Using a connection object (
JChemSearch retrieves all structures that match the search criteria from the given structure table and returns their
cd_id values in an
Oracle users may also use JChem Cartridge for Oracle to perform search and other operations via SQL commands.
It is recommended to apply MarvinSketch as a tool for drawing query structures.
Steps of creating a web page for entering query structures:
On submitting the form call
(You can also get the structure in other formats, like MDL's Molfile or SMILES, but the Marvin format is recommended as it can represent all molecule and query features that are available in Marvin Sketch. You can find more information about file formats here.)
creating a JChemSearch object , setting the following properties is necessary:
the query structure in Smiles, Molfile, or other format
specifies the connection
the table in the database where the structures are stored
In addition, various other structure search options can be specified that modify structure search behaviour. For further customization, see the
API of the JChemSearch class . Many of these options are detailed in the Substructure Search section.
Please, see the
Please, see demonstrating search types.
This search type can be used to retrieve the same molecule as the query. It is used to check whether a chemical structure already exists in the database, and also during duplicate filter import. All structural features (atom types, isotopes, stereochemistry, query features, etc.) must be the same for matching, but for example coordinates and dimensionality are usually ignored.
For this search mode there is no search per minute license limitation in JChemBase, these searches are not counted.
Java example: Throwing an exception if a given structure exists.
Substructure search finds all structures that contain the query structure as a subgraph. Sometimes not only the chemical subgraph is provided, but certain query features also that further restrict the structure. If special molecular features are present on the query (eg. stereochemistry, charge, etc.), only those targets match which also contain the feature. However, if a feature is missing from the query, it is not required to be missing (by default). For more information, see the JChem Query Guide.
Searching starts with a fast screening phase where query and database fingerprints are compared. If the result of the screening is positive (meaning that a fit is possible) for a database structure, then an atom-by-atom search (ABAS) is also performed. Query structures may contain query atoms and bonds described earlier.
The initialization of substructure searching is similar to duplicate searching , but the object needs to be created with constant value.
Since substructure searching can be time consuming, it is reasonable to create a new thread for the search. If the
runmode property of
JChemSearch is set to
The progress of the search can be checked by the following properties of
checks if searching is still running
textual information about the phase of the search process
the number of hits found so far
Java application example:
the number of hits found
returns true if the search stopped because the time that passed since the start of the searched had reached the maximum value
returns true if the search stopped because the number of hits had reached the maximum value
if an error occurred during the search these properties provide information about the problem
The two ways of retrieving the results of the search are:
The process of retrieving the results of the search from the JChemSearch object is based on the getHitsAsMolecules(. . .) and the getHitsRgDecomp(. . .)
cd_idvalues obtained by a
Create and configure a HitColoringAndAlignmentOptions object.
Generally, the following properties are set:
Specifies if substructure hit coloring should be used.
Specifies if markush structures should be hit enumerated according to the query structure.
Specifies whether unused R group definitions should be removed from the results.
Specifies what form of alignment to use for hit display.
The following values are accepted: ALIGNMENT_OFF (default), ALIGNMENT_ROTATE, ALIGNMENT_PARTIAL_CLEAN
If this options object is null, the molecules will be returned in their original form.
Objectarray elements, one for each molecule. Inside each
Objectarray will be the fetched data field values.
To display the molecules, use the
Molecule array return value.
cd_idvalues obtained by a
attachmentTypeparameter to one of the
ATTACHMENT_...constants of the
RGroupDecompositionclass (the parameter value in most cases is
Retrieve results by using methods of
The process of retrieving the results of the search from the ResultSet Object:
Use SQL statements like
cd_idvalue obtained by a
JChemSearch.getResult(...)call in the condition of the SQL statement
To display the molecule, use
cd_structure obtained from the
In the case of web applications
Please, see the
Please, see demonstrating two approaches for calculating the intersection of the result of multiple queries.
JSP example for displaying search results on a web page by a JSP script:
More JSP examples:
To store the results in a table, the name of the table should be specified by the
JChemSearch , and also the
runmode property of
JChemSearch is set to
Many times structure information is only one of several conditions that a complex query has to check. In those cases structure searches should be combined with SQL queries.
Example: Suppose that quantities on stock are stored in a table different from the structure table. We are querying compounds that contain a given substructure and their quantity on stock is not less than a given value.
Two ways of performing the combined query:
JChemSearchto save the
cd_idvalues of found compounds: set the name of the result table using the setResultsTable method.
