Renderable labels
"},{"title":"$3Dmol.StateManager","link":"StateManager","description":"$3Dmol.StateManager - StateManager creates the space to preserve the state of the ui and sync it with the GLViewer
"},{"title":"$3Dmol.StateManager#addAtomLabel","link":"addAtomLabel","description":"Adds atom label to the viewport
"},{"title":"$3Dmol.StateManager#addLabel","link":"addLabel","description":"Adds Label to the viewport specific to the selection
"},{"title":"$3Dmol.StateManager#addModel","link":"addModel","description":"Add model to the viewport
"},{"title":"$3Dmol.StateManager#addSelection","link":"addSelection","description":"Add Selection from the ui to glviewer
"},{"title":"$3Dmol.StateManager#addStyle","link":"addStyle","description":"Add style and renders it into the viewport
"},{"title":"$3Dmol.StateManager#addSurface","link":"addSurface","description":"Adds surface to the viewport
"},{"title":"$3Dmol.StateManager#checkAtoms","link":"checkAtoms","description":"Return true if the selections contain at least one atom
"},{"title":"$3Dmol.StateManager#createSelectionAndStyle","link":"createSelectionAndStyle","description":"Updates the state variable for selections and styles and trigger ui to show the
\nui elements for these selections and styles.
Creates selection and add surface with reference to that selection
\nand triggers updates in the ui
Edit the exisiting surface in the viewport
"},{"title":"$3Dmol.StateManager#exitContextMenu","link":"exitContextMenu","description":"Executes hide context menu and process the label if needed
"},{"title":"$3Dmol.StateManager#getSelectionList","link":"getSelectionList","description":"Returns the list of ids of selections that are created so far
"},{"title":"$3Dmol.StateManager#openContextMenu","link":"openContextMenu","description":"Opens context menu when called from glviewer
"},{"title":"$3Dmol.StateManager#removeAtomLabel","link":"removeAtomLabel","description":"Removes the atom label from the viewpoer
"},{"title":"$3Dmol.StateManager#removeStyle","link":"removeStyle","description":"Removes the style specified by stid
"},{"title":"$3Dmol.StateManager#removeSurface","link":"removeSurface","description":"Removes surface from the viewport
"},{"title":"$3Dmol.StateManager#setModelTitle","link":"setModelTitle","description":"Sets the value of title in ModelToolBar
"},{"title":"$3Dmol.StateManager#toggleHide","link":"toggleHide","description":"Toggle the hidden property of the selection
"},{"title":"$3Dmol.StateManager#toggleHideStyle","link":"toggleHideStyle","description":"Toggle hidden property of a style
"},{"title":"$3Dmol.StateManager#updateUI","link":"updateUI","description":"Updates the UI on viewport change
"},{"title":"$3Dmol.UI","link":"UI","description":"$3Dmol.UI - UI creates panels in the viewer to assist control of the viewport
"},{"title":"$3Dmol.UI#Form","link":"Form","description":"This is a colection of contructor to make different input element
"},{"title":"$3Dmol.UI#Form","link":"Form","description":"Creates Form input that takes input from different input element
"},{"title":"$3Dmol.UI#Form.Checkbox","link":"Checkbox","description":"Create Checkbox input for boolean values
"},{"title":"$3Dmol.UI#Form.Color","link":"Color","description":"Create Color input
"},{"title":"$3Dmol.UI#Form.EmptyElement","link":"EmptyElement","description":"Create empty element used for property that whose input cannot be taken
"},{"title":"$3Dmol.UI#Form.Input","link":"Input","description":"Create text, numeric or range Input
"},{"title":"$3Dmol.UI#Form.ListInput","link":"ListInput","description":"Create ListInput input
"},{"title":"$3Dmol.UI#Form.Slider","link":"Slider","description":"Create input for values between two numbers
"},{"title":"$3Dmol.UI#Icons","link":"Icons","description":"Generates the object to hold different icons present Icons : move, rotate, pencil, listArrow, option, minus, plus, painbrush, select, movie.play, move.pause, movie.stop, movie.next, move.previous, tick, cross, edit, remove, list, style, visible, invisible, mouse, nomouse, label, surface, molecule, change
"},{"title":"$3Dmol.UI#resize","link":"resize","description":"Resize the panel with respect to the new viewport
"},{"title":"$3Dmol.VolumeData.getIndex","link":"getIndex"},{"title":"$3Dmol.VolumeData.getIndex","link":"getIndex"},{"title":"$3Dmol.VolumeData.getVal","link":"getVal"},{"title":"$3Dmol.VolumeData.getVal","link":"getVal"},{"title":"Removes the label specific to the selection
\n(under development)
"},{"title":"Removes the selection
"},{"title":"Generates the ui and returns its reference
"},{"title":"Generate Internal alert message
"},{"title":"Generates Internal Info message
"},{"title":"Generates Internal warning message
"},{"title":"Creates all the jquery object of different UI features
"},{"title":"AmbientOcclusionStyle","link":"AmbientOcclusionStyle","description":"AmbientOcclusion style configuration parameters
"},{"title":"AmbientOcclusionStyle#radius","link":"radius","description":"Radius (in Angstroms) used to detect occlusions (default 5.0).
"},{"title":"AmbientOcclusionStyle#strength","link":"strength","description":"Strength (darkness) of shading (default 1.0)
"},{"title":"ArrowSpec","link":"ArrowSpec","description":"Arrow shape specification.
"},{"title":"ArrowSpec#color","link":"color","description":"color
"},{"title":"ArrowSpec#dir","link":"dir","description":"direction to extend from start (instead of specifying end)
"},{"title":"ArrowSpec#end","link":"end","description":"ending position
"},{"title":"ArrowSpec#hidden","link":"hidden","description":"hidden
"},{"title":"ArrowSpec#length","link":"length","description":"length to extend in dir direction from start (instead of specifying end)
"},{"title":"ArrowSpec#mid","link":"mid","description":"relative position of arrow base (0.618034 default)
"},{"title":"ArrowSpec#midpos","link":"midpos","description":"position of arrow base in length units, if negative positioned from end instead of start. Overrides mid.
"},{"title":"ArrowSpec#radius","link":"radius","description":"radius (default 0.1A)
"},{"title":"ArrowSpec#radiusRatio","link":"radiusRatio","description":"ratio of arrow base to cylinder (1.618034 default)
"},{"title":"ArrowSpec#start","link":"start","description":"starting position
"},{"title":"AtomSelectionSpec","link":"AtomSelectionSpec","description":"Atom selection object. Used to specify what atoms should be selected. Can include
\nany field from {@link AtomSpec} in which case atoms must equal the specified value.
\nAll fields must match for the selection to hold. If values
\nare provided as a list, then only one value of the list must match.
take the intersection of the provided lists of {@link AtomSelectionSpec}s
"},{"title":"AtomSelectionSpec#bonds","link":"bonds","description":"overloaded to select number of bonds, e.g. {bonds: 0} will select all nonbonded atoms
"},{"title":"AtomSelectionSpec#byres","link":"byres","description":"if set, expands the selection to include all atoms of any residue that has any atom selected
"},{"title":"AtomSelectionSpec#expand","link":"expand","description":"expands the selection to include all atoms within a given distance from the selection
"},{"title":"AtomSelectionSpec#frame","link":"frame","description":"frame index of individual frame to style; will apply to all frames if not set
"},{"title":"AtomSelectionSpec#index","link":"index","description":"index of the atom or atoms to select
"},{"title":"AtomSelectionSpec#invert","link":"invert","description":"if set, inverts the meaning of the selection
"},{"title":"AtomSelectionSpec#model","link":"model","description":"a single model or list of models from which atoms should be selected. Can also specify by numerical creation order. Reverse indexing is allowed (-1 specifies last added model).
"},{"title":"AtomSelectionSpec#not","link":"not","description":"take the inverse of the provided {@link AtomSelectionSpec}
"},{"title":"AtomSelectionSpec#or","link":"or","description":"take the union of the provided lists of {@link AtomSelectionSpec}s
"},{"title":"AtomSelectionSpec#predicate","link":"predicate","description":"user supplied function that gets passed an {@link AtomSpec} and should return true if the atom should be selected
"},{"title":"AtomSelectionSpec#resi","link":"resi","description":"overloaded to allow ranges and lists of residues, e.g. {resi: "5-10"} or {resi: [5,10,32]}
"},{"title":"AtomSelectionSpec#within","link":"within","description":"intersects the selection with the set of atoms within a given distance from another selection
"},{"title":"AtomSpec","link":"AtomSpec","description":"Atom representation. Depending on the input file format, not all fields may be defined.
"},{"title":"AtomSpec#atom","link":"atom","description":"Atom name; may be more specific than 'elem' (e.g 'CA' for alpha carbon)
"},{"title":"AtomSpec#b","link":"b","description":"Atom b factor data
"},{"title":"AtomSpec#bondOrder","link":"bondOrder","description":"Array of this atom's bond orders, corresponding to bonds identfied by 'bonds'
"},{"title":"AtomSpec#bondStyles","link":"bondStyles","description":"custom bond styling by position in bonds
"},{"title":"AtomSpec#bonds","link":"bonds","description":"Array of atom ids this atom is bonded to
"},{"title":"AtomSpec#callback","link":"callback","description":"Callback click handler function to be executed on this atom and its parent viewer
"},{"title":"AtomSpec#chain","link":"chain","description":"Chain this atom belongs to, if specified in input file (e.g 'A' for chain A)
"},{"title":"AtomSpec#clickable","link":"clickable","description":"Set this flag to true to enable click selection handling for this atom
"},{"title":"AtomSpec#color","link":"color","description":"Atom's color, as hex code or built-in color string
"},{"title":"AtomSpec#elem","link":"elem","description":"Element abbreviation (e.g. 'H', 'Ca', etc)
"},{"title":"AtomSpec#hetflag","link":"hetflag","description":"Set to true if atom is a heteroatom
"},{"title":"AtomSpec#hover_callback","link":"hover_callback","description":"Callback hover handler function to be executed on this atom and its parent viewer
"},{"title":"AtomSpec#hoverable","link":"hoverable","description":"Set this flag to true to enable hover selection handling for this atom
"},{"title":"AtomSpec#index","link":"index","description":"Index of atom in molecule
"},{"title":"AtomSpec#invert","link":"invert","description":"for selection, inverts the meaning of the selection
"},{"title":"AtomSpec#lchain","link":"lchain","description":"Label chain (not author)
"},{"title":"AtomSpec#lresi","link":"lresi","description":"Label residues number (not author)
"},{"title":"AtomSpec#lresn","link":"lresn","description":"Residue label name
"},{"title":"AtomSpec#pdbline","link":"pdbline","description":"If applicable, this atom's record entry from the input PDB file (used to output new PDB from models)
"},{"title":"AtomSpec#properties","link":"properties","description":"Optional mapping of additional properties
"},{"title":"AtomSpec#resi","link":"resi","description":"Residue number
"},{"title":"AtomSpec#resn","link":"resn","description":"Parent residue name
"},{"title":"AtomSpec#serial","link":"serial","description":"Atom's serial id number
"},{"title":"AtomSpec#singleBonds","link":"singleBonds","description":"true if this atom forms only single bonds or no bonds at all
"},{"title":"AtomSpec#ss","link":"ss","description":"Secondary structure identifier (for cartoon render; e.g. 'h' for helix)
"},{"title":"AtomSpec#style","link":"style","description":"style of atom
"},{"title":"AtomSpec#surfaceColor","link":"surfaceColor","description":"Hex code for color to be used for surface patch over this atom
"},{"title":"AtomSpec#unhover_callback","link":"unhover_callback","description":"Callback handling "unhover" to be executed on this atom and its parent viewer
"},{"title":"AtomSpec#x","link":"x","description":"Atom's x coordinate
"},{"title":"AtomSpec#y","link":"y","description":"Atom's y coordinate
"},{"title":"AtomSpec#z","link":"z","description":"Atom's z coordinate
"},{"title":"AtomStyleSpec","link":"AtomStyleSpec","description":"Atom style specification
"},{"title":"AtomStyleSpec#cartoon","link":"cartoon","description":"draw cartoon representation of secondary structure
"},{"title":"AtomStyleSpec#clicksphere","link":"clicksphere","description":"invisible style for click handling only
"},{"title":"AtomStyleSpec#cross","link":"cross","description":"draw atoms as crossed lines (aka stars)
"},{"title":"AtomStyleSpec#line","link":"line","description":"draw bonds as lines
"},{"title":"AtomStyleSpec#sphere","link":"sphere","description":"draw atoms as spheres
"},{"title":"AtomStyleSpec#stick","link":"stick","description":"draw bonds as capped cylinders
"},{"title":"BCIF","link":"BCIF"},{"title":"BondStyle","link":"BondStyle","description":"Style for individual bond.
"},{"title":"BondStyle#color1","link":"color1"},{"title":"BondStyle#color2","link":"color2"},{"title":"BondStyle#dashedBondConfig","link":"dashedBondConfig","description":"Override dashed bond colors for this specific bond
"},{"title":"BondStyle#dashedBondFlip","link":"dashedBondFlip","description":"Override which side of a fractional bond (e.g. aromatic 1.5) gets the dashed line.
\ntrue = dashed on +v side, false = dashed on -v side.
\nWhen absent, automatically determined via ring detection.
Box shape specification.
"},{"title":"BoxSpec#center","link":"center","description":"center of box
"},{"title":"BoxSpec#corner","link":"corner","description":"bottom corner of box
"},{"title":"BoxSpec#dimensions","link":"dimensions","description":"width, height, depth of box
"},{"title":"CAP","link":"CAP","description":"Enum for cylinder cap styles.
"},{"title":"CDJSON","link":"CDJSON","description":"This parses the ChemDoodle json file format. Although this is registered
\nfor the json file extension, other chemical json file formats exist that
\nthis can not parse. Check which one you have and do not assume that
\n.json can be parsed
Puts atoms specified in mmCIF fromat in str into atoms
"},{"title":"CUBE","link":"CUBE"},{"title":"CartoonStyleSpec","link":"CartoonStyleSpec","description":"A visualization of protein or nucleic acid secondary structure. Applying this to other molecules will not show anything.
\nIn nucleic acids, the base cylinders obtain their color from the atom to which the cylinder is drawn, which is 'N1' for purines (resn: 'A', 'G', 'DA', 'DG') and
\n'N3' for pyrimidines (resn: 'C', 'U', 'DC', 'DT').
\nThe different nucleobases can therefore be distinguished as by setting the colors
\nof each of these atoms. The backbone color is set from the 'P' atoms ('O5' for the 5' terminus).
whether to add arrows showing beta-sheet
\ndirectionality; does not apply to trace or ribbon
strand color, may specify as 'spectrum' which will apply reversed gradient based on residue number
"},{"title":"CartoonStyleSpec#colorfunc","link":"colorfunc","description":"Allows the user to provide a function for setting the colorschemes.
"},{"title":"CartoonStyleSpec#colorscheme","link":"colorscheme","description":"colorscheme to use on atoms; overrides color
"},{"title":"CartoonStyleSpec#gapcutoff","link":"gapcutoff","description":"If there is a gap of strictly fewer than gapcutoff missing residues
\nwithin a chain, draw a dashed line.
do not show
"},{"title":"CartoonStyleSpec#opacity","link":"opacity","description":"set opacity from 0-1; transparency is set per-chain
\nwith a warning outputted in the event of ambiguity
whether to use constant strand width, disregarding
\nsecondary structure; use thickness to adjust radius
style of cartoon rendering (trace, oval, rectangle (default), parabola, edged)
"},{"title":"CartoonStyleSpec#thickness","link":"thickness","description":"cartoon strand thickness, default is 0.4
"},{"title":"CartoonStyleSpec#tubes","link":"tubes","description":"whether to display alpha helices as simple cylinders;
\ndoes not apply to trace
cartoon strand width, default is secondary
\nstructure-dependent; does not apply to trace or ribbon
Invisible click sphere style specification. This lets you set
\nlarger (or smaller) click targets on atoms then the default radii or
\nhave clickable atoms even if they aren't being rendered visibly.
do not show sticks
"},{"title":"ClickSphereStyleSpec#radius","link":"radius","description":"fixed radius of sphere
"},{"title":"ClickSphereStyleSpec#scale","link":"scale","description":"scale VDW radius by specified amount
"},{"title":"Color","link":"Color"},{"title":"ColorSpec","link":"ColorSpec","description":"Color representation. A hex number, html color name, or object with r/g/b properties
"},{"title":"ColorschemeSpec","link":"ColorschemeSpec","description":"Colorscheme specification.
"},{"title":"ContextMenu#hide","link":"hide","description":"Hides the context menu and if needed process the propertyMenu
"},{"title":"ContextMenu#show","link":"show","description":"Shows the context menu
"},{"title":"CrossStyleSpec","link":"CrossStyleSpec","description":"Cross style specification
"},{"title":"CrossStyleSpec#color","link":"color","description":"fixed coloring
"},{"title":"CrossStyleSpec#colorfunc","link":"colorfunc","description":"Allows the user to provide a function for setting the colorschemes.
"},{"title":"CrossStyleSpec#colorscheme","link":"colorscheme","description":"colorscheme to use on atoms; overrides color
"},{"title":"CrossStyleSpec#hidden","link":"hidden","description":"do not show line
"},{"title":"CrossStyleSpec#linewidth","link":"linewidth","description":"deprecated due to vanishing browser support*
"},{"title":"CrossStyleSpec#opacity","link":"opacity","description":"opacity (zero to one), must be the same for all atoms in a model
"},{"title":"CrossStyleSpec#radius","link":"radius","description":"radius of cross
"},{"title":"CrossStyleSpec#scale","link":"scale","description":"scale VDW radius by specified amount
"},{"title":"CurveSpec","link":"CurveSpec","description":"Curve shape specification.
"},{"title":"CurveSpec#fromArrow","link":"fromArrow","description":"if an arrow should be drawn at the start
"},{"title":"CurveSpec#fromCap","link":"fromCap","description":"have cap at start
"},{"title":"CurveSpec#points","link":"points","description":"Sequence of points to draw curve through
"},{"title":"CurveSpec#radius","link":"radius","description":"radius of curve
"},{"title":"CurveSpec#smooth","link":"smooth","description":"amount of interpolation
"},{"title":"CurveSpec#toArrow","link":"toArrow","description":"if an arrow should be drawn at the end
"},{"title":"CurveSpec#toCap","link":"toCap","description":"have cap at end
"},{"title":"CustomLinear","link":"CustomLinear"},{"title":"CustomShapeSpec","link":"CustomShapeSpec","description":"Specification for adding custom shape.
"},{"title":"CustomShapeSpec#faceArr","link":"faceArr","description":"List of triangles to build the custom shape. Each triangle is defined by the indices of 3 vertices in vertexArr, so the array length should be 3 times the number of faces.
"},{"title":"CustomShapeSpec#normalArr","link":"normalArr","description":"List of normal vectors for each vertex
"},{"title":"CustomShapeSpec#vertexArr","link":"vertexArr","description":"List of vertex positions
"},{"title":"Cylinder","link":"Cylinder"},{"title":"CylinderSpec","link":"CylinderSpec","description":"Cylinder shape specification.
"},{"title":"CylinderSpec#dashLength","link":"dashLength","description":"Length of dashes (default 0.25)
"},{"title":"CylinderSpec#dashed","link":"dashed","description":"Make the cylinder dashed.
"},{"title":"CylinderSpec#end","link":"end","description":"ending position
"},{"title":"CylinderSpec#fromCap","link":"fromCap","description":"Place a cap at the start (none, flat or round)
"},{"title":"CylinderSpec#gapLength","link":"gapLength","description":"Length of gaps (default 0.25)
"},{"title":"CylinderSpec#hidden","link":"hidden","description":"hidden
"},{"title":"CylinderSpec#radius","link":"radius","description":"radius
"},{"title":"CylinderSpec#start","link":"start","description":"starting vector
"},{"title":"CylinderSpec#toCap","link":"toCap","description":"Place a cap at the end (none, flat or round)
"},{"title":"DashedBondSpec","link":"DashedBondSpec","description":"Dashed Bond style specification
"},{"title":"DashedBondSpec#dashLength","link":"dashLength","description":"length of dash (default 0.1)
"},{"title":"DashedBondSpec#dashedColor","link":"dashedColor","description":"Color for the dashed portion of aromatic bonds (default: atom color)
"},{"title":"DashedBondSpec#gapLength","link":"gapLength","description":"length of gap (default 0.25)
"},{"title":"DashedBondSpec#solidColor","link":"solidColor","description":"Color for the solid portion of aromatic bonds (default: atom color)
"},{"title":"FogSpec","link":"FogSpec","description":"Fog specification.
"},{"title":"FogSpec#fogEnd","link":"fogEnd","description":"Fraction with the slab where fog ends (nothing visible after this point). Default 1.0.
"},{"title":"FogSpec#fogStart","link":"fogStart","description":"Fraction within the slab where fog starts to be linearly added. Default 0.4.
