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JChem Base API documentation (c) 1998-2018 ChemAxon Ltd.

Packages 
Package Description
chemaxon.calculations
Contains chemical computation modules.
chemaxon.calculations.cip  
chemaxon.calculations.clean  
chemaxon.calculations.dipole  
chemaxon.calculations.hydrogenize  
chemaxon.calculations.nmr  
chemaxon.calculations.nmr.io  
chemaxon.calculations.stereo  
chemaxon.checkers
Structure checkers can be used to filter drawing mistakes or special structural elements.
chemaxon.checkers.result
This package is used to identify problems found in molecules.
chemaxon.checkers.runner
This package supports the automatic running of structure checkers.
chemaxon.checkers.runner.configuration.reader
Extension package of the automatic runner functionality.
chemaxon.clustering
Provides classes for clustering.
chemaxon.clustering.adapter
Adapter to expose LibraryMCS clustering through the (com.chemaxon.clustering) API.
chemaxon.common.util  
chemaxon.core  
chemaxon.core.calculations.stereo  
chemaxon.core.calculations.valencecheck  
chemaxon.core.util  
chemaxon.descriptors
Classes for virtual screening using Molecular Descriptors.
chemaxon.descriptors.scalars  
chemaxon.fixers
Structure fixers can be used to fix problems identified by structure checker instances.
chemaxon.formats
Provides miscellaneous utility classes for converting between various molecule file formats, importing structures, and compressing Molfiles.
chemaxon.formats.documents.jchemexcel  
chemaxon.formats.documents.jchemoffice  
chemaxon.formats.recognizer
Provides classes to recognize files of various file formats.
chemaxon.jchem.db
Provides classes for database operations.
chemaxon.jchem.db.cache  
chemaxon.jchem.file  
chemaxon.jep
Chemical Terms Evaluator classes.
chemaxon.jep.context
Specific chemical terms evaluation contexts.
chemaxon.license
Classes related licenses, license handling, validating, GUI and documentation.
chemaxon.marvin
Contains utility classes for rendering molecules.
chemaxon.marvin.alignment
The 3D molecular alignment package that can be used to align two or more 3D molecules onto each other.
chemaxon.marvin.alignment.atrop
Utilities for AtropIsomerDetector.
chemaxon.marvin.beans
Provides bean classes for creating Marvin based user interface.
chemaxon.marvin.calculations
Provides specific plugin, plugin loader and table form output implementations.
chemaxon.marvin.common
Contains a class for handling user settings.
chemaxon.marvin.io
Provides classes for molecule import and export through data streams.
chemaxon.marvin.io.formats
Core package of any import/export module.
chemaxon.marvin.io.formats.mdl
Import and export modules for MDL Molfile, SDfile, RDfile, Rxnfile and (ChemAxon) compressed molfile.
chemaxon.marvin.io.formats.smiles  
chemaxon.marvin.io.formats.vectgraphics  
chemaxon.marvin.io.image  
chemaxon.marvin.io.image.exporter  
chemaxon.marvin.modules.datatransfer
Since Marvin 5.3 this package contains the clipboard handler infrastructure in Marvin.
chemaxon.marvin.paint
Defines display options constants.
chemaxon.marvin.paint.constants  
chemaxon.marvin.plugin
Contains the classes responsible for calculator plugin loading, parameter setting, running and displaying mechanism.
chemaxon.marvin.plugin.concurrent
Classes to achieve concurrent processing of calculator plugins.
chemaxon.marvin.plugin.gui
Calculator plugin common GUI classes.
chemaxon.marvin.services
Marvin Services provides API and support for accessing remote services from Marvin Sketch and other tools.
chemaxon.marvin.services.httpservice  
chemaxon.marvin.services.json  
chemaxon.marvin.services.localservice  
chemaxon.marvin.services.soap  
chemaxon.marvin.services.xmlrpcservice  
chemaxon.marvin.sketch
Contains the sketcher's core classes and various sketching modes.
chemaxon.marvin.sketch.swing.modules.documentstyle  
chemaxon.marvin.space
Contains the core classes of MarvinSpace including the graphic canvas and the basic visualizer classes.
chemaxon.marvin.space.monitor
Classes that represent measurement and changing of coordinates according to measurements in MarvinSpace.
chemaxon.marvin.util
Contains some utilities for example for molecule cleaning and Swing.
chemaxon.marvin.util.codeassist  
chemaxon.marvin.view
Control records in MarvinView.
chemaxon.marvin.view.swing
Swing support for MarvinView tables.
chemaxon.naming
Document to Structure and Name to Structure conversion.
chemaxon.naming.document.annotate  
chemaxon.pharmacophore
Classes for pharmacophore point perception, pharmacophore fingerprint generation and pharmacophore dissimilarity calculations.
chemaxon.reaction
Classes for reaction processing related tasks.
chemaxon.sss
Contains packages for structure search and screening.
chemaxon.sss.formula  
chemaxon.sss.screen
Classes for screeening.
chemaxon.sss.search
Provides structural search capabilities.
chemaxon.sss.search.options  
chemaxon.standardizer
Contains packages for structure standardization.
chemaxon.standardizer.actions
Contains basic standardizer actions.
chemaxon.standardizer.advancedactions
Contains advanced standardizer actions.
chemaxon.standardizer.concurrent
Contains classes for concurrent execution of standardization.
chemaxon.standardizer.configuration
Contains classes for handling configurations of standardizer.
chemaxon.standardizer.configuration.reader
Contains classes for handling configuration deserialization.
chemaxon.standardizer.runner
Contains classes for executing standardization based on a configuration.
chemaxon.struc
Provides classes for implementing and manipulating chemical structures.
