ThumbFish is a simple and free utility for scientists and people working with chemical files to display and analyze common chemical formats. It integrates with Windows and provides molecule Thumbnail, Preview, Search and other useful features. ThumbFish can show you a preview of the structure contained in a particular chemical file (just like a thumbnail is generated for your JPEGs). Not just that, it can also calculate and show some common properties of that structure and all this without opening any third-party chemistry application. The best part about ThumbFish is that it sits inside Windows Explorer without interferring with other programs and is either involved automatically to generate thumbnails or manually by right-clicking on supported format file to perform some operations such as Save or Extract Molecules.

• By scientists to quickly identify chemical files during experiments and analysis
• In classrooms to quickly view chemical structures and properties
• During demos to identify the input files used and to verify the output
• By developers working on chemical programs to verify the output generated by their programs
• By software testers to identify input files for their test cases

• MOL (MDL Molfile Format - V2000 and V3000)
• RXN (Reaction file - V2000 and V3000)
• SMILES (Simplified Molecular Input Line Entry Specification)
• SMARTS (SMiles ARbitrary Target Specification)
• SDF (Structure Data File - V2000 and V3000)
• RDF (Reaction Data File - V2000 and V3000)
• CML (Chemical Markup Language)

ThumbFish is NOT dependent on any specific commercially available Chemistry application. It uses the open source organic chemistry toolkit named Indigo by GGA Software. The other open source component used in ThumbFish is Pantheios logging library.

• Thumbnail Handler: Displays thumbnails for supported formats to easily identify structure files
• Preview Handler: Displays coloured preview and calculates properties for selected file
• Search Handler: Searches for a structure based on its properties
• Context-Menu Handler: Provides additional useful options on supported structure files

1... View Thumbnails

When you open the Sample Files folder, Windows will call ThumbFish components to generate thumbnails for the files if the thumbnail view is currently active. You can switch to thumbnail view by right clicking inside the folder and selecting a View or using the View item from the menu. Try View >> Large Icons.

2... Preview

Preview Pane needs to be enabled to view molecule previews. To enable preview pane in Windows 7, click the preview pane button on the top right side in Windows Explorer (see screenshot above). In Windows 8, use the View tab and select Preview Pane. Once the preview pane is enabled, select any file to view its image and properties.

3... Search for molecules

To quickly search for molecules containing 13 atoms, type "na_13" in the search box (see screenshot above). This should filter the current view and show only 3 molecules (Adrenaline.mol. Adrenaline.smiles and Aspirin.mol). If its not working for you then you need to enable searching in "File Contents". In Windows 7, click "File Contents" in "Search Again In" section inside Windows Explorer where the thumbnails are displayed. In Windows 8, goto the "Search Tab" then "Advanced Options" and enable "File Contents". Check out Search Handler section for more details.

Components

• Connection Table Version: The connection table version is displayed on the top left as either V2 or V3 depending on whether its a V2000 or V3000 MOLFILE. Only displayed for MOL, RXN, SDF and RDF files.
• Approx Record Count: Displayed on the top right side, this is the approximate number of records in a multi-molecule file such as SDF, RDF and CML. The approximation is based on the size of first four records in the file.

• Save Structure: Saves a structure to disk in different formats: PNG, PDF, SVG, EMF and CDXML. Note that the structures can only be saved in user's AppData\LocalLow directory e.g.
  C:\Users\[USER]\AppData\LocalLow. See Known Limitations for details.
• Copy Properties: Copies the currently displayed structure properties to clipboard in Key:Value format
• Copy Structure As: Copies the current structure to clipboard in different useful formats including MDL MOL and ChemDraw's CDXML format

Setting Up Search

• Make sure Windows Search is enabled in Control Panel
  [Control Panel >> Programs and Features >> Turn Windows Features on or off >> Windows Search]
• Make sure that the folder in which you want to search is included for indexing
  [Control Panel >> Indexing Options] (your folder should be listed here)

Troubleshooting Search

• Rebuild the search index in case it is corrupt or not built because of user activity
  [Control Panel >> Indexing Options >> Advanced >> Rebuild]
  Note that this can take some time based on the number of files to index
• Enable to always search a file's content
  [Explorer >> Folder Options >> Search >> What to Search >> Always search file name and contents]
• Finally to always re-index and search
  [Explorer >> Tools >> Options >> Search >> Don't use the index when searching in file folders...]
• Still not working, check the ThumbFish Log for error messages at the following location
  C:\Users\[USER]\AppData\LocalLow\ThumbFish.log

Search Examples

• Name: name_{x} [e.g. n_benzene] Note that name is the structure name not the file name
• Formula: formula_{x} [e.g. formula_c6h6]
• NumAtoms: na_{x} [e.g. na_12]
• NumBonds: nb_{x} [e.g. nb_10]
• Molecular Weight: mweight_{x} [e.g. mweight_207]
• Implicit Hydrogens: impl_{x} [e.g. impl_4]
• Heavy Atoms: heavya_{x} [e.g. heavya_2]
• Most Abundant Mass: mamass_{x} [e.g. mamass_106]
• Mono Isotopic Mass: mimass_{x} [e.g. mimass_210]
• Chirality: chiral_{x} [e.g. chiral_yes]
• Has Coordinates: hascoord_{x} [e.g. hascoord_yes]
• Has Z Coordinates: haszcoord_{x} [e.g. haszcoord_no]
• SSSR: sssr_{x} [e.g. sssr_1]

1. Copying structure as Enhanced Metafile (EMF) Picture does not display atom labels.
2. When a structure is saved using the "Save Structure" command in Preview Handler then it can only be saved in user's AppData\LocalLow directory. This is because the Preview Handler runs in a low integrity mode under Windows and does not have access to other locations.
3. The SaveAs >> Connection Table (.ct) command saves a prettified connection table and not the standard MDLCT one. The standard one saves a line length character and then the actual line so it may contain NULL characters. Prettified one is human readable as it contains simple data lines ending with a CRLF.
4. Saving Reaction file as CDXML or CML is not supported due to issues in the provider.