sm_count()
: CUDAAccel
- device_spdpfpperfratio()
: CUDAAccel
- device_version_major()
: CUDAAccel
- device_version_minor()
: CUDAAccel
- deviceid
: latthrparms, globmembwthrparms, busbwthrparms, maddthrparms, cudadevprops
- devid
: wkf_threadpool_workerdata_struct
- devlist
: wkf_threadpool_struct
- devnum
: MsmpotCuda_t
- devpool_launch()
: CUDAAccel
- devpool_wait()
: CUDAAccel
- devs
: vmd_opencl_orbital_handle, wrap_nvml_handle
- devspeed
: wkf_threadpool_workerdata_struct
- dfdv1
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- dfdv2
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- dhlatusec
: busbwthrparms
- dhmbsec
: busbwthrparms
- diffuse
: VMDDisplayList, osp_material, ort_material, Material, anr_material
- dihedPC()
: colvar::dihedPC
- dihedral()
: colvar::dihedral
- dihedrals
: BaseMolecule
- dihedralTypeNames
: BaseMolecule
- dihedralTypes
: BaseMolecule
- dim
: VMDTracker
- dimension()
: VMDTracker, Tool
- dipole()
: atom_group
- dipole_angle()
: colvar::dipole_angle
- dipole_magnitude()
: colvar::dipole_magnitude
- dipoleV
: colvar::dipole_magnitude
- dir
: osp_directional_light, DirectionalLight, ort_directional_light, anr_directional_light
- dirs
: DirectionalLightList
- disable()
: colvardeps
- disable_stencil_stereo()
: OpenGLRenderer
- disconnect()
: VMDCollab, IMDSim
- DISP_ANTIALIAS
: Command
- DISP_AO
: Command
- DISP_AO_AMBIENT
: Command
- DISP_AO_DIRECT
: Command
- DISP_BACKGROUNDGRADIENT
: Command
- DISP_CACHEMODE
: Command
- DISP_CLIP
: Command
- DISP_CUEDENSITY
: Command
- DISP_CUEEND
: Command
- DISP_CUEMODE
: Command
- DISP_CUESTART
: Command
- DISP_CULLING
: Command
- DISP_DEPTHCUE
: Command
- DISP_DOF
: Command
- DISP_DOF_FNUMBER
: Command
- DISP_DOF_FOCALDIST
: Command
- DISP_EYESEP
: Command
- DISP_FOCALLEN
: Command
- DISP_FPS
: Command
- DISP_LIGHT_HL
: Command
- DISP_LIGHT_MOVE
: Command
- DISP_LIGHT_ON
: Command
- DISP_LIGHT_ROT
: Command
- DISP_PROJ
: Command
- DISP_RENDERMODE
: Command
- DISP_RESETVIEW
: Command
- DISP_SCRDIST
: Command
- DISP_SCRHEIGHT
: Command
- DISP_SHADOW
: Command
- DISP_STEREO
: Command
- DISP_STEREOSWAP
: Command
- DispCmdCylinder()
: DispCmdCylinder
- display
: VMDApp
- display_get_screen_distance()
: VMDApp
- display_get_screen_height()
: VMDApp
- display_get_size()
: VMDApp
- display_line()
: GeometryMol
- display_projection_is_perspective()
: VMDApp
- display_set_aa()
: VMDApp
- display_set_ao()
: VMDApp
- display_set_ao_ambient()
: VMDApp
- display_set_ao_direct()
: VMDApp
- display_set_background_mode()
: VMDApp
- display_set_cachemode()
: VMDApp
- display_set_culling()
: VMDApp
- display_set_depthcue()
: VMDApp
- display_set_dof()
: VMDApp
- display_set_dof_fnumber()
: VMDApp
- display_set_dof_focal_dist()
: VMDApp
- display_set_eyesep()
: VMDApp
- display_set_farclip()
: VMDApp
- display_set_focallen()
: VMDApp
- display_set_fps()
: VMDApp
- display_set_nearclip()
: VMDApp
- display_set_position()
: VMDApp
- display_set_projection()
: VMDApp
- display_set_rendermode()
: VMDApp
- display_set_screen_distance()
: VMDApp
- display_set_screen_height()
: VMDApp
- display_set_shadows()
: VMDApp
- display_set_size()
: VMDApp
- display_set_stereo()
: VMDApp
- display_set_stereo_swap()
: VMDApp
- display_string()
: GeometryMol
- display_titlescreen()
: VMDApp
- display_update()
: VMDApp
- display_update_cb()
: TextInterp
- display_update_on()
: VMDApp
- display_update_status()
: VMDApp
- display_update_ui()
: VMDApp
- Displayable()
: Displayable
- DisplayColor()
: DisplayColor
- DisplayDevice()
: DisplayDevice
- displayed()
: MoleculeList, Displayable
- DisplayEye
: DisplayDevice
- DisplayFltkMenu()
: DisplayFltkMenu
- displaylistcache
: OpenGLRenderer
- DisplayRocker()
: DisplayRocker
- dist
: DepthSortObject
- dist2()
: colvarvalue, colvarmodule::quaternion, colvar::alch_Flambda, colvar::alch_lambda, colvar::rmsd, colvar::euler_theta, colvar::euler_psi, colvar::euler_phi, colvar::spin_angle, colvar::tilt, colvar::orientation_proj, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::groupcoordnum, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::dipole_angle, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::dipole_magnitude, colvar::distance_inv, colvar::polar_theta, colvar::polar_phi, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, colvar::distance, colvar::cvc, colvar
- dist2_grad()
: colvarvalue, colvarmodule::quaternion
- dist2_lgrad()
: colvar::alch_Flambda, colvar::alch_lambda, colvar::rmsd, colvar::euler_theta, colvar::euler_psi, colvar::euler_phi, colvar::spin_angle, colvar::tilt, colvar::orientation_proj, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::groupcoordnum, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::dipole_angle, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::dipole_magnitude, colvar::distance_inv, colvar::polar_theta, colvar::polar_phi, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, colvar::distance, colvar::cvc, colvar
- dist2_rgrad()
: colvar::alch_Flambda, colvar::alch_lambda, colvar::rmsd, colvar::euler_theta, colvar::euler_psi, colvar::euler_phi, colvar::spin_angle, colvar::tilt, colvar::orientation_proj, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::groupcoordnum, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::dipole_angle, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::dipole_magnitude, colvar::distance_inv, colvar::polar_theta, colvar::polar_phi, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, colvar::distance, colvar::cvc, colvar
- dist_v
: colvar::distance_z, colvar::distance
- dist_v_ortho
: colvar::distance_xy
- distance()
: colvar::distance
- distance_dir()
: colvar::distance_dir
- distance_inv()
: colvar::distance_inv
- distance_pairs()
: colvar::distance_pairs
- distance_to_screen()
: DisplayDevice
- distance_vec()
: colvar::distance_vec
- distance_xy()
: colvar::distance_xy
- distance_z()
: colvar::distance_z
- divcnt
: glwin_warp_hmd
- divergence
: integrate_potential
- dL0_1
: colvarmodule::rotation
- dL0_2
: colvarmodule::rotation
- do_activate_adv_light()
: FileRenderer
- do_activate_light()
: OpenGLRenderer, FileRenderer, DisplayDevice
- do_callback()
: PickSelectionEvent, GraphLabelEvent, LogfileEvent, HelpEvent, TimestepEvent, TrajectoryReadEvent, PickAtomCallbackEvent, PickGraphicsEvent, PickAtomEvent, PickValueEvent, SpaceballEvent, MobileDeviceCommandEvent, MobileStateChangedEvent, MobileEvent, MousePositionEvent, MouseModeEvent, MoleculeEvent, InitializeStructureEvent, FrameEvent, PythonEvalEvent, TclEvalEvent, UserKeyEvent, InterpEvent
- do_color_changed()
: Stage, DisplayColor, GeometryList, FPS, DrawMolItem, DrawForce, Displayable, Axes
- do_color_rgb_changed()
: DisplayColor, DrawMolItem, Displayable
- do_color_scale_changed()
: DrawMolItem, Displayable
- do_dataset_append()
: GraphicsFltkRepFieldLines, GraphicsFltkRepOrbital, GraphicsFltkRepVolumeSlice, GraphicsFltkRepIsosurface, GraphicsFltkRepVolumetric
- do_dataset_clear()
: GraphicsFltkRepFieldLines, GraphicsFltkRepOrbital, GraphicsFltkRepVolumeSlice, GraphicsFltkRepIsosurface, GraphicsFltkRepVolumetric
- do_define_adv_light()
: FileRenderer
- do_define_light()
: OpenGLRenderer, FileRenderer, DisplayDevice
- do_dialog()
: FrameSelector
- do_event()
: SpringTool, TugTool, Tool, RotateTool, PrintTool, PinchTool, JoystickTool, GrabTool
- do_feature_side_effects()
: colvardeps, atom_group, colvar
- do_off()
: VMDTkMenu, VMDTkinterMenu, VMDFltkMenu, UIObject
- do_on()
: VMDTkMenu, VMDTkinterMenu, VMDFltkMenu, UIObject
- do_reposition_window()
: OpenGLPbufferDisplayDevice, OpenGLDisplayDevice, FltkOpenGLDisplayDevice, DisplayDevice
- do_reset()
: GraphicsFltkRepFieldLines, GraphicsFltkRepOrbital, GraphicsFltkRepVolumeSlice, GraphicsFltkRepIsosurface, GraphicsFltkRepSurf, GraphicsFltkRepQuickSurf, GraphicsFltkRepHBonds, GraphicsFltkRepNanoShaper, GraphicsFltkRepMSMS, GraphicsFltkRepSolvent, GraphicsFltkRepNewCartoon, GraphicsFltkRepCartoon, GraphicsFltkRepNewRibbons, GraphicsFltkRepRibbons, GraphicsFltkRepLicorice, GraphicsFltkRepVDW, GraphicsFltkRepPoints, GraphicsFltkRepCPK, GraphicsFltkRepDynamicBonds, GraphicsFltkRepBonds, GraphicsFltkRepLines, GraphicsFltkRep
- do_resize_window()
: OpenGLPbufferDisplayDevice, OpenGLDisplayDevice, FltkOpenGLDisplayDevice, DisplayDevice
- do_save()
: SaveTrajectoryFltkMenu
- do_start()
: VRJugglerTracker, VRJugglerButtons, SpaceballTracker, SpaceballButtons, PhoneTracker, PhoneButtons, VRPNTracker, VRPNFeedback, VRPNButtons, VMDTracker, FreeVRTracker, FreeVRButtons, Feedback, CaveTracker, CaveButtons, Buttons, MobileTracker, MobileButtons
- do_update
: AtomSel, AtomColor
- do_use_colors()
: FileRenderer, DisplayDevice
- DoCell()
: IsoContour
- DoCellGeneral()
: IsoSurface
- doCent
: Displayable
- doEvent()
: TextInterp, TclTextInterp, PythonTextInterp
- dof_enabled()
: DisplayDevice
- dof_on()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- dofEnabled
: DisplayDevice
- dofFNumber
: DisplayDevice
- dofFocalDist
: DisplayDevice
- doGlob
: Displayable
- dograb()
: Tool
- DoGridPosNorms()
: IsoSurface
- doInit()
: TextInterp, TclTextInterp
- domain
: wrap_nvmlPciInfo_t
- DONE
: CoorData
- done_waiting()
: TclTextInterp
- doRot
: Displayable
- doScale
: Displayable
- doTkUpdate()
: TextInterp, TclTextInterp, PythonTextInterp
- DOTTED
: AtomRep
- double_fctn
: SymbolTableElement
- doublesided
: DispCmdTriStrips
- downsample()
: VolumetricData
- downshift
: inthash_t, hash_t
- dpl_initialized
: OpenGLRenderer
- dpy
: glxdata, spaceballhandle, xinputhandle, oglhandle, spaceballhandle
- dpyScreen
: glxdata
- dQ0_1
: colvarmodule::rotation
- dQ0_2
: colvarmodule::rotation
- draw()
: VRJugglerScene, M_VRJapp, Scene, MainFltkMenu, My_Fl_Positioner, myFl_Chart, FreeVRScene, myglwindow, Displayable, ColorscaleLumaChart, ColorscaleImage, CaveScene
- draw_background_gradient()
: OpenGLRenderer
- draw_finished()
: VRJugglerScene, Scene
- draw_prepare()
: Displayable
- drawbufs
: glwin_fbo_target
- DrawForce()
: DrawForce
- DrawMolecule()
: DrawMolecule
- DrawMoleculeMonitor()
: DrawMoleculeMonitor
- DrawMolItem()
: DrawMolItem
- drawpixels_rgba4u()
: OpenGLDisplayDevice, DisplayDevice
- DrawTool()
: DrawTool
- drv_win
: spaceballhandle
- dS_1
: colvarmodule::rotation
- dS_2
: colvarmodule::rotation
- dsdx
: ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >
- dspin_angle_dq()
: colvarmodule::rotation
- dt()
: colvarproxy_system, colvarmodule
- dtool
: Tool
- dummy_atom_pos
: atom_group
- dump_fes
: colvarbias_meta
- dump_fes_save
: colvarbias_meta
- dump_replica_fes
: colvarbias_meta
- dup()
: Stack< T >
- duplicate_frame()
: DrawMolecule
- dval
: symbol_data, atomparser_node, YYSTYPE
- dx
: Msmpot_t, GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- dxdr1
: colvar::dipole_angle, colvar::angle
- dxdr3
: colvar::dipole_angle, colvar::angle
- dy
: Msmpot_t
- DYNAMICBONDS
: AtomRep
- dz
: Msmpot_t
- dzdv1
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- dzdv2
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- dzdx
: ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >
- e -
- Eangle
: IMDEnergies
- ebmeta
: colvarbias_meta
- ebmeta_equil_steps
: colvarbias_meta
- Ebond
: IMDEnergies
- ed
: colvar::h_bond, colvar::groupcoordnum, colvar::selfcoordnum, colvar::coordnum
- Edihe
: IMDEnergies
- Eelec
: IMDEnergies
- ef_anisotropic
: colvar::coordnum
- ef_gradients
: colvar::coordnum
- ef_null
: colvar::coordnum
- ef_rebuild_pairlist
: colvar::coordnum
- ef_use_pairlist
: colvar::coordnum
- eh
: Msmpot_t
- eigenvec
: colvar::eigenvector
- eigenvec_invnorm2
: colvar::eigenvector
- eigenvector()
: colvar::eigenvector
- Eimpr
: IMDEnergies
- elem_indices
: colvarvalue
- elem_sizes
: colvarvalue
- elem_types
: colvarvalue
- ELEMENT
: AtomColor
- element_id()
: MoleculeGraphics
- en
: colvar::h_bond, colvar::groupcoordnum, colvar::selfcoordnum, colvar::coordnum
- en_prec
: colvarmodule
- en_width
: colvarmodule
- enable()
: colvardeps
- enable_stencil_stereo()
: OpenGLRenderer
- enabled
: colvardeps::feature_state
- encache()
: OpenGLCache
- end
: atom_group, wkf_shared_iterator_struct, wkf_tasktile_struct
- end_clipgroup()
: TachyonDisplayDevice, POV3DisplayDevice, LibTachyonDisplayDevice, FileRenderer
- end_match_ptr
: match_data
- end_of_step()
: colvarproxy, colvarmodule, colvarbias, colvar
- end_offset_top
: match_data
- end_ring
: LinkagePath
- end_subject
: match_data
- endFrame
: CoorPluginData, CmdAnimDelete, CmdAnimWriteFile
- endonly
: match_data
- endtime
: wkf_timer
- energy
: colvarbias_meta::hill, Timestep
- energy_difference()
: colvarmodule, colvarbias_restraint_linear, colvarbias_restraint_harmonic, colvarbias_restraint, colvarbias
- engine_ready()
: colvarproxy
- engine_ready_
: colvarproxy
- entries
: inthash_t, hash_t
- entropy()
: colvar_grid_scalar
- Epot
: IMDEnergies
- epotmap
: Msmpot_t
- eq_and_lower_d
: watershed_gpu_state_t< GROUP_T, IMAGE_T >
- err
: NanoShaperInterface, MSMSInterface
- errcode
: occthrparms_t
- error()
: colvarproxy_vmd, colvarproxy, colvarmodule
- error_key_required()
: colvarparse
- error_output
: colvarproxy
- errorcode
: match_data
- errorstack
: wkf_threadpool_struct, wkf_threadpool_workerdata_struct
- errtol
: Msmpot_t
- Etot
: IMDEnergies
- euler_phi()
: colvar::euler_phi
- euler_psi()
: colvar::euler_psi
- euler_theta()
: colvar::euler_theta
- ev_button_press
: spaceballhandle
- ev_button_release
: spaceballhandle
- ev_command
: spaceballhandle
- ev_motion
: spaceballhandle
- evalFile()
: TextInterp, TclTextInterp, PythonTextInterp
- evalString()
: TextInterp, TclTextInterp, PythonTextInterp, PlainTextInterp
- evaluate()
: ParseTree
- evaluate_grid_point()
: Orbital
- evclasses
: xidevhandle
- evdev
: oglhandle
- Evdw
: IMDEnergies
- event
: spaceballevent
- EventCodes
: DisplayDevice
- eventdata
: VSMsgHeader_t
- eventtype
: VSMsgHeader_t
- evkey
: oglhandle
- evval
: oglhandle
- exci
: wavef_signa_t
- excl_dist
: ComputeOccupancyMap_t
- excl_energy
: ComputeOccupancyMap_t
- exclude_feature_self()
: colvardeps
- exclusions
: ComputeOccupancyMap_t
- execCmd
: FileRenderer
- execute_all()
: CommandQueue
- exists
: vmdwinjoystick
- exitFlag
: VMDApp
- exp()
: colvarmodule
- expand_atompos()
: QMData
- expand_basis_array()
: QMData
- expand_boundaries
: colvar
- expand_grids
: colvarbias_meta
- expon
: prim_t
- exponent
: colvar::distance_inv
- ext
: OpenGLShader, OpenGLRenderer, oglhandle
- ext_force_k
: colvar
- ext_gamma
: colvar
- ext_mass
: colvar
- ext_sigma
: colvar
- extcmd
: CmdRender
- extcutoff
: ComputeOccupancyMap_t
- extend()
: ResizeArray< T >
- extension()
: MolFilePlugin
- extra
: ComputeOccupancyMap_t, occthrparms_t
- extra_type
: atomparser_node
- extraflg
: BaseMolecule
- extraflt
: BaseMolecule
- extraint
: BaseMolecule
- eye_dist()
: DisplayDevice
- eyeDir
: DisplayDevice
- eyeDist
: DisplayDevice
- eyePos
: DisplayDevice
- eyeSep
: DisplayDevice
- eyesep()
: DisplayDevice
- eyeSepDir
: DisplayDevice
- eyzd
: Msmpot_t
- ezd
: Msmpot_t
- f -
- f
: Surf, osp_trimesh_v3f_n3f_c3f, IsoSurface, IsoContour, flint_t, GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >, colvar, anr_trimesh_v3f_n3f_c3f
- f_ag_active
: colvardeps
- f_ag_atom_forces
: colvardeps
- f_ag_center
: colvardeps
- f_ag_center_origin
: colvardeps
- f_ag_collect_atom_ids
: colvardeps
- f_ag_explicit_gradient
: colvardeps
- f_ag_fit_gradients
: colvardeps
- f_ag_fitting_group
: colvardeps
- f_ag_ntot
: colvardeps
- f_ag_rotate
: colvardeps
- f_ag_scalable
: colvardeps
- f_ag_scalable_com
: colvardeps
- f_cv_active
: colvardeps
- f_cv_awake
: colvardeps
- f_cv_collect_atom_ids
: colvardeps
- f_cv_collect_gradient
: colvardeps
- f_cv_corrfunc
: colvardeps
- f_cv_custom_function
: colvardeps
- f_cv_extended_Lagrangian
: colvardeps
- f_cv_external
: colvardeps
- f_cv_fdiff_velocity
: colvardeps
- f_cv_gradient
: colvardeps
- f_cv_grid
: colvardeps
- f_cv_hard_lower_boundary
: colvardeps
- f_cv_hard_upper_boundary
: colvardeps
- f_cv_hide_Jacobian
: colvardeps
- f_cv_homogeneous
: colvardeps
- f_cv_Jacobian
: colvardeps
- f_cv_Langevin
: colvardeps
- f_cv_linear
: colvardeps
- f_cv_lower_boundary
: colvardeps
- f_cv_multiple_ts
: colvardeps
- f_cv_ntot
: colvardeps
- f_cv_output_applied_force
: colvardeps
- f_cv_output_energy
: colvardeps
- f_cv_output_total_force
: colvardeps
- f_cv_output_value
: colvardeps
- f_cv_output_velocity
: colvardeps
- f_cv_periodic
: colvardeps
- f_cv_reflecting_lower_boundary
: colvardeps
- f_cv_reflecting_upper_boundary
: colvardeps
- f_cv_runave
: colvardeps
- f_cv_scalar
: colvardeps
- f_cv_scripted
: colvardeps
- f_cv_single_cvc
: colvardeps
- f_cv_subtract_applied_force
: colvardeps
- f_cv_total_force
: colvardeps
- f_cv_total_force_calc
: colvardeps
- f_cv_upper_boundary
: colvardeps
- f_cvb_active
: colvardeps
- f_cvb_apply_force
: colvardeps
- f_cvb_awake
: colvardeps
- f_cvb_bypass_ext_lagrangian
: colvardeps
- f_cvb_calc_pmf
: colvardeps
- f_cvb_calc_ti_samples
: colvardeps
- f_cvb_get_total_force
: colvardeps
- f_cvb_history_dependent
: colvardeps
- f_cvb_ntot
: colvardeps
- f_cvb_output_acc_work
: colvardeps
- f_cvb_scalar_variables
: colvardeps
- f_cvb_scale_biasing_force
: colvardeps
- f_cvb_step_zero_data
: colvardeps
- f_cvb_time_dependent
: colvardeps
- f_cvb_write_ti_pmf
: colvardeps
- f_cvb_write_ti_samples
: colvardeps
- f_cvc_active
: colvardeps
- f_cvc_collect_atom_ids
: colvardeps
- f_cvc_com_based
: colvardeps
- f_cvc_debug_gradient
: colvardeps
- f_cvc_explicit_gradient
: colvardeps
- f_cvc_gradient
: colvardeps
- f_cvc_inv_gradient
: colvardeps
- f_cvc_Jacobian
: colvardeps
- f_cvc_lower_boundary
: colvardeps
- f_cvc_ntot
: colvardeps
- f_cvc_one_site_total_force
: colvardeps
- f_cvc_pbc_minimum_image
: colvardeps
- f_cvc_periodic
: colvardeps
- f_cvc_scalable
: colvardeps
- f_cvc_scalable_com
: colvardeps
- f_cvc_scalar
: colvardeps
- f_cvc_upper_boundary
: colvardeps
- f_cvc_width
: colvardeps
- f_old
: colvar
- f_type_dynamic
: colvardeps
- f_type_not_set
: colvardeps
- f_type_static
: colvardeps
- f_type_user
: colvardeps
- fabs()
: colvarmodule
- faces
: NanoShaperInterface, MSMSInterface
- fallend
: FileRenderer::AdvancedLightState
- fallstart
: FileRenderer::AdvancedLightState
- far_clip()
: DisplayDevice
- farClip
: DisplayDevice
- fatalerror
: wkf_shared_iterator_struct
- fb
: colvar
- fb_actual
: colvar
- fbo
: glwin_fbo_target
- fcc
: compile_data
- fctn
: wkf_run_barrier_struct, SymbolTableElement
- fctns
: SymbolTable
- fdiff_velocity()
: colvar
- feature()
: colvardeps::feature
- feature_count_
: usage
- feature_paper_map_
: usage
- feature_report()
: colvarmodule
- feature_state()
: colvardeps::feature_state
- feature_states
: colvardeps
- feature_type
: colvardeps
- features()
: colvardeps, colvar::cvc, colvarbias, atom_group, colvar
- features_atomgroup
: colvardeps
- features_biases
: colvardeps
- features_colvar
: colvardeps
- features_cvc
: colvardeps
- features_hash
: colvarproxy
- Feedback()
: Feedback
- FIELDLINEDELTA
: AtomRep
- FIELDLINES
: AtomRep
- FIELDLINESEEDUSEGRID
: AtomRep
- FIELDLINESTYLE
: AtomRep
- file_in_progress()
: Molecule
- filebonds
: FileSpec
- FileChooserFltkMenu()
: FileChooserFltkMenu
- filedraw()
: Scene
- filename
: CmdRender
- fileName
: CmdAnimWriteFile
- filerender_aasamples()
: VMDApp
- filerender_aosamples()
: VMDApp
- filerender_aspectratio()
: VMDApp
- filerender_cur_format()
: VMDApp
- filerender_default_filename()
: VMDApp
- filerender_default_option()
: VMDApp
- filerender_get_format()
: VMDApp
- filerender_has_antialiasing()
: VMDApp
- filerender_has_imagesize()
: VMDApp
- filerender_imagesize()
: VMDApp
- filerender_name()
: VMDApp
- filerender_num()
: VMDApp
- filerender_numformats()
: VMDApp
- filerender_option()
: VMDApp
- filerender_prettyname()
: VMDApp
- filerender_render()
: VMDApp
- filerender_set_format()
: VMDApp
- filerender_shortname_from_prettyname()
: VMDApp
- filerender_valid()
: VMDApp
- FileRenderer()
: FileRenderer
- FileRenderList()
: FileRenderList
- FileSpec()
: FileSpec
- fileType
: CmdAnimWriteFile
- find()
: ResizeArray< T >, FileRenderList, IdList, AtomColor
- find_3D_from_2D()
: OpenGLRenderer, DisplayDevice
- find_atom_in_residue()
: BaseMolecule
- find_attribute()
: SymbolTable
- find_bonds_from_timestep()
: BaseMolecule
- find_extensions()
: OpenGLExtensions
- find_instance_images()
: DisplayDevice
- find_optimal_grid()
: Orbital
- find_pbc_cells()
: DisplayDevice
- find_pbc_images()
: DisplayDevice
- find_pretty_name()
: FileRenderList
- find_recursion()
: ParseTree
- find_renderer()
: OpenGLExtensions
- find_short_name_from_pretty_name()
: FileRenderList
- find_unique_bonds_from_timestep()
: BaseMolecule
- find_wavef_id_from_gui_specs()
: QMData
- findAtomBox()
: AtomGrid
- findAtomsGrid()
: MolData
- FindWithinData()
: FindWithinData
- first
: VMDDisplayList, FileSpec, qcprmsdthreadparms, gpuqcprmsdthreadparms
- first_atom()
: SmallRing
- first_atom_index
: Msmpot_t
- first_cb()
: FrameSelector
- first_char
: real_pcre
- first_step
: colvarbias_restraint_moving
- firstindex
: DispCmdPickPointArray
- firstsel
: AtomSel
- firstvalue
: FrameSelector
- fit_gradients
: atom_group
