Jmol JavaScript Object/JME - Revision history

AngelHerraez at 06:47, 31 May 2024

2024-05-31T06:47:36Z

AngelHerraez at 06:39, 31 May 2024

2024-05-31T06:39:24Z

AngelHerraez: /* JSME options */

2019-10-29T10:56:18Z

‎JSME options

AngelHerraez: improve documentation for JSME object

2019-10-29T09:56:16Z

improve documentation for JSME object

AngelHerraez: improve documentation for JSME object

2019-10-29T00:34:25Z

improve documentation for JSME object

AngelHerraez: improve documentation for JSME object

2019-10-28T19:58:19Z

improve documentation for JSME object

AngelHerraez: update of descriptions (mostly, Java left behind)

2019-10-27T19:09:27Z

update of descriptions (mostly, Java left behind)

AngelHerraez: update of descriptions (mostly, Java left behind)

2019-10-27T16:55:22Z

update of descriptions (mostly, Java left behind)

AngelHerraez: JME syntax

2013-02-26T19:23:23Z

JME syntax

AngelHerraez: /* JME-specific methods */

2013-02-26T19:19:32Z

‎JME-specific methods

@@ Line 5: / Line 5: @@
 == Creating and inserting JSME ==
 ''(Note that although the syntax is reminiscent of the former Java applets, no Java is currently involved here)''
 The name of the unique '''<code>Jmol</code>''' object is literal, cannot be changed.
@@ Line 21: / Line 16: @@
 In preparation, your web page must call 2 files (this is usually done in the <code>head</code> section):
 * {{file|JSmol.min.js}}
-* {{file|jsme.nocache.js}} in the {{folder|jsme}} folder of the JSmol package (this is a copy of the original JSME package). You can also include instead your own copy of the JSME package (e.g. to use a specific version not included in JSmol distribution)
+* {{file|jsme.nocache.js}}. This may be:
 To create and insert the JSME object, use:
@@ Line 38: / Line 35: @@
 * {{file|JSmol.min.js}}
 * {{file|JSmolJME.js}} in the {{folder|js}} folder of the JSmol package
-* {{file|jsme.nocache.js}} in the {{folder|jsme}} folder of the JSmol package (this is a copy of the original JSME package)
+* {{file|jsme.nocache.js}} included in JSmol distribution, in the {{folder|jsme}} folder.
 To create and insert the JSmol and JSME objects, use:

@@ Line 1: / Line 1: @@
 == Integration of JSME into JSmol ==
-'''JSME, the JavaScript Molecule Editor''' by Peter Ertl, evolved from the former [http://www.molinspiration.com/jme/ JME applet].
+'''JSME, the JavaScript Molecule Editor''' by Peter Ertl and Bruno Bienfait <sup>[1]</sup>, evolved from the former JME applet <sup>[2]</sup>.
 It provides tools for the user to draw a molecular structure in 2D. The '''JSmol object library''' includes the capability to pass information back and forth between JSME and JSmol in a seamless manner. The "information panel" that JSmol library implements can be set up to also hold the JSME object, allowing tight integration. Alternatively, JSME and JSmol objects can be set side-by-side on a web page, and communication between both objects can be handled by the page developer.
@@ Line 18: / Line 18: @@
 === Independent JSME ===
 The JSME panel takes a space of its own in the page.
 To create and insert the JSME object, use:
@@ Line 30: / Line 34: @@
 === JSME embedded in JSmol ===
 In this mode, the JSME panel shares the space in the page with a JSmol panel; only one is displayed at a time and their contents (2D vs. 3D) are automatically interconverted to match.
 To create and insert the JSmol and JSME objects, use:
@@ Line 79: / Line 88: @@
   Jmol.jmeOptions(myJME, ''options'') // to set options after the object has been created
   Jmol.jmeReset(myJME)

@@ Line 56: / Line 56: @@
 ** <code>useOpenChemLib</code> - use the [https://github.com/Actelion/openchemlib OpenChemLib library] for SMILES conversion, 2D coordinates computation and SVG export
 ** <code>exportSVG</code> - enable the menu item for SVG export
-** ...and more, all documented at [https://peter-ertl.com/jsme/ Peter Ertl's site]
+** ...and [[Jmol JavaScript Object/JME/Options|more]], all documented at [https://peter-ertl.com/jsme/ Peter Ertl's site]
 Most options are negated by prepending with "no", e.g. <code>nozoom</code>; a few have specific keywords for the opposite choice. The options are case-insensitive.

