com.discoverygate.webservice
Interface DGWS

All Superinterfaces:

java.rmi.Remote

All Known Implementing Classes:

DGWSBindingStub, DGWSProxy

public interface DGWS
extends java.rmi.Remote

DiscoveryGate Web Service end-point.

For the data model, see the WSDL and XML Schema (XSD) file. See also the Discovery Gate Web Service Developer's Guide.

Some knowledge of Accelrys searching technologies and content is assumed.

Note: To write a client application in C#.NET, you must reinterpret some Java-centric aspects of this API Reference. For example, .NET uses Properties where Java uses get and set methods.

Since:

DGWS 1.1

Author:

Accelrys

Method Summary

void	closeStatefulQuery(ServiceRequest aRequest) Terminates the stateful query specified by the statefulQueryKey in the ServiceRequest object.
java.lang.String[]	convertStructureToMolfile(ServiceRequest aRequest, java.lang.String[] aStructures) Returns the array of molecules as an array of molfiles (or the array of reactions as an array of rxnfiles).
ExistenceResult[]	findSourceMolecule(ServiceRequest aRequest, Datasource aSource, ExistenceRequest[] aRequests) Determines whether the molecules specified in the com.discoverygate.webservice.types.com.discoverygate.webservice.types.ExistenceRequest array exist in the source database.
CatalogResults	getCatalogsById(ServiceRequest aRequest, CatalogId[] aCatalogs) Returns a CatalogsResults object (a list of Catalog objects) for a given list of Catalogs IDs.
XMLResults	getCatalogsByIdXML(ServiceRequest aRequest, CatalogId[] aCatalogs) Identical to the com.discoverygate.webservice.types.com.discoverygate.webservice.types.getCatalogsById method except that the results are returned in XML format.
ClassificationVocabulary	getClassificationVocabulary(ServiceRequest aRequest, VocabularyVersion aVersion) Returns the Classification vocabulary if the VocabularyVersion passed is not equal to the current server version.
java.lang.String	getClassificationVocabularyXML(ServiceRequest aRequest, VocabularyVersion aVersion) Same as getClassificationVocabulary except that the vocabulary is returned as a string of XML.
MoleculeResults	getMoleculesByCatalogId(ServiceRequest aRequest, CatalogId aCatalog, BulkFineType aType) Returns the source molecules for a given CatalogId.
XMLResults	getMoleculesByCatalogIdXML(ServiceRequest aRequest, CatalogId aCatalog, BulkFineType aType) Same as getMoleculesByCatalogId except that the results are returned in XML format.
Molecule	getMoleculesByCatalogItem(ServiceRequest aRequest, CatalogItem[] aItems) Returns a set of source molecules for the catalog items specified by the catalog numbers.
java.lang.String	getMoleculesByCatalogItemXML(ServiceRequest aRequest, CatalogItem[] aItems) Same as getMoleculesByCatalogItem method except that the molecule container is returned as a string of XML.
MoleculeResults	getMoleculesByCatalogNumbers(ServiceRequest aRequest, java.lang.String[] aCtNums) Returns the source molecules for a given CatalogIds.
XMLResults	getMoleculesByCatalogNumbersXML(ServiceRequest aRequest, java.lang.String[] aCtNums) Same as getMoleculesByCatalogNumbers except that the results are returned in XML format.
MoleculeResults	getMoleculesByClassification(ServiceRequest aRequest, MoleculeSearch[] aCriteria, java.lang.String aClass) Returns the molecules that are classified by the class-type passed and optionally conform to the structure search specified by the parameter aCriteria.
XMLResults	getMoleculesByClassificationXML(ServiceRequest aRequest, MoleculeSearch[] aCriteria, java.lang.String aClass) Same as getMoleculesByClassification except that the results are returned in XML format.
MoleculeResults	getMoleculesById(ServiceRequest aRequest, MoleculeId[] aIds) Returns an array of Molecule within a results container for the array of Molecule IDs.
XMLResults	getMoleculesByIdXML(ServiceRequest aRequest, MoleculeId[] aIds) Identical to the com.discoverygate.webservice.types.getMoleculesById method except that the results returned are in XML format.
MoleculeResults	getMoleculesByNames(ServiceRequest aRequest, java.lang.String[] aNames) Returns an array of Molecule entities within a results container for the specified wildcard.
XMLResults	getMoleculesByNamesXML(ServiceRequest aRequest, java.lang.String[] aNames) Identical to the com.discoverygate.webservice.types.getMoleculesByName method except that the results returned are in XML format.
MoleculeResults	getMoleculesByQuery(ServiceRequest aRequest, MoleculeSearch[] aCriteria, java.lang.String aQuery) For internal use only - do not use this in your application.
XMLResults	getMoleculesByQueryXML(ServiceRequest aRequest, MoleculeSearch[] aCriteria, java.lang.String aQuery) For internal use only - do not use this in your application.
MoleculeResults	getMoleculesBySourceId(ServiceRequest aRequest, SourceId[] aIds) Returns the top-level molecules that correspond to the list of SourceId objects.
Molecule	getMoleculesBySourceIdMerged(ServiceRequest aRequest, SourceId[] aIds) Returns an unpopulated Molecule container that contains source molecule objects, as well as their hierarchies fetched with the retrieval flags.
java.lang.String	getMoleculesBySourceIdMergedXML(ServiceRequest aRequest, SourceId[] aIds) This method is the same as getMoleculeMergedBySourceId except that it returns the result as a single XML string.
XMLResults	getMoleculesBySourceIdXML(ServiceRequest aRequest, SourceId[] aIds) Same as getMoleculesBySourceId except that the results are returned in XML format.
MoleculeResults	getMoleculesByStructure(ServiceRequest aRequest, MoleculeSearch[] aCriteria) Returns an array of Molecule within a results container that satisfy the query specified by a combination of the boolean structure searches within the aCriteria parameter.
XMLResults	getMoleculesByStructureXML(ServiceRequest aRequest, MoleculeSearch[] aCriteria) Identical to the com.discoverygate.webservice.types.getMoleculesByStructure except that the results returned are in XML format.
AvailabilityFilterResults	getMoleculesFilterInfoById(ServiceRequest aRequest, MoleculeId[] aIds) Returns an array of AvailabilityFilter within a results container for the given array of Molecule IDs
XMLResults	getMoleculesFilterInfoByIdXML(ServiceRequest aRequest, MoleculeId[] aIds) Identical to the com.discoverygate.webservice.types.getMoleculesFilterInfoById method except that the results returned are in XML format.
SimilarityResult[]	getMoleculeSimilarity(ServiceRequest aRequest, MoleculeId[] aIds, Structure aStructure, SimilarityType aType) Returns the list of SimilarityResult (Molecule ID and similarity percentage) of the given IDs against the given structure, for the specified similarity type.
MoleculeSourceResults	getMoleculeSourcesByMoleculeId(ServiceRequest aRequest, Datasource aSource, MoleculeId[] aIds) For a list of com.discoverygate.webservice.types.com.discoverygate.webservice.types.MoleculeId's, determines which data sources contain the IDs.
XMLResults	getMoleculeSourcesByMoleculeIdXML(ServiceRequest aRequest, Datasource aSource, MoleculeId[] aIds) Identical to the com.discoverygate.webservice.types.com.discoverygate.webservice.types.getMoleculeSourcesByMoleculeId method except that the results returned are in XML format.
PatentResults	getPatentsByTitle(ServiceRequest aRequest, java.lang.String aCriteria) Returns the Patent entities (DGWS classes) that match the search criteria passed in the aTextQuery parameter.
XMLResults	getPatentsByTitleXML(ServiceRequest aRequest, java.lang.String aCriteria) The same as getPatentsByTitle except that the response is returned in XML form.
ProcurementVocabularies	getProcurementVocabulary(ServiceRequest aRequest, VocabularyVersion aVersion) Returns the ProcurementVocabularies object if the VocabularyVersion passed is not equal to the current server version.