Query the join of the structure table, the result table, and the stock table using an SQL SELECT statement. (See the syntax of SELECT in the documentation of your database engine.) Example:
SQL Query Followed by Structure Searching
An arbitrary SQL query can be specified as a filter for the
filterQuery property. The (first) result column should contain the allowed cd_id values.
Databases of chemical structures can contain various calculated values. These are specified upon table creation using Chemical Terms expressions and their value is calculated during database import. Please, see how calculated columns are stored in JChem tables. While executing database search these fields can be considered. Assuming that the table "
search_example" exists with the columns
pka_ac_2 a search can be executed as follows:
Please, see how to create calculated columns with JChem Manager.
Using command line tool the following command performs the same operation:
To an existing table, where the appropriate columns have been created, calculated columns can be added using jcman tool:
Please, see demonstrating the usage of calculated columns during search.
Calculated values do not need to be stored in a database field. If they should be used for a temporary filtering, they may be calculated "on the fly". These are specified for database search using theoption:
Please, see demonstrating hits ordering.
Please, see demonstrating how to filter search results based on other (possibly) database tables.
There are several other properties that modify the behavior of
The maximum number of molecules that can be found by the search.
The maximum amount of time in milliseconds, which is available for searching.
A string (like an ORDER BY sub-expression) to be appended to the SQL expression used for screening and retrieving rows from the structure table.
If set to true, information useful for testing will be written in the servlet server's error log file.
Specifies the order of the result. Java example:
Please, see the
Superstructure search finds all molecules where the query is superstructure of the target. It can be invoked in a similar fashion as Substructure search. In case of superstructure search note that except query tables the default standardization removes explicit hydrogens (see query guide) This has the effect that structures in the database are used without their explicit hydrogens as queries in these cases.
Set search type to .
A full structure search finds molecules that are equal (in size) to the query structure. (No additional fragments or heavy atoms are allowed.) Molecular features (by default) are evaluated the same way as described above for substructure search.
For this search type, theobject needs to be created with the value.
Full fragment search is between substructure and full search: the query must fully match to a whole fragment of the target. Other fragments may be present in the target, they are ignored. This search type is useful to perform a "Full structure search" that ignores salts or solvents beside the main structure in the target.
For this search type, the
Similarity searching finds molecules that are similar to the query structure. Per default the search uses Tanimoto coefficient . Tanimoto coefficient has two arguments:
the fingerprint of the molecule in the database The dissimilarity formula contains the Tanimoto coefficient and measures how dissimilar the two molecules are from each other. The formula is defined below:
where N A and N B are the number of bits set in thefingerprint of molecule A and B, respectively, N A&B is the number of bits that are set in both fingerprints.
Other dissimilarity metrics can be set by the function. Possible values:
Superstucture Tversky index can have two weights, those values are also set in the String parameter of the function using the comma as separator. For example,
The dissimilarity threshold is a number between 0 and 1, which specifies a cutoff limit in the similarity calculation. If the dissimilarity value is less than the threshold, then the query structure and the given database structure are considered similar.
See more details on fingerprints in the section .
Similarity searching should be used the same way as substructure searching . To enable similarity searching, the object need to be created with the value. If the order property is set to JChemSearch.ORDERING_BY_ID_IR_SIMILARITY (which is the default), then the hits returned by the getResult() method will be sorted in increasing order of dissimilarity.
The dissimilarity threshold is set on
Sets the dissimilarity threshold. Expects a float value between 0 and 1.
A lower threshold results in hits that are more similar to the query structure.
The dissimilarity values predicted in the similarity calculation are retrieved with the
JChemSearch instance with this function:
Returns the predicted dissimilarity value for the hit corresponding to the given index.
If a result table is generated during a similarity search, then the table will contain both the
cd_id and the calculated similarity values.
Users can open up new ways of similarity searching by using a number of built-in molecular descriptor types other than the default chemical hashed fingerprints. There are a number of built-in molecular descriptors available, including CF, PF, Burden eigenvalue descriptor (or BCUTTM) and various scalar descriptors.
The following example shows how simple it is to setup molecular descriptors for your compound library. The first command creates a table called compound_library and the second command adds the molecules from an sdf file. The third command uses the 'c' option to create the molecular descriptor with the name of the structure table set by the -a flag, and the chemicalfingerprint descriptor type set by the -k flag. The command omits the database login information that was stored previously with the -s option. See the jcman command options and the for more information. Creating and assigning molecular descriptors to database structure tables is discussed with the command.
