All Classes and Interfaces

Class
Description
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
A descendant of AbstractStructureChecker detecting abbreviations ("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in abbreviated group form.
Detects chiral molecules with no chiral flag defined
Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated, for removal: This API element is subject to removal in a future version.
Type of absolute stereo action
Detects molecules in which all asymmetric centers have absolute stereo configuration
Deprecated, for removal: This API element is subject to removal in a future version.
Abstract record reader class.
Abstract class for standardizer actions modifying S-groups.
 
 
Helper class without the requested getDescriptorGenerator method.
Abstract implementation of the StandardizerAction.
Abstract class for Filter interface.
Abstract base class of all functions checking and repairing chemical structures.
This class is the default abstract implementation of StructureFixer interface
An implementation of ConfigurationReader for parsing action strings
Absent chiral flag fixer.
Hydrogenization standardizer action
CheckerRunner implementation with advanced fixing capabilities.
StructureFixer selection is based on provided fixer class if available, or falls back to StructureCheckerResult based selection.
Supports multiple iterations of checking and fixing for the best fixing efforts.
A descendant of AbstractStructureChecker detecting atoms with alias labels.
Alias to Atom standardizer action.
Alias to Group standardizer action
3D Alignment aligns two or more 3D molecules onto each other.
Settings for the representation of a molecular shape.
 
 
Creates an AlignmentMolecule form a Molecule based on the settings.
 
Plugin layer for the AlignmentAPI
 
 
 
 
Conformational flexibility treatment during the alignment for a pair of a molecule.
 
 
Overlays two molecules using the user defined atom pairs
Example:
Aligns pairs of molecules by translating and rotating one of them and leave the one called the reference molecule intact.
Checked exception to indicate that a tool has been passed an illegal argument, typically used for CLI.
A descendant of DefaultStructureCheckerResult for identifying aromaticity problems, thus errorType property is StructureCheckerErrorType.AROMATICITY
A descendant of AbstractStructureChecker detecting aromatization problems.
Enum for aromatization methods used during the search process.
Aromatization standardizer action
Type of aromatization
Aromatizer transformer.
MDocSource implementation for an array of documents or molecules.
Callback interface for asynchronous service calls
 
Descendants of the abstract AtomChecker class check every atom for a specific error or property.
Expression evaluation context containing an input molecule and an input atom.
The identifier of an atom in the input of the reaction.
Atom index mapper.
The atom labels storage class.
A descendant of AtomChecker detecting atom maps.
Class for storing atom property enumerations.
Enumeration of the supported radicals.
A descendant of AtomChecker detecting atoms having an query property set.
A descendant of DefaultStructureCheckerResult for identifying atom query properties, thus errorType property is StructureCheckerErrorType.ATOM_QUERY_PROPERTY by default.
Selection which contains atom indexes.
A descendant of AtomChecker checking different atom types (represented by atom's symbol) in the molecule.
Settings for shape associated atom typing.
A descendant of AtomChecker detecting atoms with atom value.
Filter for atrop stereo centers.
A descendant of AbstractStructureChecker detecting atropisomers in the molecule.
Molecular mechanics based atropisomer detection.
 
Atrop stereo center implementation.
Descriptor representing atrop stereo information, the rotation of two aromatic rings connected by a single bond (axis), and at least 3 of the ligands in the ring connected to the axis has a non-ring ligand. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.ODD means that if we watch the molecule in the direction of the axis, and the ligand with the maximum index from the ligand connected to the axis is in the back, then from the higher indexed of the two ligands in the front the higher indexed in the back is clockwise. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.EVEN means that if we watch the molecule in the direction of the axis, and the ligand with the maximum index from the ligand connected to the axis is in the back, then from the higher indexed of the two ligands in the front the higher indexed in the back is counter-clockwise. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.UNKNOWN means that it can not be decided if it is clockwise or counter-clockwise, but there is no wiggly bond - like a 2D structure without wedge information.. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.WIGGLY means that there is a wiggly bond on either ligand in the ring connected to the axis, or the axis is wiggly.
Data object which contains a name and a data (String).
A descendant of AbstractStructureChecker detecting attached data in the molecule.
Attachment Point class for the Superatom S-group.
AutoMapper is a tool that performs automated chemical reaction mapping.
Option object for set common options when mapping called by static way.
Filter for axial stereo centers.
Axial stereo center implementation.
 