- fitting_group
: atom_group
- fix()
: MoleculeList, Displayable
- fixed()
: MoleculeList, Displayable
- fixed_axis
: colvar::distance_z
- fj
: colvar
- flags
: BaseMolecule, wkf_cpu_caps_struct
- flgatoms
: FindWithinData
- flgs
: FindWithinData
- floor()
: colvarmodule
- flops_per_gridpoint()
: Orbital
- FltkOpenGLDisplayDevice()
: FltkOpenGLDisplayDevice
- flush_output_stream()
: colvarproxy_io
- flush_output_streams()
: colvarproxy_io
- FogMode
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- font1pxListBase
: OpenGLRenderer
- fontNpxListBase
: OpenGLRenderer
- force
: Timestep
- force_constant()
: colvar
- force_k
: colvarbias_restraint_histogram, colvarbias_restraint_k
- force_k_incr
: colvarbias_restraint_k_moving
- force_recalc()
: DrawMolItem, DrawMolecule
- FORCEATOM
: PickModeList, Mouse
- forced_stereo_draws()
: OpenGLRenderer, DisplayDevice
- FORCEFRAG
: PickModeList, Mouse
- forceoff()
: VRPNFeedback, Tool, Feedback
- FORCERES
: PickModeList, Mouse
- forcescale
: Tool
- format
: FileRenderList, FileRenderer, CmdLabelTextFormat
- formats
: FileRenderer
- forward
: RibbonFrame
- FPS()
: FPS
- fps
: VMDApp
- fr
: colvar
- fragList
: BaseMolecule
- Fragment()
: Fragment
- fragment
: BaseMolecule, Residue
- FRAGMENT
: AtomColor
- FragmentShaderObject
: OpenGLShader, glsl_shader
- frame()
: DrawMolecule, Animation
- frame_cb()
: TextInterp, TclTextInterp, PythonTextInterp
- frame_distances
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- frame_element_distances
: ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >
- frame_index
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- framebuffer_config()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- framebuffer_destroy()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- framebuffer_map_rgb4u()
: OptiXRenderer
- framebuffer_resize()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- framebuffer_unmap()
: OptiXRenderer
- framecount
: VSMsgHeader_t
- framecrdsz
: qcprmsdthreadparms, gpuqcprmsdthreadparms
- FrameEvent()
: FrameEvent
- frames_list
: clusterparms_t
- FrameSelector()
: FrameSelector
- frameSkip
: CoorPluginData, CmdAnimDelete, CmdAnimWriteFile
- framespec
: CmdMolDrawFrames
- free_children_deps()
: colvardeps
- free_gpu_memory()
: QuickSurf
- free_opengl_ctx()
: OpenGLRenderer
- FreeVRButtons()
: FreeVRButtons
- FreeVRDisplayDevice()
: FreeVRDisplayDevice
- FreeVRScene()
: FreeVRScene
- FreeVRTracker()
: FreeVRTracker
- freeze()
: VMDMenu
- from_simple_string()
: colvarvalue, colvarmodule::quaternion, colvarmodule::rvector, colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >
- fromlen
: mobilehandle
- fromMatrix()
: Quat
- ft
: colvar::cvc, colvar
- ft_reported
: colvar
- FUNCTION
: SymbolTableElement
- function_type
: colvar::cvc
- function_types
: colvar::cvc
- fval
: eventdataunion
- g -
- g
: GRIDCELL
- gamma
: Timestep
- gaussian_blur()
: VolumetricData
- gaussian_width
: colvarbias_restraint_histogram
- GaussianBlur()
: GaussianBlur< IMAGE_T >
- gausslim
: densitythrparms
- gc
: Msmpot_t
- GelatoDisplayDevice()
: GelatoDisplayDevice
- generateChargeTexture()
: VolumeTexture
- generateColorScaleTexture()
: VolumeTexture
- generateContourLineTexture()
: VolumeTexture
- generateHSVTexture()
: VolumeTexture
- generateIndexTexture()
: VolumeTexture
- generatePosTexture()
: VolumeTexture
- GENERIC
: OpenGLExtensions
- geom
: osp_cylinder_array_color, osp_sphere_array_color, osp_trimesh_v3f_n3f_c3f, anr_cylinder_array_color, anr_sphere_array_color, anr_trimesh_v3f_n3f_c3f
- geom_list()
: GeometryList
- geom_list_index()
: GeometryList
- geom_list_name()
: GeometryList
- geom_set_name()
: GeometryMol
- GeometricPathBase()
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- geometry
: QMData
- GeometryAngle()
: GeometryAngle
- GeometryAtom()
: GeometryAtom
- GeometryBond()
: GeometryBond
- GeometryDihedral()
: GeometryDihedral
- GeometryFltkMenu()
: GeometryFltkMenu
- GeometryList()
: GeometryList
- geometryList
: VMDApp
- GeometryMol()
: GeometryMol
- GeometryMonitor()
: GeometryMonitor
- GeometrySpring()
: GeometrySpring
- geomList
: GeomListStruct
- geomValue
: GeometryMol
- get()
: Combinations, AtomGrid, AtomGridCell, GridList, IndexList
- get_accelMD_factor()
: colvarproxy_system
- get_accession()
: Molecule
- get_additional_elements()
: Symmetry
- get_alch_lambda()
: colvarproxy_vmd, colvarproxy_system
- get_ambient()
: MaterialList
- get_angletype()
: BaseMolecule
- get_angular_momentum()
: QMData
- get_angular_momentum_str()
: QMData
- get_ao_ambient()
: DisplayDevice
- get_ao_direct()
: DisplayDevice
- get_APIsupported()
: Mobile
- get_atom_applied_forces()
: colvarproxy_atoms
- get_atom_charge()
: colvarproxy_atoms
- get_atom_charges()
: colvarproxy_atoms
- get_atom_group_charge()
: colvarproxy_atom_groups
- get_atom_group_com()
: colvarproxy_atom_groups
- get_atom_group_id()
: colvarproxy_atom_groups
- get_atom_group_ids()
: colvarproxy_atom_groups
- get_atom_group_mass()
: colvarproxy_atom_groups
- get_atom_group_total_force()
: colvarproxy_atom_groups
- get_atom_group_velocity()
: colvarproxy_atom_groups
- get_atom_id()
: colvarproxy_atoms
- get_atom_ids()
: colvarproxy_atoms
- get_atom_lists()
: colvar::cvc, colvar
- get_atom_mass()
: colvarproxy_atoms
- get_atom_masses()
: colvarproxy_atoms
- get_atom_position()
: colvarproxy_atoms
- get_atom_positions()
: colvarproxy_atoms
- get_atom_total_force()
: colvarproxy_atoms
- get_atom_total_forces()
: colvarproxy_atoms
- get_atom_types()
: QMData
- get_atom_velocity()
: colvarproxy_atoms
- get_avail_occupancies()
: QMData
- get_avail_orbitals()
: QMData
- get_axisorder()
: Symmetry
- get_axistype()
: Symmetry
- get_basis()
: QMData
- get_bias_cmd_arg()
: colvarscript
- get_button_names()
: UIVR
- get_buttons()
: Tool
- get_carthessian()
: QMData
- get_category_item()
: Scene
- get_cell()
: AtomGrid
- get_charge_set()
: QMTimestep
- get_charge_type()
: QMTimestep
- get_charge_type_str()
: QMTimestep
- get_cijk()
: AtomGrid
- get_client_list()
: Mobile
- get_clip_status()
: VMDDisplayList
- get_cmd_arg()
: colvarscript
- get_cmd_prefix()
: colvarscript
- get_cmdline_help_summary()
: colvarscript
- get_cna()
: AtomGrid
- get_cnb()
: AtomGrid
- get_cnc()
: AtomGrid
- get_coeffs()
: Wavefunction
- get_colorscale_colors()
: VMDApp, Scene
- get_colorscale_minmax()
: AtomColor
- get_colvar_cmd_arg()
: colvarscript
- get_colvars_index()
: colvar_grid< T >
- get_colvars_index_bound()
: colvar_grid< T >
- get_command_arghelp()
: colvarscript
- get_command_cmdline_help()
: colvarscript
- get_command_cmdline_syntax()
: colvarscript
- get_command_full_help()
: colvarscript
- get_command_help()
: colvarscript
- get_command_n_args_max()
: colvarscript
- get_command_n_args_min()
: colvarscript
- get_command_names()
: colvarscript
- get_command_rethelp()
: colvarscript
- get_component_by_name()
: DrawMolecule
- get_component_name()
: DrawMolecule
- get_config()
: colvarparse, colvarmodule
- get_conformers()
: VolMapCreateILS
- get_copyunitcell()
: IMDMgr
- get_cuda_devpool()
: CUDAAccel
- get_cue_density()
: DisplayDevice
- get_cue_end()
: DisplayDevice
- get_cue_mode()
: DisplayDevice
- get_cue_start()
: DisplayDevice
- get_custom_singleword()
: SymbolTable
- get_cvc_param()
: colvar
- get_cvc_param_grad()
: colvar
- get_cvc_param_ptr()
: colvar
- get_d2E_dlambda2()
: colvarproxy_system
- get_data()
: AtomRep
- get_database()
: Molecule
- get_dE_dlambda()
: colvarproxy_vmd, colvarproxy_system
- get_device_names()
: UIVR
- get_diffuse()
: MaterialList
- get_dihedraltype()
: BaseMolecule
- get_dof_fnumber()
: DisplayDevice
- get_dof_focal_dist()
: DisplayDevice
- get_drawframes()
: DrawMolItem
- get_elem()
: colvarvalue
- get_element_summary()
: Symmetry
- get_energy()
: Wavefunction, colvarbias
- get_eofexit()
: VMDApp
- get_error()
: colvarmodule
- get_error_bit()
: colvarmodule
- get_error_msgs()
: colvarproxy
- get_excitation()
: QMTimestep, Wavefunction
- get_eye_dir()
: DisplayDevice
- get_eye_pos()
: DisplayDevice
- get_eye_up()
: DisplayDevice
- get_feedback()
: Tool
- get_feedback_names()
: UIVR
- get_file()
: Molecule
- get_file_specs()
: Molecule
- get_force()
: PickModeForce
- get_frame()
: DrawMolecule, colvarproxy_vmd, colvarproxy_io
- get_frame_value()
: AtomSel
- get_grad()
: integrate_potential
- get_gradients()
: QMTimestep
- get_grid_axes()
: Orbital
- get_grid_data()
: Orbital
- get_gridsize()
: Orbital
- get_highest_excitation()
: QMData
- get_homo()
: QMTimestep, Wavefunction
- get_ijk()
: AtomGrid
- get_image()
: GaussianBlur< IMAGE_T >
- get_image_d()
: GaussianBlur< IMAGE_T >
- get_imagmodes()
: QMData
- get_imdmol()
: IMDMgr
- get_impropertype()
: BaseMolecule
- get_inertia_axes()
: Symmetry
- get_inertia_eigenvals()
: Symmetry
- get_inertia_unique()
: Symmetry
- get_info()
: Wavefunction
- get_instances()
: DrawMolItem
- get_intensities()
: QMData
- get_interp()
: TclTextInterp
- get_inthessian()
: QMData
- get_keep_rate()
: IMDMgr
- get_key_string_multi_value()
: colvarparse
- get_key_string_value()
: colvarparse
- get_keyval()
: colvarparse
- get_keyval_feature()
: colvardeps
- get_last_frame()
: DrawMolecule
- get_link_key()
: SmallRingLinkages
- get_list()
: AtomGridCell
- get_lumo()
: QMTimestep
- get_max_avail_orbitals()
: QMData
- get_maxforce()
: Feedback
- get_mirror()
: MaterialList
- get_missing_elements()
: Symmetry
- get_mode_str()
: Spaceball, Mouse, Mobile
- get_module_cmd_arg()
: colvarscript
- get_molid()
: colvarproxy_vmd, colvarproxy_system
- get_move_mode()
: Mobile
- get_multiplicity()
: QMTimestep, Wavefunction
- get_na()
: AtomGrid
- get_name()
: VMDMenu
- get_nb()
: AtomGrid
- get_nc()
: AtomGrid
- get_new_frames()
: Molecule
- get_next_ts()
: IMDSimThread, IMDSimBlocking, IMDSim
- get_normalmodes()
: QMData
- get_num_active_atom_groups()
: colvarproxy_atom_groups
- get_num_active_atoms()
: colvarproxy_atoms
- get_num_atoms()
: QMData
- get_num_charge_sets()
: QMTimestep
- get_num_coeffs()
: QMTimestep, Wavefunction
- get_num_groups()
: Segmentation
- get_num_imag()
: QMData
- get_num_intcoords()
: QMData
- get_num_occupied_double()
: Wavefunction
- get_num_occupied_single()
: Wavefunction
- get_num_orbitals()
: QMTimestep, Wavefunction
- get_num_prim_per_shell()
: QMData
- get_num_processes()
: DisplayDevice
- get_num_scfiter()
: QMTimestep
- get_num_shells()
: QMData
- get_num_shells_per_atom()
: QMData
- get_num_types()
: QMData
- get_num_wavecoeff_per_atom()
: QMData
- get_num_wavef()
: QMTimestep
- get_numvoxels()
: Orbital
- get_occupancies()
: QMTimestep, Wavefunction
- get_offset()
: VMDTracker
- get_opacity()
: MaterialList
- get_orbenergies()
: Wavefunction
- get_orbids()
: Wavefunction
- get_orbital_id_from_index()
: QMTimestep
- get_orbital_index_from_id()
: QMTimestep
- get_orbital_label_from_gui_index()
: QMData
- get_orbital_occ_energy()
: QMTimestep
- get_orbitalenergy()
: QMTimestep, Wavefunction
- get_orbitalids()
: QMTimestep
- get_orientation()
: Symmetry
- get_origin()
: Orbital
- get_outline()
: MaterialList
- get_outlinewidth()
: MaterialList
- get_param()
: colvarparams
- get_param_grad()
: colvar::cvc
- get_param_grad_names()
: colvarparams
- get_param_grad_ptr()
: colvarparams
- get_param_names()
: colvarparams
- get_param_ptr()
: colvarparams
- get_pbc()
: DrawMolItem
- get_pbc_images()
: DrawMolItem
- get_planetype()
: Symmetry
- get_plugin()
: VMDApp
- get_pointgroup()
: Symmetry
- get_port()
: Mobile
- get_projection()
: DisplayDevice
- get_radii_minmax()
: BaseMolecule
- get_remarks()
: Molecule
- get_rep_molid()
: Tool
- get_rep_name()
: Tool
- get_repserialnum()
: VMDApp
- get_resolution()
: Orbital
- get_results()
: Segmentation
- get_rmsd()
: Symmetry
- get_rot_quat()
: HMDMgr
- get_rotreflectorder()
: Symmetry
- get_rotrefltype()
: Symmetry
- get_runtype_string()
: QMData
- get_scale()
: VMDTracker
- get_scfenergies()
: QMTimestep
- get_scftype_string()
: QMData
- get_shell_type_str()
: QMData
- get_shininess()
: MaterialList
- get_smoothing()
: DrawMolItem
- get_specular()
: MaterialList
- get_spin()
: QMTimestep, Wavefunction
- get_state_params()
: colvarbias_restraint_linear, colvarbias_restraint_harmonic_walls, colvarbias_restraint_harmonic, colvarbias_restraint_k_moving, colvarbias_restraint_centers_moving, colvarbias_restraint_moving, colvarbias_restraint, colvarbias_meta, colvarbias_alb, colvarbias_ti, colvarbias
- get_statistics()
: VolMapCreateILS
- get_status_string()
: QMData
- get_targeted_atom()
: Tool
- get_tcl_interp()
: UIText, colvarproxy_tcl
- get_texserialnum()
: VMDApp
- get_text()
: VMDApp
- get_time_step_factor()
: colvardeps
- get_tracker()
: Tool
- get_tracker_names()
: UIVR
- get_tracker_status()
: Spaceball, Mobile
- get_trans_rate()
: IMDMgr
- get_transform_from_cell()
: Timestep
- get_transform_vectors()
: Timestep
- get_transforms()
: Timestep
- get_transmode()
: MaterialList
- get_type()
: Wavefunction, Molecule
- get_typestr()
: Wavefunction
- get_unique_atom()
: Symmetry
- get_value()
: UIestimator::n_vector< T >, UIestimator::n_matrix
- get_vector()
: colvarmodule::quaternion
- get_version_from_string()
: colvarproxy
- get_vertex_ptrs()
: GraphLayout
- get_volmap()
: VolMapCreateILS
- get_volmap_id()
: colvarproxy_volmaps
- get_volmap_id_from_name()
: colvarproxy_volmaps
- get_volmap_ids()
: colvar
- get_volmap_value()
: colvarproxy_volmaps
- get_volume_data()
: BaseMolecule
- get_wave_energy()
: QMTimestep
- get_wave_offset()
: QMData
- get_wavecoeffs()
: QMTimestep
- get_wavef_index()
: QMTimestep
- get_wavef_typestr()
: QMTimestep
- get_wavefunction()
: QMTimestep
- get_waveid()
: QMTimestep
- get_wavenumbers()
: QMData
- get_xyz()
: AtomGrid
- GetActiveVoxelCount()
: CUDAMarchingCubes
- getActualRadius()
: MolData
- getbondorder()
: BaseMolecule
- getbondtype()
: BaseMolecule
- getdevice()
: SensorConfig
- getdevices()
: Tool
- getforcescale()
: Tool
- gethost()
: IMDMgr
- GetIsovalue()
: CUDAMarchingCubes
- getleft_rot()
: SensorConfig
- getline()
: colvarmodule
- getline_nocomments()
: colvarparse
- getLinkageEdge()
: SmallRingLinkages
- getmaxforce()
: SensorConfig
- GetMaxGridSize()
: CUDAMarchingCubes
- getname()
: SensorConfig
- getnames()
: SensorConfig
- getNum()
: GridList
- getnums()
: SensorConfig
- getoffset()
: Tool, SensorConfig
- getplace()
: SensorConfig
- getpointers()
: DispCmdPickPointArray, DispCmdWireMesh, DispCmdTriStrips, DispCmdTriMesh, DispCmdLitPointArray, DispCmdPointArray, DispCmdLatticeCubeArray, DispCmdSphereArray
- getport()
: IMDMgr
- getRadius()
: MolData
- getRawVoxels()
: Watershed< GROUP_T, IMAGE_T >
- getright_rot()
: SensorConfig
- getscale()
: Tool, SensorConfig
- getSegmentedVoxels()
: Watershed< GROUP_T, IMAGE_T >
- getsensors()
: SensorConfig
- getSimState()
: IMDSim
- getspringscale()
: Tool
- getTargetScale()
: Tool
- getTextFormat()
: GeometryList
- getTextOffset()
: GeometryList
- getTextSize()
: GeometryList
- getTextThickness()
: GeometryList
- getTextureID()
: VolumeTexture
- getTextureMap()
: VolumeTexture
- getTextureSize()
: VolumeTexture
- gettool()
: UIVR
- gettype()
: SensorConfig, Command
- getUSL()
: SensorConfig
- GetVertexCount()
: CUDAMarchingCubes
- GetVoxelCount()
: CUDAMarchingCubes
- getWandButton()
: VRJugglerScene, M_VRJapp
- getWandRotMat()
: VRJugglerScene, M_VRJapp
- getWandXYZ()
: VRJugglerScene, M_VRJapp
- gflops
: maddthrparms
- GLenum
: OpenGLExtensions
- GLfloat
: OpenGLExtensions
- GLint
: OpenGLExtensions
- glob_trans_off()
: Displayable
- glob_trans_on()
: Displayable
- glob_translating()
: Displayable
- globt
: Displayable
- GLsizei
: OpenGLExtensions
- glxsrv
: OpenGLDisplayDevice
- gmName
: GeometryMol
- goto_frame()
: Animation
- grabs
: Tool
- GrabTool()
: GrabTool
- grad
: atom
- gradient_finite_diff()
: colvar_grid_scalar, colvar_grid_count
- gradients
: integrate_potential
- graph_label_cb()
: TextInterp, TclTextInterp
- GraphicsFltkMenu()
: GraphicsFltkMenu
- GraphicsFltkRep()
: GraphicsFltkRep
- GraphicsFltkRepBeads()
: GraphicsFltkRepBeads
- GraphicsFltkRepBonds()
: GraphicsFltkRepBonds
- GraphicsFltkRepCartoon()
: GraphicsFltkRepCartoon
- GraphicsFltkRepCPK()
: GraphicsFltkRepCPK
- GraphicsFltkRepDotted()
: GraphicsFltkRepDotted
- GraphicsFltkRepDynamicBonds()
: GraphicsFltkRepDynamicBonds
- GraphicsFltkRepFieldLines()
: GraphicsFltkRepFieldLines
- GraphicsFltkRepHBonds()
: GraphicsFltkRepHBonds
- GraphicsFltkRepIsosurface()
: GraphicsFltkRepIsosurface
- GraphicsFltkRepLicorice()
: GraphicsFltkRepLicorice
- GraphicsFltkRepLines()
: GraphicsFltkRepLines
- GraphicsFltkRepMSMS()
: GraphicsFltkRepMSMS
- GraphicsFltkRepNanoShaper()
: GraphicsFltkRepNanoShaper
- GraphicsFltkRepNewCartoon()
: GraphicsFltkRepNewCartoon
- GraphicsFltkRepNewRibbons()
: GraphicsFltkRepNewRibbons
- GraphicsFltkRepOrbital()
: GraphicsFltkRepOrbital
- GraphicsFltkRepPoints()
: GraphicsFltkRepPoints
- GraphicsFltkRepQuickSurf()
: GraphicsFltkRepQuickSurf
- GraphicsFltkRepRibbons()
: GraphicsFltkRepRibbons
- GraphicsFltkRepSolvent()
: GraphicsFltkRepSolvent
- GraphicsFltkRepSurf()
: GraphicsFltkRepSurf
- GraphicsFltkRepTrace()
: GraphicsFltkRepTrace
- GraphicsFltkRepTube()
: GraphicsFltkRepTube
- GraphicsFltkRepVDW()
: GraphicsFltkRepVDW
- GraphicsFltkRepVolumeSlice()
: GraphicsFltkRepVolumeSlice
- GraphicsFltkRepVolumetric()
: GraphicsFltkRepVolumetric
- GraphLabelEvent()
: GraphLabelEvent
- GraphLayout()
: GraphLayout
- grid
: colvarbias_histogram
- grid_count
: colvarbias_reweightaMD
- grid_dV
: colvarbias_reweightaMD
- grid_dV_square
: colvarbias_reweightaMD
- grideners
: enthrparms
- GridList()
: GridList
- GridResCounter()
: GridResCounter
- grids_freq
: colvarbias_meta
- gridsize()
: VolumetricData
- GRIDSPACING
: AtomRep
- gridspacing
: densitythrparms, MolData, enthrparms
- gross_atom_mulliken_pop()
: QMData
- group
: state_t< GROUP_T, IMAGE_T >
- group1
: colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::dipole_angle, colvar::angle, colvar::distance_pairs, colvar::distance_inv, colvar::distance
- group2
: colvar::coordnum, colvar::dihedral, colvar::dipole_angle, colvar::angle, colvar::distance_pairs, colvar::distance_inv, colvar::distance
- group3
: colvar::dihedral, colvar::dipole_angle, colvar::angle
- group4
: colvar::dihedral
- groupcoordnum()
: colvar::groupcoordnum
- growthrate
: wkf_tilestack_t, ptrstack, intstack
- gspath()
: colvar::gspath
- gspathCV()
: colvar::gspathCV
- gsub()
: JString
- guess()
: Symmetry
- guess_filetype()
: VMDApp
- Gxcrds
: glwin_warp_hmd
- Gycrds
: glwin_warp_hmd
- gyration()
: colvar::gyration
- gzpath()
: colvar::gzpath
- gzpathCV()
: colvar::gzpathCV
- h -
- h_bond()
: colvar::h_bond
- handle()
: MolBrowser, myBrowser, myglwindow
- handlelist
: PluginMgr
- hard_lower_boundaries
: colvar_grid< T >
- hard_upper_boundaries
: colvar_grid< T >
- has_aa
: FileRenderer
- has_antialiasing()
: FileRenderList, FileRenderer
- has_data
: colvar_grid< T >, colvarbias
- has_imagesize()
: FileRenderList, FileRenderer
- has_imgsize
: FileRenderer
- has_inversion()
: Symmetry
- has_orbital()
: QMData
- has_parent_data
: colvar_grid< T >
- has_structure()
: BaseMolecule
- has_text()
: Command
- has_value()
: GeometryMol
- has_wavef_exci()
: QMData
- has_wavef_guitype()
: QMData
- has_wavef_signa()
: QMData
- has_wavef_spin()
: QMData
- hascompiledvertexarrayext
: OpenGLExtensions
- hasgetvideosyncsgi
: glwin_ext_fctns
- hasglarbtexnonpoweroftwo
: OpenGLExtensions
- hasglfborendertarget
: glwin_ext_fctns
- hasglfragmentshaderarb
: OpenGLExtensions, glwin_ext_fctns
- hasglgeometryshader4arb
: OpenGLExtensions, glwin_ext_fctns
- hasglpointparametersext
: OpenGLExtensions
- hasglpointspritearb
: OpenGLExtensions
- hasglsampleshadingarb
: OpenGLExtensions, glwin_ext_fctns
- hasglshaderobjectsarb
: OpenGLExtensions, glwin_ext_fctns
- hasglshadinglangarb
: OpenGLExtensions, glwin_ext_fctns
- hasglvertexshaderarb
: OpenGLExtensions, glwin_ext_fctns
- hash
: NameList< T >
- hasmultidrawext
: OpenGLExtensions
- hasmultisample
: OpenGLExtensions
- hasrescalenormalext
: OpenGLExtensions
- hasstencilbuffer
: OpenGLExtensions
- hasstereo
: OpenGLExtensions
- hastex2d
: OpenGLRenderer, OpenGLExtensions
- hastex3d
: OpenGLRenderer, OpenGLExtensions
- hasValue
: GeometryMol
- have_one_sensor()
: SensorConfig
- have_scripts
: colvarproxy_script
- have_window
: OpenGLPbufferDisplayDevice, OpenGLDisplayDevice
- havefocus
: glxdata, oglhandle
- havestencil
: oglhandle
- hb
: colvar::alpha_angles
- hb_coeff
: colvar::alpha_angles
- HBONDS
: AtomRep
- hdlatusec
: busbwthrparms
- hdmbsec
: busbwthrparms
- head
: bondsearchthrparms
- headlight_onoff()
: OSPRayRenderer, OSPRay2Renderer, ANARIRender
- HeadlightMode
: OptiXRenderer
- height
: watershed_gpu_state_t< GROUP_T, IMAGE_T >, VSMsgHeader_t, simenc_handle, oglhandle
- HELP
: colvarscript
- help_cb()
: TextInterp, TclTextInterp
- HelpEvent()
: HelpEvent
- hide()
: MoleculeList, myglwindow
- high
: netint
- highest
: netint
- highlight_adv_light()
: Scene
- highlight_light()
: Scene
- highlighted_molid
: VMDApp
- highlighted_rep
: DrawMolecule, VMDApp
- hill()
: colvarbias_meta::hill
- hill_iter
: colvarbias_meta
- hill_value
: colvarbias_meta::hill
- hill_weight