"},{"title":"GLDraw","link":"GLDraw","description":"Lower level utilities for creating WebGL shape geometries.
\nThese are not intended for general consumption.
Create a cone
"},{"title":"GLDraw.drawCylinder","link":"drawCylinder","description":"Create a cylinder
"},{"title":"GLDraw.drawSphere","link":"drawSphere","description":"Create a sphere.
"},{"title":"GLDraw.drawTorus","link":"drawTorus","description":"Draw a torus (ring/donut shape) for aromatic ring visualization.
"},{"title":"GLModel","link":"GLModel"},{"title":"GLModel#addAtomSpecs","link":"addAtomSpecs","description":"add atomSpecs to validAtomSelectionSpecs
"},{"title":"GLModel#addAtomSpecs","link":"addAtomSpecs","description":"add atomSpecs to validAtomSelectionSpecs
"},{"title":"GLModel#addAtoms","link":"addAtoms","description":"Add list of new atoms to model. Adjusts bonds appropriately.
"},{"title":"GLModel#addAtoms","link":"addAtoms","description":"Add list of new atoms to model. Adjusts bonds appropriately.
"},{"title":"GLModel#addFrame","link":"addFrame","description":"Add atoms as frames of model
"},{"title":"GLModel#addFrame","link":"addFrame","description":"Add atoms as frames of model
"},{"title":"GLModel#addMolData","link":"addMolData","description":"add atoms to this model from molecular data string
"},{"title":"GLModel#addMolData","link":"addMolData","description":"add atoms to this model from molecular data string
"},{"title":"GLModel#addPropertyLabels","link":"addPropertyLabels","description":"Create labels for atoms that show the value of the passed property.
"},{"title":"GLModel#addPropertyLabels","link":"addPropertyLabels","description":"Create labels for atoms that show the value of the passed property.
"},{"title":"GLModel#addResLabels","link":"addResLabels","description":"Create labels for residues of selected atoms.
\nWill create a single label at the center of mass of all atoms
\nwith the same chain,resn, and resi.
Create labels for residues of selected atoms.
\nWill create a single label at the center of mass of all atoms
\nwith the same chain,resn, and resi.
Assign bonds based on atomic coordinates.
\nThis currently uses a primitive distance-based algorithm that does not
\nconsider valence constraints and will only create single bonds.
Assign bonds based on atomic coordinates.
\nThis currently uses a primitive distance-based algorithm that does not
\nconsider valence constraints and will only create single bonds.
given a selection specification, return true if atom is selected.
\nDoes not support context-aware selectors like expand/within/byres.
given a selection specification, return true if atom is selected.
\nDoes not support context-aware selectors like expand/within/byres.
Calculate dashed line segments along a bond, with proper centering and two-color support.
\nThe dashes are centered along the bond using the pattern:
\n[halfGap]-[dash]-[gap]-[dash]-[gap]-...-[dash]-[halfGap]
For two-color bonds, the first half of dashes use colors[0], second half use colors[1].
"},{"title":"GLModel#createMolObj","link":"createMolObj","description":"param {AtomSpec[]} atoms
"},{"title":"GLModel#drawAtomClickSphere","link":"drawAtomClickSphere","description":"Register atom shaped click handlers
"},{"title":"GLModel#drawAtomCross","link":"drawAtomCross"},{"title":"GLModel#drawAtomSphere","link":"drawAtomSphere"},{"title":"GLModel#drawBondLines","link":"drawBondLines"},{"title":"GLModel#enableContextMenu","link":"enableContextMenu","description":"enable context menu of selected atoms
"},{"title":"GLModel#enableContextMenu","link":"enableContextMenu","description":"enable context menu of selected atoms
"},{"title":"GLModel#expandAtomList","link":"expandAtomList","description":"returns a list of atoms in the expanded bounding box, but not in the current one
\nBounding box:
\n[ [ xmin, ymin, zmin ],
\n[ xmax, ymax, zmax ],
\n[ xctr, yctr, zctr ] ]
return a VRML string representation of the model. Does not include VRML header information
"},{"title":"GLModel#exportVRML","link":"exportVRML","description":"return a VRML string representation of the model. Does not include VRML header information
"},{"title":"GLModel#getCrystData","link":"getCrystData","description":"Returns crystallographic information if present.
"},{"title":"GLModel#getCrystData","link":"getCrystData","description":"Returns crystallographic information if present.
"},{"title":"GLModel#getID","link":"getID","description":"Returns model id number
"},{"title":"GLModel#getID","link":"getID","description":"Returns model id number
"},{"title":"GLModel#getInternalState","link":"getInternalState","description":"Return object representing internal state of
\nthe model appropriate for passing to setInternalState
Return object representing internal state of
\nthe model appropriate for passing to setInternalState
Returns model's frames property, a list of atom lists
"},{"title":"GLModel#getNumFrames","link":"getNumFrames","description":"Returns model's frames property, a list of atom lists
"},{"title":"GLModel#getRadiusFromStyle","link":"getRadiusFromStyle"},{"title":"GLModel#getSymmetries","link":"getSymmetries","description":"Returns list of rotational/translational matrices if there is BIOMT data
\nOtherwise returns a list of just the ID matrix
Returns list of rotational/translational matrices if there is BIOMT data
\nOtherwise returns a list of just the ID matrix
Return viewer associated with this model.
"},{"title":"GLModel#getViewer","link":"getViewer","description":"Return viewer associated with this model.
"},{"title":"GLModel#globj","link":"globj","description":"manage the globj for this model in the possed modelGroup - if it has to be regenerated, remove and add
"},{"title":"GLModel#globj","link":"globj","description":"manage the globj for this model in the possed modelGroup - if it has to be regenerated, remove and add
"},{"title":"GLModel#hide","link":"hide","description":"Don't show this model in future renderings. Keep all styles and state
\nso it can be efficiencly shown again.
Don't show this model in future renderings. Keep all styles and state
\nso it can be efficiencly shown again.
Remove specified atoms from model
"},{"title":"GLModel#removeAtoms","link":"removeAtoms","description":"Remove specified atoms from model
"},{"title":"GLModel#removegl","link":"removegl","description":"Remove any renderable mol object from scene
"},{"title":"GLModel#removegl","link":"removegl","description":"Remove any renderable mol object from scene
"},{"title":"GLModel#selectedAtoms","link":"selectedAtoms","description":"return list of atoms selected by sel, this is specific to glmodel
"},{"title":"GLModel#selectedAtoms","link":"selectedAtoms","description":"return list of atoms selected by sel, this is specific to glmodel
"},{"title":"GLModel#setClickable","link":"setClickable","description":"Set clickable and callback of selected atoms
"},{"title":"GLModel#setClickable","link":"setClickable","description":"Set clickable and callback of selected atoms
"},{"title":"GLModel#setColorByElement","link":"setColorByElement","description":"given a mapping from element to color, set atom colors
"},{"title":"GLModel#setColorByElement","link":"setColorByElement","description":"given a mapping from element to color, set atom colors
"},{"title":"GLModel#setColorByFunction","link":"setColorByFunction"},{"title":"GLModel#setColorByFunction","link":"setColorByFunction"},{"title":"GLModel#setColorByProperty","link":"setColorByProperty"},{"title":"GLModel#setColorByProperty","link":"setColorByProperty"},{"title":"GLModel#setCoordinates","link":"setCoordinates","description":"Set coordinates for the atoms from provided trajectory file.
"},{"title":"GLModel#setCoordinates","link":"setCoordinates","description":"Set coordinates for the atoms from provided trajectory file.
"},{"title":"GLModel#setCoordinatesFromURL","link":"setCoordinatesFromURL","description":"Set coordinates from remote trajectory file.
"},{"title":"GLModel#setCoordinatesFromURL","link":"setCoordinatesFromURL","description":"Set coordinates from remote trajectory file.
"},{"title":"GLModel#setCrystData","link":"setCrystData","description":"Set crystallographic information using three angles and three lengths
"},{"title":"GLModel#setCrystData","link":"setCrystData","description":"Set crystallographic information using three angles and three lengths
"},{"title":"GLModel#setCrystMatrix","link":"setCrystMatrix","description":"Set the crystallographic matrix to the given matrix.
\nThis function removes a, b, c, alpha, beta, gamma from
\nthe crystal data.
Set the crystallographic matrix to the given matrix.
\nThis function removes a, b, c, alpha, beta, gamma from
\nthe crystal data.
Sets model's atomlist to specified frame
\nSets to last frame if framenum out of range
Sets model's atomlist to specified frame
\nSets to last frame if framenum out of range
Set hoverable and callback of selected atoms
"},{"title":"GLModel#setHoverable","link":"setHoverable","description":"Set hoverable and callback of selected atoms
"},{"title":"GLModel#setInternalState","link":"setInternalState","description":"Overwrite the internal model state with the passed state.
"},{"title":"GLModel#setInternalState","link":"setInternalState","description":"Overwrite the internal model state with the passed state.
"},{"title":"GLModel#setStyle","link":"setStyle","description":"Set atom style of selected atoms
"},{"title":"GLModel#setStyle","link":"setStyle","description":"Set atom style of selected atoms
"},{"title":"GLModel#setSymmetries","link":"setSymmetries","description":"Sets symmetries based on specified matrices in list
"},{"title":"GLModel#setSymmetries","link":"setSymmetries","description":"Sets symmetries based on specified matrices in list
"},{"title":"GLModel#show","link":"show","description":"Unhide a hidden model
"},{"title":"GLModel#show","link":"show","description":"Unhide a hidden model
"},{"title":"GLModel#toCDObject","link":"toCDObject","description":"Convert the model into an object in the format of a ChemDoodle JSON model.
"},{"title":"GLModel#toCDObject","link":"toCDObject","description":"Convert the model into an object in the format of a ChemDoodle JSON model.
"},{"title":"GLModel#vibrate","link":"vibrate","description":"If model atoms have dx, dy, dz properties (in some xyz files), vibrate populates the model's frame property based on parameters.
\nModel can then be animated
If model atoms have dx, dy, dz properties (in some xyz files), vibrate populates the model's frame property based on parameters.