@@ Line 48: / Line 48: @@
 ** <code>depict</code> - the canvas will appear without editing buttons, i.e. used for structure display only
 ** <code>zoom</code> - allow zooming of the molecular drawing
-** <code>rbutton</code> - display the R button
+** <code>rButton</code> - display the R button
 ** <code>hydrogens</code> - display hydrogens
 ** <code>query</code> - allow query features
-** <code>autoez</code> - automatic generation of SMILES with E,Z stereochemistry
+** <code>autoEZ</code> - automatic generation of SMILES with E,Z stereochemistry
 ** <code>canonize</code> - SMILES canonicalization and detection of aromaticity
 ** <code>stereo</code> - stereochemistry not considered when creating SMILES
-** <code>useopenchemlib</code> - use the [https://github.com/Actelion/openchemlib OpenChemLib library] for SMILES conversion, 2D coordinates computation and SVG export
+** <code>useOpenChemLib</code> - use the [https://github.com/Actelion/openchemlib OpenChemLib library] for SMILES conversion, 2D coordinates computation and SVG export
 ** <code>exportSVG</code> - enable the menu item for SVG export
 ** ...and more, all documented at [https://peter-ertl.com/jsme/ Peter Ertl's site]
-Most options are negated by prepending with "no", e.g. <code>nozoom</code>; a few have specific keywords for the opposite choice.
+Most options are negated by prepending with "no", e.g. <code>nozoom</code>; a few have specific keywords for the opposite choice. The options are case-insensitive.
 == JSME-specific methods ==