: colvarbias_meta
- hill_width
: colvarbias_meta
- hills
: colvarbias_meta
- hills_energy
: colvarbias_meta
- hills_energy_gradients
: colvarbias_meta
- hills_off_grid
: colvarbias_meta
- hills_traj_file_name()
: colvarbias_meta
- hist_to_pmf()
: colvarbias_reweightaMD
- histarray
: rdfthrparms
- history_freq
: colvarbias_reweightaMD
- history_index
: linenoiseState
- hlist
: gofrparms_t
- hmd_fbo
: glwin_warp_hmd
- HMDMgr()
: HMDMgr
- hmin
: Msmpot_t
- host
: CmdIMDConnect
- host_egrids
: MsmpotCuda_t
- host_lfac
: MsmpotCuda_t
- host_qgrids
: MsmpotCuda_t
- host_sinfo
: MsmpotCuda_t
- host_wt
: MsmpotCuda_t
- hx
: ComputeOccupancyMap_t, Msmpot_t, occthrparms_t
- hx_dx
: Msmpot_t
- hy
: ComputeOccupancyMap_t, Msmpot_t, occthrparms_t
- hy_dy
: Msmpot_t
- hz
: ComputeOccupancyMap_t, Msmpot_t, occthrparms_t
- hz_dz
: Msmpot_t
- i -
- i
: PointDistance, flint_t
- ID
: DispCmdVolumeTexture
- id
: Tool, BaseMolecule, atom
- idealcoor
: Best
- idealpos()
: Symmetry
- identity()
: Quat, Matrix4
- IdList()
: IdList
- ids()
: atom_group
- iend
: clusterparms_t
- ifd
: linenoiseState
- ilist
: gofrparms_t
- imagesize()
: FileRenderList
- IMD_ATTACH
: Command
- imd_connect()
: VMDApp
- imd_connected()
: VMDApp
- IMD_COPYUNITCELL
: Command
- imd_disconnect()
: VMDApp
- IMD_RATE
: Command
- imd_sendforces()
: VMDApp
- IMD_SIM
: Command
- IMDMgr()
: IMDMgr
- imdMgr
: VMDApp
- IMDOFFLINE
: IMDSim
- IMDPAUSED
: IMDSim
- IMDRUNNING
: IMDSim
- IMDSim()
: IMDSim
- IMDSimBlocking()
: IMDSimBlocking
- IMDSimThread()
: IMDSimThread
- IMDSTARTING
: IMDSim
- IMDStates
: IMDSim
- imgheight
: FileRenderer
- imgwidth
: FileRenderer
- immersadeskflip
: OpenGLRenderer
- importance
: PerRayData_radiance
- impose()
: Symmetry
- impropers
: BaseMolecule
- improperTypeNames
: BaseMolecule
- improperTypes
: BaseMolecule
- inactivate()
: MoleculeList
- incr()
: colvar_grid< T >
- incr_count()
: colvar_grid_count
- increase_depth()
: colvarmodule
- increase_refcount()
: colvarproxy_atoms
- increase_value()
: UIestimator::n_vector< T >, UIestimator::n_matrix
- ind
: Surf, osp_cylinder_array_color, osp_trimesh_v3f_n3f_c3f, osp_material, ort_material, Material, CmdMaterialDefault, anr_cylinder_array_color, anr_trimesh_v3f_n3f_c3f, anr_material
- ind1
: GridSearchPair
- ind2
: GridSearchPair
- index
: AtomEntry, atomsel_iterobject, AtomData, atom_group, atom, AtomRepDataInfo
- INDEX
: AtomColor
- index_file_names
: colvarmodule
- index_group_names
: colvarmodule
- index_groups
: colvarmodule
- index_id()
: MoleculeGraphics
- index_ok()
: colvar_grid< T >
- IndexList()
: IndexList
- indices
: osp_sphere_array_color, osp_cylinder_array_color, anr_cylinder_array_color
- indirect_lambda_biasing_force
: colvarproxy_system
- inertia()
: colvar::inertia
- inertia_z()
: colvar::inertia_z
- info
: vmdwinjoystick, wavef_signa_t
- info_id()
: MoleculeGraphics
- Inform()
: Inform
- init
: OsgNavigator, VRJugglerScene, M_VRJapp, OpenGLPbufferDisplayDevice, OpenGLDisplayDevice, NVENCMgr, DisplayDevice, colvarmodule::rotation, colvar::map_total, colvar::euler_theta, colvar::euler_psi, colvar::euler_phi, colvar::spin_angle, colvar::tilt, colvar::orientation_proj, colvar::orientation_angle, colvar::orientation, colvar::cvc, colvarbias_restraint_histogram, colvarbias_restraint_linear, colvarbias_restraint_harmonic_walls, colvarbias_restraint_harmonic, colvarbias_restraint_k_moving, colvarbias_restraint_centers_moving, colvarbias_restraint_moving, colvarbias_restraint_k, colvarbias_restraint_centers, colvarbias_restraint, colvarbias_meta, colvarbias_reweightaMD, colvarbias_histogram, colvarbias_alb, colvarbias_abf, colvarbias_ti, colvarbias, atom_group, colvar, MolAtom, watershed_gpu_state_t< GROUP_T, IMAGE_T >, group_t< IMAGE_T >
- init_angular_norm_factors()
: QMData
- init_as_angle()
: colvar::cvc
- init_as_distance()
: colvar::cvc
- init_as_periodic_angle()
: colvar::cvc
- init_atom()
: colvarproxy_vmd, colvarproxy_atoms
- init_atom_group()
: colvarproxy_atom_groups
- init_atoms()
: BaseMolecule
- init_basis()
: QMData
- init_colorchooser()
: GraphicsFltkMenu
- init_colors()
: MoleculeList
- init_components()
: colvar
- init_custom_function()
: colvar
- init_dependencies()
: colvardeps, colvar::cvc, colvarbias, atom_group, colvar
- init_ebmeta_params()
: colvarbias_meta
- init_electrons()
: QMData
- init_extended_Lagrangian()
: colvar
- init_feature()
: colvardeps
- init_from_boundaries()
: colvar_grid< T >
- init_from_colvars()
: colvar_grid< T >
- init_grid_parameters()
: colvar
- init_grids()
: colvarbias_ti
- init_materialchooser()
: GraphicsFltkMenu
- init_materials()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- init_output_flags()
: colvar
- init_positions_box()
: GraphLayout
- init_positions_circle()
: GraphLayout
- init_read()
: MolFilePlugin
- init_replicas_params()
: colvarbias_meta
- init_scalar_boundaries()
: colvar::cvc
- init_stylechooser()
: GraphicsFltkMenu
- init_tcl_pointers()
: colvarproxy_vmd, colvarproxy_tcl
- init_total_force_params()
: colvar::cvc
- init_volmap_by_id()
: colvarproxy_volmaps, colvarproxy_vmd
- init_volmap_by_name()
: colvarproxy_volmaps
- init_well_tempered_params()
: colvarbias_meta
- init_write()
: MolFilePlugin
- initfunc
: _py3_inittab
- initial_centers
: colvarbias_restraint_centers_moving
- initialize()
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >, ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >
- Initialize()
: CUDAMarchingCubes
- initialize_structure_cb()
: TextInterp, TclTextInterp, PythonTextInterp
- InitializeStructureEvent()
: InitializeStructureEvent
- inner()
: colvarmodule::quaternion
- inner_length
: colvarmodule::matrix2d< T >
- inner_opt()
: colvarvalue
- input_buffer()
: colvarproxy_io
- input_buffer_
: colvarproxy_io
- input_prefix()
: colvarproxy_io
- input_prefix_str
: colvarproxy_io
- input_stream()
: colvarproxy_io
- input_stream_error_
: colvarproxy_io
- input_stream_exists()
: colvarproxy_io
- input_streams_
: colvarproxy_io
- inrad
: vmd_ring_color
- INSERTION
: BaseMolecule
- insertionstr
: MolAtom
- instances
: VMDDisplayList, CmdMolShowInstances, BaseMolecule
- instanceset
: VMDDisplayList
- instereo
: oglhandle
- inStereo
: DisplayDevice
- int()
: glwin_ext_fctns
- int_fctn
: SymbolTableElement
- integer_power()
: colvarmodule
- integral()
: VolumetricData, colvar_grid_scalar
- integrate()
: integrate_potential
- integrate_potential()
: integrate_potential
- integratedgpu
: cudadevprops
- INTELSWR
: OpenGLExtensions
- intelswr
: OpenGLRenderer
- internal_to_angstrom()
: colvarproxy_system
- interp
: VMDTkMenu, Msmpot_t
- INTERP_EVENT
: Command
- InterpEvent()
: InterpEvent
- interpolate()
: colvarvalue
- intraFrame()
: M_VRJapp
- inv
: elementsummary
- invalidate_ss()
: DrawMolecule
- invbx
: Msmpot_t
- invby
: Msmpot_t
- invbz
: Msmpot_t
- inverse()
: Matrix4, colvarmodule::rotation
- inversion
: Best
- invert()
: Quat
- io_available()
: colvarproxy_io, colvarproxy
- is_a
: SymbolTableElement
- is_available()
: colvardeps
- is_changeable()
: SymbolTable
- is_derivative()
: colvarvalue
- is_dynamic()
: colvardeps, colvardeps::feature
- is_enabled()
: colvardeps
- IS_FLOAT
: SymbolTableElement
- is_input
: CoorPluginData
- IS_INT
: SymbolTableElement
- is_not_set()
: colvardeps
- is_orbital()
: GraphicsFltkRepOrbital, GraphicsFltkRep, AtomRep
- is_renderer_process()
: DisplayDevice
- is_scalar()
: colvarvalue
- is_spherical_top()
: Symmetry
- is_static()
: colvardeps, colvardeps::feature
- IS_STRING
: SymbolTableElement
- is_symmetric_top()
: Symmetry
- is_targeted()
: Tool
- is_top()
: MoleculeList
- is_user()
: colvardeps, colvardeps::feature
- is_volumetric()
: GraphicsFltkRepVolumetric, GraphicsFltkRep, AtomRep
- isbinwrap
: Msmpot_t
- isConnected()
: IMDSim
- isFixed
: Displayable
- isgrabbing()
: SpringTool, TugTool, Tool, RotateTool, PinchTool
- islongcutoff
: Msmpot_t
- IsoContour()
: IsoContour
- ISOLINETHICKNESS
: AtomRep
- isOn
: Displayable
- isOpened
: FileRenderer
- isorep
: isosurface_cbdata
- isort()
: SortableArray< T >
- IsoSlider()
: IsoSlider
- ISOSTEPSIZE
: AtomRep
- ISOSURFACE
: AtomRep
- IsoSurface()
: IsoSurface
- isovalue
: densitythrparms
- isperiodic
: Msmpot_t
- istart
: clusterparms_t
- isvalid
: osp_material, ort_material, OpenGLShader, glwin_fbo_target, glsl_shader, anr_material
- it
: colvarmodule, colvarbias_meta::hill
- it_restart
: colvarmodule
- it_width
: colvarmodule
- item()
: SortableArray< T >
- items()
: GeometryMol
- iter
: wkf_threadlaunch_struct, wkf_threadpool_struct, wkf_threadpool_workerdata_struct
- ival
: eventdataunion, symbol_data, atomparser_node, YYSTYPE
- ixs
: glwin_warp_hmd
- iys
: glwin_warp_hmd
- j -
- k -
- l -
- l2norm()
: integrate_potential
- LABEL_ADD
: Command
- label_add()
: VMDApp
- LABEL_ADDSPRING
: Command
- LABEL_DELETE
: Command
- label_delete()
: VMDApp
- label_get_text_size()
: VMDApp
- label_get_text_thickness()
: VMDApp
- label_set_text_size()
: VMDApp
- label_set_text_thickness()
: VMDApp
- label_set_textformat()
: VMDApp
- label_set_textoffset()
: VMDApp
- LABEL_SHOW
: Command
- label_show()
: VMDApp
- LABEL_TEXTFORMAT
: Command
- LABEL_TEXTOFFSET
: Command
- LABEL_TEXTSIZE
: Command
- LABEL_TEXTTHICKNESS
: Command
- LABELANGLE
: PickModeList, Mouse
- LABELATOM
: PickModeList, Mouse
- LABELBOND
: PickModeList, Mouse
- LABELDIHEDRAL
: PickModeList, Mouse
- lambda
: colvarmodule::rotation, ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >
- lambda_exp
: colvarbias_restraint_k_moving
- lambda_schedule
: colvarbias_restraint_moving
- last
: FileSpec, qcprmsdthreadparms, gpuqcprmsdthreadparms
- last_atom()
: SmallRing
- last_cb()
: FrameSelector
- lastbtn
: FltkOpenGLDisplayDevice
- lastevent
: FltkOpenGLDisplayDevice
- lastkeycode
: FltkOpenGLDisplayDevice
- lastres
: DispCmdCylinder
- lastsel
: AtomSel
- lastshader
: OpenGLShader, glsl_shader
- lastvalue
: FrameSelector
- lastzdelta
: FltkOpenGLDisplayDevice
- latePreFrame()
: M_VRJapp
- lcc
: match_data, compile_data
- left
: OpenGLRenderer, DisplayDevice, atomparser_node
- left_atom
: LinkageEdge
- LEFTEYE
: DisplayDevice
- len
: VSMsgHeader_t, linenoiseCompletions, abuf, linenoiseState
- length
: Vector3D, JString, bondlist, bond, IMDheader, colvarmodule::matrix2d< T >::row
- length2()
: Vector3D
- let_go()
: Tool
- LibGelatoDisplayDevice()
: LibGelatoDisplayDevice
- LibTachyonDisplayDevice()
: LibTachyonDisplayDevice
- LICORICE
: AtomRep
- LIGHT
: Mouse
- light_active()
: Scene
- light_color()
: Scene
- light_color_default()
: Scene
- light_highlight()
: VMDApp
- light_highlighted()
: Scene
- light_move()
: VMDApp
- light_on()
: VMDApp
- light_pos()
: Scene
- light_pos_default()
: Scene
- light_rotate()
: VMDApp
- light_scale
: DepthSortObject
- lightState
: FileRenderer
- likeness
: clusterparms_t
- LINE
: MoleculeGraphics
- line()
: X3DDisplayDevice, WavefrontDisplayDevice, VrmlDisplayDevice, Vrml2DisplayDevice, TachyonDisplayDevice, RenderManDisplayDevice, RayShadeDisplayDevice, RadianceDisplayDevice, R3dDisplayDevice, POV3DisplayDevice, MayaDisplayDevice, LibTachyonDisplayDevice, LibGelatoDisplayDevice, GelatoDisplayDevice, FileRenderer, ArtDisplayDevice
- line_array()
: X3DOMDisplayDevice, X3DDisplayDevice, FileRenderer
- line_marker
: colvarmodule
- linear
: Best
- linearCombination()
: colvar::linearCombination
- linearfactor
: FileRenderer::AdvancedLightState
- LINES
: AtomRep
- lineStyle
: FileRenderer, DisplayDevice
- LINETHICKNESS
: AtomRep
- lineWidth
: FileRenderer, DisplayDevice
- LinkageEdge()
: LinkageEdge
- LinkagePath()
: LinkagePath
- links
: SmallRingLinkages
- list_plugins()
: VMDApp
- lk_nlevels
: MsmpotCuda_t
- lk_padding
: MsmpotCuda_t
- lk_srad
: MsmpotCuda_t
- lm
: hersheyhandle
- load()
: X3DDisplayDevice, VrmlDisplayDevice, Vrml2DisplayDevice, FileRenderer
- load_atoms()
: colvarproxy_vmd, colvarproxy_atoms, colvarmodule
- load_coords()
: colvarproxy_vmd, colvarproxy_atoms, colvarmodule
- load_coords_xyz()
: colvarmodule
- load_sharedlibrary_plugins()
: PluginMgr
- load_static_plugins()
: PluginMgr
- loadmatrix()
: OpenGLRenderer, Matrix4, DisplayDevice
- LoadShader()
: OpenGLShader
- loc_description()
: Stage, Axes
- localization_orbital_change()
: QMData
- localization_rotation_angle()
: QMData
- location()
: Stage, Axes
- locations()
: Stage, Axes
- lock
: wkf_run_barrier_struct, barrier_struct, atomic_int_struct, AtomSelThr
- log()
: colvarproxy_vmd, colvarproxy, colvarmodule
- log_default_params()
: colvarmodule
- log_gradient_finite_diff()
: colvar_grid_count
- log_init_messages()
: colvarmodule
- log_input_files()
: colvarmodule
- log_level()
: colvarmodule
- log_output_files()
: colvarmodule
- log_user_params()
: colvarmodule
- logfile_cb()
: TextInterp, TclTextInterp
- logfile_read()
: VMDApp
- LogfileEvent()
: LogfileEvent
- logn()
: colvarmodule
- lookat()
: Matrix4
- low
: netint
- lower_boundaries
: colvar_grid< T >
- lower_boundary
: colvar::cvc, colvarbias_restraint_histogram, colvar
- lower_wall_k
: colvarbias_restraint_harmonic_walls
- lower_walls
: colvarbias_restraint_harmonic_walls
- lowest
: netint
- lx
: ComputeOccupancyMap_t, Msmpot_t
- lx0
: Msmpot_t
- ly
: ComputeOccupancyMap_t, Msmpot_t
- ly0
: Msmpot_t
- lyzd
: Msmpot_t
- lz
: ComputeOccupancyMap_t, Msmpot_t
- lz0
: Msmpot_t
- lzd
: Msmpot_t
- m -
- M
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- m
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- M_VRJapp()
: M_VRJapp
- m_x
: CmdLabelTextOffset
- m_y
: CmdLabelTextOffset
- magic_number
: real_pcre
- main
: colvarmodule, colvar::distance_z
- main_loop()
: colvar::coordnum
- MainFltkMenu()
: MainFltkMenu
- major
: cudadevprops
- make_callbacks
: UIObject
- make_top()
: MoleculeList
- make_vrpn_address()
: SensorConfig
- map
: ComputeOccupancyMap_t, occthrparms_t
- map_grid()
: colvar_grid< T >
- map_total()
: colvar::map_total
- mark_key_set_default()
: colvarparse
- mark_key_set_user()
: colvarparse
- markUnused()
: OpenGLCache
- markUsed()
: OpenGLCache
- mask
: inthash_t, hash_t
- mass
: BaseMolecule, atom
- MASS
: BaseMolecule, AtomColor
- mat
: VMDDisplayList, osp_material, ort_material, Matrix4, CmdMolMaterial, anr_material
- MAT
: CmdMolChangeRepItem
- mat_ambient
: FileRenderer
- mat_diffuse
: FileRenderer
- mat_mirror
: FileRenderer
- mat_opacity
: FileRenderer
- mat_outline
: FileRenderer
- mat_outlinewidth
: FileRenderer
- mat_shininess
: FileRenderer
- mat_specular
: FileRenderer
- mat_transmode
: FileRenderer
- match()
: JRegex, colvarmodule::quaternion
- matching_state
: colvarbias
- matcounter
: MaterialList
- matData
: FileRenderer
- MATERIAL
: MoleculeGraphics
- material()
: MoleculeList, MaterialList
- MATERIAL_ADD
: Command
- material_add()
: VMDApp
- MATERIAL_CHANGE
: Command
- material_change()
: VMDApp
- MATERIAL_DEFAULT
: Command
- MATERIAL_DELETE
: Command
- material_delete()
: VMDApp
- material_index()
: MaterialList
- material_name()
: MaterialList
- MATERIAL_RENAME
: Command
- material_rename()
: VMDApp
- material_restore_default()
: VMDApp
- material_shader_table_size()
: OptiXRenderer
- MaterialClass
: ANARIRender
- MaterialFltkMenu()
: MaterialFltkMenu
- materialIndex
: FileRenderer
- MaterialList()
: MaterialList
- materialList
: VMDApp
- MATERIALS
: MoleculeGraphics
- materials_on
: FileRenderer
- materialtag
: VMDDisplayList
- matindex
: osp_cylinder_array_color, osp_sphere_array_color, osp_trimesh_v3f_n3f_c3f, anr_cylinder_array_color, anr_sphere_array_color, anr_trimesh_v3f_n3f_c3f
- matlist
: ctxt
- matrix()
: colvarmodule::rotation
- matrix2d()
: colvarmodule::matrix2d< T >
- Matrix4()
: Matrix4
- max
: ColorScale, CmdColorScaleSettings
- max2DtexSize
: OpenGLRenderer
- max2DtexX
: OpenGLRenderer
- max2DtexY
: OpenGLRenderer
- max3DtexSize
: OpenGLRenderer
- max3DtexX
: OpenGLRenderer
- max3DtexY
: OpenGLRenderer
- max3DtexZ
: OpenGLRenderer
- max_atom_groups_applied_force()
: colvarproxy_atom_groups
- max_atoms_applied_force()
: colvarproxy_atoms
- max_atoms_applied_force_id()
: colvarproxy_atoms
- max_avail_orbs
: wavef_signa_t
- max_children
: Displayable
- max_cluster
: clusterparms_t
- max_cluster_size
: clusterparms_t
- max_coord
: VolMapCreate
- max_coupling_range
: colvarbias_alb
- max_coupling_rate
: colvarbias_alb
- max_dist
: VolMapCreateDistance
- max_energy
: occthrparms_t
- max_eyzd
: Msmpot_t
- max_ezd
: Msmpot_t
- max_idx
: group_t< IMAGE_T >
- max_lyzd
: Msmpot_t
- max_lzd
: Msmpot_t
- max_phi_x
: Msmpot_t
- max_phi_y
: Msmpot_t
- max_phi_z
: Msmpot_t
- max_primitives()
: Orbital
- max_shell_type()
: Orbital
- max_stack_size()
: Stack< T >
- max_value
: group_t< IMAGE_T >
- max_wave_f_count()
: Orbital
- maxatoms
: Msmpot_t
- MAXAXIS
: Spaceball
- maxbin
: Msmpot_t
- maxboff
: Msmpot_t
- maxforce
: Feedback
- maxframe
: gofrparms_t, FrameSelector
- maxgridpts
: MsmpotCuda_t
- maximum_value()
: colvar_grid_scalar
- maxlevels
: Msmpot_t, MsmpotCuda_t
- maxover
: Msmpot_t
- maxpairs
: bondsearchthrparms
- maxpm
: MsmpotCuda_t
- maxrows
: linenoiseState
- maxval
: GraphicsFltkRepOrbital::minmax, GraphicsFltkRepVolumetric::minmax
- maxwts
: MsmpotCuda_t
- MayaDisplayDevice()
: MayaDisplayDevice
- mButton0
: M_VRJapp
- mButton1
: M_VRJapp
- mdff_potential()
: VolumetricData
- mean()
: VolumetricData
- mean_localization_measure()
: QMData
- means
: colvarbias_alb
- membytes
: cudadevprops
- memcpygbsec
: globmembwthrparms
- memory
: QMData
- memsetgbsec
: globmembwthrparms
- MemUsageAreaCalc()
: CUDAMarchingCubes
- MemUsageMC()
: CUDAMarchingCubes
- menu_add_extension()
: VMDApp
- menu_id()
: VMDApp
- menu_location()
: VMDApp
- menu_move()
: VMDApp
- menu_name()
: VMDApp
- menu_remove_extension()
: VMDApp
- menu_select_mol()
: VMDApp
- MENU_SHOW
: Command
- menu_show()
: VMDApp
- menu_status()
: VMDApp
- MENU_TK_ADD
: Command
- MENU_TK_REMOVE
: Command
- menuname
: CmdMenuShow
- menupath
: CmdMenuExtensionAdd
- merge()
: ScaleSpaceFilter< GROUP_T, IMAGE_T >
- merge_with_watershed()
: ScaleSpaceFilter< GROUP_T, IMAGE_T >
- MESAGL
: OpenGLExtensions
- messagelabel
: FrameSelector
- method
: AtomRep, AtomColor, CmdRenderOption, CmdRender, CmdColorScaleColors, CmdColorScaleMethod
- mHead
: M_VRJapp
- mid
: ColorScale, CmdColorScaleSettings
- min
: ColorScale, CmdColorScaleSettings
- min_coord
: VolMapCreate
- min_excldist
: occthrparms_t
- min_frame_index_1
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- min_frame_index_2
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- min_frame_index_3
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- minimum_pos_value()
: colvar_grid_scalar
- minimum_value()
: colvar_grid_scalar
- minmax()
: GraphicsFltkRepOrbital::minmax, GraphicsFltkRepVolumetric::minmax
- minmaxlist
: GraphicsFltkRepOrbital, GraphicsFltkRepVolumetric
- minor
: cudadevprops
- minval
: GraphicsFltkRepOrbital::minmax, GraphicsFltkRepVolumetric::minmax
- mirror
: VMDDisplayList, Material
- mlist
: ctxt, sasathreadparms, MaterialList
- Mobile()
: Mobile
- mobile_cb()
: TextInterp, TclTextInterp
- mobile_device_command_cb()
: TextInterp, TclTextInterp
- mobile_get_APIsupported()
: VMDApp
- mobile_get_client_list()
: VMDApp
- mobile_get_mode()
: VMDApp
- mobile_get_network_port()
: VMDApp
- mobile_get_tracker_status()
: VMDApp
- MOBILE_MODE
: Command
- mobile_network_port()
: VMDApp
- mobile_sendMsg()
: VMDApp
- mobile_set_activeClient()
: VMDApp
- mobile_set_mode()
: VMDApp
- mobile_state_changed_cb()
: TextInterp, TclTextInterp
- MobileButtons()
: MobileButtons
- MobileDeviceCommandEvent()
: MobileDeviceCommandEvent
- MobileEvent()
: MobileEvent
- mobileMode
: CmdMobileMode
- MobileTracker()
: MobileTracker
- mode
: VMDClipPlane
- model
: osp_cylinder_array_color, osp_sphere_array_color, osp_trimesh_v3f_n3f_c3f
- modify_atom_applied_forces()
: colvarproxy_atoms
- modify_atom_charges()
: colvarproxy_atoms
- modify_atom_group_applied_forces()
: colvarproxy_atom_groups
- modify_atom_group_charges()
: colvarproxy_atom_groups
- modify_atom_group_masses()
: colvarproxy_atom_groups
- modify_atom_group_positions()
: colvarproxy_atom_groups
- modify_atom_group_total_forces()
: colvarproxy_atom_groups
- modify_atom_masses()
: colvarproxy_atoms
- modify_atom_positions()
: colvarproxy_atoms
- modify_atom_total_forces()
: colvarproxy_atoms
- modify_features()
: colvardeps, colvar::cvc, colvarbias, atom_group, colvar
- modify_str_result()
: colvarscript
- modify_volume_data()
: BaseMolecule
- module()
: colvarscript
- mol
: clusterparms_t
- MOL_ACTIVE
: Command
- MOL_ADDREP
: Command
- MOL_BONDRECALC
: Command
- MOL_CANCEL
: Command
- MOL_COLOR
: Command
- MOL_DEL
: Command
- MOL_DELETE
: MoleculeEvent
- MOL_DELREP
: Command
- MOL_DRAWFRAMES
: Command
- MOL_FIX
: Command
- mol_from_id()
: MoleculeList
- mol_index_from_id()
: MoleculeList
- MOL_MATERIAL
: Command
- MOL_MODREP
: Command
- MOL_MODREPITEM
: Command
- MOL_NEW
: MoleculeEvent, Command
- MOL_NUMPERIODIC
: Command
- MOL_ON
: Command
- MOL_REANALYZE
: Command
- MOL_REGEN
: MoleculeEvent, DrawMolItem
- MOL_RENAME
: MoleculeEvent, Command
- MOL_REP
: Command
- MOL_REPCOLORUPDATE
: Command
- MOL_REPSELUPDATE
: Command
- MOL_SCALEMINMAX
: Command
- MOL_SELECT
: Command
- MOL_SHOWPERIODIC
: Command
- MOL_SHOWREP
