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.