java.lang.String	getProcurementVocabularyXML(ServiceRequest aRequest, VocabularyVersion aVersion) Same as getProcurementVocabulary except that the vocabulary is returned as a string of XML.
ProductResults	getProductsByMoleculeAndSuppliers(ServiceRequest aRequest, SourceId[] aMolecules, SupplierId[] aSuppliers) Returns an array of Product within a results container for the given array of Molecule IDs and Supplier IDs.
XMLResults	getProductsByMoleculeAndSuppliersXML(ServiceRequest aRequest, SourceId[] aMolecules, SupplierId[] aSuppliers) Identical to the com.discoverygate.webservice.types.getProductsByMoleculeandSuppliers method except that the results returned are in XML format.
RxnCitationResults	getReactionCitations(ServiceRequest aRequest, CitationCriteria aCriteria) Returns the Reaction citation entities (DGWS classes) that conform to the citation criteria passed to the method.
XMLResults	getReactionCitationsXML(ServiceRequest aRequest, CitationCriteria aCriteria) Same as getReactionCitations except that the result are returned in XML format
Classification[]	getReactionClassification(ServiceRequest aRequest, Structure[] aStructs) Returns an object containing the Broad, Medium and Narrow InfoChem class-codes for each rxnfile given in the array.
ReactionResults	getReactionsById(ServiceRequest aRequest, ReactionId[] aIds) Returns an array of Reaction within a results container for the array of Reaction IDs.
XMLResults	getReactionsByIdXML(ServiceRequest aRequest, ReactionId[] aIds) Identical to the getReactionsById method except that the results returned are in XML format.
ReactionResults	getReactionsByProduct(ServiceRequest aRequest, MoleculeSearch[] aSearch, RxnProductCriteria aCriteria) Gets the reactions where at least one of the products conforms to the search created from the MoleculeSearch[] passed to the method.
XMLResults	getReactionsByProductXML(ServiceRequest aRequest, MoleculeSearch[] aSearch, RxnProductCriteria aCriteria) The same as getReactionsByProduct except that the response is returned in XML form.
ReactionResults	getReactionsByQuery(ServiceRequest aRequest, ReactionSearch[] aCriteria, java.lang.String aQuery) For internal use only - do not use this in your application.
XMLResults	getReactionsByQueryXML(ServiceRequest aRequest, ReactionSearch[] aCriteria, java.lang.String aQuery) For internal use only - do not use this in your application.
ReactionResults	getReactionsByStructure(ServiceRequest aRequest, ReactionSearch[] aCriteria) Returns an array of Reaction within a results container that satisfy the query specified.
XMLResults	getReactionsByStructureXML(ServiceRequest aRequest, ReactionSearch[] aCriteria) Identical to the com.discoverygate.webservice.types.getReactionsByStructure except that the results returned are in XML format.
ReactionResults	getReactionsByVariation(ServiceRequest aRequest, RxnVariationId[] aIds) Identical to the getReactionsById method except that the VariationId is specified.
XMLResults	getReactionsByVariationXML(ServiceRequest aRequest, RxnVariationId[] aIds) Identical to the com.discoverygate.webservice.types.getReactionsByVariation method except that the results returned are in XML format.
ReactionFilterResults	getReactionsFilterInfoById(ServiceRequest aRequest, ReactionId[] aIds) Returns an array of RxnFilterVariation within a results container for the array of Reaction IDs.
XMLResults	getReactionsFilterInfoByIdXML(ServiceRequest aRequest, ReactionId[] aIds) Identical to the com.discoverygate.webservice.types.getReactionsFilterInfoById method except that the results returned are in XML format.
ReactionVocabulary	getReactionVocabulary(ServiceRequest aRequest, VocabularyVersion aVersion) Returns the Reaction vocabulary if the VocabularyVersion passed is not equal to the current server version.
java.lang.String	getReactionVocabularyXML(ServiceRequest aRequest, VocabularyVersion aVersion) Same as getReactionVocabulary except that the vocabulary is returned as a string of XML.
java.lang.String	getSchema(ServiceRequest aRequest, SchemaType aType) Returns the Schema (XSD format) of the root-level object specified in the SchemaType.
ServiceInformation	getServiceInformation(ServiceRequest aRequest) Returns information associated with the license, such as the version string of the service, a list of retrieval flags, a list of sources and their copyright strings.
MoleculeResults	getSourceMoleculesByStructure(ServiceRequest aRequest, MoleculeSearch[] aCriteria, Datasource aSource) Searches the source database specified by the Datasource parameter for the MoleculeSearch criteria.
XMLResults	getSourceMoleculesByStructureXML(ServiceRequest aRequest, MoleculeSearch[] aCriteria, Datasource aSource) Same as getSourceMoleculesByStructure except that the results are returned in XML format.
SimilaritySourceResult[]	getSourceMoleculeSimilarity(ServiceRequest aRequest, SourceId[] aIds, Structure aStructure, SimilarityType aType) Operates in the same way as getMoleculeSimilarity except that the inputs and outputs are related to source molecule IDs.
MoleculeSourceResults	getSourceSummaryByMoleculeId(ServiceRequest aRequest, Datasource[] aSources, MoleculeId[] aIds) Determines the for a list of MoleculeId's in which data sources they exist.
XMLResults	getSourceSummaryByMoleculeIdXML(ServiceRequest aRequest, Datasource[] aSources, MoleculeId[] aIds) Identical to the com.discoverygate.webservice.types.getSourceSummaryByMoleculeId method except that the results returned are in XML format.
SupplierResults[]	getSuppliers(ServiceRequest aRequest, java.lang.String aWildcard) Returns an array of com.discoverygate.webservice.types.Supplier within a results container for the specified wildcard and procurement datasource.
SupplierResults	getSuppliersById(ServiceRequest aRequest, SupplierId[] aSuppliers) Returns a SupplierResults object (a list of Supplier objects) for a given list of Supplier IDs.
XMLResults	getSuppliersByIdXML(ServiceRequest aRequest, SupplierId[] aSuppliers) Identical to the com.discoverygate.webservice.types.getSuppliersById method except that the results are returned in XML format.
XMLResults[]	getSuppliersXML(ServiceRequest aRequest, java.lang.String aWildcard) Identical to the com.discoverygate.webservice.types.getSuppliers method except that the results returned are in XML format.
ExperimentResults	getToxicityExperiments(ServiceRequest aRequest, MoleculeSearch[] aSearch, ExperimentCriteria aCriteria) Returns the toxicity experiments that conform to the experiment criteria passed, and optionally conform to the structure search specified by the parameter aSearch.
XMLResults	getToxicityExperimentsXML(ServiceRequest aRequest, MoleculeSearch[] aSearch, ExperimentCriteria aCriteria) Same as getToxicityExperiments except that the results are returned in XML format
ToxPublication[]	getToxicityPublications(ServiceRequest aRequest, ToxCoden[] aIds) Returns a list of Toxicology publication objects for the Codens passed to the method.
ToxicityVocabulary	getToxicityVocabulary(ServiceRequest aRequest, VocabularyVersion aVersion) Returns the Toxicity vocabulary if the VocabularyVersion passed is not equal to the current server version.
java.lang.String	getToxicityVocabularyXML(ServiceRequest aRequest, VocabularyVersion aVersion) Same as getToxicityVocabulary except that the vocabulary is returned as a string of XML.
XMLResults	runProjectionQuery(ServiceRequest aRequest, java.lang.String aQuery) For internal use only - do not use this in your application.

Method Detail

closeStatefulQuery

void closeStatefulQuery(ServiceRequest aRequest)
                        throws java.rmi.RemoteException,
                               Exception

Terminates the stateful query specified by the statefulQueryKey in the ServiceRequest object. When the query closes, the key is no longer valid to produce results so the key must be re-used to start a new query. For an overview, see "stateful searches" in the Discovery Gate Web Service Developer's Guide.

