ChemDoodle 3 contains a new widget to allow you to search your hard drive and any attached storage devices for chemical structures. With the ability to interpret at least 21 chemical file formats listed below, you will be able to find the old files you thought you lost a long time ago and edit them in ChemDoodle. Just as a reminder, ChemDoodle 3 is a free upgrade for all customers that purchased ChemDoodle 1 or 2.

We have been hard at work building one of the best cheminformatics systems (in addition to a fantastic graphics system) for ChemDoodle 3. One of the many published algorithms we are including is the efficient VF2 graph isomorphism algorithm¹. This algorithm allows ChemDoodle to compare chemical data structures, and forms the basis of the engine that runs the Search widget. The following image is a breakdown of the Search widget after the result of a substructure query for pyrrole.

The Search Widget

A breakdown of the new Search widget

  1. Choose the folder to be the root of the search
  2. Set whether the entire structure should be matched, or to perform a substructure search
  3. If multiple structures are being matched, set whether queried data should result only if all structures are matched or if matching any structure is acceptable
  4. A visual progress spinner; when the query is running, clicking on this will end the process
  5. Begin the search
  6. Open the selected file in ChemDoodle
  7. Copy the current structure onto the current Doodle Sheet; you can also click and drag the structure onto the sheet
  8. Helpful information about the widget
  9. Collapse the widget
  10. The matched structures will display in this panel; hits are highlighted in red
  11. If a file contains multiple structures, clicking the grey arrows will browse through them
  12. A list of all files that contain hit molecules will be listed here, click a filename to load its matched content into panel 10
  13. During the search, the path of the file currently under investigation will be displayed here; Finished! is displayed upon completion of the query
  14. A breakdown of all files investigated: matched files/chemical files searched/all files searched

We have also added several new chemical file types as well as improved our other interpreters. The following is a complete list of all filetypes the development version of ChemDoodle 3 can currently handle (it is likely the list will grow even larger before release). All file types can be both read and written. All inclusive objects between ChemDoodle and each filetype will be handled. Given that all protocols recognized in ChemDoodle can be accessed by the Search widget, you should be able to find almost all of the chemical structures you have ever created.

  • ChemDoodle Documents: ICL
  • ChemDraw Files: CDX, CDXML
  • ISIS Sketch/Symyx Draw Files: SKC, TGF
  • ChemAxon Documents: MRV
  • Chemical Markup Language: CML
  • MDL CT Files: MOL, SDF
  • MolInspiration JME Strings: JME
  • RCSB Protein Data Bank Files: PDB
  • Schrödinger Macromodel and Maestro Files: MMD, MAE
  • Tripos Mol2 Files: MOL2
  • Standard Molecular Data: SMD
  • XYZ Data: XYZ
  • Daylight SMILES (line notation)
  • IUPAC InChI (line notation)
  • Sybyl SLN (line notation)
  • Beilstein ROSDAL (line notation)

We look forward to continuing our progress and creativity. Certainly, if you have any suggestions or comments, please feel free to contact us.

¹ Cordella, P. L.; Foggia, P.; Sansone, C.; Vento, M. An improved algorithm for matching large graphs. Proceedings of the 3rd IAPR-TC-15 International Workshop on Graph Based Representations. Italy, 2001, pp 149-159.