: Command
- MOL_SMOOTHREP
: Command
- MOL_SSRECALC
: Command
- MOL_TOP
: MoleculeEvent, Command
- MOL_VOLUME
: Command
- MolBrowser
: MolBrowser, MainFltkMenu
- molchooser_activate_selection()
: SaveTrajectoryFltkMenu
- MolData()
: MolData
- Molecule()
: Molecule
- molecule()
: MoleculeList
- MOLECULE
: AtomColor
- molecule_activate()
: VMDApp
- molecule_add_instance()
: VMDApp
- molecule_add_volumetric()
: VMDApp
- molecule_addrep()
: VMDApp
- molecule_bondsrecalc()
: VMDApp
- molecule_cancel_io()
: VMDApp
- molecule_changed_cb()
: TextInterp, TclTextInterp, PythonTextInterp
- molecule_delete()
: VMDApp
- molecule_delete_all()
: VMDApp
- molecule_delete_all_instances()
: VMDApp
- molecule_deleteframes()
: VMDApp
- molecule_display()
: VMDApp
- molecule_dupframe()
: VMDApp
- molecule_fix()
: VMDApp
- molecule_frame()
: VMDApp
- molecule_from_selection_list()
: VMDApp
- molecule_get_color()
: VMDApp
- molecule_get_material()
: VMDApp
- molecule_get_selection()
: VMDApp
- molecule_get_style()
: VMDApp
- molecule_id()
: VMDApp
- molecule_index_from_id()
: VMDApp
- molecule_is_active()
: VMDApp
- molecule_is_displayed()
: VMDApp
- molecule_is_fixed()
: VMDApp
- molecule_load()
: VMDApp
- molecule_make_top()
: VMDApp
- molecule_modrep()
: VMDApp
- molecule_name()
: VMDApp
- molecule_new()
: VMDApp
- molecule_num_instances()
: VMDApp
- molecule_numatoms()
: VMDApp
- molecule_numframes()
: VMDApp
- molecule_orblocalize()
: VMDApp
- molecule_reanalyze()
: VMDApp
- molecule_rename()
: VMDApp
- molecule_savetrajectory()
: VMDApp
- molecule_set_color()
: VMDApp
- molecule_set_dataset_flag()
: VMDApp
- molecule_set_material()
: VMDApp
- molecule_set_selection()
: VMDApp
- molecule_set_style()
: VMDApp
- molecule_ssrecalc()
: VMDApp
- molecule_top()
: VMDApp
- molecule_valid_id()
: VMDApp
- MoleculeEvent()
: MoleculeEvent
- moleculeGraphics()
: DrawMolecule
- MoleculeGraphics()
: MoleculeGraphics
- moleculeList
: VMDApp
- MoleculeList()
: MoleculeList
- moleculename
: BaseMolecule
- MolEvent
: MoleculeEvent
- MolFilePlugin()
: MolFilePlugin
- molid
: AtomSel, CmdToolRep, GeometryMonitor, CmdMolLoad, CmdIMDConnect
- molindex
: GraphicsFltkMenu
- molinfo_frame_number
: ctxt
- molinfo_get_id
: ctxt
- molinfo_get_index
: ctxt
- molinfo_get_string
: ctxt
- molList
: GeometryMol
- molname()
: BaseMolecule
- molnamelabel
: FrameSelector
- molrep_delete()
: VMDApp
- molrep_get_by_name()
: VMDApp
- molrep_get_clipplane()
: VMDApp
- molrep_get_color()
: VMDApp
- molrep_get_colorupdate()
: VMDApp
- molrep_get_drawframes()
: VMDApp
- molrep_get_instances()
: VMDApp
- molrep_get_material()
: VMDApp
- molrep_get_name()
: VMDApp
- molrep_get_pbc()
: VMDApp
- molrep_get_pbc_images()
: VMDApp
- molrep_get_scaleminmax()
: VMDApp
- molrep_get_selection()
: VMDApp
- molrep_get_selupdate()
: VMDApp
- molrep_get_smoothing()
: VMDApp
- molrep_get_style()
: VMDApp
- molrep_is_shown()
: VMDApp
- molrep_numselected()
: VMDApp
- molrep_reset_scaleminmax()
: VMDApp
- molrep_set_clipcenter()
: VMDApp
- molrep_set_clipcolor()
: VMDApp
- molrep_set_clipnormal()
: VMDApp
- molrep_set_clipstatus()
: VMDApp
- molrep_set_color()
: VMDApp
- molrep_set_colorupdate()
: VMDApp
- molrep_set_drawframes()
: VMDApp
- molrep_set_instances()
: VMDApp
- molrep_set_material()
: VMDApp
- molrep_set_pbc()
: VMDApp
- molrep_set_pbc_images()
: VMDApp
- molrep_set_scaleminmax()
: VMDApp
- molrep_set_selection()
: VMDApp
- molrep_set_selupdate()
: VMDApp
- molrep_set_smoothing()
: VMDApp
- molrep_set_style()
: VMDApp
- molrep_show()
: VMDApp
- monitor_crossings
: colvarmodule::rotation
- monitors
: GeometryMol
- motionevent
: xidevhandle
- motioneventclass
: xidevhandle
- Mouse()
: Mouse
- MOUSE_MODE
: Command
- mouse_pos_cb()
: TextInterp, TclTextInterp
- mouse_set_mode()
: VMDApp
- MouseButton
: Mouse
- mouseMode
: CmdMouseMode
- mousemode_cb()
: TextInterp, TclTextInterp
- MouseModeEvent()
: MouseModeEvent
- MousePositionEvent()
: MousePositionEvent
- mouseSetting
: CmdMouseMode
- mousex
: oglhandle
- mouseX
: DisplayDevice
- mousey
: oglhandle
- mouseY
: DisplayDevice
- MOVE
: Mobile
- move()
: VMDTkMenu, VMDTkinterMenu, VMDMenu, VMDFltkMenu
- move_adv_light()
: Scene
- move_light()
: Scene
- move_mode()
: Spaceball, Mouse, Mobile
- MOVEATOM
: PickModeList, Mouse
- MOVEFRAG
: PickModeList, Mouse
- movefrom()
: Wavefunction
- moveMode
: vmdwinjoystick
- MoveMode
: Win32Joystick, Spaceball, Mouse, Mobile
- MOVEMOL
: PickModeList, Mouse
- MOVEREP
: PickModeList, Mouse
- MOVERES
: PickModeList, Mouse
- moveto()
: VMDTracker
- mpblx
: ComputeOccupancyMap_t
- mpbly
: ComputeOccupancyMap_t
- mpblz
: ComputeOccupancyMap_t
- mScene
: VRJugglerTracker, VRJugglerButtons
- msgColvars
: colvarproxy_vmd
- msgtp
: gofrparms_t
- msmpot
: MsmpotCuda_t
- MSMS
: AtomRep
- MSMS_DIED
: MSMSInterface
- MSMSInterface()
: MSMSInterface
- MSOFTGDI
: OpenGLExtensions
- mtx
: wkf_shared_iterator_struct, wkf_tilestack_t
- mullikenpop()
: QMData
- mult
: Quat, colvar_grid< T >
- mult_scale()
: Displayable
- multiple_replicas
: colvarbias_meta
- multiplicity()
: colvar_grid< T >
- multiply_constant()
: colvar_grid< T >
- multitextureunits
: OpenGLExtensions
- multmatrix()
: X3DDisplayDevice, VrmlDisplayDevice, Vrml2DisplayDevice, OpenGLRenderer, Matrix4, FileRenderer, DisplayDevice
- multnorm3d()
: Matrix4
- multplaneeq3d()
: Matrix4
- multpoint3()
: Quat
- multpoint3d()
: Matrix4
- multpoint4d()
: Matrix4
- multpointarray_3d()
: Matrix4
- mute()
: Inform
- mWand
: M_VRJapp
- mx
: ComputeOccupancyMap_t, Msmpot_t, occthrparms_t
- my
: ComputeOccupancyMap_t, Msmpot_t, occthrparms_t
- my_color
: GeometryMol
- my_depth_sort
: DisplayDevice
- my_filename
: FileRenderer
- My_Fl_Positioner()
: My_Fl_Positioner
- myBrowser()
: myBrowser
- myFl_Chart()
: myFl_Chart
- myglwindow()
: myglwindow
- mytag
: PickModeForce
- mz
: ComputeOccupancyMap_t, Msmpot_t, occthrparms_t
- n -
- n
: Surf, osp_trimesh_v3f_n3f_c3f, flint_t, Combinations, IsoSurface, TRIANGLE, CmdLabelTextFormat, CmdLabelTextOffset, anr_trimesh_v3f_n3f_c3f
- n0
: vmd_trimesh_n3b_v3f, vmd_trimesh_n3f_v3f, vmd_trimesh_c4u_n3b_v3f, vmd_tricolor
- n1
: vmd_trimesh_n3b_v3f, vmd_trimesh_n3f_v3f, vmd_trimesh_c4u_n3b_v3f, vmd_tricolor
- n2
: vmd_trimesh_n3b_v3f, vmd_trimesh_n3f_v3f, vmd_trimesh_c4u_n3b_v3f, vmd_tricolor
- n_active_cvcs
: colvar
- N_ARGS_MAX
: colvarscript
- N_ARGS_MIN
: colvarscript
- n_clients
: wkf_run_barrier_struct, barrier_struct
- n_matrix()
: UIestimator::n_matrix
- n_permutations
: colvar::rmsd
- n_vector()
: UIestimator::n_vector< T >
- n_waiting
: wkf_run_barrier_struct, barrier_struct
- name
: NameList< T >, MolFilePlugin, GeometryMol, FileRenderList, VolumetricData, ColorScale, _py3_inittab, CmdToolDeleteDevice, CmdToolAddDevice, PointGroupDefinition, DrawMolItem, DisplayDevice, cudadevprops, CoorData, colvar::cvc, colvarbias, atom_group, colvar, CmdMolLoad, CmdMenuExtensionRemove, CmdMenuExtensionAdd, CmdColorItem, AtomRepParamStruct
- NAME
: AtomColor
- nameindex
: MolAtom
- NameList()
: NameList< T >
- names
: NameList< T >
- NANOSHAPER_DIED
: NanoShaperInterface
- NanoShaperInterface()
: NanoShaperInterface
- nAtoms
: BaseMolecule, AtomColor
- natoms
: MolFilePlugin, densitythrparms, Msmpot_t, enthrparms
- natoms1
: rdfthrparms
- natoms2
: rdfthrparms
- nbins
: rdfthrparms
- nblockhist
: rdfthrparms
- nblocks
: rdfthrparms
- nboff
: Msmpot_t
- nbrlist
: bondsearchthrparms
- nbx
: ComputeOccupancyMap_t, Msmpot_t, occthrparms_t
- nby
: ComputeOccupancyMap_t, Msmpot_t, occthrparms_t
- nbz
: ComputeOccupancyMap_t, Msmpot_t, occthrparms_t
- ncmds
: VMDDisplayList::VMDLinkIter
- nd
: colvar_grid< T >
- near_clip()
: DisplayDevice
- nearClip
: DisplayDevice
- nearest_index()
: Scene, FileRenderer
- need2flip
: IMDSim
- need_find_bonds
: BaseMolecule
- need_matrix_recalc()
: Displayable
- need_secondary_structure()
: DrawMolecule
- needRedraw()
: DisplayDevice
- needUpdate()
: Displayable
- network_port()
: Mobile
- neuralNetwork()
: colvar::neuralNetwork
- new_coords_ready
: IMDSim
- new_count()
: colvar_grid_count
- new_data
: colvar_grid< T >
- new_hill_freq
: colvarbias_meta
- new_hills_begin
: colvarbias_meta
- new_hills_off_grid_begin
: colvarbias_meta
- new_index()
: colvar_grid< T >
- new_skip_list
: clusterparms_t
- newB
: CmdColorChange
- NEWCARTOON
: AtomRep
- newDir
: CmdAnimDir
- newFrame
: CmdAnimJump
- newG
: CmdColorChange
- newname
: CmdMolRename
- newR
: CmdColorChange
- NEWRIBBONS
: AtomRep
- newSkip
: CmdAnimSkip
- newSpeed
: CmdAnimSpeed
- newStyle
: CmdAnimStyle
- next
: VMDDisplayList, MolFilePlugin, CoorPluginData, CoorData, GridSearchPairlist, GridSearchPair, inthash_node_t, hash_node_t
- next_atom_index
: Msmpot_t
- next_frame()
: Molecule
- next_molid()
: VMDApp
- next_ts_available()
: IMDSim
- next_update_d
: watershed_gpu_state_t< GROUP_T, IMAGE_T >
- next_value_d
: watershed_gpu_state_t< GROUP_T, IMAGE_T >
- nfragCyclic
: BaseMolecule
- nfragList
: BaseMolecule
- nFragments
: BaseMolecule
- nhblock
: rdfthrparms
- nimages
: CmdMolNumPeriodic
- nlevels
: Msmpot_t
- nm
: CmdLabelTextFormat, CmdLabelTextOffset
- nNucleicFragments
: BaseMolecule
- NO_AXES
: Axes
- NO_CONNECTION
: NanoShaperInterface, MSMSInterface
- NO_EVAL
: AtomSel
- NO_INITIALIZATION
: NanoShaperInterface, MSMSInterface
- NO_PARSE
: AtomSel
- NO_PORTS
: NanoShaperInterface, MSMSInterface
- NO_REGEN
: DrawMolItem
- NO_STAGE
: Stage
- NODATA
: BaseMolecule
- node
: YYSTYPE
- node_type
: atomparser_node
- nodecount
: VMDApp
- nodename
: VMDApp
- noderank
: VMDApp
- noforce
: atom_group
- NONE
: MoleculeGraphics
- norm
: colvarvalue, colvarmodule::quaternion, colvarmodule::rvector, colvarmodule::vector1d< T >, vmd_ring_color
- norm1
: DispCmdTriangle
- norm2
: colvarvalue, colvarmodule::quaternion, colvarmodule::rvector, colvarmodule::vector1d< T >, DispCmdTriangle
- norm3
: DispCmdTriangle
- norm_fac
: shell_t
- normal
: VRJugglerDisplayDevice, OpenGLRenderer, FreeVRDisplayDevice, DisplayDevice, CaveDisplayDevice, VMDClipPlane, DispCmdVolSlice
- NORMAL
: Spaceball
- normal_atom_coord()
: GeometryMol
- NORMAL_CURSOR
: DisplayDevice
- normalize()
: IsoSurface
- normalize_basis()
: QMData
- normalize_wavefunction()
: Orbital
- norml
: DispCmdSquare
- norms
: osp_trimesh_v3f_n3f_c3f, NanoShaperInterface, MSMSInterface, anr_trimesh_v3f_n3f_c3f
- NOSTEREO
: DisplayDevice
- notbol
: match_data
- NOTDONE
: CoorData
- noteol
: match_data
- NOTHING
: SymbolTableElement
- notify()
: MaterialList, GeometryMonitor, DrawMolecule, DrawMoleculeMonitor
- nover
: Msmpot_t
- npbc
: VMDDisplayList
- npoints
: DepthSortObject
- nproc
: QMData
- nProteinFragments
: BaseMolecule
- nr_linbcg_sym()
: integrate_potential
- nResidues
: BaseMolecule
- NS_SURF_BLOBBY
: NanoShaperInterface
- NS_SURF_POCKETS
: NanoShaperInterface
- NS_SURF_SES
: NanoShaperInterface
- NS_SURF_SKIN
: NanoShaperInterface
- nsamples
: sasathreadparms
- nSegments
: BaseMolecule
- nt
: colvar_grid< T >
- nthreads
: FindWithinData
- nu
: InterpParams_t
- Num
: NameList< T >
- num
: Stack< T >, SortableArray< T >, LinkagePath, SmallRing, ResizeArray< T >, NameList< T >, MoleculeList, MaterialList, Fragment, FileRenderList, IdList, Animation, Timestep, symbol_data, CmdToolDeleteDevice, CmdToolAddDevice, CmdToolOffset, CmdToolScaleSpring, CmdToolScaleForce, CmdToolScale, CmdToolDelete, CmdToolChange, osp_cylinder_array_color, osp_sphere_array_color, osp_trimesh_v3f_n3f_c3f, Combinations, anr_cylinder_array_color, anr_sphere_array_color, anr_trimesh_v3f_n3f_c3f
- num_active_cvcs()
: colvar
- num_angles()
: BaseMolecule
- num_atoms
: AtomSel
- num_atoms256
: AtomSel
- num_basis
: QMData, orbthrparms
- num_biases()
: colvarmodule
- num_biases_feature()
: colvarmodule
- num_biases_type()
: colvarmodule
- num_bin_offsets
: ComputeOccupancyMap_t
- num_binoffsets
: occthrparms_t
- num_cache_modes()
: DisplayDevice
- num_cart_func
: shell_t
- num_categories()
: Scene
- num_category_items()
: Scene
- num_children
: Displayable
- num_clipplanes()
: VMDApp
- num_color_categories()
: VMDApp
- num_color_category_items()
: VMDApp
- num_colors()
: VMDApp, Scene
- num_colorscale_methods()
: VMDApp, Scene
- num_conformers
: ComputeOccupancyMap_t, occthrparms_t
- num_coords
: ComputeOccupancyMap_t
- num_cterms()
: BaseMolecule
- NUM_CUE_MODES
: DisplayDevice
- num_cue_modes()
: DisplayDevice
- num_custom_singleword()
: SymbolTable
- num_cvcs()
: colvar
- num_devices()
: CUDAAccel
- num_df()
: colvarvalue
- num_dihedrals()
: BaseMolecule
- num_dimensions()
: colvarvalue, colvar
- num_display_processes
: DisplayDevice
- num_electrons
: QMData
- num_elements
: MoleculeGraphics, ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >
- num_extras
: ComputeOccupancyMap_t, occthrparms_t
- num_files()
: Molecule
- num_images()
: PBCControls
- num_impropers()
: BaseMolecule
- num_in_library
: PluginMgr
- num_instances()
: BaseMolecule
- num_lights
: PositionalLightList, DirectionalLightList
- num_lists()
: GeometryList
- num_menus()
: VMDApp
- num_molecules()
: VMDApp
- num_molreps()
: VMDApp
- num_prim_per_shell
: orbthrparms
- num_probes
: ComputeOccupancyMap_t, occthrparms_t
- NUM_PROJECTIONS
: DisplayDevice
- num_projections()
: DisplayDevice
- num_regular_colors()
: VMDApp, Scene
- num_render_modes()
: DisplayDevice
- num_replicas()
: colvarproxy_replicas
- num_shells
: orbthrparms
- num_shells_per_atom
: orbthrparms
- num_stereo_modes()
: DisplayDevice
- num_tool_types()
: UIVR
- num_tools()
: UIVR
- num_types()
: Orbital
- num_variables()
: colvarmodule, colvar_grid< T >, colvarbias
- num_variables_feature()
: colvarmodule
- num_vdwparms
: occthrparms_t
- num_volume_data()
: BaseMolecule
- num_wave_f
: QMData, orbthrparms
- num_wavef_signa
: QMData
- numatoms
: orbthrparms
- numaxes()
: Symmetry
- number_of_points()
: colvar_grid< T >
- number_of_points_vec()
: colvar_grid< T >
- numbonds
: bondlist
- numcol
: enthrparms
- numcoords
: IMDSim
- numcubes
: DispCmdLatticeCubeArray
- numdata
: AtomRepParamStruct
- numfacets
: DispCmdTriMesh
- numformats()
: FileRenderList, FileRenderer
- numframes
: DrawMolecule, clusterparms_t
- numinbox
: bondsearchthrparms
- numItems
: GeometryMol
- numlines
: DispCmdWireMesh
- nummultisamples
: OpenGLExtensions
- numpicks
: DispCmdPickPointArray
- numplane
: enthrparms
- numplanes()
: Symmetry
- numpoints
: DispCmdLitPointArray, DispCmdPointArray
- numprimaryaxes()
: Symmetry
- numprims
: shell_t
- numpt
: enthrparms
- numrotreflect()
: Symmetry
- numS2n()
: Symmetry
- numsels
: sasathreadparms
- numshells
: basis_atom_t
- numspheres
: DispCmdSphereArray
- numstrips
: DispCmdTriStrips
- numstripverts
: DispCmdTriStrips
- numtriangles
: Surf, IsoSurface, IsoContour
- numtris
: osp_trimesh_v3f_n3f_c3f
- numverts
: osp_trimesh_v3f_n3f_c3f, DispCmdWireMesh, DispCmdTriStrips, DispCmdTriMesh
- numvoxels
: densitythrparms, orbthrparms
- nvenc
: VMDApp
- NVENCMgr()
: NVENCMgr
- NVIDIA
: OpenGLExtensions
- nvml_cuda_device_id
: wrap_nvml_handle
- nvml_dll
: wrap_nvml_handle
- nvml_gpucount
: wrap_nvml_handle
- nvml_pci_bus_id
: wrap_nvml_handle
- nvml_pci_device_id
: wrap_nvml_handle
- nvml_pci_domain_id
: wrap_nvml_handle
- nvmlDeviceGetCount
: wrap_nvml_handle
- nvmlDeviceGetCpuAffinity
: wrap_nvml_handle
- nvmlDeviceGetFanSpeed
: wrap_nvml_handle
- nvmlDeviceGetHandleByIndex
: wrap_nvml_handle
- nvmlDeviceGetName
: wrap_nvml_handle
- nvmlDeviceGetPciInfo
: wrap_nvml_handle
- nvmlDeviceGetPowerUsage
: wrap_nvml_handle
- nvmlDeviceGetTemperature
: wrap_nvml_handle
- nvmlDeviceSetCpuAffinity
: wrap_nvml_handle
- nvmlInit
: wrap_nvml_handle
- nvmlShutdown
: wrap_nvml_handle
- nvolsets
: FileSpec
- nWaters
: BaseMolecule
- nx
: Msmpot_t, colvar_grid< T >
- nxc
: colvar_grid< T >
- ny
: Msmpot_t
- nz
: Msmpot_t
- o -
- o
: PointDistance
- obj_index()
: GeometryMol
- obj_to_str()
: colvarscript
- obj_to_str_vector()
: colvarscript
- Object_type
: colvarscript
- objIndex
: GeometryMol
- OCCUP
: AtomColor
- OCCUPANCY
: BaseMolecule
- occupancy()
: BaseMolecule
- ofd
: linenoiseState
- OFF
: Win32Joystick, Mobile
- off()
: Displayable
- Off()
: UIObject
- offset
: CmdToolOffset
- offset_end
: match_data
- offset_materialID
: osp_cylinder_array_color
- offset_max
: match_data
- offset_overflow
: match_data
- offset_radius
: osp_cylinder_array_color
- offset_v0
: osp_cylinder_array_color
- offset_v1
: osp_cylinder_array_color
- offset_vector
: match_data
- ogl_acrobat3dcapture
: OpenGLRenderer
- ogl_backcolor
: OpenGLRenderer
- ogl_backgradient
: OpenGLRenderer
- ogl_cachedebug
: OpenGLRenderer
- ogl_cacheenabled
: OpenGLRenderer
- ogl_cachelistbase
: OpenGLRenderer
- ogl_clipmode
: OpenGLRenderer
- ogl_fogmode
: OpenGLRenderer
- ogl_glslmaterialindex
: OpenGLRenderer
- ogl_glslprojectionmode
: OpenGLRenderer
- ogl_glslserial
: OpenGLRenderer
- ogl_glsltexturemode
: OpenGLRenderer
- ogl_glsltoggle
: OpenGLRenderer
- ogl_lightcolor
: OpenGLRenderer
- ogl_lightingenabled
: OpenGLRenderer
- ogl_lightpos
: OpenGLRenderer
- ogl_lightstate
: OpenGLRenderer
- ogl_mvmatrix
: OpenGLRenderer
- ogl_pmatrix
: OpenGLRenderer
- ogl_rendstateserial
: OpenGLRenderer
- ogl_textMat
: OpenGLRenderer
- ogl_transpass
: OpenGLRenderer
- ogl_useblendedtrans
: OpenGLRenderer
- ogl_useglslshader
: OpenGLRenderer
- ogl_viewport
: OpenGLRenderer
- oglambient
: OpenGLRenderer
- ogldiffuse
: OpenGLRenderer
- oglmajor
: OpenGLExtensions, glwin_ext_fctns
- oglmaterialindex
: OpenGLRenderer
- oglminor
: OpenGLExtensions, glwin_ext_fctns
- oglopacity
: OpenGLRenderer
- ogloutline
: OpenGLRenderer
- ogloutlinewidth
: OpenGLRenderer
- oglrelease
: OpenGLExtensions, glwin_ext_fctns
- oglrenderer
: OpenGLExtensions
- oglshininess
: OpenGLRenderer
- oglspecular
: OpenGLRenderer
- ogltransmode
: OpenGLRenderer
- ok()
: GeometryMol
- okbutton
: FrameSelector
- oldpos
: linenoiseState
- olist
: gofrparms_t
- omega
: InterpParams_t
- omp_lock_state
: colvarproxy_smp
- on
: Displayable, CmdToolCallback, FileRenderer::AdvancedLightState, FileRenderer::LightState, AtomSel
- On()
: UIObject
- on256
: AtomSel
- ones()
: colvarvalue
- onoff
: CmdMolShowRep
- onoroff
: CmdMolRepColorUpdate, CmdMolRepSelUpdate
- opacity
: VMDDisplayList, osp_material, ort_material, Material, anr_material
- open_file()
: WavefrontDisplayDevice, SnapshotDisplayDevice, MayaDisplayDevice, LibTachyonDisplayDevice, FileRenderer
- open_session()
: NVENCMgr
- open_traj_file()
: colvarmodule
- open_window()
: OpenGLDisplayDevice
- OpenGLCache()
: OpenGLCache
- OpenGLDisplayDevice()
: OpenGLDisplayDevice
- OpenGLExtensions()
: OpenGLExtensions
- OpenGLPbufferDisplayDevice()
: OpenGLPbufferDisplayDevice
- OpenGLRenderer()
: OpenGLRenderer
- OpenGLShader()
: OpenGLShader
- operator *
: Vector3D, colvarvalue, colvarmodule::quaternion, colvarmodule::rmatrix, colvarmodule::rvector, colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >
- operator *=()
: colvarvalue, colvarmodule::quaternion, colvarmodule::rvector, colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >
- operator const char *()
: JString
- operator cvm::quaternion()
: colvarvalue
- operator cvm::real()
: colvarvalue
- operator cvm::rvector()
: colvarvalue
- operator delete()
: VMDDisplayList, FreeVRScene, Displayable, CaveScene
- operator new()
: VMDDisplayList, FreeVRScene, Displayable, CaveScene
- operator vector1d()
: colvarmodule::matrix2d< T >::row
- operator!=()
: JString
- operator+
: Vector3D, JString, colvarvalue, colvarmodule::quaternion, colvarmodule::rvector, colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >
- operator+=()
: JString, colvarvalue, colvarmodule::quaternion, colvarmodule::rvector, colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >
- operator-
: Vector3D, colvarvalue, colvarmodule::quaternion, colvarmodule::rvector, colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >
- operator-=()
: colvarvalue, colvarmodule::quaternion, colvarmodule::rvector, colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >
- operator/
: colvarvalue, colvarmodule::quaternion, colvarmodule::rvector, colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >
- operator/=()
: colvarvalue, colvarmodule::quaternion, colvarmodule::rvector, colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >
- operator<
: PointDistance, JString, DepthSortObject, colvarbias_meta::hill
- operator<<
: SmallRingLinkages, LinkageEdge, LinkagePath, SmallRing, Inform, colvarvalue, colvarmodule::quaternion, colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >, colvarbias_meta::hill
- operator<=
: JString, colvarbias_meta::hill
- operator=()
: Wavefunction, Matrix4, JString, DisplayDevice, colvarvalue, colvarmodule::matrix2d< T >, colvarbias_meta::hill, atom, AtomRep, AtomColor
- operator==
: ColorScale, NanoShaperFace, NanoShaperCoord, MSMSFace, MSMSCoord, JString, GraphicsFltkRepOrbital::minmax, GraphicsFltkRepVolumetric::minmax, colvarbias_meta::hill
- operator>
: JString, DepthSortObject, colvarbias_meta::hill
- operator>=
: JString, colvarbias_meta::hill
- operator>>
: colvarvalue, colvarmodule::quaternion, colvarmodule::vector1d< T >, colvarparse::read_block
- operator[]()