Below is an example that runs the similarity search with the new chemical fingerprint. The molecular descriptor name, chemical_fingerprint , is set as a search option and the similarity search is run normally:
Application end-users may need further information about the molecular descriptors to select an appropriate molecular descriptor for their search. Application developers can extract this information from the database and display it to the end-user to help with selection. In this Java example, a MDTableHandler is created using the database connection and the name of the structure table. The MDTableHandler provides access to the Molecular Descriptors and the embedded configurations, metrics, and default dissimilarity thresholds.
After selecting a molecular descriptor and other desired parameters, such as the descriptor configuration and the metric, the custom molecular descriptor name is set as a search option and the similarity search is run as normal. If the descriptor name, configuration or metric is omitted, a stored default value is used.
Please, seedemonstrating how descriptors are generated and similarity searches executed on them.
Formula search is applicable for finding molecules in JChem structure tables using the cd_formula field. Formula search can be combined with other database searching methods, that is with duplicate structure search, substructure search, full structure search, full fragment search, superstructure search, and similarity search.
Types of formula search are the following:
To perform formula search in memory see Sophisticated Formula Search .
The maximum number of substructure and similarity searches allowed by the system per minute is determined by the license key entered using JChemManager. If no license key has been specified, then the program is in demo mode that allows one search per minute.
If a query is started when the number of searches has exceeded the quota,
. It is recommended to catch this exception and display a friendly message advising the user to try searching later. If this exception occurs frequently, please contact ChemAxon |mailto:'+ 'sales''@''chemaxon.com] and request a license key allowing more searches. Click here to display a table that helps you to determine the access level that suits your needs. For further details see a href="jchemtest_dev_dbconcepts_index#fingerprints"> Query guide The maximum number of substructure and similarity searches allowed by the system per minute is determined by the license key entered using JChemManager. If no license key has been specified, then the program is in demo mode that allows one search per minute.
If the files to be searchable are only available in a molecular file format in a string or stored in the file system, they have to be imported into
Molecule objects by the use of
chemaxon.util.MolHandler classes. The code example at the
MolSearch API description shows examples for the use of both classes.
Various Java examples for importing molecules using JChem API are available inand format.
An easy to use command line tool for searching and comparing molecules in files, databases or given as SMILES strings is jcsearch.
A search object of these classes compares two
Molecule objects (a query and a target) to each other. Usually a
MolSearch object is used in the following scenario:
Another way of comparing molecules is using is a descendant of
MolSearch and disposes all its methods.
StandardizedMolSearch calls standardization during the search functions automatically. If no standardization configuration is given, the default standardization is applied, which consists of an aromatization step. Hence using
StandardizedMolSearch no initial aromatization of the input molecules is required. Therefore we suggest using the
The most efficient way to decide whether there is a match between query and target.
Looks for all occurrences(matching) of query in target. Returns an array containing the matches as arrays (
Returns the number of matchings between query and target.
Please, see demonstrating the usage of
For further information, see the following resources:
Moleculeobjects in the following ways.
Generate unique SMILES representation of the Molecule objects and compare these Strings. For generating unique SMILES strings see: smiles export
For the comparison, an efficient data structure can be used (e.g. java.util.HashSet).
See the full source code.
Generate the molecules' hash codes and compare them. These hash codes are equivalent if the molecules are the same, but the equivalence of the code doesn't necessarily imply that the molecules are the same. This should be verified using structure searching. Thus this way of comparison is efficient if the number of duplicates is relatively small compared to the number of molecules.
See the full source code.
Formula search finds molecules that have matching chemical formulas to a given query. In order to use this class the formulas of the molecules need to be obtained. This can be accessed through the cd_formula column or any other used defined/calculated column of a database which contains a valid chemical formula. The ElementalAnalyser class can be used to obtain the formula or dot disconnected formula of a molecule. A method which would match two molecules by formula:
Tetrahedral centers and double bond stereo configurations are recognized during searching. The information applied by JChem for stereo recognition is
JChemSearchhandles all reasonable structures appropriately. When the query structure is specified in MDL Molfile or Marvin mrv formats for
JChemSearch, and E/Z stereoisomers are searched, the stereo search attribute (or stereo care flag) of the bonds has to be set. See the relevant section of the Query Guide . Furthermore, only the following formats supports the enhanced stereo configuration of stereocenters: MDL extended (V3000) formats, Marvin mrv, ChemAxon extended smiles/smarts. More details on these are available at the following sources: