JSME Molecule Editor Options

Q

What JSME Molecule Editor Options?

✍: FYIcenter.com

A

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 comning 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 comning 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');

 

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2020-05-18, 254👍, 0💬