: SortableArray< T >, LinkagePath, SmallRing, ResizeArray< T >, Fragment, colvarvalue, colvarmodule::quaternion, colvarmodule::rvector, colvarmodule::matrix2d< T >, colvarmodule::matrix2d< T >::row, colvarmodule::vector1d< T >, atom_group, IdList
- option
: CmdRenderOption
- options
: real_pcre_extra, real_pcre
- optix_version()
: OptiXRenderer
- OptiXDisplayDevice()
: OptiXDisplayDevice
- OptiXRenderer()
: OptiXRenderer
- orb_pair_gross_atom_mulliken_pop()
: QMData
- orbh
: orbthrparms
- orbids
: wavef_signa_t
- ORBITAL
: AtomRep
- Orbital()
: Orbital
- orbitalgrid
: orbthrparms
- orbitalindex
: GraphicsFltkRepOrbital
- orblocalize()
: QMData
- orbocc
: wavef_signa_t
- orbrep
: orbital_cbdata
- order
: bond, axis
- order_edge_atoms()
: SmallRingLinkages
- orient
: VRPNTrackerUserData, VMDTracker
- orientated
: SmallRing
- orientation()
: VMDTracker, Tool, RotateTool, colvar::orientation
- orientation_angle()
: colvar::orientation_angle
- orientation_proj()
: colvar::orientation_proj
- origin
: VolumetricData, orbthrparms, MolData, RibbonFrame, orbthrparms
- ortho()
: Matrix4
- ortho2()
: Matrix4
- ORTHOGRAPHIC
: DisplayDevice
- orthogtol
: Symmetry
- OsgNavigator()
: OsgNavigator
- OSPRay2DisplayDevice()
: OSPRay2DisplayDevice
- OSPRay2Renderer()
: OSPRay2Renderer
- OSPRay_Global_Init()
: OSPRayRenderer, OSPRayDisplayDevice, OSPRay2Renderer, OSPRay2DisplayDevice
- OSPRay_Global_Shutdown()
: OSPRayRenderer, OSPRayDisplayDevice, OSPRay2Renderer, OSPRay2DisplayDevice
- OSPRayDisplayDevice()
: OSPRayDisplayDevice
- OSPRayRenderer()
: OSPRayRenderer
- otheratoms
: FindWithinData
- out_name
: colvarbias_histogram
- out_name_dx
: colvarbias_histogram
- outer()
: colvarmodule::rvector
- outer_length
: colvarmodule::matrix2d< T >
- outfile
: FileRenderer
- outline
: VMDDisplayList, osp_material, ort_material, Material, anr_material
- outlinewidth
: VMDDisplayList, osp_material, ort_material, Material, anr_material
- output_freq
: colvarbias
- output_prefix
: colvarproxy_io, colvarmodule, colvarbias
- output_prefix_str
: colvarproxy_io
- output_stream()
: colvarproxy_io
- output_stream_error_
: colvarproxy_io
- output_stream_exists()
: colvarproxy_io
- output_streams_
: colvarproxy_io
- output_traj()
: colvarbias_meta::hill
- output_width()
: colvarvalue, colvarmodule::quaternion, colvarmodule::rvector, colvarmodule::vector1d< T >
- outrad
: vmd_ring_color
- over
: Msmpot_t
- overlap
: atom_group, axis, plane
- override_current_frame()
: DrawMolecule
- p -
- p
: GRIDCELL, TRIANGLE, SQUARECELL, LINE, hersheyhandle, colvarbias_restraint_histogram
- p2leg_opt()
: colvarvalue
- p_diff
: colvarbias_restraint_histogram
- pad
: VolumetricData, vmd_sphere_color, vmd_ring_color, vmd_cylinder
- padaction
: mobilehandle
- padcnt
: qcprmsdthreadparms, gpuqcprmsdthreadparms
- padding
: PositionalLight, DirectionalLight
- padding1
: wkf_threadlaunch_struct, wkf_threadpool_workerdata_struct, wkf_run_barrier_struct, barrier_struct, atomic_int_struct
- padding2
: wkf_threadlaunch_struct, wkf_threadpool_workerdata_struct, wkf_run_barrier_struct, barrier_struct, atomic_int_struct
- padmap
: MsmpotCuda_t
- padx
: ComputeOccupancyMap_t, mobilehandle
- pady
: ComputeOccupancyMap_t, mobilehandle
- padz
: ComputeOccupancyMap_t
- page_align_sz
: Timestep
- pageablememaccess
: cudadevprops
- pageablememaccessuseshostpagetables
: cudadevprops
- pair_localization_measure()
: QMData
- pairdist
: bondsearchthrparms
- pairlist
: GridSearchPairlist, colvar::selfcoordnum, colvar::coordnum
- pairlist_freq
: colvar::selfcoordnum, colvar::coordnum
- pairlistmutex
: bondsearchthrparms
- panels()
: Stage
- paper_bibtex_
: usage
- paper_count_
: usage
- paper_url_
: usage
- par_barrier()
: VMDApp
- par_name()
: VMDApp
- par_rank()
: VMDApp
- par_size()
: VMDApp
- param_exists()
: colvarparams
- param_grad_map
: colvarparams
- param_map
: colvarparams
- parent
: Displayable
- parms
: wkf_threadpool_workerdata_struct, wkf_run_barrier_struct
- parse
: SymbolTable, atom_group, colvarmodule
- parse_analysis()
: colvar
- parse_biases()
: colvarmodule
- parse_colvars()
: colvarmodule
- parse_config()
: colvarmodule
- parse_deprecated
: colvarparse
- parse_deprecation_warning
: colvarparse
- parse_echo
: colvarparse
- parse_echo_default
: colvarparse
- parse_fitting_options()
: atom_group
- parse_global_params()
: colvarmodule
- parse_group()
: colvar::cvc
- Parse_Mode
: colvarparse
- parse_module_config()
: colvarproxy
- parse_normal
: colvarparse
- parse_null
: colvarparse
- parse_override
: colvarparse
- parse_params()
: colvar_grid< T >
- parse_required
: colvarparse
- parse_restart
: colvarparse
- parse_silent
: colvarparse
- PARSE_SUCCESS
: AtomSel
- ParseTree()
: ParseTree
- path
: VMDTkMenu, LinkagePath
- paths
: SmallRingLinkages, LinkageEdge
- pause()
: IMDSimThread, IMDSimBlocking, IMDSim, IMDMgr
- PAUSE_OFF
: CmdIMDSim
- PAUSE_ON
: CmdIMDSim
- PAUSE_TOGGLE
: CmdIMDSim
- pbc
: VMDDisplayList, CmdMolShowPeriodic
- PBCControls()
: PBCControls
- pci_device_id
: wrap_nvmlPciInfo_t
- pci_subsystem_id
: wrap_nvmlPciInfo_t
- pdhlatusec
: busbwthrparms
- pdhmbsec
: busbwthrparms
- period
: spaceballevent, colvar::cvc, colvar
- periodic
: MolData, colvar_grid< T >
- periodic_boundaries()
: colvar
- PERSPECTIVE
: DisplayDevice
- pervertexcolors
: DispCmdTriMesh
- pervertexnormals
: DispCmdTriMesh
- pfragCyclic
: BaseMolecule
- pfragList
: BaseMolecule
- pgm
: vmd_opencl_orbital_handle
- phase
: wkf_run_barrier_struct, barrier_struct
- phdlatusec
: busbwthrparms
- phdmbsec
: busbwthrparms
- phi
: colvar::polar_theta, colvar::polar_phi
- phi_x
: Msmpot_t
- phi_y
: Msmpot_t
- phi_z
: Msmpot_t
- PhoneButtons()
: PhoneButtons
- PhoneTracker()
: PhoneTracker
- physical_time
: Timestep
- PHYSICALTIME
: AtomColor
- PICK
: PickModeList, Mouse
- pick()
: DisplayDevice
- pick_atom_callback_cb()
: TextInterp, TclTextInterp
- pick_atom_cb()
: TextInterp, TclTextInterp, PythonTextInterp
- pick_callback_clear()
: PickList
- pick_check()
: PickList
- pick_cmd_list()
: Pickable, Displayable
- PICK_CURSOR
: DisplayDevice
- pick_end()
: PickList, Pickable, DrawMolItem
- PICK_EVENT
: Command
- pick_graphics()
: PickModeMolLabel, PickMode
- pick_graphics_cb()
: TextInterp, TclTextInterp
- pick_molecule_end()
: PickModeUser, PickModeMove, PickModeMolLabel, PickModeCenter, PickModeAddBond, PickMode
- pick_molecule_move()
: PickModeMove, PickModeMolLabel, PickModeForceFragment, PickModeForceResidue, PickModeForceAtom, PickModeCenter, PickMode
- pick_molecule_start()
: PickModeUser, PickModeMove, PickModeMolLabel, PickModeForceFragment, PickModeForceResidue, PickModeForceAtom, PickModeCenter, PickModeAddBond, PickMode
- pick_move()
: Stage, PickList, Pickable, DrawMolItem, Axes
- pick_point()
: FileRenderer
- pick_selection_cb()
: TextInterp, TclTextInterp
- pick_start()
: PickList, Pickable, MoleculeGraphics, DrawMolItem
- pick_value_cb()
: TextInterp, TclTextInterp, PythonTextInterp
- pickable
: PickEvent
- Pickable()
: Pickable
- pickable_on()
: Pickable, DrawMolItem, Displayable
- PickAtomCallbackEvent()
: PickAtomCallbackEvent
- PickAtomEvent()
: PickAtomEvent
- PickEvent()
: PickEvent
- PickGraphicsEvent()
: PickGraphicsEvent
- pickList
: VMDApp
- PickList()
: PickList
- PickMode()
: PickMode
- PickModeAddBond()
: PickModeAddBond
- PickModeAngles()
: PickModeAngles
- PickModeAtoms()
: PickModeAtoms
- PickModeBonds()
: PickModeBonds
- PickModeCenter()
: PickModeCenter
- PickModeDihedrals()
: PickModeDihedrals
- PickModeForce()
: PickModeForce
- PickModeForceAtom()
: PickModeForceAtom
- PickModeForceFragment()
: PickModeForceFragment
- PickModeForceResidue()
: PickModeForceResidue
- pickModeList
: VMDApp
- PickModeList()
: PickModeList
- PickModeMolLabel()
: PickModeMolLabel
- PickModeMove()
: PickModeMove
- PickModeMoveAtom()
: PickModeMoveAtom
- PickModeMoveFragment()
: PickModeMoveFragment
- PickModeMoveMolecule()
: PickModeMoveMolecule
- PickModeMoveRep()
: PickModeMoveRep
- PickModeMoveResidue()
: PickModeMoveResidue
- PickModeUser()
: PickModeUser
- PICKPOINT
: MoleculeGraphics
- PickSelectionEvent()
: PickSelectionEvent
- PickValueEvent()
: PickValueEvent
- PinchTool()
: PinchTool
- PlainTextInterp()
: PlainTextInterp
- planar
: Best
- plane()
: Symmetry
- planes
: Best
- plen
: linenoiseState
- plugin
: CoorPluginData
- plugin_dlopen()
: VMDApp
- plugin_update()
: VMDApp
- PLUGIN_UPDATE
: Command
- pluginlist
: PluginMgr
- PluginMgr()
: PluginMgr
- plugins()
: PluginMgr
- pmx
: MsmpotCuda_t
- pmy
: MsmpotCuda_t
- pmz
: MsmpotCuda_t
- POINT
: MoleculeGraphics
- point()
: X3DDisplayDevice, WavefrontDisplayDevice, Vrml2DisplayDevice, TachyonDisplayDevice, RenderManDisplayDevice, RayShadeDisplayDevice, RadianceDisplayDevice, R3dDisplayDevice, POV3DisplayDevice, MayaDisplayDevice, LibTachyonDisplayDevice, LibGelatoDisplayDevice, GelatoDisplayDevice, FileRenderer, ArtDisplayDevice
- point_array()
: X3DDisplayDevice, FileRenderer
- point_array_lit()
: FileRenderer
- PointDistance()
: PointDistance
- pointers
: colvarmodule::matrix2d< T >
- pointgroup
: Best
- pointgrouporder
: Best
- POINTS
: AtomRep
- points
: DepthSortObject
- pointSize
: FileRenderer
- pointSphereLists
: OpenGLRenderer
- polar_phi()
: colvar::polar_phi
- polar_theta()
: colvar::polar_theta
- Polygonise()
: IsoSurface, IsoContour
- polyline_array()
: X3DOMDisplayDevice, X3DDisplayDevice, FileRenderer
- pop()
: VrmlDisplayDevice, Stack< T >, ResizeArray< T >
- population_matrix()
: Wavefunction
- port
: CmdIMDConnect
- pos
: Timestep, VRPNTrackerUserData, VMDTracker, osp_positional_light, PositionalLight, ort_positional_light, linenoiseState, FileRenderer::AdvancedLightState, FileRenderer::LightState, DispCmdPoint, atom, bondsearchthrparms, anr_positional_light
- POS
: AtomColor
- pos1
: DispCmdCone, DispCmdSquare, DispCmdTriangle, DispCmdLine
- pos2
: DispCmdCone, DispCmdSquare, DispCmdTriangle, DispCmdLine
- pos3
: DispCmdSquare, DispCmdTriangle
- pos4
: DispCmdSquare
- pos_ptr
: Timestep
- pos_r
: DispCmdSphere
- position()
: VMDTracker, Tool, RotateTool, JoystickTool
- position_derivative_inner()
: colvarmodule::quaternion
- position_distance()
: colvarproxy_system, colvarmodule
- positions()
: atom_group
- positions_shifted()
: atom_group
- posns
: PositionalLightList
- post_run()
: colvarproxy
- postag
: DispCmdPickPoint
- posterize
: CmdColorScaleSettings
- postFrame()
: M_VRJapp
- POSX
: AtomColor
- POSY
: AtomColor
- POSZ
: AtomColor
- potential_energy
: colvar
- POV3DisplayDevice()
: POV3DisplayDevice
- pow()
: colvarmodule
- preFrame()
: M_VRJapp
- prepare()
: VRJugglerScene, VMDTitle, Stage, Scene, MoleculeGraphics, Molecule, GeometrySpring, GeometryList, FreeVRScene, FPS, DrawMolItem, DrawMolecule, DrawForce, DisplayRocker, Displayable, CaveScene, Axes
- prepare3D()
: OpenGLRenderer, OpenGLDisplayDevice, FileRenderer, DisplayDevice
- prepareOpaque()
: OpenGLRenderer, DisplayDevice
- prepareTrans()
: OpenGLRenderer, DisplayDevice
- prepareVectors()
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- pretty_name()
: FileRenderList, FileRenderer
- prettyname()
: MolFilePlugin
- prev_timestep
: colvar
- prev_v_ext
: colvar
- prev_x_ext
: colvar
- previous_bin
: colvarbias_reweightaMD
- previous_colvar_forces
: colvarbias
- prim
: shell_t
- print()
: Combinations, AtomGrid
- print_atom_ids()
: atom_group
- print_cuda_devices()
: CUDAAccel
- print_input_atomic_data()
: colvarproxy
- print_output_atomic_data()
: colvarproxy
- print_properties()
: atom_group
- print_state()
: colvardeps
- print_total_forces_errning()
: colvarmodule
- print_wavefunction()
: Orbital
- PrintExtensions()
: OpenGLExtensions
- PrintInfoLog()
: OpenGLShader
- printMatrix()
: Quat
- printQuat()
: Quat
- PrintTool()
: PrintTool
- probe_vdw_params
: ComputeOccupancyMap_t
- probevdwparms
: occthrparms_t
- proc_features()
: colvarscript
- ProgramObject
: OpenGLShader, glsl_shader
- project_hills()
: colvarbias_meta
- Projection
: DisplayDevice
- projection()
: DisplayDevice
- projection_name()
: DisplayDevice
- prompt
: linenoiseState
- provide()
: colvardeps
- proxy
: colvarscript, colvarmodule
- PSDisplayDevice()
: PSDisplayDevice
- ptr
: VMDDisplayList::VMDLinkIter
- publicName
: FileRenderer
- publicPrettyName
: FileRenderer
- push()
: VrmlDisplayDevice, Stack< T >
- putdata()
: DispCmdPickPointArray, DispCmdPickPoint, DispCmdLineWidth, DispCmdLineType, DispCmdSphereType, DispCmdSphereRes, DispCmdVolumeTexture, DispCmdVolSlice, DispCmdText, DispCmdColorIndex, DispCmdCone, DispCmdCylinder, DispCmdWireMesh, DispCmdTriStrips, DispCmdTriMesh, DispCmdSquare, DispCmdTriangle, DispCmdPolyLineArray, DispCmdLineArray, DispCmdLine, DispCmdLitPointArray, DispCmdPointArray, DispCmdLatticeCubeArray, DispCmdSphereArray, DispCmdSphere, DispCmdPoint, DispCmdComment, DispCmdBeginRepGeomGroup
- px
: Msmpot_t
- px0
: Msmpot_t
- px2
: Msmpot_t
- px3
: Msmpot_t
- py
: Msmpot_t
- py0
: Msmpot_t
- py2
: Msmpot_t
- py3
: Msmpot_t
- python_cb()
: TextInterp, PythonTextInterp
- PythonEvalEvent()
: PythonEvalEvent
- PythonTextInterp()
: PythonTextInterp
- pz
: Msmpot_t
- pz0
: Msmpot_t
- pz2
: Msmpot_t
- pz3
: Msmpot_t
- q -
- r -
- r
: colvar::polar_theta, colvar::polar_phi
- r0
: colvar::h_bond, colvar::groupcoordnum, colvar::selfcoordnum, colvar::coordnum
- r0_vec
: colvar::groupcoordnum, colvar::coordnum
- r12
: colvar::dihedral
- r2
: FindWithinData
- r21
: colvar::dipole_angle, colvar::angle
- r21l
: colvar::dipole_angle, colvar::angle
- r23
: colvar::dihedral, colvar::dipole_angle, colvar::angle
- r23l
: colvar::dipole_angle, colvar::angle
- r34
: colvar::dihedral
- R3dDisplayDevice()
: R3dDisplayDevice
- RadianceDisplayDevice()
: RadianceDisplayDevice
- radii
: osp_sphere_array_color, bondsearchthrparms, anr_cylinder_array_color, anr_sphere_array_color
- radii_max
: BaseMolecule
- radii_min
: BaseMolecule
- radii_minmax_need_update
: BaseMolecule
- RADIUS
: BaseMolecule
- radius
: BaseMolecule, osp_cylinder_array_color, vmd_sphere_color, vmd_sphere, vmd_cylinder_color, vmd_cylinder, MolData, GraphicsFltkRepVDW, GraphicsFltkRepBonds, DispCmdCone
- radius2
: DispCmdCone
- radius_scale
: VolMapCreateDensity
- RadiusCounter()
: RadiusCounter
- rads
: osp_sphere_array_color, anr_cylinder_array_color, anr_sphere_array_color
- radscale
: densitythrparms
- rand_gaussian()
: colvarproxy_vmd, colvarproxy_system, colvarmodule
- rank
: colvarbias
- raw_data_in()
: colvar_grid< T >
- raw_data_num()
: colvar_grid< T >
- raw_data_out()
: colvar_grid< T >
- RayGen
: OptiXRenderer
- RayShadeDisplayDevice()
: RayShadeDisplayDevice
- RayType
: OptiXRenderer
- read_block()
: colvarparse::read_block
- read_colvar()
: colvarmodule
- read_config_file()
: colvarmodule
- read_config_line()
: colvarparse
- read_config_string()
: colvarmodule
- read_data()
: colvar::cvc
- read_event()
: OpenGLPbufferDisplayDevice, OpenGLDisplayDevice, FltkOpenGLDisplayDevice, DisplayDevice
- read_from_file()
: UIText
- read_hill()
: colvarbias_meta
- read_index_file()
: colvarmodule
- read_init()
: UIText
- read_inputfiles()
: UIestimator::UIestimator
- read_metadata()
: MolFilePlugin
- read_multicol()
: colvar_grid_gradient, colvar_grid_scalar, colvar_grid_count, colvar_grid< T >
- read_objects_state()
: colvarmodule
- read_optional_structure()
: MolFilePlugin
- read_position()
: atom
- read_positions()
: atom_group
- read_qm_data()
: MolFilePlugin
- read_raw()
: colvar_grid< T >
- read_rawgraphics()
: MolFilePlugin
- read_replica_files()
: colvarbias_meta
- read_restart()
: colvarmodule, colvar_grid< T >
- read_state()
: colvarbias, colvar
- read_state_data()
: colvarbias_restraint_linear, colvarbias_restraint_harmonic_walls, colvarbias_restraint_harmonic, colvarbias_meta, colvarbias_reweightaMD, colvarbias_histogram, colvarbias_ti, colvarbias
- read_state_data_key()
: colvarbias
- read_state_prefix()
: colvarbias
- read_state_string()
: colvarbias
- read_structure()
: MolFilePlugin
- read_timestep_pagealign_size()
: MolFilePlugin
- read_total_force()
: atom
- read_total_forces()
: atom_group
- read_traj()
: colvarmodule, colvar
- read_velocities()
: atom_group
- read_velocity()
: atom
- read_volumetric()
: MolFilePlugin
- readData()
: MolData
- reader()
: IMDSimThread
- readFile()
: MolData
- readObject()
: VRJugglerSharedData
- readpixels_rgb3u()
: OpenGLPbufferDisplayDevice, OpenGLDisplayDevice, FltkOpenGLDisplayDevice, DisplayDevice
- readpixels_rgba4u()
: OpenGLPbufferDisplayDevice, OpenGLDisplayDevice, FltkOpenGLDisplayDevice, DisplayDevice
- ReadShaderSource()
: OpenGLShader
- real
: colvarmodule
- real_value
: colvarvalue
- rebin_grids
: colvarbias_meta
- recalc_bonds()
: DrawMolecule
- recalc_mat()
: Displayable
- recalc_ss()
: DrawMolecule
- recentFrame
: CoorPluginData
- reciprocal_cell_x
: colvarproxy_system
- reciprocal_cell_y
: colvarproxy_system
- reciprocal_cell_z
: colvarproxy_system
- reComputeLambda()
: ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >
- record_database()
: Molecule
- record_file()
: Molecule
- record_remarks()
: Molecule
- recount_hills_off_grid()
: colvarbias_meta
- recurse()
: Combinations
- ref1
: colvar::distance_z
- ref2
: colvar::distance_z
- ref_count
: colvardeps::feature_state
- ref_p
: colvarbias_restraint_histogram
- ref_pos
: colvar::rmsd, colvar::orientation, colvar::eigenvector, atom_group
- ref_pos_cog
: atom_group
- ref_quat
: colvar::orientation
- reflectivity
: osp_material, ort_material, anr_material
- regen_excitationlist()
: GraphicsFltkRepOrbital
- regen_orbitallist()
: GraphicsFltkRepOrbital
- regen_wavefunctypes()
: GraphicsFltkRepOrbital
- RegenChoices
: DrawMolItem
- register_atom_group()
: colvar::cvc
- register_cb()
: PluginMgr
- register_monitor()
: DrawMolecule
- register_named_atom_group()
: colvarmodule
- register_param()
: colvarparams
- register_param_grad()
: colvarparams
- register_proc()
: VMDTkMenu
- register_UI()
: CommandQueue
- register_windowproc()
: VMDTkinterMenu
- rel_screen_pos()
: FltkOpenGLDisplayDevice, DisplayDevice
- remove()
: SortableArray< T >, ResizeArray< T >
- remove_all_children()
: colvardeps
- remove_atom()
: atom_group
- remove_child()
: Displayable, colvardeps
- remove_custom_singleword()
: SymbolTable
- remove_device()
: Tool
- remove_file()
: colvarproxy_io
- remove_last()
: LinkagePath, SmallRing
- remove_menu()
: VMDApp
- remove_pickable()
: PickList
- remove_small_values()
: colvar_grid< T >
- remove_tool()
: UIVR
- remove_volume_data()
: BaseMolecule
- removeAllClients()
: Mobile
- removeClient()
: Mobile
- rename()
: Molecule
- rename_file()
: colvarproxy_io
- rendenum
: OpenGLExtensions
- RENDER
: Command
- render()
: VRJugglerDisplayDevice, SnapshotDisplayDevice, PSDisplayDevice, OpenGLRenderer, FreeVRDisplayDevice, FileRenderList, FileRenderer, DisplayDevice, CaveDisplayDevice
- render_compile_and_validate()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- render_done()
: PSDisplayDevice, OpenGLRenderer, DisplayDevice
- render_mode()
: DisplayDevice
- render_name()
: DisplayDevice
- RENDER_OPTION
: Command
- render_to_file()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- render_to_videostream()
: OptiXRenderer
- renderer_process
: DisplayDevice
- RenderFltkMenu()
: RenderFltkMenu
- RenderManDisplayDevice()
: RenderManDisplayDevice
- renderMode
: DisplayDevice
- RenderMode
: OSPRay2Renderer, ANARIRender
- renderModes
: DisplayDevice
- renderNames
: DisplayDevice
- reopen_replica_buffer_file()
: colvarbias_meta
- REP
: CmdMolChangeRepItem
- REP_REGEN
: DrawMolItem
- repanr_context_stats()
: ANARIRender
- RepChoice()
: RepChoice
- RepChoiceSmall()
: RepChoiceSmall
- repcmd()
: GraphicsFltkRepFieldLines, GraphicsFltkRepOrbital, GraphicsFltkRepVolumeSlice, GraphicsFltkRepIsosurface, GraphicsFltkRepSurf, GraphicsFltkRepQuickSurf, GraphicsFltkRepHBonds, GraphicsFltkRepNanoShaper, GraphicsFltkRepMSMS, GraphicsFltkRepSolvent, GraphicsFltkRepNewCartoon, GraphicsFltkRepCartoon, GraphicsFltkRepNewRibbons, GraphicsFltkRepRibbons, GraphicsFltkRepTube, GraphicsFltkRepLicorice, GraphicsFltkRepTrace, GraphicsFltkRepDotted, GraphicsFltkRepBeads, GraphicsFltkRepVDW, GraphicsFltkRepPoints, GraphicsFltkRepCPK, GraphicsFltkRepDynamicBonds, GraphicsFltkRepBonds, GraphicsFltkRepLines, GraphicsFltkRep
- repcontrols
: GraphicsFltkMenu
- RepData
: CmdMolChangeRepItem
- repdata
: AtomRepParamStruct
- repData
: CmdMolChangeRepItem
- RepDataNames
: AtomRep
- repindex
: GraphicsFltkMenu
- replace_id()
: MoleculeGraphics
- replica
: colvarbias_meta::hill
- replica_comm_barrier()
: colvarproxy_replicas
- replica_comm_recv()
: colvarproxy_replicas
- replica_comm_send()
: colvarproxy_replicas
- replica_enabled()
: colvarproxy_replicas
- replica_file_name
: colvarbias_meta
- replica_hills_file
: colvarbias_meta
- replica_hills_file_pos
: colvarbias_meta
- replica_id
: colvarbias_meta
- replica_index()
: colvarproxy_replicas
- replica_list_file
: colvarbias_meta
- replica_share()
: colvarbias_meta, colvarbias
- replica_state_file
: colvarbias_meta
- replica_state_file_in_sync
: colvarbias_meta
- replica_update_freq
: colvarbias_meta
- replicas
: colvarbias_meta
- replicas_registry
: colvarbias_meta
- replicas_registry_file
: colvarbias_meta
- repList
: DrawMolecule
- RepMethod
: AtomRep
- repn