 
This is the default implementation of StandardizerActionRunner interface.
BBB score calculator.
Simple DTO that contains the predicted value, its BBB score and the BBB score multiplied with the corresponding BBB multiplier.
Base phys-chem property calculators and its score functions for BBB score calculation.
Implements BCUT descriptors.
Descriptor generator class for the BCUT descriptor.
Manages parameters for the BCUT descriptor class.
Convenience utilities for using Bemis-Murcko clustering.
Indicates that a public API entity (public class, method, or field) is subject to incompatible changes, or even removal, in a future release.
This class is the atom index based representation which can be assigned to 'endo', 'exo', 'syn', 'anti' ligands of bicyclo[x.y.z]alkanes in case of 0 dimension molecules.
Simple metrics suitable for finite length binary vectors.
Basic functionality for finite binary vector based calculations.
Simple consistency check utility.
BinaryVectorDescriptor is a Descriptor which holds a fixed length binary fingerprint.
Represents available metrics for binary vector based descriptors.
Utility methods related to bit string descriptors.
Order of components in packed representations.
Bond Angle Checker detects wrong bond angles in 2D structures.
Bond angle checker result.
Bond Angle Fixer fixes wrong bond angles in 2D structures.
Descentants of the abstract BondChecker class detect bond related problems.
Encapsulates bond info.
Bond Length Checker detects bonds with wrong length in 2D structures.
Bond angle checker result.
Bond Length Fixer fixes bonds with wrong length in 2D structures.
Provides easy lookup of bonds between pair of atoms in a molecule graph.
Checker detects bonds with reacting center bond marks.
General chemical bond types.
Detects brackets (S-groups) in molecules.
Implements a heuristic MCS algorithm using the build-up method of Takeshi Kawabata.
Generator for generic binary vector descriptors.
Parameters for generic binary vector descriptor.
Builder for BvParameters.
Interface representing BvGenerator implementation constructor
Fingerprint textual representation.
Utility class for cache registration.
An error that might occur when a calculator is initialized.
Instances of this interface are used by calculators to check if they can process an input molecule.
Common base class for calculator plugins.
 
Provides plugin cached results.
Common base class for calculator plugin displays.
Class providing plugin output in table form.
Base class for types that implement a functionality related to a specific CalculatorPlugin.
Interface providing plugin result access.
List of optional tags that can be reported by a TaggedCalculator.
Manages parameters the CustomDescriptor class.
The CFGenerator class generates topological fingerprints of molecular graphs.
Folded fixed length bit string representation of the CFP descriptor.
Manages fingerprint parameters.
Comparator for Cfp descriptor representation.
Calculates CFP (fixed length folded binary vector representation) descriptors.
CFP parameters class.
Builder class for the immutable parameter object.
Interface representing CFP generator constructor.
MDTable reader for CFP.
Factory class.
The change set of the standardization procedure.
Plugin class for partial charge calculation.
Factory for structure checkers and structure fixers.
Builder class for CheckerFixerFactory.
Descriptor of a checker class
Descriptor of a class
Descriptor of a fixer class
This annotation is responsible for adding GUI based meta data for StructureChecker implementations
The descendant of CheckerRunner interface has to provide the functionality to run StructureChecker instances automatically
on the given molecule and fix the problems with the associated StructureFixer instances.

Example:

CheckerRunner can be used directly with the checkAndWait method.
This enum defines the constants which represent the severity of the StructureChecker implementations
 
Interface of expression evaluation contexts.
Repeatable annotation used on ChemContext implementations to declare the context functions supported by the ChemContext.callContextFunction(String, List) method.
Container for the repeatable ChemContext.ProvidesFunction annotation.
The ChemicalFingerprint class implements topological fingerprints as a type of MolecularDescriptors.
Expression parser and evaluator for chemical expressions.
Implementation of AbstractStructureChecker detecting "absolute stereo flag" on molecule.
A descendant of AbstractStructureChecker detecting achiral molecules having a chiral flag set (absolute stereo flag).
Stereo calculator with the Cahn, Ingold, Prelog priority rules.
Cahn-Ingold-Prelog (CIP) stereodescriptor interface.
 