\nModel can then be animated
Custom renderable shape
"},{"title":"GLShape#GLShape","link":"GLShape","description":"Custom renderable shape
"},{"title":"GLShape#addArrow","link":"addArrow","description":"Creates an arrow shape
"},{"title":"GLShape#addArrow","link":"addArrow","description":"Creates an arrow shape
"},{"title":"GLShape#addBox","link":"addBox","description":"Creates a box
"},{"title":"GLShape#addBox","link":"addBox","description":"Creates a box
"},{"title":"GLShape#addCurve","link":"addCurve","description":"Creates a curved shape
"},{"title":"GLShape#addCurve","link":"addCurve","description":"Creates a curved shape
"},{"title":"GLShape#addCustom","link":"addCustom","description":"Creates a custom shape from supplied vertex and face arrays
"},{"title":"GLShape#addCustom","link":"addCustom","description":"Creates a custom shape from supplied vertex and face arrays
"},{"title":"GLShape#addCylinder","link":"addCylinder","description":"Creates a cylinder shape
"},{"title":"GLShape#addCylinder","link":"addCylinder","description":"Creates a cylinder shape
"},{"title":"GLShape#addDashedCylinder","link":"addDashedCylinder","description":"Creates a dashed cylinder shape
"},{"title":"GLShape#addDashedCylinder","link":"addDashedCylinder","description":"Creates a dashed cylinder shape
"},{"title":"GLShape#addIsosurface","link":"addIsosurface","description":"Create isosurface from volumetric data.
"},{"title":"GLShape#addIsosurface","link":"addIsosurface","description":"Create isosurface from volumetric data.
"},{"title":"GLShape#addLine","link":"addLine","description":"Creates a line shape
"},{"title":"GLShape#addLine","link":"addLine","description":"Creates a line shape
"},{"title":"GLShape#addSphere","link":"addSphere","description":"Creates a sphere shape
"},{"title":"GLShape#addSphere","link":"addSphere","description":"Creates a sphere shape
"},{"title":"GLShape#addVolumetricData","link":"addVolumetricData"},{"title":"GLShape#addVolumetricData","link":"addVolumetricData"},{"title":"GLShape#intersectionShape","link":"intersectionShape"},{"title":"GLShape#updateStyle","link":"updateStyle","description":"Update shape with new style specification
"},{"title":"GLShape#updateStyle","link":"updateStyle","description":"Update shape with new style specification
"},{"title":"GLViewer","link":"GLViewer"},{"title":"GLViewer#addArrow","link":"addArrow","description":"Create and add arrow shape
"},{"title":"GLViewer#addArrow","link":"addArrow","description":"Create and add arrow shape
"},{"title":"GLViewer#addAsOneMolecule","link":"addAsOneMolecule","description":"Create and add model to viewer. Given multimodel file and its format,
\nall atoms are added to one model
Create and add model to viewer. Given multimodel file and its format,
\nall atoms are added to one model
Create and add box shape. This method provides a shorthand
\nway to create a box shape object
Create and add box shape. This method provides a shorthand
\nway to create a box shape object
Create and add Curve shape
"},{"title":"GLViewer#addCurve","link":"addCurve","description":"Create and add Curve shape
"},{"title":"GLViewer#addCustom","link":"addCustom","description":"Add custom shape component from user supplied function
"},{"title":"GLViewer#addCustom","link":"addCustom","description":"Add custom shape component from user supplied function
"},{"title":"GLViewer#addCylinder","link":"addCylinder","description":"Create and add cylinder shape
"},{"title":"GLViewer#addCylinder","link":"addCylinder","description":"Create and add cylinder shape
"},{"title":"GLViewer#addIsosurface","link":"addIsosurface","description":"Construct isosurface from volumetric data. This is more flexible
\nthan addVolumetricData, but can not be used with py3Dmol.
Construct isosurface from volumetric data. This is more flexible
\nthan addVolumetricData, but can not be used with py3Dmol.
Add label to viewer
"},{"title":"GLViewer#addLabel","link":"addLabel","description":"Add label to viewer
"},{"title":"GLViewer#addLine","link":"addLine","description":"Create and add line shape
"},{"title":"GLViewer#addLine","link":"addLine","description":"Create and add line shape
"},{"title":"GLViewer#addLineDashed","link":"addLineDashed","description":"Add dashed line to shape
"},{"title":"GLViewer#addLineDashed","link":"addLineDashed","description":"Add dashed line to shape
"},{"title":"GLViewer#addMesh","link":"addMesh","description":"Adds an explicit mesh as a surface object.
"},{"title":"GLViewer#addMesh","link":"addMesh","description":"Adds an explicit mesh as a surface object.
"},{"title":"GLViewer#addModel","link":"addModel","description":"Create and add model to viewer, given molecular data and its format
"},{"title":"GLViewer#addModel","link":"addModel","description":"Create and add model to viewer, given molecular data and its format
"},{"title":"GLViewer#addModels","link":"addModels","description":"Given multimodel file and its format, add atom data to the viewer as separate models
\nand return list of these models
Given multimodel file and its format, add atom data to the viewer as separate models
\nand return list of these models
Create and add model to viewer. Given multimodel file and its format,
\ndifferent atomlists are stored in model's frame
\nproperty and model's atoms are set to the 0th frame
Create and add model to viewer. Given multimodel file and its format,
\ndifferent atomlists are stored in model's frame
\nproperty and model's atoms are set to the 0th frame
Add property labels. This will generate one label per a selected
\natom at the atom's coordinates with the property value as the label text.
Add property labels. This will generate one label per a selected
\natom at the atom's coordinates with the property value as the label text.
Add residue labels. This will generate one label per a
\nresidue within the selected atoms. The label will be at the
\ncentroid of the atoms and styled according to the passed style.
\nThe label text will be [resn][resi]
Add residue labels. This will generate one label per a
\nresidue within the selected atoms. The label will be at the
\ncentroid of the atoms and styled according to the passed style.
\nThe label text will be [resn][resi]
Add shape object to viewer
"},{"title":"GLViewer#addShape","link":"addShape","description":"Add shape object to viewer
"},{"title":"GLViewer#addSphere","link":"addSphere","description":"Create and add sphere shape. This method provides a shorthand
\nway to create a spherical shape object
Create and add sphere shape. This method provides a shorthand
\nway to create a spherical shape object
Add style properties to all selected atoms
"},{"title":"GLViewer#addSurface","link":"addSurface","description":"Add surface representation to atoms
"},{"title":"GLViewer#addSurface","link":"addSurface","description":"Add surface representation to atoms
"},{"title":"GLViewer#addUnitCell","link":"addUnitCell","description":"Create and add unit cell visualization.
"},{"title":"GLViewer#addUnitCell","link":"addUnitCell","description":"Create and add unit cell visualization.
"},{"title":"GLViewer#addVolumetricData","link":"addVolumetricData","description":"Construct isosurface from volumetric data in gaussian cube format
"},{"title":"GLViewer#addVolumetricData","link":"addVolumetricData","description":"Construct isosurface from volumetric data in gaussian cube format
"},{"title":"GLViewer#addVolumetricRender","link":"addVolumetricRender","description":"Create volumetric renderer for volumetricData
"},{"title":"GLViewer#addVolumetricRender","link":"addVolumetricRender","description":"Create volumetric renderer for volumetricData
"},{"title":"GLViewer#animate","link":"animate","description":"Animate all models in viewer from their respective frames
"},{"title":"GLViewer#animate","link":"animate","description":"Animate all models in viewer from their respective frames
"},{"title":"GLViewer#apngURI","link":"apngURI","description":"Return a promise that resolves to an animated PNG image URI of
\nviewer contents (base64 encoded) for nframes of viewer changes.
Return a promise that resolves to an animated PNG image URI of
\nviewer contents (base64 encoded) for nframes of viewer changes.
Re-center the viewer around the provided selection (unlike zoomTo, does not zoom).
"},{"title":"GLViewer#center","link":"center","description":"Re-center the viewer around the provided selection (unlike zoomTo, does not zoom).
"},{"title":"GLViewer#clear","link":"clear","description":"Clear scene of all objects
"},{"title":"GLViewer#clear","link":"clear","description":"Clear scene of all objects
"},{"title":"GLViewer#closeEnoughForClick","link":"closeEnoughForClick","description":"Determine if a positioned event is "close enough" to mouseStart to be considered a click.
\nWith a mouse, the position should be exact, but allow a slight delta for a touch interface.
Create a new model from atoms specified by sel.
\nIf extract, removes selected atoms from existing models
Create a new model from atoms specified by sel.
\nIf extract, removes selected atoms from existing models
enable context menu and callback of selected atoms
"},{"title":"GLViewer#enableContextMenu","link":"enableContextMenu","description":"enable context menu and callback of selected atoms
"},{"title":"GLViewer#enableFog","link":"enableFog","description":"Enable/disable fog for content far from the camera
"},{"title":"GLViewer#enableFog","link":"enableFog","description":"Enable/disable fog for content far from the camera
"},{"title":"GLViewer#exportJSON","link":"exportJSON","description":"Export one or all of the loaded models into ChemDoodle compatible JSON.
"},{"title":"GLViewer#exportJSON","link":"exportJSON","description":"Export one or all of the loaded models into ChemDoodle compatible JSON.
"},{"title":"GLViewer#exportVRML","link":"exportVRML","description":"return a VRML string representation of the scene. Include VRML header information
"},{"title":"GLViewer#exportVRML","link":"exportVRML","description":"return a VRML string representation of the scene. Include VRML header information
"},{"title":"GLViewer#fitSlab","link":"fitSlab","description":"Adjust slab to fully enclose selection (default everything).
"},{"title":"GLViewer#fitSlab","link":"fitSlab","description":"Adjust slab to fully enclose selection (default everything).
"},{"title":"GLViewer#getAtomsFromSel","link":"getAtomsFromSel"},{"title":"GLViewer#getCanvas","link":"getCanvas","description":"Return underlying canvas element.
"},{"title":"GLViewer#getCanvas","link":"getCanvas","description":"Return underlying canvas element.
"},{"title":"GLViewer#getConfig","link":"getConfig","description":"Return configuration of viewer
"},{"title":"GLViewer#getConfig","link":"getConfig","description":"Return configuration of viewer
"},{"title":"GLViewer#getFrame","link":"getFrame","description":"Gets the current viewer frame.
"},{"title":"GLViewer#getFrame","link":"getFrame","description":"Gets the current viewer frame.
"},{"title":"GLViewer#getInternalState","link":"getInternalState","description":"Return object representing internal state of
\nthe viewer appropriate for passing to setInternalState
Return object representing internal state of
\nthe viewer appropriate for passing to setInternalState
Return specified model
"},{"title":"GLViewer#getModel","link":"getModel","description":"Return specified model
"},{"title":"GLViewer#getNumFrames","link":"getNumFrames","description":"Returns the number of frames that the model with the most frames in the viewer has
"},{"title":"GLViewer#getNumFrames","link":"getNumFrames","description":"Returns the number of frames that the model with the most frames in the viewer has
"},{"title":"GLViewer#getPerceivedDistance","link":"getPerceivedDistance","description":"Return the z distance between the model and the camera
"},{"title":"GLViewer#getPerceivedDistance","link":"getPerceivedDistance","description":"Return the z distance between the model and the camera
"},{"title":"GLViewer#getRenderer","link":"getRenderer","description":"Return renderer element.