@@ Line 1: / Line 1: @@
-= Integration of JSME into JSmol =
+== Integration of JSME into JSmol ==
 '''JSME, the JavaScript Molecule Editor''' by Peter Ertl, evolved from the former [http://www.molinspiration.com/jme/ JME applet].
-It allows the user to draw a molecular structure in 2D. The '''JSmol object library''' includes the capability to pass information back and forth between JSME and JSmol in a seamless manner. The "information panel" that JSmol library implements can be set up to also hold the JSME object, allowing tight integration. Alternatively, JSME and JSmol objects can be set side-by-side on a web page, and communication between both objects can be handled by the page developer.
+It provides tools for the user to draw a molecular structure in 2D. The '''JSmol object library''' includes the capability to pass information back and forth between JSME and JSmol in a seamless manner. The "information panel" that JSmol library implements can be set up to also hold the JSME object, allowing tight integration. Alternatively, JSME and JSmol objects can be set side-by-side on a web page, and communication between both objects can be handled by the page developer.
 == Creating and inserting JSME ==
 ''(Note that although the syntax is reminiscent of the former Java applets, no Java is currently involved here)''
 The name of the unique '''<code>Jmol</code>''' object is literal, cannot be changed.
 On the contrary, the <code>myJME</code>, <code>myJmol</code>, <code>JmeInfo</code>, <code>JmolInfo</code> names used in these examples are user-declared variables and may be different.
-There are two ways of inserting JSME using the JSmol library:
+There are two ways of inserting JSME using the JSmol library: independent and embedded; you can see a demonstration of both at [http://jmol.org/demo/ the main Jmol website].
 === Independent JSME ===
@@ Line 20: / Line 25: @@
 * '''width''': <code>300</code>
 And the JSME panel will be inserted at the point of execution of this JavaScript code.
-If this code is to be included elsewhere, you can specify a target div where the JSME panel will be included, by adding this:
+If you need to include this code elsewhere, you can specify a target div where the JSME panel will be inserted, by adding this parameter:
-* '''divId''': "targetId"
+* '''divid''': "''my_target_div''"
-=== JSME interlinked with JSmol ===
+=== JSME embedded in JSmol ===
 In this mode, the JSME panel shares the space in the page with a JSmol panel; only one is displayed at a time and their contents (2D vs. 3D) are automatically interconverted to match.
@@ Line 29: / Line 34: @@
   Jmol.getApplet("myJmol", JmolInfo);
   Jmol.getJMEApplet("myJME", JmeInfo, myJmol);
-Where the <code>JmeInfo</code> variable must include at least:
+The 3rd argument is a pointer to the associated JSmol object, that will contain this JSME panel as a 2D input option inside its Info panel.
 * '''height''': <code>350</code>
 * '''width''': <code>300</code>
-* '''visible''': <code>true</code>  for the JSME panel to be displayed initially
+* '''visible''': <code>true</code>  for the JSME panel to be displayed initially (JSmol panel hidden)
 Other parameters that may be included in the <code>JmeInfo</code> variable are:
 * '''options''': "''comma-delimited list''"
-** <code>rbutton</code>, <code>norbutton</code> - show / hide R button
+** <code>depict</code> - the canvas will appear without editing buttons, i.e. used for structure display only
-** <code>hydrogens</code>, <code>nohydrogens</code> - display / hide hydrogens
+** <code>zoom</code> - allow zooming of the molecular drawing
-** <code>query</code>, <code>noquery</code> - enable / disable query features
+** <code>rbutton</code> - display the R button
-** <code>autoez</code>, <code>noautoez</code> - automatic generation of SMILES with E,Z stereochemistry
+** <code>hydrogens</code> - display hydrogens
-** <code>nocanonize</code> - SMILES canonicalization and detection of aromaticity supressed
+** <code>query</code> - allow query features
-** <code>nostereo</code> - stereochemistry not considered when creating SMILES
+** <code>autoez</code> - automatic generation of SMILES with E,Z stereochemistry
-** <code>reaction</code>, <code>noreaction</code> - enable / disable reaction input
+** <code>canonize</code> - SMILES canonicalization and detection of aromaticity
-** <code>multipart</code> - possibility to enter multipart structures
+** <code>stereo</code> - stereochemistry not considered when creating SMILES
-** <code>number</code> - possibility to number (mark) atoms
+** <code>useopenchemlib</code> - use the [https://github.com/Actelion/openchemlib OpenChemLib library] for SMILES conversion, 2D coordinates computation and SVG export
-** <code>depict</code> - the applet will appear without editing butons,this is used for structure display only
+** <code>exportSVG</code> - enable the menu item for SVG export
 ** ...and more, all documented at [https://peter-ertl.com/jsme/ Peter Ertl's site]
 == JSME-specific methods ==
@@ Line 59: / Line 66: @@
   Jmol.jmeGetFile(myJME, true) // molecular data in the JME format
   Jmol.jmeGetFile(myJME, false) // molecular data in the MOL format
-  Jmol.jmeSmiles(myJME, ''withStereoChemistry'') // molecular data in the SMILES format
+  Jmol.jmeSmiles(myJME, ''withStereoChemistry'') // molecular data in the SMILES format (with or without stereo information)
 For loading structures into JSME:
   Jmol.jmeReadMolecule(myJME, ''jmeOrMolData'')
-sends data as a string either in JME or MOL formats, depending on the presence of newline characters in that string
+sends data as a string that will be interpreted either in JME or MOL formats, depending on the presence of newline characters in that string.
-''Note:'' Feeding SMILES data into JSME is possible, but not currently implemented in the JSmol library.
+''Note:'' Feeding SMILES data into JSME is possible, but a dedicated method is not currently implemented in the JSmol library.
 You can achieve it using a call to an internal function:
   myJME._applet.readGenericMolecularInput( ''smilesData'' );
 For other tasks:
-  Jmol.jmeOptions(myJME, ''options'')
+  Jmol.jmeOptions(myJME, ''options'') // to set options after the object has been created
   Jmol.jmeReset(myJME)

