Application Programming Interfaces

The Marvin and JChem functionality is provided through Java and .NET Application Programming Interfaces (API's) to allow web and application developers full low and high level control of program functionalities.

Although the JChem package includes Marvin, Marvin functionalities can be accessed directly through the Marvin API.

Marvin Applets

API classes:
chemaxon/marvin/applet/JMSketch
chemaxon/marvin/applet/JMView

Marvin Beans

Java API, .NET API
chemaxon.formats.*
chemaxon.struc.* (IUPAC Naming license may be required)
chemaxon.marvin.* and sub-packages, except for non-free plugins' packages

Marvin for JavaScript

JavaScript API

Calculator Plugins

Java API, .NET API
Common classes
chemaxon.marvin.plugin.CalculatorPlugin
chemaxon.marvin.plugin.CalculatorPluginDisplay
chemaxon.marvin.plugin.CalculatorPluginOutput
chemaxon.marvin.plugin.PluginFactory
chemaxon.marvin.plugin.ParameterPanelHandler
chemaxon.marvin.plugin.gui.OptionsPane
chemaxon.marvin.plugin.gui.ParameterPanel
chemaxon.marvin.plugin.gui.ParameterTab
chemaxon.calculations.ElementalAnalyser
chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
chemaxon.marvin.calculations.ElementalAnalyserPlugin
Protonation bundle
chemaxon.marvin.calculations.pKaPlugin
chemaxon.marvin.calculations.MajorMicrospeciesPlugin
chemaxon.marvin.calculations.IsoelectricPointPlugin
Partitioning bundle
chemaxon.marvin.calculations.logPPlugin
chemaxon.marvin.calculations.logDPlugin
Charge bundle
chemaxon.marvin.calculations.ChargePlugin
chemaxon.marvin.calculations.IonChargePlugin
chemaxon.marvin.calculations.PolarizabilityPlugin
chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Isomers bundle
chemaxon.marvin.calculations.TautomerizationPlugin
chemaxon.marvin.calculations.ResonancePlugin
chemaxon.marvin.calculations.StereoizomerPlugin
Conformation bundle
chemaxon.marvin.calculations.ConformerPlugin
chemaxon.marvin.calculations.MolecularDynamics
Geometry bundle
chemaxon.calculations.TopologyAnalyser
chemaxon.marvin.calculations.TopologyAnalyserPlugin
chemaxon.marvin.calculations.GeometryPlugin
chemaxon.marvin.calculations.MSAPlugin
chemaxon.marvin.calculations.TPSAPlugin
Huckel Analysis
chemaxon.marvin.calculations.HuckelAnalysisPlugin
Refractivity
chemaxon.marvin.calculations.RefractivityPlugin
Hydrogen Bond Donor-Acceptor
chemaxon.marvin.calculations.HDBAPlugin
IUPAC Naming
chemaxon.marvin.calculations.IUPACNamingPlugin
chemaxon.marvin.modules.nameexport.IUPACNamer
Markush Enumeration
chemaxon.marvin.calculations.EnumerationPlugin
Predictor
chemaxon.marvin.calculations.PredictorPlugin

JChem Base

Java API, .NET API
All API classes from Marvin Applets
All API classes from Marvin Beans
chemaxon.util.*
chemaxon.sss.* and sub-packages (excluding chemaxon.sss.search.MCES)
chemaxon.jchem.* and sub-packages
chemaxon.jep.* and sub-packages

MolSearch

Java API, .NET API
Same as for JChem Base.

JChem Cartridge

JChem Cartridge API

Instant JChem

Instant JChem API

JChem for Excel

JChem for Excel API

JChem Web Services

JChem Web Services API

Markush Search

Java API, .NET API
  • Same as JChem Base, the difference is in the input and usable features.