 
 
 
 
 
 
 
 
 
Detection of Cahn-Ingold-Prelog (CIP) stereo descriptors: tetrahedral, axial, cis/trans and atrop stereo features.
A descendant of AbstractStructureChecker detecting circular R-group references.
Filter for CIS double bonds.
Filter for cis-trans stereo centers.
Cis-trans stereo center implementation.
 
Clean molecule graph in 2D standardizer action
Type of clean action (partial, full, template based or convert 3D to 2D)
Clean molecule graph in 3D standardizer action
Class to clean MoleculeGraphs, Molecules, SelectionMolecules and Sgroups.
A descendant of AbstractStructureFixer which cleans the molecule in 2d
Utility methods for cleaning.
Clear isotopes standardizer action
Clear stereo standardizer action
Clears wedges.
An auto-closeable wrapper for the Iterator class, so you should use this class with try-with-resources statements!
Cluster represents a group of structures.
 
CNS MPO score calculator.
Simple DTO that contains the predicted value and its CNS MPO score.
Base phys-chem property calculators and its score functions for CNS MPO calculation.
A final class which provides a static access to a color distant color creator class.
Common superclass for JKlustor tools.
Compares two sets of objects (like compound libraries) using diversity and dissimilarity calculations.
Result of a descriptor comparison.
Descendants of the abstract ComponentChecker class implement detect problems related to disconnected components (fragments).
Executes a chemical reaction: creates products from reactants with reaction center data.
Performs standardization of molecules in concurrent mode.
Molecule transformer.
This interface is provided for classes which can read the configuration of CheckerRunner.
Utility to manage standardizer configuration
Plugin class for conformer calculation.
A JavaBean for connecting to relational databases using JDBC.
 
