Help on Defining a Query

Please draw a query structure. Click on the ? sign in the drawing applet for a help on drawing.

For more details of the query features JChem offers, read the JChem Query Guide.

Input Parameters

Search type defines the way compounds are searched. Options:

Substructure
Finds all molecules containing the given substructure.
Superstructure
Finds all molecules that can be found in the given superstructure.
Full
Locates the molecule that is matching the full query structure. (no additional fragments are allowed). Molecular features (stereochemistry, isotopes, charges, etc.) are by default evaluated the same way as for substructure queries. See also Duplicate search type and Advanced search options.
Full fragment
Finds molecules where the query fully matches a fragment of the target. Other fragments may be present in the target, they are ignored. Useful to perform a Full search that ignores salts or solvents beside the main structure in the target. For a description of the differences of these search types, see the relevant section of the Query Guide or the examples page.
Similarity
Finds molecules that are similar to the query structure.
  • The default similarity calculation uses the Tanimoto coefficient of the chemical hashed fingerprints of the query structure and the molecule in the database.
    (Dissimilarity_value = 1.0 - Tanimoto_similarity)
  • Molecular Descriptor dissimilarity may also be present if descriptors are generated for the table. The descriptors can implement various calculation methods and distance metrics. For more information about the available descriptors and metrics, see the Screen documentation
Duplicate
Duplication search. All molecular features (stereochemistry, charges, isotopes, etc) equality is needed.

Dissimilarity threshold is a parameter of Similarity search. It specifies the higher limit of dissimilarity between the query and the database molecule. If the dissimilarity value is lower or equal to the threshold, then the query structure and the given database structure are considered similar.

Max. hits specifies an upper limit for the number of molecules the search engine is allowed to find.

Max. time specifies an upper limit for the length of time the search may take.

Search prev. results allows to perform a search on the hits of previous searches.

Use Substructure hit coloring to highlight the matching substructure part of the target structures.

Use Hit alignment to rotate the hits relative to the contained query substructure.

Use Return non-hits (inverse result set) to display structures that do not match the query conditions.

The fields under Conditions can be used to add extra conditions referring to non-structural data in the database table.

The Chemical Terms Filter can be used to add a complex set of rules to the search criteria. You can choose a few example filters with the help of the combo box. Please see the Chemical Terms Language Reference for more details. Note that the Chemical Terms filter is not available for similarity search and in case of Markush tables.

Advanced search options

Advanced search options are not available for similarity search, and for duplicate search only the stereochemistry and tautomer options are available.
You can find a summary of all search options here

Description of the options:

Stereochemistry
This option controls the evaluation of stereochemistry:
  • On: The default stereochemistry evaluation option: non-stereo query matches all configurations and stereo query matches only the specified stereo configuration. See examples in query guide.
  • Exact: The stereochemistry evaluation option used by duplicate search by default: equality is needed in all stereo features (eg. non-stereo query only matches non-stereo targets).
  • Off: All stereochemistry is ignored.
Double bond stereo check
This option controls the evaluation of E/Z (cis/trans) isomerism of double bonds in case of the Stereochemistry "On" setting. For examples, see the query guide.
  • All: All query double bonds are evaluated for stereochemistry.
  • Marked: Only query double bonds marked with the "stereo search flag" (visualized by a rectangle) are evaluated.
  • Off: E/Z stereochemistry is ignored.
Atom matching
These options control the evaluation of the corresponding chemical atom properties. (Charges, Isotopes, Radicals, Valences.) For examples, see the query guide. If the valence on the target is not specified, it is calculated from the atom type and bonds.
  • On: The default matching. If the query does not hold the property, it matches everything. (Eg. uncharged query matches both uncharged and charged targets.) Otherwise, the specified chemical property value must be equal.
  • Exact: The property must be equal in the query and the target. (Eg. uncharged query only matches uncharged target.)
  • Ignore: The property is ignored.
Tautomer
This search option can instruct the search engine to look for all tautomer forms the query, as generated by the Marvin plugin Tautomers.
Vague bond
These search options allow to choose between several levels of strictness in matching bond types, especially regarding aromaticity. See more information about vague bond options.

Comments

Automatically displayed (implicit) Hydrogen atoms will not be used in the query.

Searching common structures that occur frequently in the database or using vague bond options might take considerable time.