Mol Files Export Dialog
Applicability: Cranium, Synapse

There are numerous approaches used to store a molecular structure in a file format. One approach is called a mol file. Mol files are text files that contain information on the types and locations of atoms, the bond types used to connect these atoms as well as additional information describing tertiary structure.

Some example mol files are shown below:

Tip: Molfile filenames are automaticaly assigned

The file name of an exported mol file is the same as the corresponding chemical's name. Thus, acetone's mol file will have the name 'acetone.mol'.

Example: Export a mol file
  1. Open a knowledge base document. (Open a "working" document or create a copy of a document (see here) if you are just experimenting with this functionality.)
  2. Click on the File menu and select the Export Values command.
  3. The application will activate the KB Export Dialog.
  4. Select 'Mol File Format' from the Output File Format list and press the Export button. The Mol Files Export dialog is activated.
    Destination folder into which mol files will be written.
    Overwrite option - if checked, a new file will overwrite an existing file with the same name.
    List of chemicals for which mol files will be written.
    Options for adding the exported file's name to the list of associated documents of the corresponding chemical.
    Commands for selecting all chemicals, no chemicals, using bookmarks to select chemicals and using additional options to find a named chemical.
  5. Press the dialog's Browse button to select the destination folder, i.e., the folder into which the exported files will be written. Select any convenient folder.
  6. Check the 'Overwrite' box. Files generated by this export action will overwrite any existing files having the same name.
  7. Select several chemicals by clicking the left mouse button on the chemical's name shown in the 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 'aceto' into one of the Match Substrings controls and click the left mouse button on Diacetone alcohol.
    Attribute used to identify chemicals, e.g., identifier, synonym, formula, etc.
    Only those chemicals containing substrings matching these entries will be displayed in the Entities listing.
    List of names to select from.
  10. Finally, press the dialog's OK button. The identified chemical, diacetone alcohol in this example, will be selected in the list of chemicals.
  11. In the Options section, check the box in front of the "Add exported file's..." option.
  12. Finally, press the dialog's Export button. Mol files will be written for each selected chemical. An associated document entry will also be added to each chemical. For example, here is the entry added to 4-hydroxy-4-methyl-2-pentanone (synonym: diacetone alcohol). (See the documentation on the Associated Documents Section for more details on working with associated documents.)
Example Files

The following mol files were generated by exporting six chemicals (acetic acid, cyclohexanol, ethanol, ethyl acetate, n-hexane, toluene, vinyl chloride and vinyl fluoride).

Acetic acid.mol Cyclohexanol.mol Ethanol.mol Ethyl acetate.mol
n-Hexane.mol Toluene.mol Vinyl chloride.mol Vinyl fluoride.mol
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