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


API classes:
chemaxon.metabolism.*

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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