Jmol JavaScript Object/JME/Options
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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. | |