Immutable table of constants used in a Chemical Terms evaluator.
A builder for a ConstantTable.
A descendant of AbstractStructureFixer which contracts the abbreviated groups in the molecule
Standardizer action contracting s-groups of the target molecule
A descendant of AbstractStructureFixer which converts the aliases to contracted abbreviated groups in the molecule
This class contains convert relevant constants
Convert double bonds standardizer action
Type of conversion
Convert Pi-Metal coordinate bond to coordinate bond action.
A descendant of AbstractStructureFixer which converts the pseudo informations to contracted abbreviated groups in the molecule
A descendant of AbstractStructureFixer which converts the aliases to atom with atom number contained in the alias information
A descendant of AbstractStructureFixer which converts pseudo atoms to carbon atoms
A descendant of AbstractStructureFixer which sets wiggly bond to crossed double bond
A descendant of AbstractStructureFixer which converts the isotopes to non isotope atoms
Convert to enhanced stereo standardizer action
A descendant of AbstractStructureFixer which converts the incorrectly drawn (connected to bond, no charge) covalent counter ion representation into ionic form.
Converts non-stereo double bonds with invalid stereo mark (crossed, wiggly) to plain double bonds.
A descendant of AbstractStructureFixer which converts the bond to single bond.
A descendant of AbstractStructureFixer which converts crossed double bond to wiggly
Detects errors of multicenter coordination systems.
Deprecated, for removal: This API element is subject to removal in a future version.
since 5.2.1 the whole copy-paste engine was refactored.
A descendant of AbstractStructureChecker detecting covalently bonded counterions (alkaline alcoholates, carboxylates an thio analogs).
Create Group standardizer action
A descendant of BondChecker for the detection of unspecified double bonds represented by crossed bond type.
Deprecated, for removal: This API element is subject to removal in a future version.
3D transformation matrix.
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
The CustomDescriptor class implements a generic molecular descriptor class which supports third party or use defined descriptors.
Base interface for custom Chemical Terms functions.
Database constants are defined here.
Methods for reading and writing the JChemProperties table that contains information about the database and the structure tables.
Error occurred during structural search in database.
Tools that can be applied in the development of applications accessing databases.
A list of Strings to be excluded by AttachedDataChecker.
Data Sgroup.
A descendant of DefaultStructureCheckerResult for identifying Sgroup problems.
Dearomatization standardizer action
A descendant of AbstractStructureFixer which converts the aromatic rings in the molecule into Kekule representation.
Class storing RGroupDecomposition results.
This descendant of DefaultStructureCheckerResult also implements the ExternalStructureCheckerResult interface thus providing a default implementation base class for external structure checkers' results.
Work unit performing plugin calculation and returning the cached results.
Default solubility categories.
This class is the default implementation of StructureCheckerResult
Descriptor represents a molecular descriptor calculated by a specific DescriptorGenerator instance for a specific structure.
Common functionality for descriptor comparison.
Simple class for generating molecular descriptors (fingerprints).
DescriptorGenerator implements molecule to descriptor calculation functionality.
Descriptor calculator parameters base interface.
DescriptorSerializer represents descriptor IO.
Rotates a dihedral in a 3D molecule
Callback to track dihedral scan steps.
Results of a dihedral scan.
One step in a dihedral scan.
Calculates the components of the dipole vector.
Builder class for dipole moment calculation.
Dipole moment calculation result.
Dipole moment units.
Disconnect metal atoms standardizer action
DissimilarityInput represents an input set for similarity based clustering algorithm.
A descendant of AbstractStructureFixer which converts incorrectly drawn metallocenes into multicenter based coordinate bond representation.
Generate a chemically annotated HTML view of a document.
Document type enum for DocumentAnnotator.
The interface for a DocumentAnnotator progress event listener.
Represents the state of progress during a document annotation process.
Represents various options regarding how a document should be annotated, both in terms of input and output.
A builder for DocumentAnnotatorOptions, allowing for options to be built using a fluent interface.
A list of supported image formats for popups in the annotated document.
API for DocumentStyle management.
A convenience class for dealing with String-based documents, such as TXT, HTML, or XML files.
Point in three dimensional space.
Descriptor (serialized data) for the Distance range assisted shape alignment comparison.
Metrics for distance range assisted shape comparison.
ServiceArguments implementing this interface should support automatic evaluation of arguments before service call based on context.
NOTE: subclasses MUST HAVE default constructor to use from Marvin Sketch
Folded fixed length bit string representation of the ECFP descriptor family.
The ECFP class implements Extended-Connectivity Fingerprints (ECFPs) as a type of MolecularDescriptors.
Predefined atom typing settings for ECFP fingerprint family.
Comparator for Ecfp descriptor representation.
Class for representing the substructural features of ECFP fingerprints.
Class for retrieving the substructural features of ECFP fingerprints.
Calculates ECFP (fixed length folded binary vector representation) descriptors.
The ECFPGenerator class generates ECFP fingerprints of molecular graphs.
ECFP parameters class.
Manages ECFP fingerprint parameters.
Builder class for the immutable parameter object.
Interface representing ECFP generator constructor.
MDTable reader for ECFP/FCFP.
Factory class.
Calculates molecular formula, mass, MS mass and composition.
Calculates molecular formula, mass, MS mass and composition.
Represents the different result types of the elemental analyser plugin.
Calculates molecular formula, mass, MS mass and composition.
A descendant of AbstractStructureChecker detecting structures having no atoms.
File encoding information.
Please note that this class is marked with @Beta annotation, so it can be subject of incompatible changes or removal in later releases.
Enhanced stereo descriptor class.
An abstract ancestor of JavaBeans that enable exception handling in different environments.
Error processing interface.
Error reporting class.
Evaluates Chemical Terms expressions.
Expandable interface for S-groups.
Expand stoichiometry standardizer action
A descendant of AbstractStructureFixer which expands all abbreviated groups in the molecule
Standardizer action expanding s-groups of the target molecule
A descendant of AtomChecker detecting explicit hydrogens.
Deprecated, for removal: This API element is subject to removal in a future version.
A descendant of DefaultStructureCheckerResult for identifying explicit hydrogen problems, thus errorType property is StructureCheckerErrorType.EXPLICIT_H by default.
A descendant of AtomChecker detecting lone pair type atoms.
This class is a tool for exporting molecules from database tables into an OutputStream object.
ExternalStructureChecker class provides a super class for externally implemented structure checkers.
This interface is an extension of StructureCheckerResult that supports external StructureChecker development.
Enumeration of possible E/Z stereo values.
A descendant of AbstractStructureChecker detecting double bonds, that can be cis or trans.
This class implements a simple upper bound calculator for the MCS problem.
 
