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Class scilligence.JSDraw2.Editor

class scilligence.JSDraw2.Editor
Editor class - define an Editor object. 
 Example:
   <html>
   <head>
   <script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/dojo/1.11.2/dojo/dojo.js"></script>
   <script type="text/javascript" src='http://[PATH]/Scilligence.JSDraw2.js'></script>
   </head>
   <body>
   <div id='ed'></div>
   <script type='text/javascript'>
     dojo.ready(function() {
       // create a JSDraw Editor
       var editor = new JSDraw2.Editor("ed", { skin: "w8", width: 800, height: 400 });

       // create a JSDraw viewer
       //var editor = new JSDraw2.Editor("ed", { skin: "w8", width: 800, height: 400, viewonly: true });

       // create a JSDraw popup Editor
       //var editor = new JSDraw2.Editor("ed", { skin: "w8", width: 800, height: 400, popup: true });
     });
   </script>
   </body>
   </html>
Defined in Scilligence.JSDraw2.Pro.js

Property Summary
Mol atoms
Mol object
bool chiral
Molecule Chiral Flag

Constructor Summary
Editor (string dv, dictionary options)
Constructor a JSDraw Editor

Function Summary
activate (bool f, bool show)
Activate the editor and set focus
cleanupRxn()
Clean up reaction
clear (bool redraw)
Clear all contents
copy()
Copy
static create (string or DOM id, dictonary options)
Create a JSDraw Editor
This function can be called before document.onload().
new JSDraw2.Editor() can only be used in or after document.onload().
cut()
Cut
doCmd (string cmd)
Do a toolbar command
fitToWindow (number maxBondLength)
Fit the molecule to the view window
static get (string id)
Get the Editor object by its ID
getCenter (array atoms)
Get the center of a set of atoms
getExactMass()
Get exact mass
getExtinctionCoefficient()
Get Extinction Coefficient
getFormula (bool html)
Get Formula
getFragment (Atom a)
Get the fragment containing a given atom
getMolWeight()
Get molecular weight
getMolfile (bool v3000)
Get molfile data
getRxnfile (bool groupbyplus, bool v3000)
Get Rxnfile
getSmiles()
Get SMILES
getSvg()
Get SVG data
getXml (number width, number height, bool viewonly)
Get JSDraw Xml data
highlight (string or Mol query)
Highlight a query structure
static init()
Initialize all DIV HTML elements and their class marked as JSDraw, and convert all of them into JSDraw Editor
This function can be called before document.onload().
new JSDraw2.Editor() can only be used in or after document.onload().
moveCenter()
Move the structure to center of the view window
past (Point pos)
Paste
pushundo()
Push the current status into undo stack
readCookie (string name)
Read the structure from a saved cookie
redo()
Redo once
redraw()
Redraw the molecule
refresh (bool modified)
Refresh the display
resetScale()
Reset scaling
rotate (array atoms, Point origin, deg atoms)
Rotate atoms around a point
scale (number s, Point origin)
Scale the molecule
selectAll()
Select all object
setFile (string data, string filetype)
Load file data
setJdx (string data)
Set Secptrum JDX data
setModified (bool f)
Set modified flag
setMol (Mol mol)
Load a Mol object
setMolFile (string molfile)
Load a molfile
setRxnFile (string rxnfile)
Load a rxnfile
setXml (string xml)
Set JSDraw Xml data
static showAbout()
Show JSDraw About box
static showPopup (string title, string btnText, function(editor) btnFn, number zindex)
Show JSDraw Poup Editor
undo()
Undo once
writeCookie (string name, number days)
Write the current structure into a cookie, so it can be reloaded next time

Event Summary
bool ondatachange (Editor editor)
Called when the structure is changed

Property Details

property Mol atoms

Mol object

property bool chiral

Molecule Chiral Flag

Constructor Details

constructor Editor

Editor(string dv, dictionary options)
Constructor a JSDraw Editor
Parameters:
dv - the id of the div placeholder
options - the options for the editor:
  • background - background color
  • biology - Set this flag to false to hide seqence button
  • buttonshape - circle, or square
  • data - actual data
  • dataformat - data format. It can be molfile, rxnfile, html
  • height
  • focusbox - indicate if show focusing box if focused. default: true
  • focuscolor - the border color when focused
  • inktools - set this flag to false to hide ink tools
  • highlighterrors - set this flag to false not to highlight errors in reb box
  • ondatachange - datachange event handler
  • plugins - plugins, as an array [{iconurl, tooltips, onclick}, ...]
  • popup - Create a viewer, and double-click to show popup editor
  • popupheight - Popup Editor height
  • popupwidth - Popup Editor width
  • query - Set this flag to false to disable query atoms (A, R, X, Q, *, etc.) in periodic table
  • removeHydrogens - Remove hydrogen atoms before show the structure
  • rxn - Set this flag to false to disable reaction buttons on toolbar
  • scale - A factore to zoom the whole editor, including toolbars. This is useful for iPad applications
  • sendquery - Set this flag to false to hide PubChem, ChemSpider search button
  • skin - set this to "w8" to display the editor in JSDraw2 mode; leave this parameter to empty to display editor in classic mode (2.0)
  • showcarbon - all or terminal
  • showfilemenu - set this flag to false to hide file menus
  • showimplicithydrogens - Set flag to false to hide implicit hydrogens
  • showtoolbar - set this flag to false not to show toolbar
  • viewonly
  • width