"},{"title":"GLViewer#getRenderer","link":"getRenderer","description":"Return renderer element.
"},{"title":"GLViewer#getSlab","link":"getSlab","description":"Get slab of view (contents outside of slab are clipped).
"},{"title":"GLViewer#getSlab","link":"getSlab","description":"Get slab of view (contents outside of slab are clipped).
"},{"title":"GLViewer#getSurface","link":"getSurface","description":"Return surface object
"},{"title":"GLViewer#getSurface","link":"getSurface","description":"Return surface object
"},{"title":"GLViewer#getUniqueValues","link":"getUniqueValues","description":"Returns valid values for the specified attribute in the given selection
"},{"title":"GLViewer#getUniqueValues","link":"getUniqueValues","description":"Returns valid values for the specified attribute in the given selection
"},{"title":"GLViewer#getView","link":"getView","description":"Returns an array representing the current viewpoint.
\nTranslation, zoom, and rotation quaternion.
Returns an array representing the current viewpoint.
\nTranslation, zoom, and rotation quaternion.
Return true if volumetric rendering is supported (WebGL 2.0 required)
"},{"title":"GLViewer#hasVolumetricRender","link":"hasVolumetricRender","description":"Return true if volumetric rendering is supported (WebGL 2.0 required)
"},{"title":"GLViewer#hideAllLabels","link":"hideAllLabels","description":"Hide all labels in viewer
"},{"title":"GLViewer#hideAllLabels","link":"hideAllLabels","description":"Hide all labels in viewer
"},{"title":"GLViewer#isAnimated","link":"isAnimated","description":"Return true if viewer is currently being animated, false otherwise
"},{"title":"GLViewer#isAnimated","link":"isAnimated","description":"Return true if viewer is currently being animated, false otherwise
"},{"title":"GLViewer#jmolMoveTo","link":"jmolMoveTo","description":"return Jmol moveto command to position this scene
"},{"title":"GLViewer#jmolMoveTo","link":"jmolMoveTo","description":"return Jmol moveto command to position this scene
"},{"title":"GLViewer#linkViewer","link":"linkViewer","description":"Synchronize this view matrix of this viewer to the passed viewer.
\nWhen the viewpoint of this viewer changes, the other viewer will
\nbe set to this viewer's view.
Synchronize this view matrix of this viewer to the passed viewer.
\nWhen the viewpoint of this viewer changes, the other viewer will
\nbe set to this viewer's view.
Add specified properties to all atoms matching input argument
"},{"title":"GLViewer#mapAtomProperties","link":"mapAtomProperties","description":"Add specified properties to all atoms matching input argument
"},{"title":"GLViewer#modelToScreen","link":"modelToScreen","description":"Convert model coordinates to screen coordinates.
"},{"title":"GLViewer#modelToScreen","link":"modelToScreen","description":"Convert model coordinates to screen coordinates.
"},{"title":"GLViewer#pauseAnimate","link":"pauseAnimate","description":"Pause animation of all models in viewer
"},{"title":"GLViewer#pauseAnimate","link":"pauseAnimate","description":"Pause animation of all models in viewer
"},{"title":"GLViewer#pdbData","link":"pdbData","description":"Return pdb output of selected atoms (if atoms from pdb input)
"},{"title":"GLViewer#pdbData","link":"pdbData","description":"Return pdb output of selected atoms (if atoms from pdb input)
"},{"title":"GLViewer#pngURI","link":"pngURI","description":"Return image URI of viewer contents (base64 encoded). *
"},{"title":"GLViewer#pngURI","link":"pngURI","description":"Return image URI of viewer contents (base64 encoded). *
"},{"title":"GLViewer#removeAllLabels","link":"removeAllLabels","description":"Remove all labels from viewer
"},{"title":"GLViewer#removeAllLabels","link":"removeAllLabels","description":"Remove all labels from viewer
"},{"title":"GLViewer#removeAllModels","link":"removeAllModels","description":"Delete all existing models
"},{"title":"GLViewer#removeAllModels","link":"removeAllModels","description":"Delete all existing models
"},{"title":"GLViewer#removeAllShapes","link":"removeAllShapes","description":"Remove all shape objects from viewer
"},{"title":"GLViewer#removeAllShapes","link":"removeAllShapes","description":"Remove all shape objects from viewer
"},{"title":"GLViewer#removeAllSurfaces","link":"removeAllSurfaces","description":"Remove all surfaces.
"},{"title":"GLViewer#removeAllSurfaces","link":"removeAllSurfaces","description":"Remove all surfaces.
"},{"title":"GLViewer#removeLabel","link":"removeLabel","description":"Remove label from viewer
"},{"title":"GLViewer#removeLabel","link":"removeLabel","description":"Remove label from viewer
"},{"title":"GLViewer#removeModel","link":"removeModel","description":"Delete specified model from viewer
"},{"title":"GLViewer#removeModel","link":"removeModel","description":"Delete specified model from viewer
"},{"title":"GLViewer#removeShape","link":"removeShape","description":"Remove shape object from viewer
"},{"title":"GLViewer#removeShape","link":"removeShape","description":"Remove shape object from viewer
"},{"title":"GLViewer#removeSurface","link":"removeSurface","description":"Remove surface with given ID
"},{"title":"GLViewer#removeSurface","link":"removeSurface","description":"Remove surface with given ID
"},{"title":"GLViewer#removeUnitCell","link":"removeUnitCell","description":"Remove unit cell visualization from model.
"},{"title":"GLViewer#removeUnitCell","link":"removeUnitCell","description":"Remove unit cell visualization from model.
"},{"title":"GLViewer#render","link":"render","description":"Render current state of viewer, after
\nadding/removing models, applying styles, etc.
Render current state of viewer, after
\nadding/removing models, applying styles, etc.
Replicate atoms in model to form a super cell of the specified dimensions.
\nOriginal cell will be centered as much as possible.
Replicate atoms in model to form a super cell of the specified dimensions.
\nOriginal cell will be centered as much as possible.
Resize viewer according to containing HTML element's dimensions
"},{"title":"GLViewer#resize","link":"resize","description":"Resize viewer according to containing HTML element's dimensions
"},{"title":"GLViewer#resumeAnimate","link":"resumeAnimate","description":"Resume animation of all models in viewer
"},{"title":"GLViewer#resumeAnimate","link":"resumeAnimate","description":"Resume animation of all models in viewer
"},{"title":"GLViewer#rotate","link":"rotate","description":"Rotate scene by angle degrees around axis
"},{"title":"GLViewer#rotate","link":"rotate","description":"Rotate scene by angle degrees around axis
"},{"title":"GLViewer#screenOffsetToModel","link":"screenOffsetToModel","description":"For a given screen (x,y) displacement return model displacement
"},{"title":"GLViewer#screenOffsetToModel","link":"screenOffsetToModel","description":"For a given screen (x,y) displacement return model displacement
"},{"title":"GLViewer#screenToModelDistance","link":"screenToModelDistance","description":"Distance from screen coordinate to model coordinate assuming screen point
\nis projected to the same depth as model coordinate
Distance from screen coordinate to model coordinate assuming screen point
\nis projected to the same depth as model coordinate
return list of atoms selected by sel
"},{"title":"GLViewer#selectedAtoms","link":"selectedAtoms","description":"return list of atoms selected by sel
"},{"title":"GLViewer#setAutoEyeSeparation","link":"setAutoEyeSeparation","description":"Used for setting an approx value of eyeSeparation. Created for calling by StereoViewer object
"},{"title":"GLViewer#setAutoEyeSeparation","link":"setAutoEyeSeparation","description":"Used for setting an approx value of eyeSeparation. Created for calling by StereoViewer object
"},{"title":"GLViewer#setBackgroundColor","link":"setBackgroundColor","description":"Set the background color (default white)
"},{"title":"GLViewer#setBackgroundColor","link":"setBackgroundColor","description":"Set the background color (default white)
"},{"title":"GLViewer#setCameraParameters","link":"setCameraParameters","description":"Set camera parameters (distance to the origin and field of view)
"},{"title":"GLViewer#setCameraParameters","link":"setCameraParameters","description":"Set camera parameters (distance to the origin and field of view)
"},{"title":"GLViewer#setClickable","link":"setClickable","description":"Set click-handling properties to all selected atoms. Important: render must be called for this to take effect.
"},{"title":"GLViewer#setClickable","link":"setClickable","description":"Set click-handling properties to all selected atoms. Important: render must be called for this to take effect.
"},{"title":"GLViewer#setColorByElement","link":"setColorByElement"},{"title":"GLViewer#setColorByElement","link":"setColorByElement"},{"title":"GLViewer#setColorByProperty","link":"setColorByProperty"},{"title":"GLViewer#setColorByProperty","link":"setColorByProperty"},{"title":"GLViewer#setConfig","link":"setConfig","description":"Set the configuration object. Note that some settings may only
\nhave an effect at viewer creation time.
Set the configuration object. Note that some settings may only
\nhave an effect at viewer creation time.
Change the viewer's container element
\nAlso useful if the original container element was removed from the DOM.
Change the viewer's container element
\nAlso useful if the original container element was removed from the DOM.
Set the default cartoon quality for newly created models. Default is 5.
\nCurrent models are not affected.
Set the default cartoon quality for newly created models. Default is 5.
\nCurrent models are not affected.
Sets the atomlists of all models in the viewer to specified frame.
\nShapes and labels can also be displayed by frame.
\nSets to last frame if framenum out of range
Sets the atomlists of all models in the viewer to specified frame.
\nShapes and labels can also be displayed by frame.
\nSets to last frame if framenum out of range
Set viewer height independently of the HTML container. This is probably not what you want.
"},{"title":"GLViewer#setHeight","link":"setHeight","description":"Set viewer height independently of the HTML container. This is probably not what you want.
"},{"title":"GLViewer#setHoverDuration","link":"setHoverDuration","description":"Set the duration of the hover delay
"},{"title":"GLViewer#setHoverDuration","link":"setHoverDuration","description":"Set the duration of the hover delay
"},{"title":"GLViewer#setHoverable","link":"setHoverable","description":"Set hoverable and callback of selected atoms
"},{"title":"GLViewer#setHoverable","link":"setHoverable","description":"Set hoverable and callback of selected atoms
"},{"title":"GLViewer#setInternalState","link":"setInternalState","description":"Overwrite internal state of the viewer with passed object
\nwhich should come from getInternalState.
