What JSME Molecule Editor Options?

JSME Molecule Editor Options are parameters that can be passed to the editor through the API to change it behavior.

Here are the options supported by JSME:

• xbutton, noxbutton - show / hide the X button (default is xbutton)
• rbutton, norbutton - show / hide the R button (to mark connection of substituent with the main scaffold)
• atommovebutton, noatommovebutton - show / hide the atom move button (default is noatommovebutton)
• hydrogens, nohydrogens - display / hide hydrogens on heteroatom labels (default is hydrogens)
• keephs, removehs - remove hydrogens when reading a molecule with explicit hydrogens (default is keephs). This option can be used to remove hydrogens when pasting a structure with explicit hydrogens coming from e.g. the PubChem database
• keephs, removehsc - remove hydrogens bounded to C when reading a molecule with explicit hydrogens (default is keephs). This option can be used to remove hydrogens when pasting a structure with explicit hydrogens coming from e.g. the PubChem database
• query, noquery - enable / disable query features (default is noquery). In query mode, a SMARTS is generated when a smiles is requested.
• autoez, noautoez - automatic generation of SMILES with E,Z stereochemistry (default is autoez)
• canonize,nocanonize - SMILES canonicalization and detection of aromaticity supressed (default is canonize)
• stereo,nostereo - stereochemistry not considered when creating SMILES (default is stereo)
• reaction, noreaction - enable / disable reaction input
• multipart, nomultipart - possibility to enter multipart structures (default multipart)
• addnewpart, noaddnewpart when reading or pasting a new molecule, add it to the existing molecules or replace them (used only if option multipart is set)
• polarnitro, nopolarnitro - prevent automatic conversion of nitro (and similar) groups into nonpolar form (default is nopolarnitro)
• number / autonumber - possibility to number (mark) atoms
• star, nostar - possibility to highlight an atom (default is nostar). All highlighted atoms will have an atom number equal to 1. The atom numbers are included in the exported SMILES and MOL.
• depict, nodepict - the applet will appear without editing buttons, this is used for structure display only (default nodepict)
• depictaction, nodepictaction - allow structure editing in depict mode
• toggle, notoggle - allow to switch automatically between editing and depict mode (default is notoggle)
• paste, nopaste - enabling and disabling the paste action including drop of a MOL/RXN on the applet., can be used together with the depict option to have a read only depiction
• border, noborder (used together with the depict option) - displays a border around depicted molecule (default is noborder)
• newlook, oldlook - turn on/off the old Java based JME look (default is newlook)
• exportinchi, noexportinchi - enable / disable the menu item for InChI export (http://www.inchi-trust.org/)
• exportinchikey, noexportinchikey - enable / disable the menu item for InChI key export (http://www.inchi-trust.org/)
• exportinchiauxinfo, noexportinchiauxinfo - enable / disable the menu item for InChI auxinfo export (http://www.inchi-trust.org/)
• searchinchiKey, nosearchinchiKey - enable / disable the menu item to search InChI key on the web (http://www.inchi-trust.org/)
• useopenchemlib, nouseopenchemlib - use the OpenChemLib library (https://github.com/Actelion/openchemlib) for SMILES conversion, 2D coordinates computation and SVG export
• exportSVG, noexportSVG - enable / disable the menu item for SVG export (useopenchemlib must be set))
• useOclidcode, nouseOclidcode - enable / disable the menu item for OCL export (useopenchemlib must be set))
• zoom, nozoom - turn on/off zooming of the molecular drawing area
• showdraganddropsymbolindepictmode, noshowdraganddropsymbolindepictmode show or hide the drag and drop symbol (blue triangle) in depict mode
• atombg - atom background color - see the demo JSME_atom_highlight_demo.html for an example
• depictbg - background color for the depict mode in hex format - no test yet

You can call JSME API options(options) function to pass any options to the editor. For example, the following JacaScript statement passes 3 options to the editor identified by "jsme":

jsmeObj.options('paste,query,exportSVG');

⇒ Loading JSME JavaScript in "body"

⇐ Refresh Molecule in JSME Editor

⇑ JSME JavaScript API

⇑⇑ JSME Tutorials