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Chemistry

Components

Chemical structure editor and viewer

Supported plugins:

Plugin Version License Editor Viewer Molfile V2000 support Molfile V3000 support JSF Component
OpenChemLib JS v7.4.1 BSD-3-Clause [x] [x] [x] [x] <mol:openChemLibJSPlugin>
MolPaintJS v0.3.5-alpha Apache License 2.0 [x] [x] [x] [x] <mol:molPaintJSPlugin>
Marvin JS 21.1.0 proprietary [x] [x] [x] requires web services <mol:marvinJSPlugin>

Supported attributes

  • border (boolean, default: false): render with a border
  • converter (java.faces.convert.Converter, no default): FacesConverter for the component
  • format (String, default: "MDLV2000"): chemical file format used by the component; possible values: "MDLV2000" and "MDLV3000"
  • height (int, default: 400): height of the plugin in pixels
  • readonly (boolean, default: false): render in view-only mode or as structure editor; do not decode the submitted component value if set to true
  • widgetVar (String, no default): client-side variable name of a Promise object that embeds the plugin's JavaScript instance
  • width (int, default: 400): width of the plugin in pixels

Composite components <mol:molecule> and <mol:moleculeRepeatable>

In case you want to switch between the plugin types dynamically, you can use these two composite components. They pass all the attributes mentioned above to the chosen component.

Additional attribute:
  • pluginType (String, default: "OpenChemLibJS"): type of the plugin; possible values: "OpenChemLibJS", "MolPaintJS" and "MarvinJS"
Use in iterations:

The component <mol:molecule> uses the JSTL tag <c:if test="..."> internally for switching the plugin type. Thus, it shall not be used inside iterating JSF components like <h:dataTable> or <ui:repeat> if they iterate the pluginType attribute. The functionally identical component <mol:moleculeRepeatable> is available for this case, which uses <ui:fragment rendered="..."> internally. Note: This component adds all possible plugin components to the component tree (including JS and CSS resources rendered via JSF), but renders only one of them.

Known issues:
  • Passthrough attributes added via the component attribute pt:myattribute="value" and the XML namespace xmlns:pt="http://xmlns.jcp.org/jsf/passthrough" are not applied to composite components. You can use <f:passThroughAttribute name="myattribute" value="value"> instead.
  • (Mojarra only, tested with Glassfish 5.0) When using other composite components on the same facelet page, you will receive an error like javax.faces.view.facelets.FaceletException: components/molecule.xhtml @0,0 <> Cannot create composite component tag handler for composite-source element in taglib.xml file.

Use in modals

Popular JSF component frameworks such as BootsFaces and PrimeFaces offer modal components, which can include MolecularFaces' plugin components. It might be necessary to execute the init() method of the JavaScript object provided via the widgetVar attribute to reinitialize the plugin.

Example using a BootsFaces modal:

<b:container>
  <b:form>
    <b:commandButton value="open modal" ajax="true" update="modalform" oncomplete="$('.modalPseudoClass').modal('show');editorInModal.then(e => e.init());" />
  </b:form>
</b:container>
<b:modal styleClass="modalPseudoClass">
  <b:form id="modalform">
    <mol:molecule id="editorInModal" value="#{testBean.structure}" pluginType="OpenChemLibJS" widgetVar="editorInModal" />
  </b:form>
</b:modal>

Known issues:

  • The Marvin JS editor component drops an exception via a JavaScript alert() as soon as it initializes in a hidden modal - not very user friendly.

OpenChemLib JS

All resource dependencies (openchemlib-full.js) are included in the jar build pipeline.

Context-params:

  • de.ipb_halle.molecularfaces.OPENCHEMLIBJS_URL (optional): location of openchemlib-full.js relative to the application's context root

MolPaintJS

All resource dependencies (molpaint.js) are included in the jar build pipeline.

Context-params:

  • de.ipb_halle.molecularfaces.MOLPAINTJS_URL (optional): location of molpaint.js relative to the application's context root

Marvin JS

The resource dependencies are not part of the jar build pipeline. It is necessary to download the platform independent core archive (e.g. marvinjs-21.1.0-core.zip) from ChemAxon's website, extract it and supply its location via a context-param in web.xml.

Marvin JS does not support import/export via the MDL Molfile V3000 format natively. This extended functionality requires the installation of additional webservices. Note: This has not been tested extensively.

Context-params:

  • de.ipb_halle.molecularfaces.MARVINJS_BASE_URL (required): location of the extracted Marvin JS core archive
  • de.ipb_halle.molecularfaces.MARVINJS_LICENSE_URL (required): location of Marvin JS' license file (marvin4js-license.cxl) relative to de.ipb_halle.molecularfaces.MARVINJS_BASE_URL
  • de.ipb_halle.molecularfaces.MARVINJS_WEBSERVICES (optional): if set to "true", use webservices (embeds editorws.html or loads webservices.js)

Converters

The FacesConverters molecularfaces.MDLV2000Converter and molecularfaces.MDLV3000Converter may be used to convert Molfile V2000 and V3000 strings to CDK's IAtomContainer objects. The converters use CDK's reader and writer classes for conversion.

Bean validators

@Molfile: validate Molfiles

  • parameters: format (Molfile version; possible values: Format.V2000 or Format.V3000) and mode (strictness mode of the CDK reader used for validation; possible values: Mode.RELAXED or Mode.STRICT)