Overwrite internal state of the viewer with passed object
\nwhich should come from getInternalState.
Modify existing label's style
"},{"title":"GLViewer#setLabelStyle","link":"setLabelStyle","description":"Modify existing label's style
"},{"title":"GLViewer#setLabelText","link":"setLabelText","description":"Modify existing label's text
"},{"title":"GLViewer#setLabelText","link":"setLabelText","description":"Modify existing label's text
"},{"title":"GLViewer#setPerceivedDistance","link":"setPerceivedDistance","description":"Set the distance between the model and the camera
\nEssentially zooming. Useful while stereo rendering.
Set the distance between the model and the camera
\nEssentially zooming. Useful while stereo rendering.
Set view projection scheme. Either orthographic or perspective.
\nDefault is perspective. Orthographic can also be enabled on viewer creation
\nby setting orthographic to true in the config object.
Set view projection scheme. Either orthographic or perspective.
\nDefault is perspective. Orthographic can also be enabled on viewer creation
\nby setting orthographic to true in the config object.
Set slab of view (contents outside of slab are clipped).
\nMust call render to update.
Set slab of view (contents outside of slab are clipped).
\nMust call render to update.
Set a callback to call when the view has potentially changed.
"},{"title":"GLViewer#setStateChangeCallback","link":"setStateChangeCallback","description":"Set a callback to call when the view has potentially changed.
"},{"title":"GLViewer#setStyle","link":"setStyle","description":"Set style properties to all selected atoms
"},{"title":"GLViewer#setSurfaceMaterialStyle","link":"setSurfaceMaterialStyle","description":"Set the surface material to something else, must render change
"},{"title":"GLViewer#setSurfaceMaterialStyle","link":"setSurfaceMaterialStyle","description":"Set the surface material to something else, must render change
"},{"title":"GLViewer#setView","link":"setView","description":"Sets the view to the specified translation, zoom, and rotation.
"},{"title":"GLViewer#setView","link":"setView","description":"Sets the view to the specified translation, zoom, and rotation.
"},{"title":"GLViewer#setViewChangeCallback","link":"setViewChangeCallback","description":"Set a callback to call when the view has potentially changed.
"},{"title":"GLViewer#setViewChangeCallback","link":"setViewChangeCallback","description":"Set a callback to call when the view has potentially changed.
"},{"title":"GLViewer#setViewStyle","link":"setViewStyle","description":"Set global view styles.
"},{"title":"GLViewer#setViewStyle","link":"setViewStyle","description":"Set global view styles.
"},{"title":"GLViewer#setWidth","link":"setWidth","description":"Set viewer width independently of the HTML container. This is probably not what you want.
"},{"title":"GLViewer#setWidth","link":"setWidth","description":"Set viewer width independently of the HTML container. This is probably not what you want.
"},{"title":"GLViewer#setZoomLimits","link":"setZoomLimits","description":"Set lower and upper limit stops for zoom.
"},{"title":"GLViewer#setZoomLimits","link":"setZoomLimits","description":"Set lower and upper limit stops for zoom.
"},{"title":"GLViewer#showAllLabels","link":"showAllLabels","description":"Show all labels in viewer
"},{"title":"GLViewer#showAllLabels","link":"showAllLabels","description":"Show all labels in viewer
"},{"title":"GLViewer#spin","link":"spin","description":"Continuously rotate a scene around the specified axis.
\nCall spin(false) to stop spinning.
Continuously rotate a scene around the specified axis.
\nCall spin(false) to stop spinning.
Stop animation of all models in viewer
"},{"title":"GLViewer#stopAnimate","link":"stopAnimate","description":"Stop animation of all models in viewer
"},{"title":"GLViewer#targetedObjects","link":"targetedObjects","description":"Return a list of objects that intersect that at the specified viewer position.
"},{"title":"GLViewer#targetedObjects","link":"targetedObjects","description":"Return a list of objects that intersect that at the specified viewer position.
"},{"title":"GLViewer#translate","link":"translate","description":"Translate current view by x,y screen coordinates
\nThis pans the camera rather than translating the model.
Translate current view by x,y screen coordinates
\nThis pans the camera rather than translating the model.
Translate current models by x,y screen coordinates
\nThis translates the models relative to the current view. It does
\nnot change the center of rotation.
Translate current models by x,y screen coordinates
\nThis translates the models relative to the current view. It does
\nnot change the center of rotation.
User specified function for handling a context menu event.
\nHandler is passed the selected object, x and y in canvas coordinates,
\nand original event.
User specified function for handling a context menu event.
\nHandler is passed the selected object, x and y in canvas coordinates,
\nand original event.
If atoms have dx, dy, dz properties (in some xyz files), vibrate populates each model's frame property based on parameters.
\nModels can then be animated
If atoms have dx, dy, dz properties (in some xyz files), vibrate populates each model's frame property based on parameters.
\nModels can then be animated
Zoom current view by a constant factor
"},{"title":"GLViewer#zoom","link":"zoom","description":"Zoom current view by a constant factor
"},{"title":"GLViewer#zoomTo","link":"zoomTo","description":"Zoom to center of atom selection. The slab will be set appropriately for
\nthe selection, unless an empty selection is provided, in which case there will be no slab.
Zoom to center of atom selection. The slab will be set appropriately for
\nthe selection, unless an empty selection is provided, in which case there will be no slab.
Initialize webgl objects for rendering
"},{"title":"GLVolumetricRender#globj","link":"globj","description":"Initialize webgl objects for rendering
"},{"title":"GRO","link":"GRO","description":"Parse a gro file from str and create atoms
"},{"title":"GradientSpec","link":"GradientSpec","description":"Gradient specification.
"},{"title":"IsoSurfaceSpec","link":"IsoSurfaceSpec","description":"Isosurface style specification
"},{"title":"IsoSurfaceSpec#coords","link":"coords","description":"coordinates around which to include data; use viewer.selectedAtoms() to convert an AtomSelectionSpec to coordinates
"},{"title":"IsoSurfaceSpec#isoval","link":"isoval","description":"specifies the isovalue to draw surface at
"},{"title":"IsoSurfaceSpec#seldist","link":"seldist","description":"distance around coords to include data [default = 2.0]
"},{"title":"IsoSurfaceSpec#selection","link":"selection","description":"selection around which to include data (alternative to coords)
"},{"title":"IsoSurfaceSpec#smoothness","link":"smoothness","description":"amount to smooth surface (default 1)
"},{"title":"IsoSurfaceSpec#voldata","link":"voldata","description":"volumetric data for vertex coloring, can be VolumeData object or raw data if volformat is specified
"},{"title":"IsoSurfaceSpec#volformat","link":"volformat","description":"format of voldata if not a $3Dmol.VolumeData object
"},{"title":"IsoSurfaceSpec#volscheme","link":"volscheme","description":"coloring scheme for mapping volumetric data to vertex color, if not a Gradient object, show describe a builtin gradient one by providing an object with gradient, min, max, and (optionally) mid fields.
"},{"title":"IsoSurfaceSpec#voxel","link":"voxel","description":"if true uses voxel style rendering
"},{"title":"Label#hide","link":"hide","description":"Hide this label.
"},{"title":"Label#hide","link":"hide","description":"Hide this label.
"},{"title":"Label#show","link":"show","description":"Show a hidden label.
"},{"title":"Label#show","link":"show","description":"Show a hidden label.
"},{"title":"LabelSpec","link":"LabelSpec","description":"Label style specification
"},{"title":"LabelSpec#alignment","link":"alignment","description":"how to orient the label w/respect to position: "topLeft" (default),
\n"topCenter", "topRight", "centerLeft", "center", "centerRight",
\n"bottomLeft", "bottomCenter", "bottomRight", or an arbitrary offset
color of background, default black
"},{"title":"LabelSpec#backgroundImage","link":"backgroundImage","description":"An elment to draw into the label. Any CanvasImageSource is allowed. Label is resized to size of image
"},{"title":"LabelSpec#backgroundOpacity","link":"backgroundOpacity","description":"opacity of background, default 1.0
"},{"title":"LabelSpec#borderColor","link":"borderColor","description":"color of border, default backgroundColor
"},{"title":"LabelSpec#borderOpacity","link":"borderOpacity","description":"opacity of border
"},{"title":"LabelSpec#borderThickness","link":"borderThickness","description":"line width of border around label, default 0
"},{"title":"LabelSpec#font","link":"font","description":"font name, default sans-serif
"},{"title":"LabelSpec#fontColor","link":"fontColor","description":"font color, default white
"},{"title":"LabelSpec#fontOpacity","link":"fontOpacity","description":"font opacity, default 1
"},{"title":"LabelSpec#fontSize","link":"fontSize","description":"height of text, default 18
"},{"title":"LabelSpec#frame","link":"frame","description":"if set, only display in this frame of an animation
"},{"title":"LabelSpec#inFront","link":"inFront","description":"always put labels in front of model
"},{"title":"LabelSpec#position","link":"position","description":"coordinates for label
"},{"title":"LabelSpec#screenOffset","link":"screenOffset","description":"x,y,z pixel offset of label from position; for screen labels z is a z-index
"},{"title":"LabelSpec#showBackground","link":"showBackground","description":"show background rounded rectangle, default true
"},{"title":"LabelSpec#useScreen","link":"useScreen","description":"position is in screen (not model) coordinates which are pixel offsets from the upper left corner
"},{"title":"LineSpec","link":"LineSpec","description":"Line shape specification. Default to wireframe.
"},{"title":"LineSpec#dashed","link":"dashed","description":"make dashed
"},{"title":"LineSpec#end","link":"end","description":"Ending position
"},{"title":"LineSpec#start","link":"start","description":"Starting position
"},{"title":"LineStyleSpec","link":"LineStyleSpec","description":"Line style specification
"},{"title":"LineStyleSpec#color","link":"color","description":"fixed coloring
"},{"title":"LineStyleSpec#colorfunc","link":"colorfunc","description":"Allows the user to provide a function for setting the colorschemes.
"},{"title":"LineStyleSpec#colorscheme","link":"colorscheme","description":"colorscheme to use on atoms; overrides color
"},{"title":"LineStyleSpec#hidden","link":"hidden","description":"do not show line
"},{"title":"LineStyleSpec#linewidth","link":"linewidth","description":"deprecated due to vanishing browser support*
"},{"title":"LineStyleSpec#opacity","link":"opacity","description":"opacity (zero to one), must be the same for all atoms in a model
"},{"title":"LineStyleSpec#wireframe","link":"wireframe","description":"wireframe style
"},{"title":"MMTFparser","link":"MMTFparser"},{"title":"MOL2","link":"MOL2"},{"title":"Matrix3","link":"Matrix3"},{"title":"Matrix4","link":"Matrix4"},{"title":"OFFSETS","link":"OFFSETS"},{"title":"OutlineStyle","link":"OutlineStyle","description":"Outline style configuration parameters
"},{"title":"OutlineStyle#color","link":"color","description":"Color of the outline
"},{"title":"OutlineStyle#maxpixels","link":"maxpixels","description":"Maximum width in screen pixels of outline.
