Mariner: Daylight's JSP toolkit

Mariner Interface:

• A set of beans that can be invoked from any JSP page
• A partial description of the interface
  • SimSearch
    A Tanimoto Similarity Search bean for use with JSP pages
    • public String getSmiles()
      Returns the SMILES to be used for similarity searching through a form
    • public void setSmiles(String smiles)
      Interface that permits a form element to set the SMILES to use for similarity searching, transparently via JSP
    • public void setSimThreshold(double simThreshold)
      Sets the similarity threshold to be used for similarity searches
    • public double getSimThreshold()
      Returns the similarity threshold currently used for similarity searches
    • public boolean hasAllParameters()
      Returns true if the SMILES and Similarity threshold to be used for searches has been set. Returns false otherwise
    • public String getSimilarStructures()
      Looks up the database via JDBC (for Daycart), retrieves the rows, replaces the SMILES row with images, and then outputs all this data in a HTML table
  • AbsSmilesSearch
    • public String getAbsSmilesStructure
      Looks up the give Absolute SMILES to search for. Retrieves any rows with the same and formats the output to a HTML form, replacing the SMILES column with an image
    • public String getSmiles()
      Returns the SMILES that may have been set through a form.
    • public void setSmiles(String smiles)
      Interface that permits a form element to set the absolute SMILES to search transparently via JSP
  • AgentSearch
  • AvMolWtSearch
  • CanSmilesSearch
  • ClogpSearch
  • DayServe
  • EuclidSearch
  • GraphSearch
  • MolFormulaSearch
  • NetChargeSearch
  • NumHydrogensSearch
  • ProductSearch
  • ReactantSearch
  • SmartsSearch
  • SmilesSearch
  • SuperStrSearch
  • TautomerSearch
  • TverskySearch
• Along with this interface a set of search forms for each kind of search are provided.
• Any search form can be altered to suit corporate needs provided it obeys a simple set of rules
• Consider this similarity search web-app and its source.
• Only HTML and a smattering of Java are needed for creating webapps
• No knowledge of SQL or C-toolkit programming required
• Demonstration of some Mariner functionality
• At release, more outputs will be possible for search results (e.g. ECS Table object, graph output for selected rows)
• There will also be a hook to add your own output method to embellish output(Delegation)
• Suggestions for addition
  • Interface for getting data such as images or Word files associated with a row, so that they are linked to display the data in their appropriate viewers
  • Mechanism to view structures & accept input from ChemDraw & IsisDraw
  • Capability to depict molecules with coordinates obtained from rowdata
• Both search & input classes will be extensible and hence configurable with a supported interface
• Email me any more function requests
• Will be a similar interface to Daylight at time of release
• Will be fairly optimized

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