@@ Line 4: / Line 4: @@
 == Creating and inserting JSME ==
 ''(Note that although the syntax is reminiscent of the former Java applets, no Java is currently involved here)''
-The 3rd argument, if provided, is a pointer to a JSmol object that will contain this JSME drawing panel as a 2D input option inside its Info panel.
+The name of the unique '''<code>Jmol</code>''' object is literal, cannot be changed.
-Parameters making the <code>Info</code> variable (with default values shown):
+There are two ways of inserting JSME using the JSmol library:
-* '''height''' <code>300</code>
-* '''width''' <code>300</code>
+=== Independent JSME ===
-* '''j2sPath''' <code>"j2s"</code>
+The JSME panel takes a space of its own in the page.
-* '''options''' <code>"autoez"</code>
 ** <code>rbutton</code>, <code>norbutton</code> - show / hide R button
 ** <code>hydrogens</code>, <code>nohydrogens</code> - display / hide hydrogens
@@ Line 25: / Line 50: @@
 ** <code>number</code> - possibility to number (mark) atoms
 ** <code>depict</code> - the applet will appear without editing butons,this is used for structure display only
-** ...and more, documented at [https://peter-ertl.com/jsme/ Peter Ertl's site]
+** ...and more, all documented at [https://peter-ertl.com/jsme/ Peter Ertl's site]
 == JSME-specific methods ==
-All these functions must be applied to the unique '''<code>Jmol</code>''' object (this name is literal, cannot be changed):
+All the following functions must be applied to the unique '''<code>Jmol</code>''' object (this name is literal, cannot be changed).
-  Jmol.jmeGetFile(myJME, asJME)
+The <code>myJME</code> name used in these examples is, in contrast, a user-declared variable and may be different.
-  Jmol.jmeOptions(myJME, options)
-  Jmol.jmeReadMolecule(myJME, jmeOrMolData)
+For retrieving data from JSME:
-  Jmol.jmeReset(myJME)
+  Jmol.jmeGetFile(myJME, true) // molecular data in the JME format
-  Jmol.jmeSmiles(myJME, withStereoChemistry)
+  Jmol.jmeGetFile(myJME, false) // molecular data in the MOL format

@@ Line 1: / Line 1: @@
-= Integration of JME into Jmol-JSO =
+= Integration of JSME into JSmol =
-The [http://www.molinspiration.com/jme/ JME applet] (Java Molecular Editor by Peter Ertl) allows the user to draw a molecular structure in 2D. '''Jmol-JSO''' includes the capability to pass information back and forth between JME and Jmol in a seamless manner. The "information panel" that Jmol-JSO implements can be set up to hold the JME applet, allowing tight integration. Alternatively, the JME applet and the Jmol applet can be set side-by-side on a web page, and applet-applet communication can be handled by the page developer.
+JSME, the JavaScript Molecular Editor by Peter Ertl, evolved from the former [http://www.molinspiration.com/jme/ JME applet].
-== Creating and inserting the JME applet ==
+== Creating and inserting JSME ==
-To create a JME applet, use for example:
+To create a JSME object, use for example:
-  var myJME = Jmol.getJMEApplet("myJME", Info, myJmol)
+  var myJME = Jmol.getJMEApplet("myJME", Info, myJmol);
-The 3rd argument, if provided, is a pointer to a Jmol JavaScript Object that will contain this JME drawing panel as a 2D input option inside its Info panel.
+The 3rd argument, if provided, is a pointer to a JSmol object that will contain this JSME drawing panel as a 2D input option inside its Info panel.
-Parameters making the <code>Info</code> variable (with default values shown between angular brackets):
+Parameters making the <code>Info</code> variable (with default values shown):
-* '''height''' <<code>300</code>>
+* '''height''' <code>300</code>
-* '''width''' <<code>300</code>>
+* '''width''' <code>300</code>
-* '''jarPath''' <<code>.</code>>
+* '''j2sPath''' <code>"j2s"</code>
-* '''jarFile''' <<code>JME.jar</code>>
+* '''options''' <code>"autoez"</code>
 ** rbutton, norbutton - show / hide R button
 ** hydrogens, nohydrogens - display / hide hydrogens
@@ Line 26: / Line 27: @@
 ** Documented at [http://www2.chemie.uni-erlangen.de/services/fragment/editor/jme_functions.html]
-== JME-specific methods ==
+== JSME-specific methods ==
 All these functions must be applied to the unique '''<code>Jmol</code>''' object (this name is literal, cannot be changed):
   Jmol.jmeGetFile(myJME, asJME)

@@ Line 32: / Line 32: @@
 Syntax:
-  Jmol.jmeGetFile = function(jme, asJME)
+  Jmol.jmeGetFile(myJME, asJME)
-  Jmol.jmeOptions = function(jme, options)
+  Jmol.jmeOptions(myJME, options)
-  Jmol.jmeReadMolecule = function(jme, jmeOrMolData)
+  Jmol.jmeReadMolecule(myJME, jmeOrMolData)
-  Jmol.jmeReset = function(jme)
+  Jmol.jmeReset(myJME)
-  Jmol.jmeSmiles = function(jme, withStereoChemistry)
+  Jmol.jmeSmiles(myJME, withStereoChemistry)