Fingerprint generator used in Chemical Terms match functions.
This annotation is responsible for adding UI based meta data for StructureFixer implementations
Comparator of structure fixer for priority Default fixer and order of fixers is defined this way.
This annotation is used to annotate the StructureFixer implementations which StructureCheckerErrorType can be fixed by the current fixer
This annotation is used to annotate the StructureFixer implementations which error codes (identified by a unqie String) can be fixed by the current fixer
fix mode options
 
Flips wedge bonds.
Float vector based calculations.
Various utility methods related to float vector comparation.
FloatVectorDescriptor is a Descriptor which holds a float vector fingerprint.
Simple metrics for float vectors.
Molecular formula generation settings.
Chemical formula based search class.
Results of a framework based clustering.
Generator for generic binary vector descriptors.
Parameters for generic float vector descriptor.
Builder for FvParameters.
Representation of the vector coordinates.
Optimization for sparse vectors.
Abstract class to handle common export options.
 
 
 
GenerateMD provides a high level Application Program Interface (API) with comprehensive functionality for the generation of various Molecular Descriptors.
Plugin class for geometric properties calculations.
Pattern of a group.
Represents guarded entities.
Guarded checking utility.
Create new guard object.
Implements hydrogen bond acceptor atom count as a scalar descriptor.
Option type describing the error handling behaviour.
Filter stereo centers which contains attached data.
Hash code generator for molecules.
Plugin class for H bond acceptor/donor calculation.
Manages parameters for the HDon and HAcc scalar descriptor classes.
Implements hidrogen bond donor atom count as a scalar descriptor.
Implements HeavyAtomCount (number of non-hydrogen atoms) as a scalar descriptor.
hERG activity predictor.
The possible values of hERG class prediction.
hERG class predictor.
Represents a group (cluster) of structures, possibly divided into further non overlapping clusters.
A grouping of structures into disjunct hierarchical groups.
Level interpretation.
Class for specifying coloring and alignment options.
Class for displaying hit results with hit coloring, alignment, partial clean, etc.
Class providing some utility tools for displaying hit results with hit coloring, alignment, partial clean, etc.
Calculates hydrophilic-lipophilic balance (HLB) of a molecule.
Builder class for HlbPlugin.
Option type describing the scope of homology matching.
Deprecated, for removal: This API element is subject to removal in a future version.
Will be removed, no replacement.
HTTP Request based ServiceDescriptor implementation for HTTP POST/GET based services
ServiceHandler implementation for HTTP Services
Plugin class for Huckel Analysis calculation.
Hybridization state constants.
Addition and removal of explicit hydrogens or lone pairs.
Assign levels to IDBasedHierarchicClustering.
An ID based cluster level assigner builder.
Builder for ID based non-hierarchic clustering.
Allowing fluent API calls to IDBasedHierarchicClusterBuilder.
A Hierarchic cluster over integers, preferably IDs; having associated integral ClusterID.
Builder for integer ID based hierarchic cluster building.
A Hierarchic clustering over integers, preferably IDs.
A SingleLevelClustering of clusters containing Integer IDs.
Extends ImageExportBaseUtil with additional methods.
Tool for importing molecules to database tables from a File or InputStream object.
Common interface for ImportOptions classes to use in ServiceLoader.
Incorrect Tetrahedral Stereo Checker detects stereo wedge configurations around chiral atoms which are not possible.
Maps int values of a range [0..size-1] to other int values.
An extremal checker implementation indicating error in the configuration imported from XML or action string
 