Parameters:

aRequest - the service request

Throws:

java.rmi.RemoteException

Exception

convertStructureToMolfile

java.lang.String[] convertStructureToMolfile(ServiceRequest aRequest,
                                             java.lang.String[] aStructures)
                                             throws java.rmi.RemoteException

Returns the array of molecules as an array of molfiles (or the array of reactions as an array of rxnfiles).

• Supported molfile/rxnfile formats: SMILES and Chime string.
• License access required: any valid license.

Parameters:

aRequest - the service request

aStructures - the array of structures to be converted

Returns:

the molfiles in the same order as the input structures

Throws:

java.rmi.RemoteException

findSourceMolecule

ExistenceResult[] findSourceMolecule(ServiceRequest aRequest,
                                     Datasource aSource,
                                     ExistenceRequest[] aRequests)
                                     throws java.rmi.RemoteException,
                                            Exception

Determines whether the molecules specified in the com.discoverygate.webservice.types.com.discoverygate.webservice.types.ExistenceRequest array exist in the source database.

• Each request specifies both the structure and the user's own ID for the structure.
• An com.discoverygate.webservice.types.com.discoverygate.webservice.types.ExistenceResult object
is returned for each Molecule found and it indicates the Symyx Molecule ID and the user's own ID for the structure.
• License access required: the target datasource.

Parameters:

aRequest - the service request

aSource - a data source

aRequests - the molecules to search for

Returns:

an array of Molecules found and their IDs

Throws:

java.rmi.RemoteException

Exception

getCatalogsById

CatalogResults getCatalogsById(ServiceRequest aRequest,
                               CatalogId[] aCatalogs)
                               throws java.rmi.RemoteException,
                                      Exception

Returns a CatalogsResults object (a list of Catalog objects) for a given list of Catalogs IDs.

• The catalogs IDs can come from any of the procurement sources that the license-holder is entitled to.
• The Catalog objects are of type Catalog, regardless of the source providing the object.
• Each object can be inspected to discover the provider source.
• License access required: ACD or SCD.

Parameters:

aRequest - the service request

aCatalogs - the list of Catalog Id objects

Returns:

the CatalogResults object containing a list of Catalog objects

Throws:

java.rmi.RemoteException

Exception

getCatalogsByIdXML

XMLResults getCatalogsByIdXML(ServiceRequest aRequest,
                              CatalogId[] aCatalogs)
                              throws java.rmi.RemoteException,
                                     Exception

Identical to the com.discoverygate.webservice.types.com.discoverygate.webservice.types.getCatalogsById method except that the results are returned in XML format.

Parameters:

aRequest - the service request

aCatalogs - the list of Catalog ID objects

Returns:

an XML container for the CatalogResults object containing a list of Catalog objects

Throws:

java.rmi.RemoteException

Exception

getClassificationVocabulary

ClassificationVocabulary getClassificationVocabulary(ServiceRequest aRequest,
                                                     VocabularyVersion aVersion)
                                                     throws java.rmi.RemoteException,
                                                            Exception

Returns the Classification vocabulary if the VocabularyVersion passed is not equal to the current server version.

• The ClassificationVocabulary inherits VocabularyVersion. Therefore, the object can be serialized on the client-side to either return the latest version or to confirm that the holder already has the latest version.
• sourceFilter of the ServiceRequest: supported.
• License access required: Toxicity, CMC, or MDDR. The vocabulary contains items from Toxicity, Medicinal, and Drug databases depending on entitlement.

Parameters:

aRequest - the ServiceRequest describing at least the License

aVersion - the current version of the vocabulary held by caller

Returns:

the ClassificationVocabulary object that either contains the vocabulary and related version id, or the current id and a null vocabulary

Throws:

java.rmi.RemoteException

Exception

getClassificationVocabularyXML

java.lang.String getClassificationVocabularyXML(ServiceRequest aRequest,
                                                VocabularyVersion aVersion)
                                                throws java.rmi.RemoteException,
                                                       Exception

Same as getClassificationVocabulary except that the vocabulary is returned as a string of XML.

Parameters:

aRequest - the ServiceRequest describing at least the License

aVersion - the current version of the vocabulary held by caller

Returns:

string of XML representing the ClassificationVocabulary object that contains either the vocabulary and related version id, or the current id and a null vocabulary

Throws:

java.rmi.RemoteException

Exception

getMoleculeSimilarity

SimilarityResult[] getMoleculeSimilarity(ServiceRequest aRequest,
                                         MoleculeId[] aIds,
                                         Structure aStructure,
                                         SimilarityType aType)
                                         throws java.rmi.RemoteException,
                                                Exception

Returns the list of SimilarityResult (Molecule ID and similarity percentage) of the given IDs against the given structure, for the specified similarity type. The method can be used in conjuction with the results from a SIMILARITY-type structure search to find the similarity percentage of the hits returned.

Parameters:

aRequest - the service request

aIds - list of Molecule ID objects normally from the resultset of a previous search

aStructure - structure used in the comparison of the similarity search

aType - similarity type to use for the comparison

Returns:

list of Similairty results

Throws:

java.rmi.RemoteException

Exception

getMoleculeSourcesByMoleculeId

MoleculeSourceResults getMoleculeSourcesByMoleculeId(ServiceRequest aRequest,
                                                     Datasource aSource,
                                                     MoleculeId[] aIds)
                                                     throws java.rmi.RemoteException,
                                                            Exception

For a list of com.discoverygate.webservice.types.com.discoverygate.webservice.types.MoleculeId's, determines which data sources contain the IDs. This method can be used for a fast lookup whether a given molecule or list of molecules exist in a given datasource.

Parameters:

aRequest - the service request

aSource - a data source to be searched. If set to null, all datasources of a given MoleculeId will be returned

aIds - an array of com.discoverygate.webservice.types.com.discoverygate.webservice.types.MoleculeId's

Returns:

a com.discoverygate.webservice.types.com.discoverygate.webservice.types.MoleculeSourceResults container with a list of com.discoverygate.webservice.types.com.discoverygate.webservice.types.MoleculeSource entities.

Throws:

java.rmi.RemoteException

Exception

getMoleculeSourcesByMoleculeIdXML

XMLResults getMoleculeSourcesByMoleculeIdXML(ServiceRequest aRequest,
                                             Datasource aSource,
                                             MoleculeId[] aIds)
                                             throws java.rmi.RemoteException,
                                                    Exception

Identical to the com.discoverygate.webservice.types.com.discoverygate.webservice.types.getMoleculeSourcesByMoleculeId method except that the results returned are in XML format.

Parameters:

aRequest - the service request

aSource - a data source to be searched. If set to null, all datasources of a given MoleculeId will be returned

aIds - an array of MoleculeId's

Returns:

an XML results container with the MoleculeSourceResults

Throws:

java.rmi.RemoteException

Exception

getMoleculesByCatalogId

MoleculeResults getMoleculesByCatalogId(ServiceRequest aRequest,
                                        CatalogId aCatalog,
                                        BulkFineType aType)
                                        throws java.rmi.RemoteException,
                                               Exception

Returns the source molecules for a given CatalogId. The caller must specify whether the molecules returned should be available in BULK quantities, FINE quantities, or both BULK and FINE.

• Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags, and the ID_ONLY flag.
• Licence access required: ACD or SCD.

Parameters:

aRequest - the ServiceRequest describing at least the License and retrieval flags.

aCatalog - the catalog Id of the catalog to search

aType - the Bulk/Fine Flag used to filter the molecules from the catalog

Returns:

a molecule container

Throws:

java.rmi.RemoteException

Exception

getMoleculesByCatalogIdXML

XMLResults getMoleculesByCatalogIdXML(ServiceRequest aRequest,
                                      CatalogId aCatalog,
                                      BulkFineType aType)
                                      throws java.rmi.RemoteException,
                                             Exception

Same as getMoleculesByCatalogId except that the results are returned in XML format.

