Difference between revisions of "Jmol JavaScript Object/JME/Options"
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AngelHerraez (talk | contribs) (improve documentation for JSME object) |
AngelHerraez (talk | contribs) (improve documentation for JSME object) |
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| + | [[File:JSME toolbar.png|frame|right|Top toolbar in JSME under several settings]] | ||
| + | [[Jmol JavaScript Object/JME|Parent page]] | ||
| + | |||
| + | <div style="clear: both"></div> | ||
== "Options" parameter for JSME == | == "Options" parameter for JSME == | ||
| − | + | Option key words are case-insensitive. | |
The default values are shown in bold. | The default values are shown in bold. | ||
| + | Original documentation at [https://peter-ertl.com/jsme/ Peter Ertl's site]. | ||
{| class="wikitable sortable" | {| class="wikitable sortable" | ||
| Line 7: | Line 12: | ||
!colspan="3"| option keywords !! description | !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) | | 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 | + | | '''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. | | query || '''NOquery''' || || Display or not the query button, which opens a dialog. In query mode, a SMARTS is generated when a SMILES is requested. | ||
| Line 19: | Line 24: | ||
| atomMoveButton || '''NOatomMoveButton''' || || Display or not the atom move 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). | | depict || '''NOdepict''' || || Display only the canvas, without any toolbars for editing (useful for display of structure). | ||
| Line 57: | Line 62: | ||
| useOCLidCode || '''NOuseOCLidCode''' || || Display or hide the menu item for exporting OCL (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 [ | + | | '''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 [ | + | | '''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 | + | | '''searchInChIkey''' || NOsearchInChIkey || || Display or hide the menu item for searching on the web using the current InChIKey. |
|} | |} | ||
Latest revision as of 16:36, 31 October 2019
Top toolbar in JSME under several settings
"Options" parameter for JSME
Option key words are case-insensitive. The default values are shown in bold. Original documentation at Peter Ertl's site.
| option keywords | description | ||
|---|---|---|---|
| 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) | |
| number 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. | |
| 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 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 InChI | |
| exportInChIauxInfo | NOexportInChIauxInfo | Display or hide the menu item for exporting InChI AuxInfo. | |
| exportInChIkey | NOexportInChIkey | Display or hide the menu item for exporting InChIKey | |
| searchInChIkey | NOsearchInChIkey | Display or hide the menu item for searching on the web using the current InChIKey. | |