Serialization of these classes is `standardized' in Marvin 5.3.
chemaxon.struc.graphics
Contains graphics MDocument elements.
chemaxon.struc.prop
Utility classes that represent molecular properties and convert molecular property Strings to values and vice versa.
chemaxon.struc.sgroup
S-group related classes and interfaces.
Serialization of the classes is `standardized' in Marvin 3.1.4.
chemaxon.util
Provides general utility classes.
chemaxon.util.concurrent
Provides utility classes for concurrent processing.
chemaxon.util.concurrent.marvin
Provides utility classes for concurrent processing in Marvin.
chemaxon.util.concurrent.processors
Provides utility classes for concurrent processing.
chemaxon.util.iterator
Provides iterator classes for molecules and their components.
com.chemaxon.apidiscovery
API Discovery framework.
com.chemaxon.apidiscovery.annotations
Annotations used by the API Discovery framework.
com.chemaxon.apidiscovery.interfaces
Interfaces introduced for the API Discovery framework.
com.chemaxon.apidiscovery.util
Various utilities.
com.chemaxon.calculations.common
Common components of Calculator APIs.
com.chemaxon.calculations.elemanal
API of the elemental analysis functionality.
com.chemaxon.calculations.io  
com.chemaxon.calculations.solubility  
com.chemaxon.calculations.stereoanal
API of the Stereo Analysis Plugin.
com.chemaxon.calculations.stereoanal.filters
Core filter classes.
com.chemaxon.calculations.stereoanal.filters.atrop
Atrop stereo filter implementations.
com.chemaxon.calculations.stereoanal.filters.axial
Axial stereo filter implementations.
com.chemaxon.calculations.stereoanal.filters.cistrans
Cis-trans stereo filter implementations.
com.chemaxon.calculations.stereoanal.filters.tetrahedral
Tetrahedral stereo filter implementations.
com.chemaxon.calculations.stereoanal.stereocenters
Stereocenter implementations of Stereo Analysis API.
com.chemaxon.calculations.stereoisomers  
com.chemaxon.calculations.util
Various utilities used in calculations, descriptors, clustering and overlap analysis.
com.chemaxon.clustering.common
Common components of clustering related APIs.
com.chemaxon.clustering.framework
Hierarchic structural framework based clustering.
com.chemaxon.clustering.singlelinkage
Single linkage clustering algorithm.
com.chemaxon.clustering.sphex
Sphere exclusion clustering algorithm.
com.chemaxon.clustering.util
Clustering related utilities.
com.chemaxon.clustering.wards
Ward's minimum variance implemented as a generic agglomerative hierarchical clustering algorithm.
com.chemaxon.common.annotations  
com.chemaxon.descriptors.alignment
3D flexible alignment based molecular shape similarity calculation.
com.chemaxon.descriptors.common
Unguarded descriptor handling.
com.chemaxon.descriptors.db
Interfaces for database import/export.
com.chemaxon.descriptors.fingerprints.cfp
API of the Chemaxon hashed fingerprint family molecular descriptors.
com.chemaxon.descriptors.fingerprints.ecfp
API of the ECFP fingerprint family molecular descriptors.
com.chemaxon.descriptors.fingerprints.maccs
ChemAxon implementation of the MACCS 166 bit fingerprints.
com.chemaxon.descriptors.fingerprints.pf2d
API of the 2D pharmacophore fingerprint family molecular descriptors.
com.chemaxon.descriptors.metrics
Common descriptor comparison metrics.
com.chemaxon.descriptors.vectors.binary
Generic binary vector descriptors.
com.chemaxon.descriptors.vectors.floats
Generic floating point vector descriptors.
com.chemaxon.mapper  
com.chemaxon.markush.composer  
com.chemaxon.markush.overlap  
com.chemaxon.overlap.io  
com.chemaxon.search
Tools for chemical search.
com.chemaxon.search.mcs
Contains classes for finding the maximum common substructure (MCS) of molecular structures.
com.chemaxon.search.mcs.buildup
Contains MCS algorithm implementation based on the "build up" method.
com.chemaxon.search.mcs.maxclique
Contains MCS algorithm implementation based on the "maximum clique" method.
com.chemaxon.search.mcs.upperbound
Contains classes for calculating upper bound estimations for maximum common substructure (MCS) search.
com.chemaxon.search.transformation  
com.chemaxon.search.transformation.transformers  
com.chemaxon.version  
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