Jmol JavaScript Object/JME/Options - Revision history

AngelHerraez: improve documentation for JSME object

2019-10-31T16:36:57Z

improve documentation for JSME object

AngelHerraez: improve documentation for JSME object

2019-10-29T14:44:20Z

improve documentation for JSME object

AngelHerraez: improve documentation for JSME object

2019-10-29T11:28:49Z

improve documentation for JSME object

AngelHerraez at 10:57, 29 October 2019

2019-10-29T10:57:03Z

AngelHerraez: improve documentation for JSME object

2019-10-29T10:55:08Z

improve documentation for JSME object

New page

== "Options" parameter for JSME ==

The default values are shown in bold.

{| class="wikitable sortable"
|-
!colspan="3"| option keywords !! description
|-
| '''xButton''' || NOxButton || || Display or not the X button (left side, under the elements)
|-
| rButton || '''NOrButton''' || || Display or not the R button, to mark connection of substituent with the main scaffold (left side, under the elements)
|-
| '''number'''<br>autonumber || star || noStar || Possibility to mark atoms with a number or a circular highlight. All highlighted atoms will have an atom number equal to 1. The atom numbers are included in the exported SMILES and MOL.
|-
| query || '''NOquery''' || || Display or not the query button, which opens a dialog. In query mode, a SMARTS is generated when a SMILES is requested.
|-
| reaction || '''NOreaction''' || || Enable or disable reaction input, and display or not the reaction button.
|-
| atomMoveButton || '''NOatomMoveButton''' || || Display or not the atom move button.
|-
| oldLook || '''newLook''' || || Style of the toolbar buttons and the interface.
|-
| depict || '''NOdepict''' || || Display only the canvas, without any toolbars for editing (useful for display of structure).
|-
| depictAction || '''NOdepictAction''' || || Allow structure editing in depict mode.
|-
| toggle || '''NOtoggle''' || || Allow to switch automatically between editing and depict modes.
|-
| border || '''NOborder''' || || When in depict mode, displays a border around the molecule.
|-
| '''showDragAndDrop SymbolInDepictMode''' || NOshowDragAndDrop SymbolInDepictMode || || Display or not the drag and drop symbol (blue triangle at lower-right corner) in depict mode.
|-
| paste || NOpaste || || Enable or not the paste action, including drop of a MOL/RXN; this can be used together with the depict option to have a read-only depiction.
|-
| '''zoom''' || NOzoom || || Allow zooming of the drawing area (mouse wheel).
|-
| '''hydrogens''' || NOhydrogens || || Display or hide hydrogens on heteroatoms.
|-
| '''keepHs''' || removeHs || removeHsC || Remove hydrogens (all or just those bound to C) when reading a molecule with explicit hydrogens (e.g. from the PubChem database).
|-
| '''stereo''' || NOstereo || || Keep or ignore stereochemistry when generating SMILES.
|-
| '''autoEZ''' || NOautoEZ || || Inclusion of E,Z stereochemistry when generating SMILES.
|-
| '''canonize''' || NOcanonize || || Keep or suppress SMILES canonicalization and detection of aromaticity.
|-
| polarNitro || '''NOpolarNitro''' || || Convert or not nitro (and similar) groups into a nonpolar form.
|-
| '''multiPart''' || NOmultiPart || || Allow to enter multipart structures (display the NEW button).
|-
| addNewPart || NOaddNewPart || || If multipart is enabled, when reading or pasting a new molecule, add it to the existing molecules or replace these.
|-
| '''useOpenChemLib''' || NOuseOpenChemLib || || Use the [https://github.com/Actelion/openchemlib OpenChemLib library] for SMILES conversion, 2D coordinates computation and SVG export.
|-
| '''exportSVG''' || NOexportSVG || || Display or hide the menu item for exporting SVG (useOpenChemLib must be set).
|-
| useOCLidCode || '''NOuseOCLidCode''' || || Display or hide the menu item for exporting OCL (useOpenChemLib must be set).
|-
| '''exportInChI''' || NOexportInChI || || Display or hide the menu item for exporting [http://www.inchi-trust.org/ InChI]
|-
| exportInChIauxInfo || '''NOexportInChIauxInfo''' || || Display or hide the menu item for exporting InChI AuxInfo.
|-
| '''exportInChIkey''' || NOexportInChIkey || || Display or hide the menu item for exporting [http://www.inchi-trust.org/ InChI key]
|-
| '''searchInChIkey''' || NOsearchInChIkey || || Display or hide the menu item for searching on the web using the current InChI key.
|}

