Jmol JavaScript Object/JME/Options

From Jmol
Jump to navigation Jump to search
Top toolbar in JSME under several settings

Parent page

"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)
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.