: CmdMolShowRep, CmdMolSmoothRep, CmdMolDrawFrames, CmdMolScaleMinmax, CmdMolShowInstances, CmdMolNumPeriodic, CmdMolShowPeriodic, CmdMolDeleteRep, CmdMolRepColorUpdate, CmdMolRepSelUpdate, CmdMolChangeRepItem, CmdMolChangeRep
- repnum
: CmdToolRep
- repNumber
: DrawMolItem
- report()
: usage
- report_context_stats()
: OptiXRenderer
- reposition_window()
: DisplayDevice
- reposp_context_stats()
: OSPRayRenderer, OSPRay2Renderer
- representation()
: MoleculeList
- representation_index()
: DrawMolItem
- request_actual_value()
: colvar_grid< T >
- request_deletion()
: colvarproxy_vmd, colvarproxy
- request_group1_gradients()
: colvarmodule::rotation
- request_group2_gradients()
: colvarmodule::rotation
- request_total_force()
: colvarproxy_vmd, colvarproxy_system, colvarmodule
- require_cave_name()
: SensorConfig
- require_feature_alt()
: colvardeps
- require_feature_children()
: colvardeps
- require_feature_self()
: colvardeps
- require_freevr_name()
: SensorConfig
- require_local()
: SensorConfig
- require_volume_texture()
: OpenGLRenderer
- requires_alt
: colvardeps::feature
- requires_children
: colvardeps::feature
- requires_exclude
: colvardeps::feature
- requires_self
: colvardeps::feature
- res
: DispCmdSphereRes, DispCmdCone
- res0
: wrap_nvmlPciInfo_t
- res1
: wrap_nvmlPciInfo_t
- res2
: wrap_nvmlPciInfo_t
- res3
: wrap_nvmlPciInfo_t
- rescale_colorscale_minmax()
: AtomColor
- rescale_voxel_value_range()
: VolumetricData
- reset
: Win32Joystick, UIObject, Spaceball, OpenGLShader, Mouse, Mobile, Inform, GraphicsFltkRep, colvarvalue, colvarmodule::quaternion, colvarmodule::rmatrix, colvarmodule::rvector, colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >, colvarproxy_volmaps, colvarproxy, colvarproxy_atom_groups, colvarproxy_atoms, colvarmodule, colvar_grid< T >, colvarbias, CmdMolScaleMinmax
- reset_and_free()
: VMDDisplayList
- reset_atoms_data()
: atom_group
- reset_bias_force()
: colvar
- reset_data()
: atom
- reset_device_menus()
: ToolFltkMenu
- reset_disp_list()
: Displayable
- reset_index_groups()
: colvarmodule
- reset_lights()
: Scene
- reset_orientation()
: HMDMgr
- reset_pbc_lattice()
: colvarproxy_system
- reset_rep()
: GraphicsFltkMenu
- reset_rotation()
: colvarmodule::quaternion
- reset_state()
: FileRenderer
- reset_tool_list()
: ToolFltkMenu
- reset_transformation()
: Displayable
- ResetViewPending
: VMDApp
- reshape()
: OpenGLPbufferDisplayDevice, OpenGLDisplayDevice, FltkOpenGLDisplayDevice, DisplayDevice
- resid
: Residue, MolAtom
- RESID
: AtomColor
- Residue()
: Residue
- residue()
: BaseMolecule
- residue_id
: colvarmodule
- residueList
: BaseMolecule
- residues
: Fragment
- residueType
: Residue, MolAtom
- resize()
: colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >
- resize_window()
: DisplayDevice
- ResizeArray()
: ResizeArray< T >
- RESNAME
: AtomColor
- resnameindex
: MolAtom
- resNames
: BaseMolecule
- resolution
: GraphicsFltkRepVDW, GraphicsFltkRepBonds
- resolution_changed()
: GraphicsFltkRepQuickSurf
- ResolutionCounter()
: ResolutionCounter
- restart_frequency_engine
: colvarproxy_io
- restart_keep_hills
: colvarbias_meta
- restart_out_freq
: colvarmodule
- restart_out_name
: colvarmodule
- restart_output_prefix()
: colvarproxy_io
- restart_output_prefix_str
: colvarproxy_io
- restart_version()
: colvarmodule
- restart_version_int
: colvarmodule
- restart_version_number()
: colvarmodule
- restart_version_str
: colvarmodule
- restore_children_deps()
: colvardeps
- restore_default()
: MaterialList
- restraint_convert_k()
: colvarbias_alb
- restraint_FE
: colvarbias_restraint_k_moving
- restraint_force()
: colvarbias_restraint_linear, colvarbias_restraint_harmonic_walls, colvarbias_restraint_harmonic, colvarbias_restraint, colvarbias_alb
- restraint_potential()
: colvarbias_restraint_linear, colvarbias_restraint_harmonic_walls, colvarbias_restraint_harmonic, colvarbias_restraint, colvarbias_alb
- RESTYPE
: AtomColor
- resTypes
: MoleculeList
- result
: barrier_struct, PerRayData_radiance
- returns_a
: SymbolTableElement
- rev
: CmdColorScaleSettings
- reverse()
: SmallRing
- RGB3F
: CUDAQuickSurf, CUDAMarchingCubes
- RGB4U
: CUDAQuickSurf, CUDAMarchingCubes
- RIBBONS
: AtomRep
- right
: OpenGLRenderer, DisplayDevice, RibbonFrame, atomparser_node
- right_atom
: LinkageEdge
- right_eye_dir()
: DisplayDevice
- RIGHTEYE
: DisplayDevice
- ring_array_color()
: OptiXRenderer
- rm
: hersheyhandle
- rmap_x
: Msmpot_t
- rmap_y
: Msmpot_t
- rmap_z
: Msmpot_t
- rmatrix()
: colvarmodule::rmatrix
- rmin
: rdfthrparms
- rms_atom_groups_applied_force()
: colvarproxy_atom_groups
- rms_atoms_applied_force()
: colvarproxy_atoms
- rmsd
: colvar::rmsd, Best
- rmsdmat
: qcprmsdthreadparms, gpuqcprmsdthreadparms
- ROCKOFF
: Command
- ROCKON
: Command
- root
: Scene, MaterialList, oglhandle
- rootWindowID
: glxdata
- rot
: Matrix4, FileRenderer, DispCmdCylinder, colvar::orientation, atom_group
- rot_basis_quat()
: HMDMgr
- rot_off()
: Displayable
- rot_on()
: Displayable
- rot_orient
: VMDTracker
- rot_point_quat()
: HMDMgr
- ROTATE
: Mobile, Command
- rotate()
: Quat, PickModeMoveRep, PickModeMoveMolecule, PickModeMoveFragment, PickModeMoveResidue, PickModeMoveAtom, PickModeMove, colvarmodule::rotation, colvarmodule::quaternion
- rotate_2x2_orbitals()
: QMData
- rotate_axis()
: Matrix4
- rotate_light()
: Scene
- RotateTool()
: RotateTool
- rotating()
: Displayable
- rotation()
: colvarmodule::rotation
- ROTATION
: Win32Joystick, Mouse
- rotation_matrix()
: colvarmodule::quaternion
- rotm
: Displayable
- rotMat
: CmdRotMat
- ROTMAT
: Command
- rotmatrix
: mobilehandle
- rotreflect()
: Symmetry
- rotreflections
: Best
- row
: colvarmodule::matrix2d< T >::row, colvarmodule::matrix2d< T >
- rows
: colvarmodule::matrix2d< T >
- rslt
: wkf_run_barrier_struct
- rsltparms
: wkf_run_barrier_struct
- RT_BACKGROUND_TEXTURE_SKY_ORTHO_PLANE
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- RT_BACKGROUND_TEXTURE_SKY_SPHERE
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- RT_BACKGROUND_TEXTURE_SOLID
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- RT_CLIP_NONE
: OptiXRenderer
- RT_CLIP_PLANE
: OptiXRenderer
- RT_CLIP_SPHERE
: OptiXRenderer
- RT_CUBEMAP
: OptiXRenderer
- RT_DOME_MASTER
: OptiXRenderer
- RT_EQUIRECTANGULAR
: OptiXRenderer
- RT_FOG_EXP
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- RT_FOG_EXP2
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- RT_FOG_LINEAR
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- RT_FOG_NONE
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- RT_HEADLIGHT_OFF
: OptiXRenderer
- RT_HEADLIGHT_ON
: OptiXRenderer
- RT_OCULUS_RIFT
: OptiXRenderer
- RT_ORTHOGRAPHIC
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- RT_PATHTRACER
: OSPRay2Renderer
- RT_PERSPECTIVE
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- RT_RAY_GEN_ACCUMULATE
: OptiXRenderer
- RT_RAY_GEN_CLEAR_ACCUMULATION_BUFFER
: OptiXRenderer
- RT_RAY_GEN_COPY_FINISH
: OptiXRenderer
- RT_RAY_GEN_COUNT
: OptiXRenderer
- RT_RAY_TYPE_COUNT
: OptiXRenderer
- RT_RAY_TYPE_RADIANCE
: OptiXRenderer
- RT_RAY_TYPE_SHADOW
: OptiXRenderer
- RT_SCIVIS
: OSPRay2Renderer
- RT_SHADOWS_OFF
: OSPRayRenderer, OSPRay2Renderer, ANARIRender
- RT_SHADOWS_ON
: OSPRayRenderer, OSPRay2Renderer, ANARIRender
- RT_VERB_DEBUG
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- RT_VERB_MIN
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- RT_VERB_TIMING
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- RtShadowMode
: OSPRayRenderer, OSPRay2Renderer, ANARIRender
- run()
: colvarscript
- run_ave()
: colvar
- run_colvar_callback()
: colvarproxy_vmd, colvarproxy_script
- run_colvar_gradient_callback()
: colvarproxy_vmd, colvarproxy_script
- run_force_callback()
: colvarproxy_vmd, colvarproxy_script
- run_tcl_script()
: colvarmodule
- runave
: colvar
- runave_length
: colvar
- runave_outfile
: colvar
- runave_stride
: colvar
- runave_variance
: colvar
- runbar
: wkf_threadpool_struct
- runcommand()
: UIObject, CommandQueue
- runtitle
: QMData
- runtype
: QMData
- rvector()
: colvarmodule::rvector
- rvector_value
: colvarvalue
- rx
: mobilehandle, spaceballevent
- Rxcrds
: glwin_warp_hmd
- ry
: mobilehandle, spaceballevent
- Rycrds
: glwin_warp_hmd
- rz
: mobilehandle, spaceballevent
- s -
- S
: elementsummary, colvarmodule::rotation
- s
: wkf_tilestack_t, ptrstack, intstack, GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >, ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >, CmdScale, atomparser_string
- S_backup
: colvarmodule::rotation
- S_eigval
: colvarmodule::rotation
- S_eigvec
: colvarmodule::rotation
- safely_read_restart
: colvarbias_meta
- samples
: colvar_grid_gradient, colvar_grid_scalar
- sasalist
: sasathreadparms
- save_state()
: VMDApp, UIText
- saved_exec_string()
: FileRenderer
- SaveTrajectoryFltkMenu()
: SaveTrajectoryFltkMenu
- sball
: glxdata, oglhandle
- sballevent
: glxdata, oglhandle
- scalable_group_coms()
: colvarproxy_atom_groups
- scalar_add()
: VolumetricData
- SCALE
: Command
- scale
: Matrix4, FileRenderer, colvarbias_meta::hill, CmdToolScaleSpring, CmdToolScaleForce, CmdToolScale, Displayable
- scale_by()
: VolumetricData
- SCALE_CURSOR
: DisplayDevice
- scale_factor()
: MoleculeGraphics, FileRenderer, DrawMolecule
- scale_off()
: Displayable
- scale_on()
: Displayable
- scale_radius()
: FileRenderer
- scale_volume()
: VolumetricData
- scalemax
: CmdMolScaleMinmax
- scalemin
: CmdMolScaleMinmax
- SCALEROTZ
: Mobile
- ScaleSpaceFilter()
: ScaleSpaceFilter< GROUP_T, IMAGE_T >
- SCALING
: Win32Joystick, Spaceball, Mouse
- scaling()
: Displayable
- scene
: M_VRJapp, VMDApp, Displayable
- Scene()
: Scene
- scene_resetview()
: VMDApp
- scene_resetview_newmoldata()
: VMDApp
- scene_rock()
: VMDApp
- scene_rockoff()
: VMDApp
- scene_rotate_by()
: VMDApp
- scene_rotate_to()
: VMDApp
- scene_scale_by()
: VMDApp
- scene_scale_to()
: VMDApp
- scene_stoprotation()
: VMDApp
- scene_translate_by()
: VMDApp
- scene_translate_to()
: VMDApp
- scftype
: QMData
- score_axis()
: Symmetry
- score_inversion()
: Symmetry
- score_plane()
: Symmetry
- score_rotary_reflection()
: Symmetry
- scramble_array()
: AtomGrid
- screen_height()
: DisplayDevice
- screenX
: DisplayDevice
- screenY
: DisplayDevice
- script
: colvarproxy_script
- scripted_forces()
: colvarmodule
- scripted_function
: colvar
- scripting_after_biases
: colvarmodule
- scrnum
: oglhandle
- search()
: JRegex
- segment()
: Segmentation
- Segmentation()
: Segmentation
- segments_d
: watershed_gpu_state_t< GROUP_T, IMAGE_T >
- SEGNAME
: AtomColor
- segnameindex
: MolAtom
- segNames
: BaseMolecule
- SEL
: CmdMolChangeRepItem
- sel
: VolMapCreate, qcprmsdthreadparms, clusterparms_t, AtomSelThr, gpuqcprmsdthreadparms, CmdMolColor, CmdMolRep, CmdMolSelect
- SEL_REGEN
: DrawMolItem
- selbuilder
: GraphicsFltkMenu
- sele
: atomparser_node
- select_atoms()
: SaveTrajectoryFltkMenu
- select_tool()
: ToolFltkMenu
- select_tool_type()
: ToolFltkMenu
- selected
: AtomSel
- selected_molid
: SaveTrajectoryFltkMenu
- selection
: MoleculeList, FileSpec, CoorPluginData
- SelectionBuilder()
: SelectionBuilder
- selectiontext()
: GraphicsFltkMenu
- selectmol()
: VMDMenu, SaveTrajectoryFltkMenu, GraphicsFltkMenu, FileChooserFltkMenu
- self
: orbital_cbdata, isosurface_cbdata, quicksurf_cbdata
- selfcoordnum()
: colvar::selfcoordnum
- sellist
: sasathreadparms
- selupdate
: clusterparms_t
- send()
: Inform
- send_alch_lambda()
: colvarproxy_vmd, colvarproxy_system
- send_cylinder_buffer()
: OSPRayDisplayDevice, OSPRay2DisplayDevice, OptiXDisplayDevice
- send_forces()
: IMDSimThread, IMDSimBlocking, IMDSim, IMDMgr
- send_sphere_buffer()
: OptiXDisplayDevice
- send_triangle_buffer()
: OSPRayDisplayDevice, OSPRay2DisplayDevice, OptiXDisplayDevice, ANARIDisplayDevice
- sendforce()
: VRPNFeedback, Tool, Feedback
- sendMsgToClient()
: Mobile
- SensorConfig()
: SensorConfig
- seqnum
: mobilehandle
- serial
: VMDDisplayList
- set()
: AtomGrid, AtomGridCell, colvarmodule::quaternion, colvarmodule::rvector, colvarmodule::matrix2d< T >::row
- set_aa_samples()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_aasamples()
: FileRenderer
- set_activeClient()
: Mobile
- set_alch_lambda()
: colvarproxy_system
- set_alignsel()
: VolMapCreateILS
- set_ambient()
: MaterialList
- set_angletype()
: BaseMolecule
- set_angular_momenta()
: QMData
- set_angular_momentum()
: QMData
- set_angular_momentum_str()
: QMData
- set_ao_ambient()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, DisplayDevice, ANARIRender
- set_ao_direct()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, DisplayDevice, ANARIRender
- set_ao_mode()
: DisplayDevice
- set_ao_samples()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_aosamples()
: FileRenderer
- set_array()
: DispCmdTriangle
- set_aspectratio()
: FileRenderer
- set_autoupdate()
: GraphicsFltkMenu
- set_backgradient()
: OpenGLRenderer, FileRenderer, DisplayDevice
- set_background()
: OpenGLRenderer, FileRenderer, DisplayDevice
- set_background_mode()
: Scene, DisplayDevice
- set_bg_color()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_bg_color_grad_bot()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_bg_color_grad_top()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_bg_gradient()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_bg_gradient_botval()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_bg_gradient_topval()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_bg_mode()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_buttons()
: UIVR
- set_cache_mode()
: OpenGLRenderer, DisplayDevice
- set_callbacks()
: UIObject
- set_camera_dof_fnumber()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_camera_dof_focal_dist()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_camera_projection()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_camera_stereo_convergence_dist()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_camera_stereo_eyesep()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_camera_zoom()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- set_carthessian()
: QMData
- set_category_item()
: Scene
- set_cent_trans()
: Displayable
- set_charges()
: QMTimestep
- set_checkbonds()
: Symmetry
- set_checkpoint()
: VolMapCreate
- set_clip_center()
: VMDDisplayList, Displayable
- set_clip_color()
: VMDDisplayList, Displayable
- set_clip_normal()
: VMDDisplayList, Displayable
- set_clip_sphere()
: OptiXRenderer
- set_clip_status()
: VMDDisplayList, Displayable
- set_clipview_mode()
: OptiXRenderer
- set_coeffs()
: Wavefunction
- set_color()
: X3DDisplayDevice, VrmlDisplayDevice, Vrml2DisplayDevice, RadianceDisplayDevice, MoleculeList, GeometryMol, FileRenderer
- set_color_rgb3fv()
: IsoSurface
- set_color_value()
: Scene
- set_color_voltex_rgb3fv()
: IsoSurface
- set_colorscale_colors()
: VMDApp, Scene
- set_colorscale_method()
: Scene
- set_colorscale_minmax()
: AtomColor
- set_colorscale_params()
: Scene
- set_colorupdate()
: GraphicsFltkMenu
- set_copyunitcell()
: IMDMgr
- set_coupling
: colvarbias_alb
- set_cue_density()
: DisplayDevice
- set_cue_end()
: DisplayDevice
- set_cue_mode()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, DisplayDevice, ANARIRender
- set_cue_start()
: DisplayDevice
- set_cursor()
: OpenGLPbufferDisplayDevice, OpenGLDisplayDevice, FltkOpenGLDisplayDevice, DisplayDevice
- set_cvc_flags()
: colvar
- set_cvc_param()
: colvar
- set_data()
: NameList< T >, myFl_Chart
- set_dataset_flag()
: BaseMolecule
- set_default_color()
: MoleculeList
- set_default_material()
: MoleculeList
- set_default_representation()
: MoleculeList
- set_default_selection()
: MoleculeList
- set_diffuse()
: MaterialList
- set_dihedraltype()
: BaseMolecule
- set_div()
: integrate_potential
- set_dof_fnumber()
: DisplayDevice
- set_dof_focal_dist()
: DisplayDevice
- set_dof_mode()
: DisplayDevice
- set_double_fctn
: SymbolTableElement
- set_drawframes()
: DrawMolItem
- set_dummy()
: atom_group
- set_dummy_pos()
: atom_group
- set_elem()
: colvarvalue
- set_enabled()
: colvardeps
- set_eofexit()
: VMDApp
- set_error_bits()
: colvarmodule
- set_exec_string()
: FileRenderer
- set_eye_defaults()
: DisplayDevice
- set_eye_dir()
: DisplayDevice
- set_eye_dist()
: DisplayDevice
- set_eye_pos()
: DisplayDevice
- set_eye_up()
: DisplayDevice
- set_eyesep()
: DisplayDevice
- set_far_clip()
: DisplayDevice
- set_fctn
: SymbolTableElement
- set_feedback()
: UIVR
- set_force()
: PickModeForce
- set_force_scale()
: UIVR
- set_forcescale()
: ToolFltkMenu
- set_format()
: FileRenderList, FileRenderer
- set_frame()
: colvarproxy_vmd, colvarproxy_io
- set_from_euler_angles()
: colvarmodule::quaternion
- set_function_type()
: colvar::cvc
- set_glob_trans()
: Displayable
- set_gradients()
: QMTimestep
- set_grid()
: Orbital
- set_grid_stepsize()
: GraphicsFltkRepOrbital, GraphicsFltkRepIsosurface
- set_grid_to_bbox()
: Orbital
- set_gridspacing_multiplier()
: GraphicsFltkRepQuickSurf
- set_headlight_onoff()
: OptiXRenderer
- set_imagesize()
: FileRenderer
- set_imagmodes()
: QMData
- set_impropertype()
: BaseMolecule
- set_instances()
: DrawMolItem
- set_int_fctn
: SymbolTableElement
- set_intensities()
: QMData
- set_inthessian()
: QMData
- set_keep_rate()
: IMDMgr
- set_keyword_double
: SymbolTableElement
- set_keyword_int
: SymbolTableElement
- set_keyword_single
: SymbolTableElement
- set_keyword_string
: SymbolTableElement
- set_left_rot()
: VMDTracker
- set_line_style()
: OpenGLRenderer, FileRenderer
- set_line_width()
: POV3DisplayDevice, OpenGLRenderer, FileRenderer
- set_material()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, MoleculeList, FileRenderer, ANARIRender
- set_max_stride()
: Spaceball, Mobile
- set_maxenergy()
: VolMapCreateILS
- set_maxforce()
: Feedback
- set_maxnumatoms()
: Symmetry
- set_minmax()
: VolMapCreateILS, VolMapCreate
- set_mirror()
: MaterialList
- set_mouse_callbacks()
: VMDApp
- set_mouse_rocking()
: VMDApp
- set_name()
: VolumetricData, NameList< T >, MaterialList
- set_natoms()
: MolFilePlugin
- set_near_clip()
: DisplayDevice
- set_normalmodes()
: QMData
- set_null_region()
: Spaceball
- set_occupancies()
: Wavefunction
- set_offset()
: ToolFltkMenu, VMDTracker
- set_ones()
: colvarvalue
- set_opacity()
: MaterialList
- set_orbenergies()
: Wavefunction
- set_orbids()
: Wavefunction
- set_orbitalenergies()
: QMTimestep
- set_outline()
: MaterialList
- set_outlinewidth()
: MaterialList
- set_overlaptol()
: Symmetry
- set_param()
: colvarparams, colvar::cvc
- set_pbc()
: VolMapCreateILS, GraphicsFltkMenu, DrawMolItem
- set_pbc_images()
: DrawMolItem
- set_persp()
: OpenGLRenderer
- set_pick()
: GeometrySpring, GeometryMol, GeometryDihedral, GeometryBond, GeometryAtom, GeometryAngle
- set_pick_mode()
: PickModeList
- set_pick_selection()
: GeometryMol
- set_pick_value()
: GeometryMol
- set_position_scale()
: UIVR
- set_positionscale()
: ToolFltkMenu
- set_positive()
: colvarmodule::quaternion
- set_probe()
: VolMapCreateILS
- set_probe_symmetry()
: VolMapCreateILS
- set_projection()
: DisplayDevice
- set_radii_changed()
: BaseMolecule
- set_random()
: colvarvalue
- set_render_mode()
: OpenGLRenderer, DisplayDevice
- set_render_option()
: FileRenderList
- set_representation()
: MoleculeList
- set_resolution()
: Orbital
- set_result_colvarvalue()
: colvarscript
- set_result_colvarvalue_vec()
: colvarscript
- set_result_int()
: colvarscript
- set_result_int_vec()
: colvarscript
- set_result_long_int()
: colvarscript
- set_result_long_int_vec()
: colvarscript
- set_result_real()
: colvarscript
- set_result_real_vec()
: colvarscript
- set_result_rvector()
: colvarscript
- set_result_rvector_vec()
: colvarscript
- set_result_str()
: colvarscript
- set_result_text()
: colvarscript
- set_right_rot()
: VMDTracker
- set_rocking()
: Mouse
- set_rot()
: Displayable
- set_scale()
: VMDTracker, Displayable
- set_scfenergies()
: QMTimestep
- set_screen_pos()
: DisplayDevice
- set_selection()
: SelectionBuilder, MoleculeList
- set_sensitivity()
: Spaceball
- set_shadow_mode()
: DisplayDevice
- set_shininess()
: MaterialList
- set_single_fctn
: SymbolTableElement
- set_size()
: ResizeArray< T >
- set_sizes()
: colvar_grid< T >
- set_smoothing()
: DrawMolItem
- set_specular()
: MaterialList
- set_sphere_mode()
: OpenGLRenderer
- set_sphere_res()
: OpenGLRenderer, FileRenderer
- set_sphere_style()
: FileRenderer
- set_spring_scale()
: UIVR
- set_springscale()
: ToolFltkMenu
- set_state_params()
: colvarbias_restraint_linear, colvarbias_restraint_harmonic_walls, colvarbias_restraint_harmonic, colvarbias_restraint_k_moving, colvarbias_restraint_centers_moving, colvarbias_restraint_moving, colvarbias_restraint, colvarbias_meta, colvarbias_alb, colvarbias_ti, colvarbias
- set_stereo_mode()
: VRJugglerDisplayDevice, OpenGLRenderer, FreeVRDisplayDevice, DisplayDevice, CaveDisplayDevice
- set_stereo_swap()
: DisplayDevice
- set_string()
: colvarparse
- set_string_fctn
: SymbolTableElement
- set_target_bitrate_Mbps()
: VideoStream
- set_target_frame_rate()
: VideoStream
- set_target_temperature()
: colvarproxy_system
- set_tcl_interp()
: colvarproxy_tcl
- set_text()
: VMDApp
- set_text_format()
