Report:SureChem/Search Interface/The Search Forms/Chemical Search Form
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Chemical Structure Search Form
The Chemical Structure search form features the ability to search SureChem’s databases via a drawing assisted SMILES interface. In SureChem, users can search any combination of the databases via checkboxes.
In the Structure Search area, users can use the embedded Java drawing app (MarvinSketch) to draw a chemical structure. A multitude of options are available in MarvinSketch that include templates and 3D view options. Users can load structures of interest from a local directory, and new files created in MarvinSketch can also be saved locally. After confirming the correct structure, users can click on the search button to search full text for the chemical structure related to the SMILES tag. Users can decide whether to search with exact match, similarity >=.95 or >=.8, or substructure options. Similarity and substructure searching are powered by ChemAxon's JChemBase chemical search structure engine.
MarvinSketch can be used to upload MOL files, and may also be used to preview SMILES code by pasting the code directly into the app. The Structure Search area is the only way to specify the similarity or substructure searching desired by the searcher. SureChem Pro users can also specify which fields to search as well as a display format.
Java version 1.6 (Java 6) or later is required to use MarvinSketch. MarvinSketch has many supported features such as:
- support for multiple file types (MOL, MOL2, SDF, RX, RDF, SMILES, many more)
- 3D and 2D geometry editing and generation
- advanced query features (generic atoms and bonds, atom lists/not lists, many more)
- creating and editing molecule sets (without a database)
- structure annotation
- structure based calculations
- error checking (valence and reaction error checking)
- support for isotopes, charges, radicals, lone pairs and aliases
SureChem additionally boasts the ability to limit searches to titles, abstracts, claims, or description sections, as well as the option to select the display format between structures and patents containing structures.
The drawing tool MarvinSketch is a very deep and state of the art chemical drawing tool. This tool offers many viewing options ranging from display of hydrogen to the style of the drawing. Users with knowledge of SMILES will find this search form to be effective and simple, while still offering depth. The further ability to import MOL extension files will be appreciated by users of the common chemical structure protocol.The option to search using exact match, similarity scores, or as a substructure gives users the ability to find relevant results that may not match the exact structure present in MarvinSketch. The additional options allow users to further narrow and specify their search.
- ↑ SureChem Pro FAQ. SureChem website, http://www.surechem.org/help.html. Accessed on April 30, 2009.
- ↑ "Introduction to MarvinSketch." SureChem website, http://www.surechem.org/chemical/marvin/help/sketch/sketch-intro.html. Accessed on March 10, 2009.