Implementation of StandardizerAction representing an invalid instance of a standardizer action.
Plugin class for charge calculation on ionized microspecies.
Plugin class for isoelectric point and pH - charge distribution calculation.
IsotopeChecker detects isotopes (non-elemental atoms).
Deprecated, for removal: This API element is subject to removal in a future version.
The IteratorFactory class provides implementations of Iterator to ease the handling of atoms and bonds used in Molecule objects and its descendants.
IUPAC name generator plugin.
Performs variable-length Jarvis-Patrick clustering based on binary fingerprints (bits strings) and/or other data stored in a database table or a file.
JavaBean for structure searching in structure tables of relational databases.
Class for presenting the available dissimilarity metrics for similarity search.
Class to encapsulate search parameters used by JChemSearch.
Provides version information of JChem products.
Exception thrown during the compilation or evaluation of Chemical Terms exceptions.
Service descriptor of JSON type requests.
request method
Service handler for JSON type requests.
Filter for known atrop stereo centers.
Filter for known axial centers.
Filter for known (CIS or TRANS) double bonds.
Filter for known, resolved tetrahedral centers.
Agglomerative hierarchical clustering implementation for Lance-Williams algorithm family.
Instances represent a cluster distance update for agglomerative clusterings.
Singleton instances of various cluster merge operations.
Average linkage clustering, also known as UPGMA.
Complete linkage clustering, also known as farthest neighbor clustering.
Single linkage clustering also known as nearest neighbor clustering.
Ward's minimum variance clustering.
Manages parameters for the LogD scalar descriptor class.
Deprecated, for removal: This API element is subject to removal in a future version.
This class has been renamed and moved to a new package, import and use it from its new location: LegacyLibraryMcsAdapter.
API adapter to use LibraryMcs clustering with the new clustering API.
Parameters for LibraryMcs clustering implementation.
Assigns levels for clusters and leaves.
The LibraryMCS class computes the maximum common substructure (MCS) of a set of compounds.
Deprecated, for removal: This API element is subject to removal in a future version.
This class has been renamed and moved to a new package, import and use it from its new location: LibraryMcs.
 
 
Service Descriptor for java based local services.
Implements logD value as a scalar descriptor.
Plugin class for logD calculation.
Implements LogP value as a scalar descriptor.
logP calculation method.
Plugin class for logP calculation.
Interface to define a compatible descriptor framework for the MACCS fingerprint
Interface to define a compatible comparator for the MACCS fingerprint
Interface to define the MACCS fingerprint generator
Class for MACSS fingerprint parameters.
Build parameters for MACCS fingerprint descriptor generation.
Interface representing Maccs generator constructor.
Comman base class for Marvin actions.
Common base class for all plugins with possible major microspecies input.
Plugin class that calculates the major microspecies on a given pH.
 
Map standardizer action
A descendant of AbstractStructureFixer which maps the atoms of the molecule incrementally
Provides support for mapping parts of <T> instances by finding the matching parts and mark them with the same identifier.
Available mapping styles by Mapper
Map reaction standardizer action
A descendant of AbstractStructureFixer which maps the reaction with AutoMapper.
Option type describing the way aromaticity is handled in Markush structures.
Plugin class for enumerating Markush molecules.
Deprecated, for removal: This API element is subject to removal in a future version.
Generates RgMolecule output that covers the specified targets with the specified scaffold.
Ancestor of the Marvin Beans.
Ancestor of Marvin's BeanInfo classes that are needed by GUI builders.
Abstract Adapter implementation of the MTransferable interface used by Marvin.
Implements Mass (total mass of molecule) value as a scalar descriptor.
Atom assigner to connect two atoms.
Class to encapsulate Match count option parameters used by JChemSearch.
Point fixed to the location of one or more atoms.
Implements a heuristic MCS algorithm based on maximum clique detection.
Abstract base class of the algorithms for finding the maximum common substructure (MCS) of two molecules.
Max search frequency quota exceeded.
String property.
Bracket object.
Wrapper for the EasyChart module.
Molecule graph object.
Collection of properties.
Align molecules using the maximum common substructure (MCS) of the given molecules.
Usage examples:
Factory class for ConformationAlignment.
Result class for MCS alignment calculation.
Interface for custom matching of atoms and bonds for MaxCommonSubstructure search.
Factory interface for creating McsCustomMatcher objects.
Options class for MaxCommonSubstructure (MCS) search.
Builder class for creating immutable instances of the enclosing McsSearchOptions class.
Class for representing the result of a MaxCommonSubstructure (MCS) search.
Reads MolecularDescriptors from an array.
Class for reading MolecularDescriptors from a database.
Class for inserting Molecular Descriptors into database tables.
Reads MDSet objects from a text file.
Writes chemical descriptor sets (MDSet)s into text files.
Base class for all kinds of MolecularDescriptor generators.
Exception definition for the MolecularDescriptor.generate() interface.
Retrieves statistical information from a test screen on a set of molecules.
Generic definitions for molecular descriptor hypotheses.
Hypothesis generator interface.
Molfile compression.
Optimization of metric parameters for dissimilarity based screening.
Marvin document source.
Sparse dynamic document storage and reader.
Document production listener.
Marvin document.
Provides informations for Structure Checker higlight
Double array property.
Double floating point property.
MolecularDescriptor parameter settings.
MDParametersException reports all kinds of parametrization related failures.
Base class definitions for MDSet input streams.
Exception definition for all MDReader classes.
Factory class for MDTableReader.
MDset combines several MolecularDescriptors into one entity.
Parameters settings for MDSet-s.
Performs similarity comparisons between MDSets (see MDSet (for example set of chemical fingerprints and/or pharmacophore fingerprints).
Base class for prointing results produced by MDSimilarity.
Class for handling Molecular Descriptor tables.
Deserialize fingerprint from MDTable (JChem).
Base class definitions for MDSet output streams.
Exception definition for the MDWriter class.
Electron flow arrow.
Representing the movement of one or two electrons in a reaction as a curved arrow.
Electron flow can start from any atom or bond, but not from any atom pairs that has no connection bond.
The logic of the electron flows: If the source is an Atom, the sink can be: any Atom Bond connected to this Atom an atom pair from this atom and any other atom (incipient bond) If the source is a Bond, the sink can be: one of the Atoms on the end of this Bond a Bond connected to this Bond (has common ending Atom) an atom pair from one of the Atoms on the end of this Bond and any other atom (incipient bond) If only the sink/source is in an sgroup, the sink/source must be the attachment point.
Electron flow arrow base point.
 