: GeometryMol
- set_text_offset()
: GeometryMol
- set_text_size()
: GeometryMol
- set_text_thickness()
: GeometryMol
- set_toolrep()
: ToolFltkMenu
- set_tracker()
: UIVR
- set_trans_rate()
: IMDMgr
- set_transform()
: VolMapCreateILS
- set_transmode()
: MaterialList
- set_transrate()
: IMDSimThread, IMDSimBlocking, IMDSim
- set_unit_system()
: colvarproxy_vmd, colvarproxy_system
- set_value()
: colvar_grid< T >, colvar::cvc, UIestimator::n_vector< T >, UIestimator::n_matrix
- set_values()
: GraphicsFltkRepFieldLines, GraphicsFltkRepOrbital, GraphicsFltkRepVolumeSlice, GraphicsFltkRepIsosurface, GraphicsFltkRepSurf, GraphicsFltkRepQuickSurf, GraphicsFltkRepHBonds, GraphicsFltkRepNanoShaper, GraphicsFltkRepMSMS, GraphicsFltkRepSolvent, GraphicsFltkRepNewCartoon, GraphicsFltkRepNewRibbons, GraphicsFltkRepRibbons, GraphicsFltkRepLicorice, GraphicsFltkRepVDW, GraphicsFltkRepPoints, GraphicsFltkRepCPK, GraphicsFltkRepDynamicBonds, GraphicsFltkRepBonds, GraphicsFltkRepLines, GraphicsFltkRep
- set_volume_axes()
: VolumetricData
- set_volume_gradient()
: VolumetricData
- set_volume_origin()
: VolumetricData
- set_wavef_idtag()
: QMTimestep
- set_wavefunction()
: QMTimestep
- set_wavenumbers()
: QMData
- set_weighted_gradient()
: atom_group
- set_window_title()
: OpenGLRenderer, OpenGLDisplayDevice
- set_zero_minimum()
: integrate_potential
- setbondorder()
: BaseMolecule
- setbondtype()
: BaseMolecule
- setconstraint()
: Tool
- setforcefield()
: Tool
- setforcescale()
: Tool
- setGridData()
: VolumeTexture
- setids
: FileSpec
- SetIsovalue()
: CUDAMarchingCubes
- setoffset()
: Tool
- setplaneconstraint()
: Tool
- setscale()
: Tool
- setScene()
: M_VRJapp
- setspringscale()
: SpringTool, TugTool, Tool, PinchTool
- setString()
: TextInterp, TclTextInterp
- SetSubVolume()
: CUDAMarchingCubes
- setTextFormat()
: GeometryList
- setTextOffset()
: GeometryList
- setTextSize()
: GeometryList
- setTextThickness()
: GeometryList
- setup()
: colvarproxy_vmd, colvarproxy, colvar_grid< T >, colvar::cvc, atom_group, colvar
- setup_context()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- setup_initial_opengl_state()
: OpenGLRenderer
- setup_input()
: colvarmodule
- setup_output()
: colvarmodule, colvarbias_meta, colvarbias
- setvalue()
: RepChoiceSmall, RepChoice
- SetVolumeData()
: CUDAMarchingCubes
- shadowEnabled
: DisplayDevice
- ShadowMode
: DisplayDevice
- shadows_enabled()
: DisplayDevice
- SHADOWS_OFF
: DisplayDevice
- shadows_on()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- SHADOWS_ON
: DisplayDevice
- Shapes
: MoleculeGraphics
- sharedData
: M_VRJapp
- sharesLinkageEdges()
: SmallRingLinkages
- shearstereo
: OpenGLRenderer
- shell
: basis_atom_t
- shell_symmetry
: orbthrparms
- shell_types
: orbthrparms
- SHIFT
: DisplayDevice
- shift_state()
: OpenGLPbufferDisplayDevice, OpenGLDisplayDevice, FltkOpenGLDisplayDevice, DisplayDevice
- shininess
: VMDDisplayList, osp_material, ort_material, Material, anr_material
- ShortSlider()
: ShortSlider
- show()
: MoleculeList
- show_geometry()
: GeometryList
- show_rep()
: DrawMolecule
- show_repcontrols()
: GraphicsFltkMenu
- show_stride_message()
: VMDApp
- sigma
: VolumetricData, Symmetry, elementsummary
- sigma_scale()
: VolumetricData
- sigmas
: colvarbias_meta::hill
- sign
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- simplegraphics
: OpenGLRenderer
- simstate
: IMDSim
- simulation_continuing()
: colvarproxy
- simulation_running()
: colvarproxy
- sin()
: colvarmodule
- single_fctn
: SymbolTableElement
- single_replica
: colvarbias_meta
- singleword
: atomsel_ctxt
- SINGLEWORD
: SymbolTableElement
- sint
: netint
- size
: Stage, IndexList, colvarvalue, colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >, colvarmodule, atom_group, wkf_tilestack_t, ptrstack, intstack, inthash_t, hash_t, DispCmdLitPointArray, DispCmdPointArray, CmdLabelTextSize
- sizeHints
: glxdata
- sizes()
: colvar_grid< T >
- skip()
: MolFilePlugin, Animation
- skip_list
: clusterparms_t
- slice()
: colvarmodule::vector1d< T >
- sliceassign()
: colvarmodule::vector1d< T >
- SmallRing()
: SmallRing
- SmallRingLinkages()
: SmallRingLinkages
- smcount
: cudadevprops
- smp_biases_loop()
: colvarproxy_smp
- smp_biases_script_loop()
: colvarproxy_smp
- smp_colvars_loop()
: colvarproxy_smp
- smp_enabled()
: colvarproxy_smp
- smp_lock()
: colvarproxy_smp
- smp_num_threads()
: colvarproxy_smp
- smp_thread_id()
: colvarproxy_smp
- smp_trylock()
: colvarproxy_smp
- smp_unlock()
: colvarproxy_smp
- smtdepth
: wkf_cpu_caps_struct
- SnapshotDisplayDevice()
: SnapshotDisplayDevice
- sock
: IMDSim
- sockaddr
: mobilehandle
- sockfd
: mobilehandle
- solidSphereLists
: OpenGLRenderer
- SOLVENT
: AtomRep
- sort_items()
: GeometryMol
- sort_orbitals()
: QMTimestep, Wavefunction
- sort_wave_coefficients()
: Wavefunction
- SortableArray()
: SortableArray< T >
- sorted_atoms_ids
: atom_group
- sorted_atoms_ids_map
: atom_group
- sorted_cvc_values
: colvar
- sorted_ids()
: atom_group
- sorted_ids_map()
: atom_group
- spaceball()
: OpenGLPbufferDisplayDevice, OpenGLDisplayDevice, FltkOpenGLDisplayDevice, DisplayDevice
- Spaceball()
: Spaceball
- spaceball_cb()
: TextInterp, TclTextInterp
- spaceball_get_tracker_status()
: VMDApp
- SPACEBALL_MODE
: Command
- spaceball_set_mode()
: VMDApp
- spaceball_set_null_region()
: VMDApp
- spaceball_set_sensitivity()
: VMDApp
- SpaceballButtons()
: SpaceballButtons
- SpaceballEvent()
: SpaceballEvent
- spaceballMode
: CmdSpaceballMode
- SpaceballTracker()
: SpaceballTracker
- spdpfpperfratio
: cudadevprops
- spec
: CmdMolLoad
- specular
: VMDDisplayList, osp_material, ort_material, Material, anr_material
- speed()
: Animation
- sphere()
: X3DDisplayDevice, VrmlDisplayDevice, Vrml2DisplayDevice, TachyonDisplayDevice, RenderManDisplayDevice, RayShadeDisplayDevice, RadianceDisplayDevice, R3dDisplayDevice, POV3DisplayDevice, OptiXDisplayDevice, MayaDisplayDevice, LibTachyonDisplayDevice, LibGelatoDisplayDevice, GelatoDisplayDevice, FileRenderer, ArtDisplayDevice
- SPHERE
: MoleculeGraphics
- sphere_array()
: TachyonDisplayDevice, OSPRayRenderer, OSPRayDisplayDevice, OSPRay2Renderer, OSPRay2DisplayDevice, OptiXRenderer, OptiXDisplayDevice, LibTachyonDisplayDevice, FileRenderer, ANARIRender, ANARIDisplayDevice
- sphere_array_color()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- SphereList
: OpenGLRenderer
- sphereMode
: DisplayDevice
- spherepts
: sasathreadparms
- SPHERERAD
: AtomRep
- sphereres
: DispCmdSphereArray
- SPHERERES
: AtomRep
- sphereRes
: DisplayDevice
- sphereResolution
: FileRenderer
- sphereStyle
: FileRenderer
- SPHERETUBE
: MoleculeGraphics
- sphericaltop
: Best
- spin
: wavef_signa_t
- spin_angle()
: colvarmodule::rotation, colvar::spin_angle
- spline_basis
: DrawMolItem
- split
: Msmpot_t
- split_string()
: colvarparse
- spotdir
: FileRenderer::AdvancedLightState
- spoton
: FileRenderer::AdvancedLightState
- springscale
: Tool
- SpringTool()
: SpringTool
- sqrt()
: colvarmodule
- square()
: RenderManDisplayDevice, RadianceDisplayDevice, LibGelatoDisplayDevice, GelatoDisplayDevice, FileRenderer, ArtDisplayDevice
- srad
: sasathreadparms
- srv_check_ui_event()
: VideoStream
- srv_connect()
: VideoStream
- srv_connected()
: VideoStream
- srv_disconnect()
: VideoStream
- srv_get_last_event_type()
: VideoStream
- srv_get_last_keyboard()
: VideoStream
- srv_get_last_rotate_by()
: VideoStream
- srv_get_last_scale_by()
: VideoStream
- srv_get_last_translate_by()
: VideoStream
- srv_gethost()
: VideoStream
- srv_getport()
: VideoStream
- srv_listen()
: VideoStream
- srv_process_all_events()
: VideoStream
- srv_send_frame()
: VideoStream
- ssd
: colvarbias_alb
- sstruct
: Residue
- st
: atomparser_string
- Stack()
: Stack< T >
- stack_size()
: Stack< T >
- stage
: VMDApp, colvarbias_restraint_moving
- Stage()
: Stage
- STAGE_BEHIND
: Stage
- STAGE_LEFT
: Stage
- STAGE_LOWER
: Stage
- STAGE_ORIGIN
: Stage
- STAGE_RIGHT
: Stage
- stage_set_location()
: VMDApp
- stage_set_numpanels()
: VMDApp
- stage_set_size()
: VMDApp
- STAGE_UPPER
: Stage
- StagePos
: Stage
- STAGEPOS_TOTAL
: Stage
- start
: VMDTracker, Feedback, Buttons, wkf_shared_iterator_struct, wkf_tasktile_struct, vmd_cylinder_color, vmd_cylinder
- start_after_steps
: colvarbias_reweightaMD
- start_bits
: real_pcre_extra
- start_clipgroup()
: TachyonDisplayDevice, POV3DisplayDevice, LibTachyonDisplayDevice, FileRenderer
- start_ring
: LinkagePath
- start_rocking()
: DisplayRocker
- start_subject
: match_data
- start_tug()
: SpringTool, TugTool, PinchTool
- starting_force_k
: colvarbias_restraint_k_moving
- startserver()
: VMDCollab
- stat
: Buttons
- state()
: Buttons, PBCControls
- state_file_prefix()
: colvarmodule
- state_file_step
: colvarbias
- state_keyword
: colvarbias
- status
: QMData
- steal_sensor()
: Tool
- stencil
: InterpParams_t
- step
: qcprmsdthreadparms, gpuqcprmsdthreadparms
- step_absolute()
: colvarmodule
- step_number
: colvarmodule
- step_relative()
: colvarmodule
- StepCounter()
: StepCounter
- steps
: CmdRockOn, CmdRotate
- stereo_mode()
: DisplayDevice
- stereo_name()
: DisplayDevice
- stereo_swap()
: DisplayDevice
- stereodrawforced
: OpenGLExtensions
- stereoModes
: DisplayDevice
- stereoNames
: DisplayDevice
- stereoSwap
: DisplayDevice
- STLDisplayDevice()
: STLDisplayDevice
- stop_rocking()
: DisplayRocker
- stop_rotation()
: Mouse
- STOPROT
: Command
- stopserver()
: VMDCollab
- store()
: AtomGrid
- storeData()
: AtomList
- storeFile()
: AtomList
- str
: CmdMolChangeRepItem
- str_result()
: colvarscript
- str_result_
: colvarscript
- stride
: FileSpec
- stridevalue
: FrameSelector
- string_fctn
: SymbolTableElement
- STRINGFCTN
: SymbolTableElement
- stringfctn_fctn
: SymbolTableElement
- strip_values()
: colvarparse
- STRUCTURE
: AtomRep, AtomColor
- subcube_total
: MsmpotCuda_t
- sum
: colvarvalue, colvarmodule::vector1d< T >, barrier_struct
- summary
: PointGroupDefinition
- sup_coeff
: colvar::cvc
- sup_np
: colvar::cvc
- super_load()
: FileRenderer
- super_materials()
: FileRenderer
- super_multmatrix()
: FileRenderer
- super_rot()
: FileRenderer
- super_scale()
: FileRenderer
- super_set_color()
: FileRenderer
- super_set_material()
: FileRenderer
- super_translate()
: FileRenderer
- supersample()
: VolumetricData
- supports_gui()
: VRJugglerDisplayDevice, OpenGLRenderer, OpenGLPbufferDisplayDevice, DisplayDevice
- surf
: anr_cylinder_array_color, anr_sphere_array_color, anr_trimesh_v3f_n3f_c3f
- Surf()
: Surf
- SURF
: AtomRep
- surface_type
: NanoShaperFace, MSMSFace
- sval
: symbol_data
- sW
: colvarbias_meta::hill
- swap()
: SortableArray< T >
- swap4_aligned()
: IMDSim
- switching_function()
: colvar::coordnum
- symbol_data()
: symbol_data
- SymbolTable()
: SymbolTable
- SymbolTableElement()
: SymbolTableElement
- symdesc
: SymbolTableElement
- symmetrictop
: Best
- Symmetry()
: Symmetry
- symtype
: SymbolTableElement
- sz
: gpuseg_temp_storage
- t -
- T
: IMDEnergies
- t
: DispCmdVolSlice
- t_name
: yytoktype
- t_val
: yytoktype
- table
: atomsel_ctxt
- tables
: real_pcre
- TachyonDisplayDevice()
: TachyonDisplayDevice
- tag
: PickEvent, DispCmdPickPoint
- target()
: Tool
- target_centers
: colvarbias_restraint_centers_moving
- target_dist
: colvarbias_meta
- target_equil_steps
: colvarbias_restraint_k_moving
- target_force_k
: colvarbias_restraint_k_moving
- target_nstages
: colvarbias_restraint_moving
- target_nsteps
: colvarbias_restraint_moving
- target_temperature()
: colvarproxy_system
- target_temperature_
: colvarproxy_system
- tcl_available()
: colvarproxy_tcl
- tcl_cb()
: TextInterp, TclTextInterp
- tcl_get_str()
: colvarproxy_tcl
- tcl_interp_
: colvarproxy_tcl
- tcl_run_colvar_callback()
: colvarproxy_tcl
- tcl_run_colvar_gradient_callback()
: colvarproxy_tcl
- tcl_run_file()
: colvarproxy_tcl
- tcl_run_force_callback()
: colvarproxy_tcl
- tcl_run_script()
: colvarproxy_tcl
- TclEvalEvent()
: TclEvalEvent
- TclTextInterp()
: TclTextInterp
- test_dataset_flag()
: BaseMolecule
- testloops
: latthrparms, maddthrparms
- tex
: glwin_fbo_target
- texmap
: DispCmdVolumeTexture
- texmode
: DispCmdVolSlice
- TEXT
: MoleculeGraphics
- text
: X3DOMDisplayDevice, X3DDisplayDevice, Vrml2DisplayDevice, TachyonDisplayDevice, RenderManDisplayDevice, R3dDisplayDevice, POV3DisplayDevice, OSPRayDisplayDevice, OSPRay2DisplayDevice, OptiXDisplayDevice, LibTachyonDisplayDevice, Inform, GelatoDisplayDevice, FileRenderer, DepthSortObject
- text_format()
: GeometryMol
- text_offset()
: GeometryMol
- TextInterp()
: TextInterp
- textinterp_change()
: VMDApp
- texturecache
: OpenGLRenderer
- theta
: colvar::dihedPC, colvar::alpha_angles, colvar::polar_theta, colvar::polar_phi
- theta_ref
: colvar::alpha_angles
- theta_tol
: colvar::alpha_angles
- thickness
: GraphicsFltkRepRibbons, CmdLabelTextThickness
- thrdensitymaps
: densitythrparms
- threadcount
: wkf_threadlaunch_struct, wkf_threadpool_workerdata_struct, clusterparms_t, gofrparms_t, bondsearchthrparms
- threadid
: wkf_threadlaunch_struct, wkf_threadpool_workerdata_struct, clusterparms_t, gofrparms_t, bondsearchthrparms
- threads
: wkf_threadpool_struct
- threshold
: MolData
- THROB
: AtomColor
- thrpool
: wkf_threadpool_workerdata_struct, VMDApp
- thrvoltexmaps
: densitythrparms
- ti_avg_forces
: colvarbias_ti
- ti_bin
: colvarbias_ti
- ti_count
: colvarbias_ti
- ti_system_forces
: colvarbias_ti
- tid
: FindWithinData
- tilt()
: colvar::tilt
- time_dependent_biases()
: colvarmodule
- time_step_factor
: colvardeps
- timer
: wkfmsgtimer
- Timestep()
: Timestep
- timestep()
: AtomSel
- TIMESTEP
: AtomColor
- timestep_cb()
: TextInterp, TclTextInterp, PythonTextInterp
- TimestepEvent()
: TimestepEvent
- timesteps
: Timestep
- tm
: Displayable, CoorPluginData
- tmp_d
: gpuseg_temp_storage
- TO
: CmdScale, CmdTranslate, CmdRotate, CmdRotMat
- to_camel()
: JString
- to_lower_cppstr()
: colvarparse
- to_simple_string()
: colvarvalue, colvarmodule::quaternion, colvarmodule::rvector, colvarmodule::matrix2d< T >, colvarmodule::vector1d< T >
- to_str()
: colvarmodule
- togglepause()
: IMDMgr
- tolerance
: colvar::selfcoordnum, colvar::coordnum
- Tool()
: Tool
- TOOL_ADD_DEVICE
: Command
- TOOL_CALLBACK
: Command
- TOOL_CHANGE
: Command
- tool_change_type()
: VMDApp
- tool_create()
: VMDApp
- TOOL_CREATE
: Command
- tool_delete()
: VMDApp
- TOOL_DELETE
: Command
- TOOL_DELETE_DEVICE
: Command
- tool_location_update()
: Tool
- tool_name()
: UIVR
- TOOL_OFFSET
: Command
- TOOL_REP
: Command
- TOOL_SCALE
: Command
- TOOL_SCALE_FORCE
: Command
- TOOL_SCALE_SPRING
: Command
- tool_set_force_scale()
: VMDApp
- tool_set_position_scale()
: VMDApp
- tool_set_spring_scale()
: VMDApp
- tool_type()
: UIVR
- ToolFltkMenu()
: ToolFltkMenu
- toolnum
: CmdToolRep
- top
: Stack< T >, MoleculeList, wkf_tilestack_t, ptrstack, intstack
- top_backref
: real_pcre
- top_bracket
: real_pcre
- TOTAL
: Command, AtomRep, AtomColor
- total_bias_energy
: colvarmodule
- TOTAL_BUTTONS
: DisplayDevice
- total_charge
: atom_group
- total_force
: colvar::cvc, atom_group, colvar, atom
- total_force_requested
: colvarproxy_system
- total_forces()
: atom_group
- total_forces_enabled()
: colvarproxy_system
- total_forces_same_step()
: colvarproxy_system
- total_frames
: ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >
- total_mass
: atom_group
- total_shells()
: Orbital
- totalcharge
: QMData
- totalframes
: CoorPluginData
- totb
: FindWithinData, bondsearchthrparms
- touchcnt
: mobilehandle
- touchid
: mobilehandle
- TouchMode
: Mobile
- TRACE
: AtomRep
- TRACKER
: Spaceball, Mobile
- trajectory_cb()
: TextInterp, TclTextInterp, PythonTextInterp
- TrajectoryReadEvent()
: TrajectoryReadEvent
- TRANS_CURSOR
: DisplayDevice
- transcnt
: PerRayData_radiance
- TRANSFER
: CmdIMDRate
- transformed_atom_coord()
: GeometryMol
- translate()
: PickModeMoveRep, PickModeMoveMolecule, PickModeMoveFragment, PickModeMoveResidue, PickModeMoveAtom, PickModeMove, Matrix4, FileRenderer
- TRANSLATE
: Mobile, Command
- TRANSLATION
: Win32Joystick, Mouse
- transMat
: FileRenderer, DisplayDevice
- transmode
: VMDDisplayList, osp_material, ort_material, Material, anr_material
- transpose()
: Matrix4, colvarmodule::rmatrix
- transvec()
: Matrix4
- transvecinv()
: Matrix4
- transX
: VMDDisplayList
- transXinv
: VMDDisplayList
- transY
: VMDDisplayList
- transYinv
: VMDDisplayList
- transZ
: VMDDisplayList
- transZinv
: VMDDisplayList
- TRIANGLE
: MoleculeGraphics
- triangle()
: X3DDisplayDevice, WavefrontDisplayDevice, VrmlDisplayDevice, Vrml2DisplayDevice, TachyonDisplayDevice, STLDisplayDevice, RenderManDisplayDevice, RayShadeDisplayDevice, RadianceDisplayDevice, R3dDisplayDevice, POV3DisplayDevice, OSPRayDisplayDevice, OSPRay2DisplayDevice, OptiXDisplayDevice, MayaDisplayDevice, LibTachyonDisplayDevice, LibGelatoDisplayDevice, GelatoDisplayDevice, FileRenderer, ArtDisplayDevice, ANARIDisplayDevice
- TRICOLOR
: MoleculeGraphics
- tricolor()
: X3DDisplayDevice, Vrml2DisplayDevice, TachyonDisplayDevice, RenderManDisplayDevice, R3dDisplayDevice, POV3DisplayDevice, OSPRayDisplayDevice, OSPRay2DisplayDevice, OptiXDisplayDevice, LibTachyonDisplayDevice, LibGelatoDisplayDevice, GelatoDisplayDevice, FileRenderer, ANARIDisplayDevice
- tricolor_list()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- trifan_singlecolor()
: FileRenderer
- trimesh_c3f_n3f_v3f()
: FileRenderer
- trimesh_c4n3v3()
: X3DDisplayDevice, WavefrontDisplayDevice, Vrml2DisplayDevice, TachyonDisplayDevice, RenderManDisplayDevice, POV3DisplayDevice, OSPRayRenderer, OSPRayDisplayDevice, OSPRay2Renderer, OSPRay2DisplayDevice, OptiXRenderer, OptiXDisplayDevice, LibGelatoDisplayDevice, GelatoDisplayDevice, FileRenderer, ANARIRender, ANARIDisplayDevice
- trimesh_c4u_n3b_v3f()
: X3DDisplayDevice, WavefrontDisplayDevice, Vrml2DisplayDevice, TachyonDisplayDevice, RenderManDisplayDevice, POV3DisplayDevice, OSPRayRenderer, OSPRayDisplayDevice, OSPRay2Renderer, OSPRay2DisplayDevice, OptiXRenderer, OptiXDisplayDevice, FileRenderer, ANARIRender, ANARIDisplayDevice
- trimesh_c4u_n3f_v3f()
: OSPRayRenderer, OSPRayDisplayDevice, OSPRay2Renderer, OSPRay2DisplayDevice, OptiXRenderer, OptiXDisplayDevice, FileRenderer, ANARIRender, ANARIDisplayDevice
- trimesh_n3b_v3f()
: OSPRayRenderer, OSPRayDisplayDevice, OSPRay2Renderer, OSPRay2DisplayDevice, OptiXRenderer, OptiXDisplayDevice, FileRenderer, ANARIRender, ANARIDisplayDevice
- trimesh_n3f_v3f()
: OSPRayRenderer, OSPRayDisplayDevice, OSPRay2Renderer, OSPRay2DisplayDevice, OptiXRenderer, OptiXDisplayDevice, FileRenderer, ANARIRender, ANARIDisplayDevice
- trimesh_n3fopt_v3f()
: OptiXDisplayDevice, FileRenderer
- trimesh_singlecolor()
: FileRenderer
- trimesh_v3f()
: OptiXRenderer
- TRINORM
: MoleculeGraphics
- tristrip()
: X3DOMDisplayDevice, X3DDisplayDevice, WavefrontDisplayDevice, Vrml2DisplayDevice, TachyonDisplayDevice, RenderManDisplayDevice, POV3DisplayDevice, OSPRayRenderer, OSPRayDisplayDevice, OSPRay2Renderer, OSPRay2DisplayDevice, OptiXRenderer, OptiXDisplayDevice, LibTachyonDisplayDevice, LibGelatoDisplayDevice, GelatoDisplayDevice, FileRenderer, ANARIRender, ANARIDisplayDevice
- tristrip_singlecolor()
: FileRenderer
- truncatelastn()
: ResizeArray< T >
- TS_LAST
: AtomSel
- TS_NOW
: AtomSel
- ts_page_align_sz
: CoorPluginData
- tstep
: IMDEnergies
- TUBE
: AtomRep
- tug()
: Tool
- TugTool()
: TugTool
- turnOn
: CmdMenuShow
- tx
: mobilehandle, spaceballevent
- ty
: mobilehandle, spaceballevent
- TYPE
: AtomColor
- Type
: colvarvalue
- type
: colvarvalue, VSMsgHeader_t, ColorScaleTypeInfo, shell_t, wavef_signa_t, symbol_data, CmdToolChange, CmdToolCreate, axis, plane, IMDheader, DispCmdLineType, DispCmdSphereType, colvardeps::feature, CmdMolLoad
- type_3vector
: colvarvalue
- type_all
: colvarvalue
- type_checking()
: colvarvalue
- type_desc()
: colvarvalue
- type_keyword()
: colvarvalue
- type_name()
: SpringTool, TugTool, Tool, RotateTool, PrintTool, PinchTool, JoystickTool, GrabTool
- type_notset
: colvarvalue
- type_quaternion
: colvarvalue
- type_quaternionderiv
: colvarvalue
- type_scalar
: colvarvalue
- type_unit3vector
: colvarvalue
- type_unit3vectorderiv
: colvarvalue
- type_vector
: colvarvalue
- typecode()
: NameList< T >
- typeindex
: MolAtom
- tz
: wkf_timer, mobilehandle, spaceballevent
- u -
- UIestimator()
: UIestimator::UIestimator
- UIObject()
: UIObject
- UIText()
: UIText
- uiText
: VMDApp
- uivr
: VMDApp
- UIVR()
: UIVR
- uivs
: VMDApp
- undef_op()
: colvarvalue
- unfix()
: MoleculeList, Displayable
- unfreeze()
: VMDMenu
- ungrab()
: Tool
- uniq_resid
: MolAtom
- unique_name()
: GeometryMol
- uniquegmName
: GeometryMol
- unit()
: colvarmodule::rvector
- unit_cell_x
: colvarproxy_system
- unit_cell_y
: colvarproxy_system
- unit_cell_z
: colvarproxy_system
- units
: colvarproxy_system
- unmute()
: Inform
- unpause()
: IMDSimThread, IMDSimBlocking, IMDSim, IMDMgr
- unregister_monitor()
: DrawMolecule
- unregister_named_atom_group()
: colvarmodule
- unregister_UI()
: CommandQueue
- unset_dataset_flag()
: BaseMolecule
- unsupported_op()
: colvarscript
- up
: RibbonFrame
- upcase()
: JString
- update()