Parameters:

aRequest - the ServiceRequest describing at least the License and retrieval flags.

aCatalog - the catalog Id of the catalog to search

aType - the Bulk/Fine Flag used to filter the molecules from the catalog

Returns:

an XML results container

Throws:

java.rmi.RemoteException

Exception

getMoleculesByCatalogItem

Molecule getMoleculesByCatalogItem(ServiceRequest aRequest,
                                   CatalogItem[] aItems)
                                   throws java.rmi.RemoteException,
                                          Exception

Returns a set of source molecules for the catalog items specified by the catalog numbers.

• Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags.
• Note: The source molecules automatically have the PROCUREMENT_PRICING flag specified. However, the sub-level data is already filtered to only show the product to which the catalog item is related.

Parameters:

aRequest - the ServiceRequest describing at least the License

aItems - the list of catalog items from the procurement database(s)

Returns:

a single molecule container that contains source molecules relating to the items requested

Throws:

java.rmi.RemoteException

Exception

getMoleculesByCatalogItemXML

java.lang.String getMoleculesByCatalogItemXML(ServiceRequest aRequest,
                                              CatalogItem[] aItems)
                                              throws java.rmi.RemoteException,
                                                     Exception

Same as getMoleculesByCatalogItem method except that the molecule container is returned as a string of XML.

Parameters:

aRequest - the ServiceRequest describing at least the License

aItems - the list of catalog items from the procurement database(s)

Returns:

a String of XML that contains source molecules relating to the items requested

Throws:

java.rmi.RemoteException

Exception

getMoleculesByCatalogNumbers

MoleculeResults getMoleculesByCatalogNumbers(ServiceRequest aRequest,
                                             java.lang.String[] aCtNums)
                                             throws java.rmi.RemoteException,
                                                    Exception

Returns the source molecules for a given CatalogIds.

• Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags, and the ID_ONLY flag.

Parameters:

aRequest - the ServiceRequest describing at least the License and retrieval flags.

aCtNums - the catalog Ids of the catalog to search

Returns:

a molecule container

Throws:

java.rmi.RemoteException

Exception

getMoleculesByCatalogNumbersXML

XMLResults getMoleculesByCatalogNumbersXML(ServiceRequest aRequest,
                                           java.lang.String[] aCtNums)
                                           throws java.rmi.RemoteException,
                                                  Exception

Same as getMoleculesByCatalogNumbers except that the results are returned in XML format.

Parameters:

aRequest - the ServiceRequest describing at least the License and retrieval flags.

aCtNums - the catalog Ids of the catalog to search

Returns:

an XML results container

Throws:

java.rmi.RemoteException

Exception

getMoleculesByClassification

MoleculeResults getMoleculesByClassification(ServiceRequest aRequest,
                                             MoleculeSearch[] aCriteria,
                                             java.lang.String aClass)
                                             throws java.rmi.RemoteException,
                                                    Exception

Returns the molecules that are classified by the class-type passed and optionally conform to the structure search specified by the parameter aCriteria.

• The aClass string passed must be one of those found in the classification vocabulary returned from getClassificationVocabulary (or getMoleculesByClassificationXML).
• Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags, ID_ONLY.
• sourceFilter of the ServiceRequest: supported.
• License access required: Toxicity, CMC or MDDR. Depending on your entitlements, the method will search Toxicity, Medicinal, and Drug-related information.

Parameters:

aRequest - the ServiceRequest describing at least the License, Page information, and com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags.

aCriteria - the molecule search criteria by which to narrow the citations returned from the method. This argument can be null.

aClass - the classification from the vocabulary on which to search, such as com.discoverygate.webservice.types.com.symyx.refdata.types.vocabulary.ClassificationVocabulary.

Returns:

the molecules that match the search criteria

Throws:

Exception

java.rmi.RemoteException

getMoleculesByClassificationXML

XMLResults getMoleculesByClassificationXML(ServiceRequest aRequest,
                                           MoleculeSearch[] aCriteria,
                                           java.lang.String aClass)
                                           throws java.rmi.RemoteException,
                                                  Exception

Same as getMoleculesByClassification except that the results are returned in XML format.

Parameters:

aRequest - the ServiceRequest describing at least the License, Page information, and com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags.

aCriteria - the molecule search criteria by which to narrow the citations returned from the method

aClass - the classification from the vocabulary on which to search

Returns:

the molecules that match the search criteria

Throws:

java.rmi.RemoteException

Exception

getMoleculesById

MoleculeResults getMoleculesById(ServiceRequest aRequest,
                                 MoleculeId[] aIds)
                                 throws java.rmi.RemoteException,
                                        Exception

Returns an array of Molecule within a results container for the array of Molecule IDs.

• The MoleculeId is a base class to many types of objects returned from the service. Therefore this method can consume the output from other methods without conversion.
• The data retrieved from within the Molecule is controlled by the com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags specified in the ServiceRequest object.
• To control sub-level Reaction data returned, specify the com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags.
• Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags (and ReactionRetrievalFlags for sub-level Reaction data)
• sourceFilter of the ServiceRequest: supported.

Parameters:

aRequest - the service request

aIds - the molecule IDs of the target molecules

Returns:

a results container with the Molecule hits

Throws:

java.rmi.RemoteException

Exception

getMoleculesByIdXML

XMLResults getMoleculesByIdXML(ServiceRequest aRequest,
                               MoleculeId[] aIds)
                               throws java.rmi.RemoteException,
                                      Exception

Identical to the com.discoverygate.webservice.types.getMoleculesById method except that the results returned are in XML format.

Parameters:

aRequest - the service request

aIds - the molecule IDs of the target molecules

Returns:

an XML results container with the Molecule hits

Throws:

java.rmi.RemoteException

Exception

getMoleculesByNames

MoleculeResults getMoleculesByNames(ServiceRequest aRequest,
                                    java.lang.String[] aNames)
                                    throws java.rmi.RemoteException,
                                           Exception

Returns an array of Molecule entities within a results container for the specified wildcard.

• The wildcard character '%' is used to specify multiple-character wildcards and the '_' for a single character wildcard.
• The name specified can be the chemical name, CAS number, NEMA key, or OHS name, and is case-insensitive
• To control the data retrieved from within the Molecule, specify com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags in the ServiceRequest object.
• To control sub-level Reaction data returned, specify the com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags.
• To control the number and offset of records retrieved, use the DataPage of the ServiceRequest object.
• Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags, ID_ONLY.
• sourceFilter of the ServiceRequest: supported.

Parameters:

aRequest - the service request

aNames - the search name with optional wildcard characters

Returns:

a results container with the Molecule hits

Throws:

java.rmi.RemoteException

Exception

getMoleculesByNamesXML

XMLResults getMoleculesByNamesXML(ServiceRequest aRequest,
                                  java.lang.String[] aNames)
                                  throws java.rmi.RemoteException,
                                         Exception

Identical to the com.discoverygate.webservice.types.getMoleculesByName method except that the results returned are in XML format.

Parameters:

aRequest - the service request

aNames - the search name with optional wildcard characters

Returns:

an XML results container with the Reaction hits

Throws:

java.rmi.RemoteException

Exception

getMoleculesByQuery

MoleculeResults getMoleculesByQuery(ServiceRequest aRequest,
                                    MoleculeSearch[] aCriteria,
                                    java.lang.String aQuery)
                                    throws java.rmi.RemoteException,
                                           Exception

For internal use only - do not use this in your application.