"},{"title":"OutlineStyle#width","link":"width","description":"Width of the outline
"},{"title":"PDB","link":"PDB","description":"Parse pdb file from str and create atoms if computeStruct is true will always perform secondary structure analysis,
\notherwise only do analysis of SHEET/HELIX comments are missing
Parse a pqr file from str and create atoms. A pqr file is assumed to be a whitespace delimited PDB with charge and radius fields.
"},{"title":"PRMTOP","link":"PRMTOP","description":"Parse a prmtop file from str and create atoms
"},{"title":"ParserOptionsSpec","link":"ParserOptionsSpec","description":"Parser options specification. Used to specify the options of a GLModel. Depending on the input file format, not all fields may be defined.
"},{"title":"ParserOptionsSpec#altLoc","link":"altLoc","description":"which alternate location to select, if present; '*' to load all ; supported by pdb
"},{"title":"ParserOptionsSpec#assemblyIndex","link":"assemblyIndex","description":"index of the assembly in symmetry ; supported by mmtf
"},{"title":"ParserOptionsSpec#assignBonds","link":"assignBonds","description":"for formats without explicit bonds (e.g. PDB, xyz) infer bonding (default true).
"},{"title":"ParserOptionsSpec#doAssembly","link":"doAssembly","description":"boolean dictating weather or not to do assembly ; supported by mcif, pdb
"},{"title":"ParserOptionsSpec#dontConnectDuplicatedAtoms","link":"dontConnectDuplicatedAtoms","description":"do not detect bonds between symmetries generated with duplicateAssemblyAtoms (cif only - other formats never make bonds between symmetries)
"},{"title":"ParserOptionsSpec#duplicateAssemblyAtoms","link":"duplicateAssemblyAtoms","description":"Set to true if you wish to duplicate assembly atoms otherwise false ; supported by all formats with symmetries. Not duplicating will result in faster rendering but it will not be possible to individually style symmetries.
"},{"title":"ParserOptionsSpec#frames","link":"frames","description":"true if you want to add to a new frame and false otherwise ; supported by all
"},{"title":"ParserOptionsSpec#hbondCutoff","link":"hbondCutoff","description":"maximum distance used for identifying hydrogen bonds when computing secondary structure; supported by pdb, mmtf, cif
"},{"title":"ParserOptionsSpec#keepH","link":"keepH","description":"do not strip hydrogens ; supported by sdf,mol2
"},{"title":"ParserOptionsSpec#multimodel","link":"multimodel","description":"specifies whether or not multiple models are being defined ; supported by xyz,sdf, or mol2
"},{"title":"ParserOptionsSpec#noComputeSecondaryStructure","link":"noComputeSecondaryStructure","description":"do not compute ss ; supported by pdb, mmtf, cif
"},{"title":"ParserOptionsSpec#noSecondaryStructure","link":"noSecondaryStructure","description":"boolean dictating the presence of a secondary structure ; supported by pdb
"},{"title":"ParserOptionsSpec#normalizeAssembly","link":"normalizeAssembly","description":"shift symmetry mates so their centroid is in the unit cell
"},{"title":"ParserOptionsSpec#onemol","link":"onemol","description":"specifies weather or not the model is of one molecule ; Supported by xyz , sdf , mol2
"},{"title":"ParserOptionsSpec#parseStyle","link":"parseStyle","description":"used to define ChemDoodle styles ; supported by cdjson
"},{"title":"ParserOptionsSpec#style","link":"style","description":"set model to this style after parsing
"},{"title":"ParserOptionsSpec#unboundCations","link":"unboundCations","description":"for formats without explicit bonds, if assigning bonds to not assign bonds to common cations
"},{"title":"ParserOptionsSpec#vibrate","link":"vibrate","description":"object specifying the vibration behavior ; supported by all
"},{"title":"ParserOptionsSpec#wrapAtoms","link":"wrapAtoms","description":"Set to true with duplicateAssemblyAtoms to individually wrap atoms (from symmetries) into unit cell
"},{"title":"Quaternion","link":"Quaternion"},{"title":"ROYGB","link":"ROYGB"},{"title":"RWB","link":"RWB"},{"title":"Ray","link":"Ray"},{"title":"SDF","link":"SDF"},{"title":"ShapeSpec","link":"ShapeSpec","description":"GLShape style specification
"},{"title":"ShapeSpec#callback","link":"callback","description":"function to call on click
"},{"title":"ShapeSpec#clickable","link":"clickable","description":"if true, user can click on object to trigger callback
"},{"title":"ShapeSpec#color","link":"color","description":"Either a single color for the whole object or an array specifying the color at each vertex ({@link CustomShapeSpec}).
"},{"title":"ShapeSpec#contextMenuEnabled","link":"contextMenuEnabled","description":"if true, user can right-click or long press to trigger callback
"},{"title":"ShapeSpec#frame","link":"frame","description":"if set, only display in this frame of an animation
"},{"title":"ShapeSpec#hidden","link":"hidden","description":"if true, do not display object
"},{"title":"ShapeSpec#hover_callback","link":"hover_callback","description":"hover callback
"},{"title":"ShapeSpec#hoverable","link":"hoverable","description":"if true, user can hover on object to trigger callback
"},{"title":"ShapeSpec#linewidth","link":"linewidth","description":"width of line for wireframe rendering No longer supported by most browsers
"},{"title":"ShapeSpec#opacity","link":"opacity","description":"transparency, between 0 (invisible) and 1 (opaque)
"},{"title":"ShapeSpec#unhover_callback","link":"unhover_callback","description":"unhover callback
"},{"title":"ShapeSpec#wireframe","link":"wireframe","description":"draw as wireframe, not surface
"},{"title":"Sinebow","link":"Sinebow"},{"title":"Sphere","link":"Sphere"},{"title":"SphereSpec","link":"SphereSpec","description":"Sphere shape specification. Extends {@link ShapeSpec}.
"},{"title":"SphereSpec#center","link":"center","description":"center of sphere
"},{"title":"SphereSpec#quality","link":"quality","description":"quality metric, higher uses more triangles (default 2)
"},{"title":"SphereSpec#radius","link":"radius","description":"radius of sphere
"},{"title":"SphereStyleSpec","link":"SphereStyleSpec","description":"Sphere (spacefill) style specification
"},{"title":"SphereStyleSpec#color","link":"color","description":"fixed coloring
"},{"title":"SphereStyleSpec#colorfunc","link":"colorfunc","description":"Allows the user to provide a function for setting the colorschemes.
"},{"title":"SphereStyleSpec#colorscheme","link":"colorscheme","description":"colorscheme to use on atoms; overrides color
"},{"title":"SphereStyleSpec#hidden","link":"hidden","description":"do not show sticks
"},{"title":"SphereStyleSpec#opacity","link":"opacity","description":"opacity (zero to one), must be the same for all atoms in a model
"},{"title":"SphereStyleSpec#radius","link":"radius","description":"fixed radius of sphere
"},{"title":"SphereStyleSpec#scale","link":"scale","description":"scale VDW radius by specified amount
"},{"title":"StickStyleSpec","link":"StickStyleSpec","description":"Stick (cylinder) style specification
"},{"title":"StickStyleSpec#aromaticStyle","link":"aromaticStyle","description":"Style for rendering aromatic (bond order 4) bonds.
\n"dashed" = one solid + one dashed bond (default)
\n"circle" = single bond + circle/torus inside the aromatic ring
fixed coloring
"},{"title":"StickStyleSpec#colorfunc","link":"colorfunc","description":"Allows the user to provide a function for setting the colorschemes.
"},{"title":"StickStyleSpec#colorscheme","link":"colorscheme","description":"colorscheme to use on atoms; overrides color
"},{"title":"StickStyleSpec#dashedBondConfig","link":"dashedBondConfig","description":"dashed bond properties
"},{"title":"StickStyleSpec#dashedBonds","link":"dashedBonds","description":"draw all bonds as dashed bonds
"},{"title":"StickStyleSpec#doubleBondScaling","link":"doubleBondScaling","description":"radius scaling factor for drawing double bonds (default 0.4)
"},{"title":"StickStyleSpec#hidden","link":"hidden","description":"do not show sticks
"},{"title":"StickStyleSpec#opacity","link":"opacity","description":"opacity (zero to one), must be the same for all atoms in a model
"},{"title":"StickStyleSpec#radius","link":"radius","description":"radius of stick
"},{"title":"StickStyleSpec#showNonBonded","link":"showNonBonded","description":"display nonbonded atoms as spheres
"},{"title":"StickStyleSpec#singleBonds","link":"singleBonds","description":"draw all bonds as single bonds
"},{"title":"StickStyleSpec#tripleBondScaling","link":"tripleBondScaling","description":"radius scaling factor for drawing triple bonds (default 0.25)
"},{"title":"Style#updateStyle","link":"updateStyle"},{"title":"StyleBox#addStyle","link":"addStyle"},{"title":"Surface","link":"Surface"},{"title":"Surface#editSurface","link":"editSurface","description":"Finalizes the surface card with value specified in the surfaceSpec
"},{"title":"Surface#getSymmetries","link":"getSymmetries","description":"Returns list of rotational/translational matrices if there is BIOMT data
\nOtherwise returns a list of just the ID matrix
Returns list of rotational/translational matrices if there is BIOMT data
\nOtherwise returns a list of just the ID matrix
Sets symmetries based on specified matrices in list
"},{"title":"Surface#setSymmetries","link":"setSymmetries","description":"Sets symmetries based on specified matrices in list
"},{"title":"SurfaceMenu#addSurface","link":"addSurface","description":"Add Surface in the Surface Menu
"},{"title":"SurfaceMenu#empty","link":"empty","description":"Clear all the surface cards
"},{"title":"SurfaceStyleSpec","link":"SurfaceStyleSpec"},{"title":"SurfaceStyleSpec#color","link":"color","description":"fixed coloring, overrides colorscheme
"},{"title":"SurfaceStyleSpec#colorscheme","link":"colorscheme","description":"element based coloring
"},{"title":"SurfaceStyleSpec#onesided","link":"onesided","description":"one sided material - back is transparent
"},{"title":"SurfaceStyleSpec#opacity","link":"opacity","description":"sets the transparency: 0 to hide, 1 for fully opaque
"},{"title":"SurfaceStyleSpec#voldata","link":"voldata","description":"volumetric data for vertex coloring, can be VolumeData object or raw data if volformat is specified
"},{"title":"SurfaceStyleSpec#volformat","link":"volformat","description":"format of voldata if not a {VolumeData} object
"},{"title":"SurfaceStyleSpec#volscheme","link":"volscheme","description":"coloring scheme for mapping volumetric data to vertex color, if not a Gradient object, show describe a builtin gradient one by providing an object with gradient, min, max, and (optionally) mid fields.