← Older revision		Revision as of 10:57, 29 October 2019
Line 1:		Line 1:
		+	[[Jmol JavaScript Object/JME\|Parent page]]
		+
	== "Options" parameter for JSME ==		== "Options" parameter for JSME ==

@@ Line 12: / Line 12: @@
 !colspan="3"| option keywords !! description
 |-
-| '''xButton''' || NOxButton ||  || Display or not the X button (left side, under the elements)
+| '''xButton''' || NOxButton ||  || Display or not the X button (left side, under the elements; to insert a ''nonstandard atom'', e.g. any other element)
 |-
 | rButton || '''NOrButton''' ||  || Display or not the R button, to mark connection of substituent with the main scaffold (left side, under the elements)
@@ Line 62: / Line 62: @@
 | useOCLidCode || '''NOuseOCLidCode''' || || Display or hide the menu item for exporting OCL (useOpenChemLib must be set).
 |-
-| '''exportInChI''' || NOexportInChI || || Display or hide the menu item for exporting          [http://www.inchi-trust.org/ InChI]
+| '''exportInChI''' || NOexportInChI || || Display or hide the menu item for exporting          [https://www.inchi-trust.org/technical-faq-2/#2.1 InChI]
 |-
-| exportInChIauxInfo || '''NOexportInChIauxInfo''' || || Display or hide the menu item for exporting InChI AuxInfo.
+| exportInChIauxInfo || '''NOexportInChIauxInfo''' || || Display or hide the menu item for exporting [https://www.inchi-trust.org/technical-faq-2/#11.1 InChI AuxInfo].
 |-
-| '''exportInChIkey''' || NOexportInChIkey || || Display or hide the menu item for exporting          [http://www.inchi-trust.org/ InChI key]
+| '''exportInChIkey''' || NOexportInChIkey || || Display or hide the menu item for exporting          [https://www.inchi-trust.org/technical-faq-2/#2.7 InChIKey]
 |-
-| '''searchInChIkey''' || NOsearchInChIkey || || Display or hide the menu item for searching on the web using the current InChI key.
+| '''searchInChIkey''' || NOsearchInChIkey || || Display or hide the menu item for searching on the web using the current InChIKey.
 |}

@@ Line 6: / Line 6: @@
 Option key words are case-insensitive.
 The default values are shown in bold.
 {| class="wikitable sortable"
@@ Line 23: / Line 24: @@
 | atomMoveButton || '''NOatomMoveButton''' || || Display or not the atom move button.
 |-
-| oldLook || '''newLook''' ||  || Style of the toolbar buttons and the interface.
+| '''oldLook''' || newLook ||  || Style of the toolbar buttons and the interface.
 |-
 | depict || '''NOdepict''' ||  || Display only the canvas, without any toolbars for editing (useful for display of structure).

@@ Line 1: / Line 1: @@
 [[Jmol JavaScript Object/JME|Parent page]]
 == "Options" parameter for JSME ==
+Option key words are case-insensitive.
 The default values are shown in bold.
@@ Line 13: / Line 15: @@
 | rButton || '''NOrButton''' ||  || Display or not the R button, to mark connection of substituent with the main scaffold (left side, under the elements)
 |-
-| '''number'''<br>autonumber || star || noStar || Possibility to mark atoms with a number or a circular highlight. All highlighted atoms will have an atom number equal to 1. The atom numbers are included in the exported SMILES and MOL.
+| '''number'''<br>autonumber || star || noStar || Possibility to mark atoms with a number or a circular highlight. All highlighted atoms will have an atom number equal to 1. The atom numbers will be included in the exported SMILES and MOL.
 |-
 | query || '''NOquery''' ||  || Display or not the query button, which opens a dialog. In query mode, a SMARTS is generated when a SMILES is requested.