Function Details

function activate

activate(bool f, bool show)
Activate the editor and set focus
Parameters:
f - indicate setting focus or name
show - indicate if redrawing the structure
Returns:
null

function cleanupRxn

cleanupRxn()
Clean up reaction
Returns:
true if it is a reaction

function clear

clear(bool redraw)
Clear all contents
Parameters:
redraw - indicate if redrawing the view wndow
Returns:
null

function copy

copy()
Copy
Returns:
null

function create

static create(string or DOM id, dictonary options)
Create a JSDraw Editor
This function can be called before document.onload().
new JSDraw2.Editor() can only be used in or after document.onload().
Parameters:
id - the ID of DIV placehold, or the DIV DOM object
options - creating options. Please check Editor contructor for details

function cut

cut()
Cut
Returns:
null

function doCmd

doCmd(string cmd)
Do a toolbar command
Parameters:
cmd - the command name
Returns:
null

function fitToWindow

fitToWindow(number maxBondLength)
Fit the molecule to the view window
Parameters:
maxBondLength - maximum bond length
Returns:
null

function get

static get(string id)
Get the Editor object by its ID
Parameters:
id - the Editor ID
Returns:
the Editor object

function getCenter

getCenter(array atoms)
Get the center of a set of atoms
Parameters:
atoms - an array of atoms
Returns:
a Point object

function getExactMass

getExactMass()
Get exact mass
Returns:
a number

function getExtinctionCoefficient

getExtinctionCoefficient()
Get Extinction Coefficient
Returns:
a number

function getFormula

getFormula(bool html)
Get Formula
Parameters:
html - indicate if rendering Formula in HTML format
Returns:
a string

function getFragment

getFragment(Atom a)
Get the fragment containing a given atom
Parameters:
a - the given atom
Returns:
the fragement as a Mol object

function getMolWeight

getMolWeight()
Get molecular weight
Returns:
a number

function getMolfile

getMolfile(bool v3000)
Get molfile data
Parameters:
v3000 - indicate if rendering it in mol v3000 format
Returns:
the molfile string

function getRxnfile

getRxnfile(bool groupbyplus, bool v3000)
Get Rxnfile
Parameters:
groupbyplus - indicate if grouping reactants/products based on explicit plus signs
v3000 - indicate if rendering in v3000 format
Returns:
a string

function getSmiles

getSmiles()
Get SMILES
Returns:
a string

function getSvg

getSvg()
Get SVG data
Returns:
the svg string

function getXml

getXml(number width, number height, bool viewonly)
Get JSDraw Xml data
Parameters:
width - the view width
height - the view height
viewonly - indicate if it is viewonly mode
Returns:
a string

function highlight

highlight(string or Mol query)
Highlight a query structure
Parameters:
query - the query structure
Returns:
true or false

function init

static init()
Initialize all DIV HTML elements and their class marked as JSDraw, and convert all of them into JSDraw Editor
This function can be called before document.onload().
new JSDraw2.Editor() can only be used in or after document.onload().

function moveCenter

moveCenter()
Move the structure to center of the view window
Returns:
null

function past

past(Point pos)
Paste
Parameters:
pos - place the pasted structure to this location
Returns:
the Mol

function pushundo

pushundo()
Push the current status into undo stack
Returns:
null

function readCookie

readCookie(string name)
Read the structure from a saved cookie
Parameters:
name - cookie name
Returns:
null

function redo

redo()
Redo once
Returns:
null

function redraw

redraw()
Redraw the molecule
Returns:
null

function refresh

refresh(bool modified)
Refresh the display
Parameters:
modified - modified flag
Returns:
null

function resetScale

resetScale()
Reset scaling
Returns:
null

function rotate

rotate(array atoms, Point origin, deg atoms)
Rotate atoms around a point
Parameters:
atoms - an array of atom
origin - rotating orgin
atoms - rotating degree
Returns:
null

function scale

scale(number s, Point origin)
Scale the molecule
Parameters:
s - the scaling factor
origin - the scaling origin
Returns:
null

function selectAll

selectAll()
Select all object
Returns:
true or false

function setFile

setFile(string data, string filetype)
Load file data
Parameters:
data - the file contents
filetype - the file type: mol, rxn, xml. Other file types can be loaded with JSDraw.WebServices
Returns:
the Mol object loaded

function setJdx

setJdx(string data)
Set Secptrum JDX data
Parameters:
data - JDX string

function setModified

setModified(bool f)
Set modified flag
Parameters:
f - true or false
Returns:
null

function setMol

setMol(Mol mol)
Load a Mol object
Parameters:
mol - the Mol object to be loaded
Returns:
true or false

function setMolFile

setMolFile(string molfile)
Load a molfile
Parameters:
molfile - the mol file contents
Returns:
null

function setRxnFile

setRxnFile(string rxnfile)
Load a rxnfile
Parameters:
rxnfile - the rxn file contents
Returns:
null

function setXml

setXml(string xml)
Set JSDraw Xml data
Parameters:
xml - the JSDraw Xml string
Returns:
the Mol object loaded

function showAbout

static showAbout()
Show JSDraw About box
Returns:
null

function showPopup

static showPopup(string title, string btnText, function(editor) btnFn, number zindex)
Show JSDraw Poup Editor
Parameters:
title - the title of the Popup dialog
btnText - the button text of the Popup dialog
btnFn - the callback function when user clicks on the button
zindex - the zIndex of the dialog DOM

function undo

undo()
Undo once
Returns:
null

function writeCookie

writeCookie(string name, number days)
Write the current structure into a cookie, so it can be reloaded next time
Parameters:
name - cookie name
days - cookie valid days
Returns:
null

Event Details

event ondatachange

bool ondatachange(Editor editor)
Called when the structure is changed
Parameters:
editor this Editor
Returns:
null