SD File Export Dialog
Applicability: Cranium, Synapse (core versions 0315+)

A Structure Data (SD) file is a text-based formatted file containing molecular structure information and chemical property values. SD files are based upon the same format used by Mol files. (Mol files are detailed in the documentation on Mol Files Export dialog.)

The general format of an SD file is one or more sets of a mol file followed by a series of property data entries. Each property data entry is of the form 'keyword line' followed by 'data line'. There is no standard listing of keywords - they can be any descriptive term you wish to use.

Two example SD files are shown below. The first file contains structures and property values for several common chemicals. The second file contains the structure and several property values for ethanol.

Example: Export an SD File
  1. Open a Knowledge Base document using either Cranium or Synapse.
  2. To follow this example, change the current units for the temperature to C and the liquid density to kg/m3. (See the Property Units dialog for details on changing units.)
  3. Click on the File menu and select the Export Values command.
  4. The application will activate the KB Export Dialog.
  5. Select 'SD File Format' from the Output File Format list and press the Export button. The Creat an SD File dialog is activated.
    1
    		 Destination file into which values will be written.
    2
    		 List of selected chemicals whose structure and property values will be exported.
    3
    		 Command buttons for selecting all entities, no entities, selecting entities using a bookmark, showing details about the selected chemicals and selecting an entity using the Find Entity dialog.
    4
    		 Table of selected properties to export. Each table row specifies the information needed to retrieve a specific property value.
    5
    		 Commands for editing table rows as well as saving and loading export property specifications.
    6
    		 Export button
  6. Press the dialog's Browse button to select the destination file, i.e., the file into which the exported structures and property values will be written.
  7. Select several chemicals by clicking the left mouse button on the chemical's name shown in the Select Chemicals list.
  8. Press the Find button. This enables you to search for a chemical by name or synonym. The application will activate the Find Chemical dialog.
  9. Select Synonym from the attributes list, type 'ethanoate' into one of the Match Substrings controls and click the left mouse button on Ethyl ethanoate (ethyl aceate).
    1
    		 When the mouse cursor is positioned over an entity, the application will display a tool-tip containing the entity's name.
  10. Finally, press the dialog's OK button. The identified chemical, ethyl acetate in this example, will be selected in the list of chemicals.
  11. Click on the first row of the Select Properties table and press the Edit button. The application will activate the SD File Property dialog. The attributes you select in this dialog will be used by Cranium and Synapse to retrieve a single property value to be written into the destination file.
    1
    		 Property: the property whose value is being retrieved.
    2
    		 Status: the type of value to be exported. Choices are Data Only, Estimates Only or Data or Estimates.
    3
    		 Temperature: the temperature for which values will be retrieved. For example, a chemical may have many data values for liquid density. Entering a value of 25 C in this control will instruct the application to retrieve the first datum with a temperature value near (see next) 25 C. (Note that this control will only be enabled if the selected physical property depends upon temperature.)
    4
    		 Temperature Range: this enables you to specify a range of values that will match the entered temperature. For example, entering a temperature value of 25 C and a range of ±5 will instruct the application to retrieve the first datum with a temperature value between 20 C and 30 C. (Note that this control will only be enabled if the selected physical property depends upon temperature.)
    5
    		 Pressure: this value is entered in the same manner as the value for temperature. (Note that this control will only be enabled if the selected physical property depends upon pressure.)
    6
    		 Pressure Range: this value is entered in the same manner as the value for temperature range. (Note that this control will only be enabled if the selected physical property depends upon pressure.)
    7
    		 Property Term: this is the keyword text value that will be written into the destination file. Any text string may be entered except that the string cannot contain the characters '>' or '<'.
    8
    		 Default: pressing the Default button will cause the application to create a default keyword and enter it into the Property Term control. The default value is formed using the property name, the entered state variables and their units and the property's units.
    9
    		 Units: pressing the Units button will insert the units of the selected property into the Property Term control. The functionality is useful for ensuring the property term (the keyword) properly documents the property value being exported.
  12. In the SD File Property dialog select the following entries:
    • Property: Density, Liquid - f(T)
    • Status: Data Only
    • Temp: 25
    • Temp Range: 5
  13. Press the dialog's Default button. The application will enter the value 'Density, Liquid (25 C) [kg/m3]' into the Property Term control.
  14. Press the dialog's OK button. The entered value specifications will be entered on the selected table row.
  15. Finally, press the dialog's Export button. The molecular structure and specified physical property values will be retrieved from the selected chemicals and written into the destination file.
Tip: Save column specifications for reuse

Entering the specifications for a number of properties can take some time. We thus recommend that you save your entered specifications for later retrieval. Even if you wish to enter different specifications, starting from a saved set can often save time.

Once you have entered a set of property specifications, press the Save button, located to the right of the Select Properties table, to write the entered specifications into a file that can be loaded again at a different time.

Example Files

The following SD files were generated using Cranium's and Synapse's text export capabilities.

Example File Description
SDFileExportFile01.sdf An SD file containing molecular structure and physical property values for several common chemicals.
SDFileExportFile02.sdf An SD file containing the molecular structure and several physical property values for ethanol.
Using SD Files in Other Software

Many other chemical software programs can use the SD files generated by Cranium and Synapse. MarvinView by ChemAxon (website) is one such program. Opening the SDFileExportFile01.sdf example file listed above with MarvinView will show the following window.

SD files are also accepted by the Elsevier's Reaxys chemical data search engine. This is a very useful tool when combined with Synapse's chemical product design capabilities. Once you have generated a set of chemical candidates, you can easily search Reaxys to determine if they are known to the chemical literature. See documentation on Searching Elsevier's Reaxys for details.)

Related Documentation
Topic Description
Estimating Chemical Properties a short video demonstrating how to estimate the physical properties of pure chemical using either Synapse or Cranium.
Estimating Mixture Properties a short video demonstrating how to estimate the physical properties of mixtures using either Synapse or Cranium.
Getting Started using Cranium provides a quick tour of Cranium's capabilities including physical property estimation and a discussion of structure editing.
Getting Started using Synapse provides a quick tour of Synapse's capabilities including examples of chemical product design.