Package com.im.df.api.capabilities

Interface JChemEntityCapability

    • Field Detail

      • PROP_STANDARDIZER_CONFIG

        static final java.lang.String PROP_STANDARDIZER_CONFIG
        See Also:
        Constant Field Values

      • PROP_ABSOLUTE_STEREO

        static final java.lang.String PROP_ABSOLUTE_STEREO
        See Also:
        Constant Field Values

      • PROP_DUPLICATE_FILTERING

        static final java.lang.String PROP_DUPLICATE_FILTERING
        See Also:
        Constant Field Values

      • PROP_TAUTOMER_DUPLICATE_CHECKING

        static final java.lang.String PROP_TAUTOMER_DUPLICATE_CHECKING
        See Also:
        Constant Field Values

      • PROP_EMPTY_STRUCTURES_ALLOWED

        static final java.lang.String PROP_EMPTY_STRUCTURES_ALLOWED
        See Also:
        Constant Field Values

      • PROP_NUMBER_OF_EDGES

        static final java.lang.String PROP_NUMBER_OF_EDGES
        See Also:
        Constant Field Values

      • PROP_JCHEM_TABLE_TYPE

        static final java.lang.String PROP_JCHEM_TABLE_TYPE
        See Also:
        Constant Field Values

      • PROP_STRUCTURE_COLUMN_NAME

        static final java.lang.String PROP_STRUCTURE_COLUMN_NAME
        See Also:
        Constant Field Values

      • IMPORT_OPTION_SET_CHIRAL_FLAG

        static final java.lang.String IMPORT_OPTION_SET_CHIRAL_FLAG
        See Also:
        Constant Field Values

    • Method Detail

      • getNumberOfInts

        int getNumberOfInts()
        The number of INTEGER columns that will contain the fingerprint info (each column will contain 4 bytes). See https://docs.chemaxon.com/display/CD/Home

        Beware that the UpdateHandler doesn't enforce the FP options to be valid for the current JChem table type, so it's not safe to assume you can always construct a fingerprint or new JChem entity with these parameters.

        Returns:
        The fingerprint length (x4 bytes)

      • getNumberOfOnes

        int getNumberOfOnes()
        The number of bits to be set for each substructure pattern. For more info click here

        Beware that the UpdateHandler doesn't enforce the FP options to be valid for the current JChem table type, so it's not safe to assume you can always construct a fingerprint or new JChem entity with these parameters.

        Returns:
        The number of bits to be set for each substructure pattern

      • getNumberOfEdges

        int getNumberOfEdges()
        The maximum length (number of bonds) of linear substructure patterns used for fingerprints. See https://docs.chemaxon.com/display/CD/Home

        Beware that the UpdateHandler doesn't enforce the FP options to be valid for the current JChem table type, so it's not safe to assume you can always construct a fingerprint or new JChem entity with these parameters.

        Returns:
        The pattern length

      • isAbsoluteStereo

        boolean isAbsoluteStereo()
        Getter for property absoluteStereo.
        Returns:
        Value of property absoluteStereo.

      • setAbsoluteStereo

        void setAbsoluteStereo​(boolean absoluteStereo,
                       com.im.commons.progress.DFEnvironmentRW env)
        Setter for property absoluteStereo.
        Parameters:
        absoluteStereo - New value of property absoluteStereo.
        env - environment

      • isDuplicateFiltering

        boolean isDuplicateFiltering()
        Is duplicate filtering currently turned on or off.
        Returns:
        Value of property duplicateFiltering.

      • setDuplicateFiltering

        void setDuplicateFiltering​(boolean duplicateFiltering,
                           com.im.commons.progress.DFEnvironmentRW env)
        Setter for property duplicateFiltering.
        Parameters:
        duplicateFiltering - New value of property duplicateFiltering.
        env - environment

      • isTautomerDuplicateChecking

        boolean isTautomerDuplicateChecking()
        Does this JChem table use tautomer duplicate checking. If not then exact search is used. This affects how the JChem table is generated.
        Returns:
        Whether tautomer checking is used for duplicates.

      • setEmptyStructuresAllowed

        void setEmptyStructuresAllowed​(boolean emptyStructuresAllowed,
                               com.im.commons.progress.DFEnvironmentRW env)
        Setter for property emptyStructuresAllowed.
        Parameters:
        emptyStructuresAllowed - New value of property emptyStructuresAllowed.
        env - environment

      • getStandardizerConfig

        java.lang.String getStandardizerConfig()
        Getter for property standardizerConfig.
        Returns:
        Value of property standardizerConfig.

      • setStandardizerConfig

        void setStandardizerConfig​(java.lang.String standardizerConfig,
                           com.im.commons.progress.DFEnvironmentRW env)
        Setter for property standardizerConfig.
        Parameters:
        standardizerConfig - New value of property standardizerConfig.
        env - environment

      • getEntityStandardizer

        chemaxon.standardizer.Standardizer getEntityStandardizer()
        Get the standardiser. If custom standardisation is not defined or is invalid, it returns the default standardiser. The default standardiser performs aromatisation and dehydrogenisation.
        Returns:
        The standardiser.
        Since:
        5.12

      • getEntityDefaultStandardizer

        chemaxon.standardizer.Standardizer getEntityDefaultStandardizer()

      • getCurrentVersionNumber

        java.lang.String getCurrentVersionNumber()
        Get the version of this entity as it is in the database. This is a Chemaxon JChem tables version number increasing usually with each release. This can be used somewhere in UI, but has no reason for the entity existence. If table is not up to date, it is upgraded automatically by DFSchemaProvider implementation during schema initialisation process.
        Returns:
        version number
        Since:
        6.4

      • getSupportedVersionNumber

        int getSupportedVersionNumber()
        Deprecated.
        TODO P2 - this method will be removed from API. Upgrade of tables is done transparently during schema init process. Schema should not be returned from API if entity is not current.

        Returns:
        the version of this entity that is supported by this version of IJC.

      • getJChemPropertyTable

        com.im.commons.db.util.SchemaQualifiedName getJChemPropertyTable()
        Gets the name of the JChem properties table associated with this Entity. Never returns null.
        Returns:
        The name of JChem Property table

      • getMolecularDescriptors

        java.util.List<chemaxon.descriptors.MolecularDescriptor> getMolecularDescriptors()
        Returns:
        the available molecular descriptors for this JChem table

      • getDissimilarityMetrics

        chemaxon.jchem.db.JChemSearch.DissimilarityMetrics getDissimilarityMetrics()
        Returns:
        the built in dissimilarity metrics for this JChem table

      • getStructureField

        DFField getStructureField()
        Get the structure field.
        Returns:
        The structure field

      • supportsNonHits

        default boolean supportsNonHits()
        Description copied from interface: StructureEntityCapability
        Says if this structure entity supports non-hit search (set complement of a search).
        Specified by:
        supportsNonHits in interface StructureEntityCapability
        Returns:
        true if this structure entity supports non-hit search, false otherwise

      • newJChemSearchOptionsFromOld

        default chemaxon.sss.search.JChemSearchOptions newJChemSearchOptionsFromOld​(chemaxon.sss.search.JChemSearchOptions oldOptions,
                                                                            DFOperator op)
        Description copied from interface: StructureEntityCapability
        Creates new JChemSearchOptions based on old options for the specific operator. Sets default values.
        Specified by:
        newJChemSearchOptionsFromOld in interface StructureEntityCapability
        Parameters:
        oldOptions - original JChemSearchOptions, can be null
        op - structure operator
        Returns:
        new JChemSearchOptions instance