Search Options

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Specify the query structure

There are four possibilities to specify the query structure:

  1. Dragging the file containing the query structure over the picture box.
  2. Double-clicking the picture box and drawing the structure for the query or open a file in the structure editor window.
  3. Paste a structure from the clipboard by using the Paste right-click menu item over the picture box.

(You can find additional information in Structure Filter topic of the separate User's Guide of JChem for Excel.)




Basic Search Options

When opening Import from Database dialog and connecting to a database table this search option group drop-down list is opened by default, the other groups remain closed. In this group most frequently used search options are collected. Depending on the selected search type, different options will be present in this group, e.g. when selecting Substructure search all options are available as in the image above. But when selecting Similarity search, only three options are displayed, the others are located at their original place, e.g. Chemistry or General Search Options.


If you change from default value "Substructure Search" to "Duplicate Search", the value of Stereochemistry option is automatically set to Exact.




Similarity Search

  1. Select Similarity search and specify a Similarity Threshold (from 0 to 1). Please, note that this is implemented in 6.1 or higher version of JChem for Office.
  2. Follow the general database import process (Mapping Results to a New Worksheet, Selecting Columns for Import, Running the Search).
  3. The results will be displayed on the sheet with the fields selected during import. In the structure cell similarity values are displayed, the structures are not sorted. If the structures have any matching substructures with the query molecule, the matching parts will be highlighted in the result structures, which can be removed with Remove Hit Coloring ribbon button in Filter box, but in this case similarity values will be removed as well.




Please note, that Similarity Threshold option is NOT available in the Structure Filter menu, because the structure search method is different than the one implemented in Import from Database.


Maximum Hits

You can also determine the maximum number of results to be displayed.


Return Non-Hits

If you set this option from False to True on the sheet only those structures and data will be displayed, which don't fit the search criteria. This option is active with all types of databases and searches, except Oracle databases with cartridge search.


Chemistry Search Options

There are some chemistry related parameters to be applied in the search. The detailed description of different search criteria can be found here:


General Search Options




Chemical Terms Filter

You can specify a filter using chemical terms by using different expressions described in Chemical Terms Reference Table.

Maximum Time

The maximum time interval of running the search can be specified here.

Query Structure

The query structure applied for the search when importing is specified here.

Search Method

You can select JChem Cartridge and JChem Base search method. In case of views, it is not possible to recognize the indexed columns from schema, therefore all possible search methods are displayed. You have to select manually both the search method and the column with structure.

Target Column

Structure columns available in the connected database table are listed here and can be selected from the drop-down list.

In case of views the users can select which one of the listed columns should be handled as structure column. The following column names will be selected by default in the following order: CD_STRUCTURE, STRUCTURE, CD_SMILES, SMILES. If none of these columns are available the first will be set as target column.


Hit Coloring

Hit Alignment Mode: You can read a detailed description of this option here:

Hit Color and Non hit color: You can specify the color of hit structures and non-hit structures with this  option.

Hit Coloring: by setting this option to True or False, you can display hit structures with the selected colors.


Hit coloring and hit alignment can be applied separately by setting the Hit Alignment Mode to Rotate (or Partial) and Hit Coloring option to True or False. This way you can display hit structures rotated as the query structure without coloring them.

(Default values:

Hit Alignment Mode: Off

Hit Color: Red

Hit Coloring: True

Non Hit Color: Grey)


Other query options can be specified in the property grid. You can find additional information about the JChem query options at

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