"},{"title":"SurfaceStyleSpec#wireframe","link":"wireframe","description":"Display as wireframe
"},{"title":"SurfaceType","link":"SurfaceType","description":"Surface types
"},{"title":"Triangle","link":"Triangle"},{"title":"UnitCellStyleSpec","link":"UnitCellStyleSpec","description":"Style specification ofr unit cell shape.
"},{"title":"UnitCellStyleSpec#alabel","link":"alabel","description":"label for "a" axis
"},{"title":"UnitCellStyleSpec#alabelstyle","link":"alabelstyle","description":"label style for a axis
"},{"title":"UnitCellStyleSpec#astyle","link":"astyle","description":"arrow specification of the "a" axis
"},{"title":"UnitCellStyleSpec#blabel","link":"blabel","description":"label for "b" axis
"},{"title":"UnitCellStyleSpec#blabelstyle","link":"blabelstyle","description":"label style for b axis
"},{"title":"UnitCellStyleSpec#box","link":"box","description":"line style used to draw box
"},{"title":"UnitCellStyleSpec#bstyle","link":"bstyle","description":"arrow specification of the "b" axis
"},{"title":"UnitCellStyleSpec#clabel","link":"clabel","description":"label for "c" axis
"},{"title":"UnitCellStyleSpec#clabelstyle","link":"clabelstyle","description":"label style for c axis
"},{"title":"UnitCellStyleSpec#cstyle","link":"cstyle","description":"arrow specification of the "c" axis
"},{"title":"VASP","link":"VASP"},{"title":"Vector2","link":"Vector2"},{"title":"Vector3","link":"Vector3"},{"title":"ViewStyle","link":"ViewStyle","description":"View style configuration
"},{"title":"ViewStyle#color","link":"color","description":"Color of the outline
"},{"title":"ViewStyle#radius","link":"radius","description":"Ambient occlusion radius (in Angstroms) used to detect occlusions (default 5.0).
"},{"title":"ViewStyle#strength","link":"strength","description":"Ambient occlusion strength (darkness) of shading (default 1.0)
"},{"title":"ViewStyle#style","link":"style","description":"How to style viewer: outline|ambientOcclusion|none
"},{"title":"ViewStyle#width","link":"width","description":"Width of the outline
"},{"title":"ViewerGridSpec","link":"ViewerGridSpec","description":"Grid GLViewer input specification
"},{"title":"ViewerGridSpec#cols","link":"cols","description":"number of columns in grid
"},{"title":"ViewerGridSpec#control_all","link":"control_all","description":"if true, mouse events are linked
"},{"title":"ViewerGridSpec#rows","link":"rows","description":"number of rows in grid
"},{"title":"ViewerSpec","link":"ViewerSpec","description":"GLViewer input specification
"},{"title":"ViewerSpec#ambientOcclusion","link":"ambientOcclusion","description":"Ambient occlusion settings
"},{"title":"ViewerSpec#antialias","link":"antialias","description":"Enable antialiasing
"},{"title":"ViewerSpec#backgroundAlpha","link":"backgroundAlpha","description":"Alpha transparency of canvas background
"},{"title":"ViewerSpec#backgroundColor","link":"backgroundColor","description":"Color of the canvas background
"},{"title":"ViewerSpec#callback","link":"callback","description":"Callback function to be executed with this viewer after setup is complete
"},{"title":"ViewerSpec#camerax","link":"camerax"},{"title":"ViewerSpec#canvas","link":"canvas"},{"title":"ViewerSpec#cartoonQuality","link":"cartoonQuality","description":"default 10
"},{"title":"ViewerSpec#col","link":"col"},{"title":"ViewerSpec#cols","link":"cols"},{"title":"ViewerSpec#control_all","link":"control_all"},{"title":"ViewerSpec#defaultcolors","link":"defaultcolors","description":"Object defining default atom colors as atom => color property value pairs for all models within this viewer
"},{"title":"ViewerSpec#disableFog","link":"disableFog","description":"Disable fog, default to false
"},{"title":"ViewerSpec#hoverDuration","link":"hoverDuration"},{"title":"ViewerSpec#id","link":"id","description":"id of the canvas
"},{"title":"ViewerSpec#lowerZoomLimit","link":"lowerZoomLimit"},{"title":"ViewerSpec#minimumZoomToDistance","link":"minimumZoomToDistance"},{"title":"ViewerSpec#nomouse","link":"nomouse","description":"Whether to disable disable handling of mouse events.
\nIf you want to use your own mouse handlers, set this then bind your handlers to the canvas object.
\nThe default 3Dmol.js handlers are available for use:
\n'mousedown touchstart': viewer._handleMouseDown,
\n'DOMMouseScroll mousewheel': viewer._handleMouseScroll
\n'mousemove touchmove': viewer._handleMouseMove
Orthographic instead of perspective rendering. Default false.
"},{"title":"ViewerSpec#outline","link":"outline","description":"Outline parameters
"},{"title":"ViewerSpec#row","link":"row"},{"title":"ViewerSpec#rows","link":"rows"},{"title":"ViewerSpec#style","link":"style","description":"outline or ambientOcclusion deprecated
"},{"title":"ViewerSpec#upperZoomLimit","link":"upperZoomLimit"},{"title":"ViewerSpec#upscale","link":"upscale","description":"Render upscaled to 2x resolution. Defaults to antialiasing setting. Ignored for Retina displays.
"},{"title":"VolumeData","link":"VolumeData"},{"title":"VolumetricRendererSpec","link":"VolumetricRendererSpec","description":"VolumetricRenderer style specification
"},{"title":"VolumetricRendererSpec#coords","link":"coords","description":"coordinates around which to include data; use viewer.selectedAtoms() to convert an AtomSelectionSpec to coordinates
"},{"title":"VolumetricRendererSpec#seldist","link":"seldist","description":"distance around coords to include data [default = 2.0]
"},{"title":"VolumetricRendererSpec#selection","link":"selection","description":"selection around which to include data
"},{"title":"VolumetricRendererSpec#subsamples","link":"subsamples","description":"number of times to sample each voxel approximately (default 5)
"},{"title":"VolumetricRendererSpec#transferfn","link":"transferfn","description":"list of objects containing @color, @opacity and @value properties to specify color per voxel data value
"},{"title":"WithinSelectionSpec","link":"WithinSelectionSpec","description":"Within selection object. Used to find the subset of an atom selection that is within
\nsome distance from another atom selection. When added as a field of an {@link AtomSelectionSpec},
\nintersects the set of atoms in that selection with the set of atoms within a given
\ndistance from the given {@link AtomSelectionSpec}.
the distance in angstroms away from the atom selection to include atoms in the parent selection
"},{"title":"WithinSelectionSpec#invert","link":"invert","description":"if set, selects atoms not within distance range for intersection
"},{"title":"WithinSelectionSpec#sel","link":"sel","description":"the selection of atoms against which to measure the distance from the parent atom selection
"},{"title":"XYZ","link":"XYZ"},{"title":"XYZ","link":"XYZ","description":"Read an XYZ file from str and return result
"},{"title":"XYZ#x","link":"x"},{"title":"XYZ#y","link":"y"},{"title":"XYZ#z","link":"z"},{"title":"addBond","link":"addBond","description":"Add a bond between two atoms (bidirectional).
"},{"title":"apply3DmolStyle","link":"apply3DmolStyle","description":"Apply a 3DMOL_STYLE JSON block to atom bond styles and model data.
\nJSON format:
\n{"stick":{"radius":0.15},"bonds":{"1-5":{"color1":"red","color2":"blue"}}}
built in color schemes
\nThe user can pass these strings directly as the colorscheme
secondary structure pymol
"},{"title":"builtinGradients","link":"builtinGradients","description":"built in gradient schemes
\nThe user can pass these strings directly as the gradient
Create and initialize an appropriate viewer at supplied HTML element using specification in config
"},{"title":"createViewerGrid","link":"createViewerGrid","description":"Create and initialize an appropriate a grid of viewers that share a WebGL canvas
"},{"title":"decode","link":"decode","description":"Fixed point, delta, RLE, integer packing adopted from https://github.com/rcsb/mmtf-javascript/
\nby Alexander Rose alexander.rose@weirdbyte.de, MIT License, Copyright (c) 2016
Parse a lammps trajectory file from str and create atoms
"},{"title":"download","link":"download","description":"Load a PDB/PubChem structure into existing viewer. Automatically calls 'zoomTo' and 'render' on viewer after loading model
"},{"title":"elementColors","link":"elementColors","description":"Preset element coloring - from individual element colors to entire mappings (e.g. 'elementColors.Jmol' colors atoms with Jmol stylings)
"},{"title":"elementColors.Jmol","link":"Jmol","description":"Jmol-like element colors
"},{"title":"elementColors.rasmol","link":"rasmol","description":"rasmol-like element colors
"},{"title":"get","link":"get","description":"Fetch data from URL
"},{"title":"getColorFromStyle","link":"getColorFromStyle","description":"Return proper color for atom given style
"},{"title":"getbin","link":"getbin","description":"Download binary data (e.g. a gzipped file) into an array buffer and provide
\narraybuffer to callback.
Parse SDF data items (property blocks) that follow M END.
\nPer the CTfile spec, each data item consists of:
\nThe record ends at the $$$$ delimiter.
"},{"title":"parseV3000","link":"parseV3000"},{"title":"residues.amino","link":"amino"},{"title":"residues.nucleic","link":"nucleic"},{"title":"residues.shapely","link":"shapely"},{"title":"setSyncSurface","link":"setSyncSurface"},{"title":"ssColors","link":"ssColors","description":"Preset secondary structure color scheme
"},{"title":"syncSurface","link":"syncSurface","description":"Render surface synchronously if true
"},{"title":"viewers","link":"viewers","description":"Contains a dictionary of embedded viewers created from HTML elements
\nwith a the viewer_3Dmoljs css class indexed by their id (or numerically
\nif they do not have an id).