Standardizer

Java API, .NET API
chemaxon.reaction.Standardizer
chemaxon.reaction.ConcurrentStandardizerProcessor

Structure Checker

Java API, .NET API
Checkers
chemaxon.checkers.StructureChecker
chemaxon.checkers.* (Structure Checker implementations)
Checker result
chemaxon.checkers.result.ExternalStructureCheckerResult
chemaxon.checkers.result.StructureCheckerResult
chemaxon.checkers.result.AromaticityCheckerResult
chemaxon.checkers.result.DefaultStructureCheckerResult
chemaxon.checkers.result.ExplicitHydrogenResult
chemaxon.checkers.result.SgroupCheckerResult
Runners
chemaxon.checkers.runner.CheckerRunner
chemaxon.checkers.runner.AdvancedCheckerRunner
chemaxon.checkers.runner.BasicCheckerRunner
chemaxon.checkers.runner.CheckerRunnerImpl
chemaxon.checkers.runner.SketchCheckerRunner
Configuration readers
chemaxon.checkers.runner.configuration.reader.ConfigurationReader
chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader
Fixers
chemaxon.fixers.StructureFixer
chemaxon.fixers.Fixes
chemaxon.fixers.* (Structure Fixer implementations)

Screen

Java API, .NET API
Standard
chemaxon.descriptors.CDParameters
chemaxon.descriptors.CFGenerator
chemaxon.descriptors.CFParameters
chemaxon.descriptors.ChemicalFingerprint
chemaxon.descriptors.CustomDescriptor
chemaxon.descriptors.GenerateMD
chemaxon.descriptors.MDArrayReader
chemaxon.descriptors.MDHypothesisCreator
chemaxon.descriptors.MDHypothesisGenerator
chemaxon.descriptors.MDParameters
chemaxon.descriptors.MDReader
chemaxon.descriptors.MDSet
chemaxon.descriptors.MDSetParameters
chemaxon.descriptors.MDSimilarity
chemaxon.descriptors.MDSimilarityResultWriter
chemaxon.descriptors.MDWriter
chemaxon.descriptors.Metrics
chemaxon.descriptors.MolecularDescriptorGenerator
chemaxon.descriptors.MolecularDescriptor
chemaxon.descriptors.ScalarDescriptor
chemaxon.descriptors.SDParameters
chemaxon.descriptors.scalars.* (additional plugin licenses may be required)
chemaxon.descriptors.BCUTGenerator (additional plugin licenses may be required)
chemaxon.descriptors.BCUT
chemaxon.descriptors.BCUTParameters
chemaxon.pharmacophore.*
Professional
All API classes from Screen Standard
chemaxon.descriptors.*

Reactor

Java API, .NET API
chemaxon.reaction.Reactor
chemaxon.reaction.ConcurrentReactorProcessor
chemaxon.reaction.Reaction - deprecated

Metabolizer Preview

API classes:
chemaxon.metabolizer.*

Fragmenter

Java API, .NET API
chemaxon.reaction.Fragmenter
chemaxon.reaction.ExhaustiveFragmenter
chemaxon.reaction.CutBondReviser
chemaxon.reaction.Recap
chemaxon.sss.search.RGroupDecomposition

JKlustor

Java API, .NET API
Basic
chemaxon.clustering.*
chemaxon.descriptors.CFGenerator
chemaxon.descriptors.CFParameters
chemaxon.descriptors.ChemicalFingerprint
chemaxon.descriptors.GenerateMD
chemaxon.descriptors.MDFileReader
chemaxon.descriptors.MDFileWriter
chemaxon.descriptors.MDParameters
chemaxon.descriptors.MDReader
chemaxon.descriptors.MDWriter
chemaxon.descriptors.MolecularDescriptor
Standard
All API classes from JKlustor Basic
chemaxon.pharmacophore.*
chemaxon.clustering.LibraryMCS
chemaxon.descriptors.*
chemaxon.sss.search.RGroupDecomposition

Compound Registration

Java API
Basic
com.chemaxon.registry.RegistryService

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