Throws:

java.rmi.RemoteException

Exception

getMoleculesByQueryXML

XMLResults getMoleculesByQueryXML(ServiceRequest aRequest,
                                  MoleculeSearch[] aCriteria,
                                  java.lang.String aQuery)
                                  throws java.rmi.RemoteException,
                                         Exception

For internal use only - do not use this in your application.

Throws:

java.rmi.RemoteException

Exception

getMoleculesBySourceId

MoleculeResults getMoleculesBySourceId(ServiceRequest aRequest,
                                       SourceId[] aIds)
                                       throws java.rmi.RemoteException,
                                              Exception

Returns the top-level molecules that correspond to the list of SourceId objects.

• The IDs can be from any data source known to the service, including 3rd-party databases.
• Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags.
• sourceFilter of the ServiceRequest: supported.

Parameters:

aRequest - the ServiceRequest describing at least the License, page parameters, and retrieval flags.

aIds - the list of IDs for which the top-level molecules are to be retrieved

Returns:

a molecule results container

Throws:

java.rmi.RemoteException

Exception

getMoleculesBySourceIdMerged

Molecule getMoleculesBySourceIdMerged(ServiceRequest aRequest,
                                      SourceId[] aIds)
                                      throws java.rmi.RemoteException,
                                             Exception

Returns an unpopulated Molecule container that contains source molecule objects, as well as their hierarchies fetched with the retrieval flags.

• Finds the source molecule information from the SourceId specified.
• Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags.
• License access required: the specific datasource requested

Parameters:

aRequest - the ServiceRequest describing at least the License and retrieval flags.

aIds - the list of IDs for which to fetch the source molecules.

Returns:

a molecule container

Throws:

java.rmi.RemoteException

Exception

getMoleculesBySourceIdMergedXML

java.lang.String getMoleculesBySourceIdMergedXML(ServiceRequest aRequest,
                                                 SourceId[] aIds)
                                                 throws java.rmi.RemoteException,
                                                        Exception

This method is the same as getMoleculeMergedBySourceId except that it returns the result as a single XML string.

Parameters:

aRequest - the ServiceRequest describing at least the License and retrieval flags.

aIds - the list of IDs for which to fetch the source molecules.

Returns:

a single XML string

Throws:

java.rmi.RemoteException

Exception

See Also:

getMoleculeMergedBySourceId

getMoleculesBySourceIdXML

XMLResults getMoleculesBySourceIdXML(ServiceRequest aRequest,
                                     SourceId[] aIds)
                                     throws java.rmi.RemoteException,
                                            Exception

Same as getMoleculesBySourceId except that the results are returned in XML format.

Parameters:

aRequest - the ServiceRequest describing at least the License, page parameters and retrieval flags.

aIds - the list of IDs for which the top-level molecules are to be retrieved

Returns:

an XML results container

Throws:

java.rmi.RemoteException

Exception

getMoleculesByStructure

MoleculeResults getMoleculesByStructure(ServiceRequest aRequest,
                                        MoleculeSearch[] aCriteria)
                                        throws java.rmi.RemoteException,
                                               Exception

Returns an array of Molecule within a results container that satisfy the query specified by a combination of the boolean structure searches within the aCriteria parameter.

• The data retrieved from within the Molecule is controlled by the com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags specified in the ServiceRequest object.
• To control sub-level Reaction data returned, specify the com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags.
• To control the number and offset of records retrieved, use the DataPage of the ServiceRequest object.
• Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags, ID_ONLY.
• sourceFilter of the ServiceRequest: supported.
• License access required: at least one Reaction datasource.

Parameters:

aRequest - the service request

aCriteria - the structure search combination

Returns:

a results container with the Molecule hits

Throws:

java.rmi.RemoteException

Exception

getMoleculesByStructureXML

XMLResults getMoleculesByStructureXML(ServiceRequest aRequest,
                                      MoleculeSearch[] aCriteria)
                                      throws java.rmi.RemoteException,
                                             Exception

Identical to the com.discoverygate.webservice.types.getMoleculesByStructure except that the results returned are in XML format.

Parameters:

aRequest - the service request

aCriteria - the structure search combination

Returns:

an XML results container with the Molecule hits in XML format

Throws:

java.rmi.RemoteException

Exception

getMoleculesFilterInfoById

AvailabilityFilterResults getMoleculesFilterInfoById(ServiceRequest aRequest,
                                                     MoleculeId[] aIds)
                                                     throws java.rmi.RemoteException,
                                                            Exception

Returns an array of AvailabilityFilter within a results container for the given array of Molecule IDs

Parameters:

aRequest - the service request

aIds - the molecule IDs

Returns:

a results container

Throws:

java.rmi.RemoteException

Exception

getMoleculesFilterInfoByIdXML

XMLResults getMoleculesFilterInfoByIdXML(ServiceRequest aRequest,
                                         MoleculeId[] aIds)
                                         throws java.rmi.RemoteException,
                                                Exception

Identical to the com.discoverygate.webservice.types.getMoleculesFilterInfoById method except that the results returned are in XML format. Returns an array of AvailabilityFilter within a results container for the given array of Molecule IDs

Parameters:

aRequest - the service request

aIds - the molecule IDs

Returns:

an XML results container with the AvailabilityFilterResults

Throws:

java.rmi.RemoteException

Exception

getPatentsByTitle

PatentResults getPatentsByTitle(ServiceRequest aRequest,
                                java.lang.String aCriteria)
                                throws java.rmi.RemoteException,
                                       Exception

Returns the Patent entities (DGWS classes) that match the search criteria passed in the aTextQuery parameter.

• The search criteria must be in the form of an Oracle text query and therefore can contain single words, groups of words (found as a group), or boolean logic such as "ligand and inhibitor", which would search titles that contain both 'ligand' and 'inhibitor' in any order.
• Flag support: Molecule Retrieval Flags that are drug-related.
• License access required: MDDR.

Parameters:

aRequest - the ServiceRequest describing at least the License, Page information, and the com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags required

aCriteria - search criteria in the form of an Oracle text query

Returns:

the reactions that match the search criteria

Throws:

java.rmi.RemoteException

Exception

getPatentsByTitleXML

XMLResults getPatentsByTitleXML(ServiceRequest aRequest,
                                java.lang.String aCriteria)
                                throws java.rmi.RemoteException,
                                       Exception

The same as getPatentsByTitle except that the response is returned in XML form.

Parameters:

aRequest - the ServiceRequest describing at least the License, Page information, and the com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags required

aCriteria - search criteria in the form of an Oracle text query

Returns:

the reactions that match the search criteria

Throws:

java.rmi.RemoteException

Exception

getProcurementVocabulary

ProcurementVocabularies getProcurementVocabulary(ServiceRequest aRequest,
                                                 VocabularyVersion aVersion)
                                                 throws java.rmi.RemoteException,
                                                        ServiceFault

Returns the ProcurementVocabularies object if the VocabularyVersion passed is not equal to the current server version.

• The ProcurementVocabularies object inherits VocabularyVersion. Therefore, the object can be serialized on the client-side to either return the latest version or to confirm that the holder already has the latest version.
• The vocabulary contains a ProcurementVocabulary object for each procurement database the caller has access to.
• sourceFilter of the ServiceRequest: supported.
• License access required: ACD and/or SCD.

Parameters:

aRequest - the ServiceRequest describing at least the License

aVersion - the current version of the vocabulary held by caller

Returns:

the ProcurementVocabularies object that either contains the vocabularies and related version id, or the current id and a null vocabulary list

Throws:

java.rmi.RemoteException

Exception

ServiceFault

getProcurementVocabularyXML

java.lang.String getProcurementVocabularyXML(ServiceRequest aRequest,
                                             VocabularyVersion aVersion)
                                             throws java.rmi.RemoteException,
                                                    Exception

Same as getProcurementVocabulary except that the vocabulary is returned as a string of XML.