: VRJugglerTracker, OsgNavigator, VRJugglerDisplayDevice, VRJugglerButtons, SpaceballTracker, SpaceballButtons, PhoneTracker, PhoneButtons, VRPNTracker, VRPNFeedback, VRPNButtons, VMDTracker, FreeVRTracker, FreeVRButtons, Feedback, CaveTracker, CaveButtons, Buttons, OpenGLPbufferDisplayDevice, OpenGLDisplayDevice, MolBrowser, MobileTracker, MobileButtons, AtomSelThr, IMDSimBlocking, IMDSim, HMDMgr, PBCControls, GeometryMol, FreeVRDisplayDevice, FltkOpenGLDisplayDevice, FileRenderer, DisplayDevice, colvarbias_restraint_histogram, colvarbias_restraint_linear, colvarbias_restraint_harmonic_walls, colvarbias_restraint_harmonic, colvarbias_restraint_k_moving, colvarbias_restraint_centers_moving, colvarbias_restraint_moving, colvarbias_restraint, colvarbias_meta, colvarbias_reweightaMD, colvarbias_histogram, colvarbias_alb, colvarbias_abf, colvarbias_ti, colvarbias, UIestimator::UIestimator, CaveDisplayDevice
- update_acc_work()
: colvarbias_restraint_k_moving, colvarbias_restraint_centers_moving
- update_active_cvc_square_norm()
: colvar
- update_atomic_properties()
: colvarproxy_vmd
- update_avail_orbs()
: QMData
- update_bias()
: colvarbias_meta
- update_calls
: colvarbias_alb
- update_centers()
: colvarbias_restraint_centers_moving
- update_charge()
: atom
- update_colvar_forces()
: colvarmodule
- update_completion_list()
: TclTextInterp
- update_cvc_config()
: colvar
- update_cvc_flags()
: colvar
- update_div_local()
: integrate_potential
- update_div_neighbors()
: integrate_potential
- update_engine_parameters()
: colvarmodule
- update_exec_cmd()
: TachyonDisplayDevice, FileRenderer
- update_extended_Lagrangian()
: colvar
- update_forces_energy()
: colvar
- update_freq
: colvarbias_alb
- update_grid_data()
: colvarbias_meta
- update_grid_params()
: colvarbias_meta
- update_input()
: colvarproxy_vmd, colvarproxy
- update_lists()
: OpenGLRenderer
- update_macrobrowser()
: SelectionBuilder
- update_mass()
: atom
- update_material()
: Displayable
- update_molchooser()
: GraphicsFltkMenu
- update_output()
: colvarproxy
- update_output_filename()
: UIestimator::UIestimator
- update_pbc()
: GraphicsFltkMenu
- update_pbc_lattice()
: colvarproxy_system
- update_rendering_state()
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- update_rep()
: GraphicsFltkMenu
- update_repbrowser()
: GraphicsFltkMenu
- update_repindex()
: GraphicsFltkMenu
- update_replicas_registry()
: colvarbias_meta
- update_replist()
: ToolFltkMenu
- update_scaleimage()
: ColorFltkMenu
- update_selection()
: SelectionBuilder, GraphicsFltkMenu
- update_shader_uniforms()
: OpenGLRenderer
- update_status
: colvarbias_meta
- update_system_forces()
: colvarbias_ti
- update_toolrep_choosers()
: ToolFltkMenu
- update_total_charge()
: atom_group
- update_total_mass()
: atom_group
- updated_charges()
: colvarproxy_atoms
- updated_charges_
: colvarproxy_atoms
- updated_masses()
: colvarproxy_atoms
- updated_masses_
: colvarproxy_atoms
- UpdateDisplay
: VMDApp
- updateDistanceToReferenceFrames()
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >, ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >
- updatetime
: wkfmsgtimer
- upDir
: DisplayDevice
- upid
: mobilehandle
- upper_boundaries
: colvar_grid< T >
- upper_boundary
: colvar::cvc, colvarbias_restraint_histogram, colvar
- upper_wall_k
: colvarbias_restraint_harmonic_walls
- upper_walls
: colvarbias_restraint_harmonic_walls
- usage()
: usage
- usage_
: colvarmodule
- use_actual_value
: colvar_grid< T >
- use_bias
: colvarscript
- use_color()
: MoleculeGraphics
- use_colors()
: DisplayDevice
- use_colorscale_auto()
: GraphicsFltkMenu
- use_colorscale_minmax()
: GraphicsFltkMenu
- use_colvar
: colvarscript
- use_context()
: ParseTree
- use_grids
: colvarbias_meta
- use_material()
: MoleculeGraphics
- use_materials()
: MoleculeGraphics
- use_module
: colvarscript
- use_molecule()
: SelectionBuilder
- use_scripted_forces
: colvarmodule
- use_second_closest_frame
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- use_third_closest_frame
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- use_z_square
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- UseColor()
: CUDAMarchingCubes
- used
: Buttons
- usepbc
: rdfthrparms
- user
: Timestep
- USER
: Win32Joystick, Spaceball, Mobile, AtomColor
- user2
: Timestep
- USER2
: AtomColor
- user3
: Timestep
- USER3
: AtomColor
- user4
: Timestep
- USER4
: AtomColor
- user_minmax
: VolMapCreate
- userkey_cb()
: TextInterp, TclTextInterp, PythonTextInterp
- userKeyDesc
: VMDApp
- UserKeyEvent()
: UserKeyEvent
- userKeys
: VMDApp
- USERPOINT
: Mouse
- uses_colorscale()
: AtomColor
- UseShader()
: OpenGLShader
- USL
: CmdToolCreate
- v -
- v
: Surf, osp_trimesh_v3f_n3f_c3f, axis, plane, IsoSurface, IsoContour, DispCmdVolSlice, anr_trimesh_v3f_n3f_c3f
- v0
: vmd_trimesh_v3f, vmd_trimesh_n3b_v3f, vmd_trimesh_n3f_v3f, vmd_trimesh_c4u_n3b_v3f, vmd_tricolor, DispCmdVolumeTexture
- v1
: vmd_trimesh_v3f, vmd_trimesh_n3b_v3f, vmd_trimesh_n3f_v3f, vmd_trimesh_c4u_n3b_v3f, vmd_tricolor, DispCmdVolumeTexture, GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- v12
: colvar::distance_xy
- v13
: colvar::distance_xy
- v1v1
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- v1v3
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- v1v4
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- v2
: vmd_trimesh_v3f, vmd_trimesh_n3b_v3f, vmd_trimesh_n3f_v3f, vmd_trimesh_c4u_n3b_v3f, vmd_tricolor, DispCmdVolumeTexture, GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- v2v2
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- v3
: DispCmdVolumeTexture, GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- v3v3
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- v4
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- v4v4
: GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- v_ext
: colvar
- v_fdiff
: colvar
- v_reported
: colvar
- val
: atomic_int_struct, GRIDCELL, SQUARECELL
- value
: GeometryMol, colvar_grid< T >, colvar::cvc, colvarbias_meta::hill, colvar, state_t< GROUP_T, IMAGE_T >
- value_input()
: colvar_grid_gradient, colvar_grid_scalar, colvar_grid_count, colvar_grid< T >
- value_output()
: colvar_grid_gradient, colvar_grid_scalar, colvar_grid< T >
- value_to_bin_scalar()
: colvar_grid< T >
- value_to_bin_scalar_bound()
: colvar_grid< T >
- value_to_bin_scalar_fraction()
: colvar_grid< T >
- value_type
: colvarvalue
- valuePos
: GeometryMol
- variables()
: colvarmodule, colvarbias
- variables_active()
: colvarmodule
- variables_active_smp()
: colvarmodule
- variables_active_smp_items()
: colvarmodule
- VDW
: AtomRep
- vdw_params
: ComputeOccupancyMap_t
- vdw_type
: ComputeOccupancyMap_t
- vdwparms
: occthrparms_t
- vdwtype
: AtomPosType
- vector1d()
: colvarmodule::vector1d< T >
- vector1d_value
: colvarvalue
- vector_gradient_finite_diff()
: colvar_grid_scalar
- vector_value()
: colvar_grid_gradient
- vel
: Timestep, atom
- velocities()
: atom_group
- VELOCITY
: AtomColor
- velocity()
: colvar
- verbose
: densitythrparms
- Verbosity
: OSPRayRenderer, OSPRay2Renderer, OptiXRenderer, ANARIRender
- version()
: colvarmodule
- version_int
: colvarproxy
- version_number()
: colvarproxy, colvarmodule
- version_string
: QMData
- vertex
: NanoShaperFace, MSMSFace
- vertexfusion()
: IsoSurface
- VertexInterp()
: IsoSurface, IsoContour
- VertexShaderObject
: OpenGLShader, glsl_shader
- verts
: osp_trimesh_v3f_n3f_c3f, anr_cylinder_array_color, anr_trimesh_v3f_n3f_c3f
- vertsrads
: osp_cylinder_array_color
- video_frame_force_Iframe()
: VideoStream
- video_frame_pending()
: VideoStream
- VideoStream()
: VideoStream
- visible_name()
: FileRenderer
- VMD
: colvarscript
- vmd
: colvarproxy_vmd
- vmd_choose_file()
: VMDApp
- VMDApp()
: VMDApp
- vmdapp
: DisplayDevice
- VMDClipPlane()
: VMDClipPlane
- vmdcollab
: VMDApp
- VMDCollab()
: VMDCollab
- VMDDisplayList()
: VMDDisplayList
- VMDexit()
: VMDApp
- VMDFltkMenu()
: VMDFltkMenu
- vmdGetProcAddress()
: OpenGLExtensions
- VMDinit()
: VMDApp
- VMDMenu()
: VMDMenu
- vmdmol
: colvarproxy_vmd
- vmdmol_frame
: colvarproxy_vmd
- vmdmolid
: colvarproxy_vmd
- vmdQueryExtension()
: OpenGLExtensions
- vmdQueryGLVersion()
: OpenGLExtensions
- VMDTempFile()
: VMDTempFile
- VMDTitle()
: VMDTitle
- VMDTkinterMenu()
: VMDTkinterMenu
- VMDTkMenu()
: VMDTkMenu
- VMDTracker()
: VMDTracker
- VMDupdate()
: VMDApp
- void()
: OpenGLExtensions
- void_fctn
: SymbolTableElement
- vol
: IsoSurface, IsoContour
- volindex_update()
: GraphicsFltkMenu
- volindex_visible()
: GraphicsFltkMenu
- volmap
: VolMapCreate
- volmap_flag_gradients
: colvarproxy_volmaps
- volmap_flag_null
: colvarproxy_volmaps
- volmap_flag_use_atom_field
: colvarproxy_volmaps
- volmap_id
: colvar::map_total
- volmap_ids_
: colvar
- volmap_index
: colvar::map_total
- volmap_name
: colvar::map_total
- VolMapCreate()
: VolMapCreate
- VolMapCreateCoulombPotential()
: VolMapCreateCoulombPotential
- VolMapCreateCoulombPotentialMSM()
: VolMapCreateCoulombPotentialMSM
- VolMapCreateDensity()
: VolMapCreateDensity
- VolMapCreateDistance()
: VolMapCreateDistance
- VolMapCreateILS()
: VolMapCreateILS
- VolMapCreateInterp()
: VolMapCreateInterp
- VolMapCreateMask()
: VolMapCreateMask
- VolMapCreateOccupancy()
: VolMapCreateOccupancy
- volmaps_available()
: colvarproxy_volmaps
- volmaps_ids
: colvarproxy_volmaps
- volmaps_max_applied_force_
: colvarproxy_volmaps
- volmaps_new_colvar_forces
: colvarproxy_volmaps
- volmaps_refcount
: colvarproxy_volmaps
- volmaps_rms_applied_force_
: colvarproxy_volmaps
- volmaps_values
: colvarproxy_volmaps
- VOLSLICE
: AtomRep
- VolTexFormat
: CUDAQuickSurf, CUDAMarchingCubes
- VOLUME
: AtomColor
- volume_index()
: AtomColor
- volume_texture_off()
: TachyonDisplayDevice, LibTachyonDisplayDevice, FileRenderer
- volume_texture_on()
: TachyonDisplayDevice, LibTachyonDisplayDevice, FileRenderer
- volumeList
: BaseMolecule
- VolumeTexture()
: VolumeTexture
- VolumetricData()
: VolumetricData
- voxel_coord()
: VolumetricData
- voxel_coord_from_cartesian_coord()
: VolumetricData
- voxel_gradient_fast()
: VolumetricData
- voxel_gradient_from_coord()
: VolumetricData
- voxel_gradient_interpolate()
: VolumetricData
- voxel_gradient_interpolate_from_coord()
: VolumetricData
- voxel_gradient_safe()
: VolumetricData
- voxel_index_from_coord()
: VolumetricData
- voxel_value()
: VolumetricData
- voxel_value_from_coord()
: VolumetricData
- voxel_value_from_coord_safe()
: VolumetricData
- voxel_value_interpolate()
: VolumetricData
- voxel_value_interpolate_from_coord()
: VolumetricData
- voxel_value_interpolate_from_coord_safe()
: VolumetricData
- voxel_value_safe()
: VolumetricData
- voxelsize
: orbthrparms
- VRJugglerButtons()
: VRJugglerButtons
- VRJugglerDisplayDevice()
: VRJugglerDisplayDevice
- VRJugglerScene()
: VRJugglerScene
- VRJugglerTracker()
: VRJugglerTracker
- Vrml2DisplayDevice()
: Vrml2DisplayDevice
- VrmlDisplayDevice()
: VrmlDisplayDevice
- VRPNButtons()
: VRPNButtons
- VRPNFeedback()
: VRPNFeedback
- VRPNTracker()
: VRPNTracker
- vs_connect()
: VMDApp
- vs_connected()
: VMDApp
- vs_disconnect()
: VMDApp
- VS_EV_KEYBOARD
: VideoStream
- VS_EV_NONE
: VideoStream
- VS_EV_ROTATE_BY
: VideoStream
- VS_EV_SCALE_BY
: VideoStream
- VS_EV_TRANSLATE_BY
: VideoStream
- VSEventDev
: VideoStream
- vSize
: DisplayDevice
- vx
: vmdwinjoystick
- vy
: vmdwinjoystick
- vz
: vmdwinjoystick
- w -
- W
: colvarbias_meta::hill
- wait()
: TclTextInterp
- WAIT_ALL
: FileSpec
- WAIT_BACK
: FileSpec
- WAIT_CURSOR
: DisplayDevice
- wait_cv
: wkf_run_barrier_struct, barrier_struct
- waitfor
: FileSpec
- WaitFor
: FileSpec
- waitForKernelStop()
: VRJugglerScene
- want_command()
: UIObject
- warningflags
: FileRenderer
- wasgrabbing
: Tool
- Watershed()
: Watershed< GROUP_T, IMAGE_T >
- watershed()
: Watershed< GROUP_T, IMAGE_T >
- wave_f
: orbthrparms
- WAVEFNCEXCITATION
: AtomRep
- wavefncexcitation
: GraphicsFltkRepOrbital
- WAVEFNCSPIN
: AtomRep
- wavefncspin
: GraphicsFltkRepOrbital
- WAVEFNCTYPE
: AtomRep
- wavefnctype
: GraphicsFltkRepOrbital
- WavefrontDisplayDevice()
: WavefrontDisplayDevice
- Wavefunction()
: Wavefunction
- weight
: colvarbias_meta::hill, VolMapCreateInterp, VolMapCreateDensity, axis, plane
- weight_mutable
: VolMapCreateInterp, VolMapCreateDensity
- weight_string
: VolMapCreateInterp, VolMapCreateDensity
- weights
: clusterparms_t, colvar_grid_gradient, colvarbias_histogram, ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >
- well_tempered
: colvarbias_meta
- where()
: VMDTkMenu, VMDTkinterMenu, VMDMenu, VMDFltkMenu
- which_frame
: AtomSel, atomsel_ctxt
- whichEye
: DisplayDevice
- whichFrame
: CmdAnimDup
- whichMol
: CmdMolShowRep, CmdMolSmoothRep, CmdMolDrawFrames, CmdMolScaleMinmax, CmdMolShowInstances, CmdMolNumPeriodic, CmdMolShowPeriodic, CmdMolRename, CmdMolVolume, CmdMolSSRecalc, CmdMolBondsRecalc, CmdMolReanalyze, CmdMolDeleteRep, CmdMolRepColorUpdate, CmdMolRepSelUpdate, CmdMolChangeRepItem, CmdMolChangeRep, CmdMolAddRep, CmdMolTop, CmdMolOn, CmdMolFix, CmdMolActive, CmdMolDelete, CmdMolCancel, CmdAnimDup, CmdAnimDelete, CmdAnimWriteFile
- white_space
: colvarparse
- width
: watershed_gpu_state_t< GROUP_T, IMAGE_T >, VSMsgHeader_t, simenc_handle, oglhandle, DispCmdLineWidth, colvar::cvc, colvarbias_restraint_histogram, colvar
- widths
: colvar_grid< T >
- win
: xinputhandle, oglhandle
- Win32Joystick()
: Win32Joystick
- WIN_KBD
: DisplayDevice
- WIN_KBD_DELETE
: DisplayDevice
- WIN_KBD_DOWN
: DisplayDevice
- WIN_KBD_END
: DisplayDevice
- WIN_KBD_ESCAPE
: DisplayDevice
- WIN_KBD_F1
: DisplayDevice
- WIN_KBD_F10
: DisplayDevice
- WIN_KBD_F11
: DisplayDevice
- WIN_KBD_F12
: DisplayDevice
- WIN_KBD_F2
: DisplayDevice
- WIN_KBD_F3
: DisplayDevice
- WIN_KBD_F4
: DisplayDevice
- WIN_KBD_F5
: DisplayDevice
- WIN_KBD_F6
: DisplayDevice
- WIN_KBD_F7
: DisplayDevice
- WIN_KBD_F8
: DisplayDevice
- WIN_KBD_F9
: DisplayDevice
- WIN_KBD_HOME
: DisplayDevice
- WIN_KBD_INSERT
: DisplayDevice
- WIN_KBD_LEFT
: DisplayDevice
- WIN_KBD_PAGE_DOWN
: DisplayDevice
- WIN_KBD_PAGE_UP
: DisplayDevice
- WIN_KBD_RIGHT
: DisplayDevice
- WIN_KBD_UP
: DisplayDevice
- WIN_LEFT
: DisplayDevice
- WIN_MIDDLE
: DisplayDevice
- WIN_MOUSEX
: DisplayDevice
- WIN_MOUSEY
: DisplayDevice
- WIN_NOEVENT
: DisplayDevice
- WIN_REDRAW
: DisplayDevice
- WIN_RIGHT
: DisplayDevice
- WIN_WHEELDOWN
: DisplayDevice
- WIN_WHEELUP
: DisplayDevice
- window()
: Matrix4
- windowID
: glxdata
- windowProc
: VMDTkMenu
- winsize
: CmdMolSmoothRep
- wiregl
: OpenGLRenderer
- WIREGL
: OpenGLExtensions
- wiremesh()
: FileRenderer
- wmDeleteWindow
: oglhandle
- Workarounds
: ANARIRender
- workercount
: wkf_threadpool_struct
- workerdata
: wkf_threadpool_struct
- wrap()
: colvar_grid< T >, colvar::euler_psi, colvar::euler_phi, colvar::spin_angle, colvar::dihedral, colvar::polar_phi, colvar::distance_z, colvar::cvc, colvar
- wrap_center
: colvar::cvc, colvar
- wrap_edge()
: colvar_grid< T >
- wrap_string()
: colvarmodule
- wrap_xyz()
: AtomGrid
- wrapCoords()
: MolData
- write_1D_integral()
: colvar_grid_gradient
- write_1D_pmf()
: UIestimator::UIestimator
- write_acf()
: colvar
- write_cindexmaterial()
: X3DDisplayDevice
- write_colormaterial()
: X3DDisplayDevice
- write_count()
: colvarbias_reweightaMD
- write_cumulant_expansion_pmf()
: colvarbias_reweightaMD
- write_dx_file()
: VolMapCreate
- write_exponential_reweighted_pmf()
: colvarbias_reweightaMD
- write_files()
: UIestimator::UIestimator
- write_header()
: X3DDisplayDevice, WavefrontDisplayDevice, VrmlDisplayDevice, Vrml2DisplayDevice, TachyonDisplayDevice, STLDisplayDevice, RenderManDisplayDevice, RayShadeDisplayDevice, RadianceDisplayDevice, R3dDisplayDevice, PSDisplayDevice, POV3DisplayDevice, OSPRayDisplayDevice, OSPRay2DisplayDevice, OptiXDisplayDevice, MayaDisplayDevice, LibTachyonDisplayDevice, LibGelatoDisplayDevice, GelatoDisplayDevice, FileRenderer, ArtDisplayDevice, ANARIDisplayDevice
- write_interal_data()
: UIestimator::UIestimator
- write_map()
: VolMapCreateILS, VolMapCreate
- write_multicol()
: colvar_grid_gradient, colvar_grid_scalar, colvar_grid_count, colvar_grid< T >
- write_opendx()
: colvar_grid_gradient, colvar_grid_scalar, colvar_grid_count, colvar_grid< T >
- write_output_files()
: colvarmodule, colvarbias_restraint_histogram, colvarbias_meta, colvarbias_reweightaMD, colvarbias_histogram, colvarbias_ti, colvarbias, colvar
- write_params()
: colvar_grid< T >
- write_pmf()
: colvarbias_meta
- write_raw()
: colvar_grid< T >
- write_replica_state_file()
: colvarbias_meta
- write_restart()
: colvarmodule, colvar_grid< T >
- write_restart_file()
: colvarmodule
- write_restart_string()
: colvarmodule
- write_state()
: colvarbias, colvar
- write_state_data()
: colvarbias_restraint_linear, colvarbias_restraint_harmonic_walls, colvarbias_restraint_harmonic, colvarbias_meta, colvarbias_reweightaMD, colvarbias_histogram, colvarbias_ti, colvarbias
- write_state_prefix()
: colvarbias
- write_state_string()
: colvarbias
- write_state_to_replicas()
: colvarbias_meta, colvarbias
- write_structure()
: MolFilePlugin
- write_timestep()
: MolFilePlugin
- write_trailer()
: X3DDisplayDevice, WavefrontDisplayDevice, VrmlDisplayDevice, Vrml2DisplayDevice, TachyonDisplayDevice, STLDisplayDevice, RenderManDisplayDevice, RayShadeDisplayDevice, RadianceDisplayDevice, R3dDisplayDevice, PSDisplayDevice, POV3DisplayDevice, OSPRayDisplayDevice, OSPRay2DisplayDevice, OptiXDisplayDevice, MayaDisplayDevice, LibTachyonDisplayDevice, LibGelatoDisplayDevice, GelatoDisplayDevice, FileRenderer, ArtDisplayDevice, ANARIDisplayDevice
- write_traj()
: colvarmodule, colvarbias_restraint_histogram, colvarbias_restraint_linear, colvarbias_restraint_harmonic_walls, colvarbias_restraint_harmonic, colvarbias_restraint_k_moving, colvarbias_restraint_centers_moving, colvarbias_restraint, colvarbias_alb, colvarbias, colvar
- write_traj_files()
: colvarmodule
- write_traj_label()
: colvarmodule, colvarbias_restraint_histogram, colvarbias_restraint_linear, colvarbias_restraint_harmonic_walls, colvarbias_restraint_harmonic, colvarbias_restraint_k_moving, colvarbias_restraint_centers_moving, colvarbias_restraint, colvarbias_alb, colvarbias, colvar
- write_volumetric()
: MolFilePlugin
- writehead()
: UIestimator::UIestimator
- writeObject()
: VRJugglerSharedData
- wrot
: glwin_warp_hmd
- wsx
: glwin_warp_hmd
- wsy
: glwin_warp_hmd
- x -
- x
: OpenGLPbufferDisplayDevice, OpenGLDisplayDevice, FltkOpenGLDisplayDevice, DisplayDevice, AtomPosType, AtomEntry, NanoShaperCoord, MSMSCoord, Vector3D, XYZ, XY, colvarmodule::rvector, colvar::cvc, colvar, CmdTranslate
- x0
: ComputeOccupancyMap_t, occthrparms_t
- X3DDisplayDevice()
: X3DDisplayDevice
- X3DOMDisplayDevice()
: X3DOMDisplayDevice
- x_ext
: colvar
- x_history
: colvar
- x_history_p
: colvar
- x_old
: colvar::cvc, colvar
- x_reported
: colvar
- x_restart
: colvar
- xad
: IsoSurface
- xax
: IsoSurface, IsoContour
- xaxis
: VolumetricData
- xb
: FindWithinData
- xcrds
: glwin_warp_hmd
- xinp
: glxdata
- xmax
: Msmpot_t
- xmin
: Msmpot_t
- xOrig
: DisplayDevice
- xpos
: oglhandle
- xrange
: vmdwinjoystick
- xsize
: VolumetricData, DispCmdVolumeTexture
- xSize
: DisplayDevice
- xx
: colvarmodule::rmatrix
- xy
: colvarmodule::rmatrix
- xytotb
: FindWithinData
- xyz
: FindWithinData, osp_sphere_array_color, rdfthrparms, anr_sphere_array_color
- xyz2array
: rdfthrparms
- xyz_reader_use_count
: colvarmodule
- xyzr
: densitythrparms, osp_sphere_array_color
- xz
: colvarmodule::rmatrix
- y -
- y
: OpenGLPbufferDisplayDevice, OpenGLDisplayDevice, FltkOpenGLDisplayDevice, DisplayDevice, AtomPosType, AtomEntry, Vector3D, XYZ, XY, colvarmodule::rvector, CmdTranslate
- y0
: ComputeOccupancyMap_t, occthrparms_t
- yad
: IsoSurface
- yax
: IsoSurface, IsoContour
- yaxis
: VolumetricData
- yb
: FindWithinData
- ycrds
: glwin_warp_hmd
- ymax
: Msmpot_t
- ymin
: Msmpot_t
- yn
: CmdMolOn, CmdMolFix, CmdMolActive
- yOrig
: DisplayDevice
- ypos
: oglhandle
- yrange
: vmdwinjoystick
- ySize
: DisplayDevice
- ysize
: VolumetricData, DispCmdVolumeTexture
- yx
: colvarmodule::rmatrix
- yy
: colvarmodule::rmatrix
- yy_at_bol
: yy_buffer_state
- yy_buf_pos
: yy_buffer_state
- yy_buf_size
: yy_buffer_state
- yy_buffer_status
: yy_buffer_state
- yy_ch_buf
: yy_buffer_state
- yy_fill_buffer
: yy_buffer_state
- yy_input_file
: yy_buffer_state
- yy_is_interactive
: yy_buffer_state
- yy_is_our_buffer
: yy_buffer_state
- yy_n_chars
: yy_buffer_state
- yz
: colvarmodule::rmatrix
- z -
- z
: AtomPosType, AtomEntry, Vector3D, XYZ, colvarmodule::rvector, GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >, ArithmeticPathCV::ArithmeticPathBase< element_type, scalar_type, path_type >, CmdTranslate
- z0
: ComputeOccupancyMap_t, occthrparms_t
- zad
: IsoSurface
- zax
: IsoSurface, IsoContour
- zaxis
: VolumetricData
- zb
: FindWithinData
- zDist
: DisplayDevice
- zero_values()
: Timestep
- zeroforce()
: VRPNFeedback, Feedback
- zmax
: Msmpot_t
- zmin
: Msmpot_t
- zrange
: vmdwinjoystick
- zsize
: VolumetricData, DispCmdVolumeTexture
- zx
: colvarmodule::rmatrix
- zy
: colvarmodule::rmatrix
- zz
: colvarmodule::rmatrix, GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >
- ~ -
Generated on Thu Dec 5 02:44:11 2024 for VMD (current) by
1.2.14 written by Dimitri van Heesch,
© 1997-2002