TouchMol Configuration

TouchMol is architected and implmented for integration to corporate systems . TouchMol can be configured to integrated with:

  1. Private Web Services
  2. Coporation Compound Database
  3. ELN Database
  4. Assay Database
  5. Inventory Database

to load compound properties, compound structures, reactions, assay data, and availability.

TouchMol configuration is a file called scilligence.config store in the following folder:

- XP: C:\Documents and Settings\All Users\Application Data\Scilligence\Common\

- Vista/Windows7/Windows8: C:\ProgramData\Scilligence\Common\

I. Connect TouchMol to Corporation Compound Database

TouchMol can be configured to talk to Corporation Compound Database, so users can load structures by using Compound IDs.  There are two ways to do this:

  1. Talk to Web Service

    • - This is recommended way to connect TouchMol to Corporation Compound Database, because it won't need to install Oracle client and has some security control

    • - Settings in scilligence.config:

      <add key="molengine.lookup.1" value="compound" />

      <add key="molengine.lookup.1.provider" value="ws" />

      <add key="molengine.lookup.1.url" value="http://server/JSDraw/Service.aspx?cmd=name2structure&amp;q={q}&amp;{user}=&amp;wrapper=raw" />

      NOTE: the Service.aspx take compound ID {q}, and windows user name {user}, as inputs, and returns a structure file, such as molfile, smiles etc.

  2. Directly connect to database
    • - Connect to Oracle DB.  Here is settings in scilligence.config:
      <add key="molengine.lookup.1" value="compound" />
      <add key="molengine.lookup.1.provider" value="oracle" />
      <add key="molengine.lookup.1.connectionstring" value="Data Source=CORP_COMP_DB;User Id=USRID;Password=PWD;"/>
      <add key="molengine.lookup.1.sql" value="select Mol from test where compoundid={q}" />
      NOTE: Oracle client has to be installed.
    • - Connection SQL Server DB.  Here is settings in scilligence.config:
      <add key="molengine.lookup.1" value="compound" />
      <add key="molengine.lookup.1.provider" value="sqlserver" />
      <add key="molengine.lookup.1.connectionstring" value="Data Source=DB;initial catalog=USRID;Integrated Security=True;" />
      <add key="molengine.lookup.1.sql" value="select Mol from test where compoundid={q}" />

II. Configuration to Detect Compound ID

TouchMol can scan and hilight Compound ID in word documents, and make it easier for scientists to mine the unstructured document.  In order to do so, the following item has be added to scilligence.config:

  • <add key="compounddetector.pattern" value="SCI-[0-9]{2,20}-[0-9]{2,2}"/>

III. Compute Custom Properties, and Load Custom Data by Calling Web Services

TouchMol calculates some basic in silico properties by default using MolEngine, but it is able to let TouchMol to connect to other Web Services to calculate custom properties using in-house tools, or load in-house data.  First specify the web service URL:

  • <add key="molengine.compoundprofile" value="http://server/JSDraw/compprofile.aspx"/>

    <add key="molengine.remoteproperties.1" value="http://server/JSDraw/compprofile.aspx" />
    <add key="molengine.remoteproperties.1.properties" value="pKi,pKa,CLogP" />
    <add key="molengine.remoteproperties.1.category" value="Demo Properties" />

TouchMol will send the following parameter to the web service using HTTP POST:

  1. SMILES - SMILES of query structure
  2. Molfile - Molfile of query structure
  3. Property - Requested property name
  4. User - User name for security check

Required XML format of results:

<result>
<item name='logp' value='1.5' category='in silico'/>
...
</result>

An full example of scilligence.config.

IV. Use MolEngine/JSDraw Web Services

MolEngine/JSDraw web services make it easy to set up the service side for TouchMol enterprise integration.

MolEngine/JSDraw web services is build on IIS/ASP.NET based on MolEngine.  Those web services can be configured to directly talking to in-house databased.  And the APIs can be extended to provide extra functions.

V. Add Custom Search Menu

Custom Search Menu can be configured to search some special web sites or web applications.  Here are those configurations:

<add key="touchmol.customsearch.1" value="Customized Search (Baidu)" />
<add key="touchmol.customsearch.1.url" value="http://www.baidu.com/s?wd={inchikey}&smiles={smiles}" />