Parameters:

aRequest - the ServiceRequest describing at least the License

aVersion - the current version of the vocabulary held by caller

Returns:

a string of XML that represents the ProcurementVocabulary object that contains either the vocabulary and related version id, or the current id and a null vocabulary

Throws:

java.rmi.RemoteException

Exception

getProductsByMoleculeAndSuppliers

ProductResults getProductsByMoleculeAndSuppliers(ServiceRequest aRequest,
                                                 SourceId[] aMolecules,
                                                 SupplierId[] aSuppliers)
                                                 throws java.rmi.RemoteException,
                                                        Exception

Returns an array of Product within a results container for the given array of Molecule IDs and Supplier IDs.

• The MoleculeId is a base class to many types of objects returned from the service. Therefore this method can consume the output from other methods without conversion.
• The data retrieved is NOT controlled by the com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags. Therefore all Packages and Catalogs for each Product hit by the search are returned.
• The DataPage of the ServiceRequest object is ignored and all Products that match the criteria are returned.
• License access required: ACD or SCD

Parameters:

aRequest - the service request

aMolecules - the molecule IDs of the target molecules

aSuppliers - the supplier IDs of the target Companies

Returns:

a results container with the Product hits

Throws:

java.rmi.RemoteException

Exception

getProductsByMoleculeAndSuppliersXML

XMLResults getProductsByMoleculeAndSuppliersXML(ServiceRequest aRequest,
                                                SourceId[] aMolecules,
                                                SupplierId[] aSuppliers)
                                                throws java.rmi.RemoteException,
                                                       Exception

Identical to the com.discoverygate.webservice.types.getProductsByMoleculeandSuppliers method except that the results returned are in XML format.

Parameters:

aRequest - the service request

aMolecules - the molecule IDs of the target molecules

aSuppliers - the supplier IDs of the target Companies

Returns:

an XML results container with the Reaction hits

Throws:

java.rmi.RemoteException

Exception

getReactionCitations

RxnCitationResults getReactionCitations(ServiceRequest aRequest,
                                        CitationCriteria aCriteria)
                                        throws java.rmi.RemoteException,
                                               Exception

Returns the Reaction citation entities (DGWS classes) that conform to the citation criteria passed to the method.

• Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags, and therefore the caller is able to create a hierarchy from the results with citations on top.
• sourceFilter of the ServiceRequest: supported.
• License access required: any reaction database.

Parameters:

aRequest - the ServiceRequest describing at least the License, Page information, and com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags required

aCriteria - the criteria on which to narrow the citations returned from the method

Returns:

the Citations that match the search criteria

Throws:

java.rmi.RemoteException

Exception

getReactionCitationsXML

XMLResults getReactionCitationsXML(ServiceRequest aRequest,
                                   CitationCriteria aCriteria)
                                   throws java.rmi.RemoteException,
                                          Exception

Same as getReactionCitations except that the result are returned in XML format

Parameters:

aRequest - the ServiceRequest describing at least the License, Page information, and com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags required

aCriteria - the criteria by which to narrow the citations returned from the method

Returns:

the Citations that match the search criteria

Throws:

java.rmi.RemoteException

Exception

getReactionClassification

Classification[] getReactionClassification(ServiceRequest aRequest,
                                           Structure[] aStructs)
                                           throws java.rmi.RemoteException,
                                                  Exception

Returns an object containing the Broad, Medium and Narrow InfoChem class-codes for each rxnfile given in the array.

• The Structure is a base class to many types of objects returned from the service. Therefore this method can consume the output from other methods without conversion.
• License access required: at least one Reaction datasource.

Parameters:

aRequest - the service request

aStructs - an array of RxnFile reaction structures

Returns:

an object containing class-codes

Throws:

java.rmi.RemoteException

Exception

getReactionVocabulary

ReactionVocabulary getReactionVocabulary(ServiceRequest aRequest,
                                         VocabularyVersion aVersion)
                                         throws java.rmi.RemoteException,
                                                Exception

Returns the Reaction vocabulary if the VocabularyVersion passed is not equal to the current server version.

• The ReactionVocabulary inherits VocabularyVersion. Therefore, the object can be serialzied on the client-side to return the latest version or confirm that the holder already has the latest version.
• The vocabulary contains items only from those reaction databases the caller has access to.
• sourceFilter of the ServiceRequest: supported.
• License access required: any reaction database.

Parameters:

aRequest - the ServiceRequest describing at least the License

aVersion - the current version of the vocabulary held by caller

Returns:

the ReactionVocabulary object that either contains the vocabulary and related version id, or the current id and a null vocabulary

Throws:

java.rmi.RemoteException

Exception

getReactionVocabularyXML

java.lang.String getReactionVocabularyXML(ServiceRequest aRequest,
                                          VocabularyVersion aVersion)
                                          throws java.rmi.RemoteException,
                                                 Exception

Same as getReactionVocabulary except that the vocabulary is returned as a string of XML.

Parameters:

aRequest - the ServiceRequest describing at least the License

aVersion - the current version of the vocabulary held by caller

Returns:

a string of XML that represents the ReactionVocabulary object that either contains the vocabulary and related version id, or the current id and a null vocabulary

Throws:

java.rmi.RemoteException

Exception

getReactionsById

ReactionResults getReactionsById(ServiceRequest aRequest,
                                 ReactionId[] aIds)
                                 throws java.rmi.RemoteException,
                                        Exception

Returns an array of Reaction within a results container for the array of Reaction IDs.

• The ReactionId is a base class to many types of objects returned from the service.
Therefore this method can consume the output from other methods without conversion.
• To control the data retrieved from within the Reaction, specify com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags in the ServiceRequest object.
• To control sub-level Molecule data returned, specify the com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags
• Flag support: ReactionRetrievalFlags (and MoleculeRetrievalFlags for sub-level Molecule data)
• sourceFilter of the ServiceRequest: supported.
• License access required: at least one Reaction datasource.

Parameters:

aRequest - the service request

aIds - the reaction IDs of the target reactions

Returns:

a results container with the Reaction hits

Throws:

java.rmi.RemoteException

Exception

getReactionsByIdXML

XMLResults getReactionsByIdXML(ServiceRequest aRequest,
                               ReactionId[] aIds)
                               throws java.rmi.RemoteException,
                                      Exception

Identical to the getReactionsById method except that the results returned are in XML format.

Parameters:

aRequest - the service request

aIds - the reaction IDs of the target reactions

Returns:

an XML results container with the Reaction hits

Throws:

java.rmi.RemoteException

Exception

getReactionsByProduct

ReactionResults getReactionsByProduct(ServiceRequest aRequest,
                                      MoleculeSearch[] aSearch,
                                      RxnProductCriteria aCriteria)
                                      throws java.rmi.RemoteException,
                                             Exception

Gets the reactions where at least one of the products conforms to the search created from the MoleculeSearch[] passed to the method.

• The reactions returned can be further filtered on the product yield by passing a RxnProductCriteria object.
• Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags, ID_ONLY flag.
• sourceFilter of the ServiceRequest: supported.
• License access required: any reaction database.

Parameters:

aRequest - the ServiceRequest describing at least the License, Page information, and the com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags required

aSearch - the array of MoleculeSearch objects that describes how to search the products (optional)

aCriteria - the criteria for which to narrow the candidate products. This parameter can be null.

Returns:

the reactions that match the search criteria

Throws:

java.rmi.RemoteException

Exception

getReactionsByProductXML

XMLResults getReactionsByProductXML(ServiceRequest aRequest,
                                    MoleculeSearch[] aSearch,
                                    RxnProductCriteria aCriteria)
                                    throws java.rmi.RemoteException,
                                           Exception

The same as getReactionsByProduct except that the response is returned in XML form.

Parameters:

aRequest - the ServiceRequest describing at least the License, Page information, and the com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags required

aSearch - the array of MoleculeSearch objects that describes how to search the products (optional)

aCriteria - the criteria by which to narrow the candidate products. This parameter can be null.

