JChem Base API documentation (c) 1998-2025 Chemaxon Ltd.
Packages
Package
Description
Contains chemical computation modules.
BBB score calculator.
CNS MPO score calculator.
Structure checkers can be used to filter drawing mistakes or special structural elements.
This package is used to identify problems found in molecules.
This package supports the automatic running of structure checkers.
Extension package of the automatic runner functionality.
Provides classes for clustering.
Adapter to expose
LibraryMcs clustering through the (com.chemaxon.clustering) API.Provides general utility classes.
Classes for virtual screening using Molecular Descriptors.
Structure fixers can be used to fix problems identified by structure checker instances.
Provides miscellaneous utility classes for converting between various
molecule file formats, importing structures, and compressing Molfiles.
Provides classes to recognize files of various file formats.
Provides classes for database operations.
Chemical Terms Evaluator classes.
Specific chemical terms evaluation contexts.
Classes related licenses, license handling, validating, GUI and documentation.
Contains utility classes for rendering molecules.
The 3D molecular alignment package that can be used to align two or more 3D molecules onto each other.
Utilities for atropisomer detection.
Provides bean classes for creating Marvin based user interface.
Provides specific plugin, plugin loader and table form output implementations.
Contains a class for handling user settings.
Provides classes for molecule import and export through data streams.
Core package of any import/export module.
Import and export modules for MDL Molfile, SDfile, RDfile, Rxnfile and (Chemaxon) compressed molfile.
Since Marvin 5.3 this package contains the clipboard handler
infrastructure in Marvin.
Contains the classes responsible for calculator plugin loading, parameter setting,
running and displaying mechanism.
Classes to achieve concurrent processing of calculator plugins.
Calculator plugin common GUI classes.
Marvin Services provides API and support for accessing remote
services from Marvin Sketch and other tools.
Contains the sketcher's core classes and various sketching modes.
Contains some utilities for example for molecule cleaning and Swing.
Control records in MarvinView.
Swing support for MarvinView tables.
Name to Structure conversion.
Document to Structure (D2S) conversion.
Classes for pharmacophore point perception, pharmacophore fingerprint generation
and pharmacophore dissimilarity calculations.
Classes for reaction processing related tasks.
Contains packages for structure search and screening.
Classes for screeening.
Provides structural search capabilities.
Contains packages for structure standardization.
Contains basic standardizer actions.
Contains advanced standardizer actions.
Contains classes for concurrent execution of standardization.
Contains classes for handling configurations of standardizer.
Contains classes for handling configuration deserialization.
Contains classes for executing standardization based on a configuration.
Provides classes for implementing and manipulating chemical structures.
Serialization of these classes is `standardized' in Marvin 5.3.
Serialization of these classes is `standardized' in Marvin 5.3.
Contains graphics MDocument elements.
Utility classes that represent molecular properties and convert molecular property Strings to values and vice versa.
S-group related classes and interfaces.
Serialization of the classes is `standardized' in Marvin 3.1.4.
Serialization of the classes is `standardized' in Marvin 3.1.4.
Provides iterator classes for molecules and their components.
Common components of Calculator APIs.
API of the elemental analysis functionality.
API of the Stereo Analysis Plugin.
Core filter classes.
Atrop stereo filter implementations.
Axial stereo filter implementations.
Cis-trans stereo filter implementations.
Tetrahedral stereo filter implementations.
Stereocenter implementations of Stereo Analysis API.
Common components of clustering related APIs.
Hierarchic structural framework based clustering.
Single linkage clustering algorithm.
Sphere exclusion clustering algorithm.
Clustering related utilities.
Ward's minimum variance implemented as a generic agglomerative hierarchical clustering algorithm.
Provides annotations for Chemaxon classes.
3D flexible alignment based molecular shape similarity calculation.
Unguarded descriptor handling.
Interfaces for database import/export.
API of the Chemaxon hashed fingerprint family molecular descriptors.
API of the ECFP fingerprint family molecular descriptors.
ChemAxon implementation of the MACCS 166 bit fingerprints.
API of the 2D pharmacophore fingerprint family molecular descriptors.
Common descriptor comparison metrics.
Generic binary vector descriptors.
Generic floating point vector descriptors.
Tools for chemical search.
Contains classes for finding the maximum common substructure (MCS) of molecular structures.
Contains MCS algorithm implementation based on the "build up" method.
Contains MCS algorithm implementation based on the "maximum clique" method.
Contains classes for calculating upper bound estimations for maximum common substructure (MCS) search.
This package contains an
Iterator wrapper that can be used to perform calculations simultaneously
on multiple elements provided by the wrapped iterator, and returns the calculation results while preserving the
original order of elements.