Returns:

the reactions that match the search criteria

Throws:

java.rmi.RemoteException

Exception

getReactionsByQuery

ReactionResults getReactionsByQuery(ServiceRequest aRequest,
                                    ReactionSearch[] aCriteria,
                                    java.lang.String aQuery)
                                    throws java.rmi.RemoteException,
                                           Exception

For internal use only - do not use this in your application.

Throws:

java.rmi.RemoteException

Exception

getReactionsByQueryXML

XMLResults getReactionsByQueryXML(ServiceRequest aRequest,
                                  ReactionSearch[] aCriteria,
                                  java.lang.String aQuery)
                                  throws java.rmi.RemoteException,
                                         Exception

For internal use only - do not use this in your application.

Throws:

java.rmi.RemoteException

Exception

getReactionsByStructure

ReactionResults getReactionsByStructure(ServiceRequest aRequest,
                                        ReactionSearch[] aCriteria)
                                        throws java.rmi.RemoteException,
                                               Exception

Returns an array of Reaction within a results container that satisfy the query specified.

• The data retrieved from within the Reaction is controlled by the com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags specified in the ServiceRequest object.
• To control sub-level Molecule data returned, specify the com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags
• To control the number and offset of records retrieved, use the DataPage of the ServiceRequest object
• Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags, ID_ONLY.
• sourceFilter of the ServiceRequest: supported.
• License access required: at least one Reaction datasource.

Parameters:

aRequest - the service request

aCriteria - the structure search combination

Returns:

a results container with the Reaction hits

Throws:

java.rmi.RemoteException

Exception

getReactionsByStructureXML

XMLResults getReactionsByStructureXML(ServiceRequest aRequest,
                                      ReactionSearch[] aCriteria)
                                      throws java.rmi.RemoteException,
                                             Exception

Identical to the com.discoverygate.webservice.types.getReactionsByStructure except that the results returned are in XML format.

Parameters:

aRequest - the service request

aCriteria - the structure search combination

Returns:

an XML results container with the Reaction hits in XML format

Throws:

java.rmi.RemoteException

Exception

getReactionsByVariation

ReactionResults getReactionsByVariation(ServiceRequest aRequest,
                                        RxnVariationId[] aIds)
                                        throws java.rmi.RemoteException,
                                               Exception

Identical to the getReactionsById method except that the VariationId is specified.

Parameters:

aRequest - the service request

aIds - the reaction validation IDs of the target reactions

Returns:

a results container with the Reaction hits

Throws:

java.rmi.RemoteException

Exception

getReactionsByVariationXML

XMLResults getReactionsByVariationXML(ServiceRequest aRequest,
                                      RxnVariationId[] aIds)
                                      throws java.rmi.RemoteException,
                                             Exception

Identical to the com.discoverygate.webservice.types.getReactionsByVariation method except that the results returned are in XML format.

Parameters:

aRequest - the service request

aIds - the reaction variation IDs of the target reactions

Returns:

an XML results container with the Reaction hits

Throws:

java.rmi.RemoteException

Exception

getReactionsFilterInfoById

ReactionFilterResults getReactionsFilterInfoById(ServiceRequest aRequest,
                                                 ReactionId[] aIds)
                                                 throws java.rmi.RemoteException,
                                                        Exception

Returns an array of RxnFilterVariation within a results container for the array of Reaction IDs.

• The ReactionId is a base class to many types of objects returned from the service.
Therefore this method can consume the output from other methods without conversion.
• To control the data retrieved from within the RxnFilterVariation, specify com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags in the ServiceRequest object.
• Flag support: ReactionRetrievalFlags
• License access required: at least one Reaction datasource.

Parameters:

aRequest - the service request

aIds - the reaction IDs of the target reactions

Returns:

a results container with the Reaction hits

Throws:

java.rmi.RemoteException

Exception

getReactionsFilterInfoByIdXML

XMLResults getReactionsFilterInfoByIdXML(ServiceRequest aRequest,
                                         ReactionId[] aIds)
                                         throws java.rmi.RemoteException,
                                                Exception

Identical to the com.discoverygate.webservice.types.getReactionsFilterInfoById method except that the results returned are in XML format. Returns an array of RxnFilterVariation within a results container for the given array of Reaction IDs

Parameters:

aRequest - the service request

aIds - the Reaction IDs

Returns:

an XML results container with the ReactionFilterResults

Throws:

java.rmi.RemoteException

Exception

getSchema

java.lang.String getSchema(ServiceRequest aRequest,
                           SchemaType aType)
                           throws java.rmi.RemoteException,
                                  Exception

Returns the Schema (XSD format) of the root-level object specified in the SchemaType.

Note: If the Type chosen is the complete object, the parameters of the ServiceRequest are ignored and the entire schema is retrieved. Otherwise the schema returned supports the flags and the sourceFilter specified in the ServiceRequest object.

Parameters:

aRequest - the ServiceRequest describing at least the License

aType - the type of schema to be returned

Returns:

the Schema XML in XSD format

Throws:

java.rmi.RemoteException

Exception

getServiceInformation

ServiceInformation getServiceInformation(ServiceRequest aRequest)
                                         throws java.rmi.RemoteException

Returns information associated with the license, such as the version string of the service, a list of retrieval flags, a list of sources and their copyright strings. See ServiceInformation. This method is typically the first method called against the service.

Parameters:

aRequest - the service request

Returns:

the ServiceInformation object

Throws:

java.rmi.RemoteException

getSourceMoleculeSimilarity

SimilaritySourceResult[] getSourceMoleculeSimilarity(ServiceRequest aRequest,
                                                     SourceId[] aIds,
                                                     Structure aStructure,
                                                     SimilarityType aType)
                                                     throws java.rmi.RemoteException,
                                                            Exception

Operates in the same way as getMoleculeSimilarity except that the inputs and outputs are related to source molecule IDs.

• License access required: the specific datasource requested.

Parameters:

aRequest - the ServiceRequest describing at least the License

aIds - the list of source Id objects by which to compare for percentage similarity

aStructure - the structure used for comparison

aType - the type of simiarity to use for comparison

Returns:

a result container

Throws:

java.rmi.RemoteException

Exception

See Also:

getMoleculeSimilarity

getSourceMoleculesByStructure

MoleculeResults getSourceMoleculesByStructure(ServiceRequest aRequest,
                                              MoleculeSearch[] aCriteria,
                                              Datasource aSource)
                                              throws java.rmi.RemoteException,
                                                     Exception

Searches the source database specified by the Datasource parameter for the MoleculeSearch criteria.

• The results are added into the Molecule object at the source molecule level.
• The top-level data is not retrieved.
• Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags that relate to the source being searched, and the ID_ONLY flag.
• A licence with access to the specific datasource requested is required by this method.

Parameters:

aRequest - the ServiceRequest describing at least the License, Page, Molecule, and com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags

aCriteria - the molecule search criteria by which to narrow the citations returned from the method

aSource - the source database on which to search

Returns:

a molecule container

Throws:

java.rmi.RemoteException

Exception

getSourceMoleculesByStructureXML

XMLResults getSourceMoleculesByStructureXML(ServiceRequest aRequest,
                                            MoleculeSearch[] aCriteria,
                                            Datasource aSource)
                                            throws java.rmi.RemoteException,
                                                   Exception

Same as getSourceMoleculesByStructure except that the results are returned in XML format.

Parameters:

aRequest - the ServiceRequest describing at least the License

aCriteria - the molecule search criteria by which to narrow the citations returned from the method

aSource - the source database on which to search

an - XML results container

Throws:

java.rmi.RemoteException

Exception

getSourceSummaryByMoleculeId

MoleculeSourceResults getSourceSummaryByMoleculeId(ServiceRequest aRequest,
                                                   Datasource[] aSources,
                                                   MoleculeId[] aIds)
                                                   throws java.rmi.RemoteException,
                                                          Exception

Determines the for a list of MoleculeId's in which data sources they exist. This method can be used for a fast lookup whether a given molecule or list of molecules exist in a given datasource. This method is provides the exact same result as com.discoverygate.webservice.types.getMoleculeSourcesByMoleculeId, except that it accepts an array of datasources instead of just a single datasource.

Parameters:

aRequest - the service request

aSources - an array Datasource to be searched. If set to null, all datasources of a given MoleculeId will be returned

aIds - an array of MoleculeId's

Returns:

a MoleculeSourceResults container with a list of MoleculeSource entities.

Throws:

java.rmi.RemoteException

Exception

getSourceSummaryByMoleculeIdXML

XMLResults getSourceSummaryByMoleculeIdXML(ServiceRequest aRequest,
                                           Datasource[] aSources,
                                           MoleculeId[] aIds)
                                           throws java.rmi.RemoteException,
                                                  Exception

Identical to the com.discoverygate.webservice.types.getSourceSummaryByMoleculeId method except that the results returned are in XML format.

Parameters:

aRequest - the service request

aSources - an array Datasource to be searched. If set to null, all datasources of a given MoleculeId will be returned

aIds - an array of MoleculeId's

Returns:

an XML results container with the MoleculeSourceResults

Throws:

java.rmi.RemoteException

Exception

getSuppliers

SupplierResults[] getSuppliers(ServiceRequest aRequest,
                               java.lang.String aWildcard)
                               throws java.rmi.RemoteException,
                                      Exception

Returns an array of com.discoverygate.webservice.types.Supplier within a results container for the specified wildcard and procurement datasource.

• Depending on the licensee's entitlement, this method can return more than one results container, one for each procurement source.
• Each results container specifies the datasource of the results contained within it.
• The wildcard character '%' is used to specify multiple-character wildcards and the '_' for a single character wildcard.
• The name specified is that of the full company name and is case-insensitive.
• The data retrieved is NOT controlled by the com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags, and therefore the data returned differs from the Supplier retrieval flag in that the associated Distributor information is associated with each Supplier.
• To control the number and offset of records retrieved, use the DataPage of the ServiceRequest object.
• sourceFilter of the ServiceRequest: supported.
• License access required: the procurement datasource presented.

Parameters:

aRequest - the service request

aWildcard - the search name, with optional wildcard characters, which can be null

Returns:

a results container with the Molecule hits

Throws:

java.rmi.RemoteException

Exception

getSuppliersById

SupplierResults getSuppliersById(ServiceRequest aRequest,
                                 SupplierId[] aSuppliers)
                                 throws java.rmi.RemoteException,
                                        Exception

Returns a SupplierResults object (a list of Supplier objects) for a given list of Supplier IDs.

• The supplier IDs can come from any of the procurement sources that the license-holder is entitled to.
• The Supplier objects are of type Supplier regardless of the source providing the object.
• Each object can be inspected to discover the provider source.
• Note: The method serializes all of the Company entity (DGWS class), and therefore both the Catalog and Distributors are included in the Company data.
• License access required: ACD or SCD.

Parameters:

aRequest - the service request

aSuppliers - the list of Supplier ID objects

Returns:

the SupplierResults object containing a list of Supplier objects

Throws:

java.rmi.RemoteException

Exception

getSuppliersByIdXML

XMLResults getSuppliersByIdXML(ServiceRequest aRequest,
                               SupplierId[] aSuppliers)
                               throws java.rmi.RemoteException,
                                      Exception

Identical to the com.discoverygate.webservice.types.getSuppliersById method except that the results are returned in XML format.

Parameters:

aRequest - the service request

aSuppliers - the list of Supplier ID objects

Returns:

the SupplierResults object containing a list of Supplier objects

Throws:

java.rmi.RemoteException

Exception

getSuppliersXML

XMLResults[] getSuppliersXML(ServiceRequest aRequest,
                             java.lang.String aWildcard)
                             throws java.rmi.RemoteException,
                                    Exception

Identical to the com.discoverygate.webservice.types.getSuppliers method except that the results returned are in XML format.

Parameters:

aRequest - the service request

aWildcard - the search name with optional wildcard characters

Returns:

an XML results container with the Reaction hits

Throws:

java.rmi.RemoteException

Exception

getToxicityExperiments

ExperimentResults getToxicityExperiments(ServiceRequest aRequest,
                                         MoleculeSearch[] aSearch,
                                         ExperimentCriteria aCriteria)
                                         throws java.rmi.RemoteException,
                                                Exception

Returns the toxicity experiments that conform to the experiment criteria passed, and optionally conform to the structure search specified by the parameter aSearch.

• Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags related to Toxicity data.
• License access required: Toxicity.

Parameters:

aRequest - the ServiceRequest describing at least the License, Page information and com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags.

aSearch - the molecule search criteria by which to narrow the citations returned from the method. This argument can be null.

aCriteria - the classification from the vocabulary on which to search

Returns:

the molecules that match the search criteria

Throws:

java.rmi.RemoteException

Exception

getToxicityExperimentsXML

XMLResults getToxicityExperimentsXML(ServiceRequest aRequest,
                                     MoleculeSearch[] aSearch,
                                     ExperimentCriteria aCriteria)
                                     throws java.rmi.RemoteException,
                                            Exception

Same as getToxicityExperiments except that the results are returned in XML format

Parameters:

aRequest - the ServiceRequest describing at least the License, Page information, and com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags.

aSearch - the molecule search criteria by which to narrow the citations returned from the method

aCriteria - the classification from the vocabulary on which to search

Returns:

the molecules that match the search criteria

Throws:

java.rmi.RemoteException

Exception

getToxicityPublications

ToxPublication[] getToxicityPublications(ServiceRequest aRequest,
                                         ToxCoden[] aIds)
                                         throws java.rmi.RemoteException

Returns a list of Toxicology publication objects for the Codens passed to the method.

• These codens normally originate from the toxiciology information returned when using the MoleculeRetrievalFlags.LITERATURE flag.
• License access required: Toxicity.

Parameters:

aRequest - the service request

aIds - the codens

Returns:

a list of Publication objects from the Toxicology source database

Throws:

java.rmi.RemoteException

getToxicityVocabulary

ToxicityVocabulary getToxicityVocabulary(ServiceRequest aRequest,
                                         VocabularyVersion aVersion)
                                         throws java.rmi.RemoteException

Returns the Toxicity vocabulary if the VocabularyVersion passed is not equal to the current server version.

• The ToxicityVocabulary inherits VocabularyVersion. Therefore, the object can be serialized on the client-side to either return the latest version or to confirm that the holder already has the latest version.
• License access required: Toxicity.

Parameters:

aRequest - the ServiceRequest describing at least the License

aVersion - the current version of the vocabulary held by caller

Returns:

the ToxicityVocabulary object that either contains the vocabulary and related version id, or the current id and a null vocabulary

Throws:

java.rmi.RemoteException

getToxicityVocabularyXML

java.lang.String getToxicityVocabularyXML(ServiceRequest aRequest,
                                          VocabularyVersion aVersion)
                                          throws java.rmi.RemoteException

Same as getToxicityVocabulary except that the vocabulary is returned as a string of XML.

Parameters:

aRequest - the ServiceRequest describing at least the License

aVersion - the current version of the vocabulary held by caller

Returns:

a string of XML that represents the ToxicityVocabulary object that contains the vocabulary and related version id, or the current id and a null vocabulary

Throws:

java.rmi.RemoteException

runProjectionQuery

XMLResults runProjectionQuery(ServiceRequest aRequest,
                              java.lang.String aQuery)
                              throws java.rmi.RemoteException,
                                     Exception

For internal use only - do not use this in your application.

Throws:

java.rmi.RemoteException

Exception