 
Ellipse object.
Mesomerize standardizer action
 
MetalloceneErrorChecker detects metallocenes represented in ionic or covalently bonded formats, that are not coordinate multicenters.
A descendant of AbstractStructureFixer which converts a single incorrectly drawn metallocene into multicenter based coordinate bond representation.
Represents available metrics.
Metric Metadata contains info about a specific metric.
The Metrics class implements dissimilarity metrics for MolecularDescriptors.
 
Abstract class for extracting fields (properties) from input and storing them.
File format descriptor class.
File format related utility functions.
Font wrapper class that does not require an X server.
Font property to store in PropertyContainer
Linked hash map of properties.
3D coordinates array property.
Calculates the minimum or maximum intermolecular Cartesian distance between atoms by rotating flexible bonds.
Integer array property.
Integer property.
MissingAtomMapChecker detects unmapped atoms.
A descendant of AbstractStructureChecker detecting missing R-group definition errors.
Property list property.
Middle point in a line.
Fixed middle point that can be a point of a polyline.
Molecule animation.
Molecule property.
Molecule string property.
3D Molecular alignment that uses the maximum common substructure to align a pair of structures.
Input property settings for MMPAlignment.
Results of the MMPAlignment process.
Name Text box object to display IUPAC name.
Paintable object.
Property that stores any object.
Tool for aligning a target molecule to a pattern molecule.
Atom object and the properties of the elements.
Chemical bond.
Interface for comparing atoms, bonds, etc.
Deprecated, for removal: This API element is subject to removal in a future version.
Will be removed soon.
Expression evaluation context containing a single molecule.
Converts between molecule file formats.
MolConverter builder.
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 5.2.3, use MolConverter.Builder instead.
Generic definition of molecular descriptors.
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
Molecular Dynamics plugin.
Static utility methods related to molecular formula calculations.
Deprecated, for removal: This API element is subject to removal in a future version.
Molecule class.
MoleculeChargeChecker detects molecules where the sum of the formal atom charges is not zero.
A graph consisting of MolAtom nodes and MolBond edges.
Deprecated, for removal: This API element is subject to removal in a future version.
Molecule importer.
Interface for molecule importer classes.
Molecule iterator.
Molecule iterator factory.
Interface for molecule object for which valence calculations can be performed.
Exports MDL Molfile, SDfile, RGfile, RDfile, Rxnfile and (Chemaxon) compressed molfile.
Molecule exporter class.
Molecule export exception.
Abstract base class of molecule export modules.
Factory interface for MolExportModules.
MDL molfile related utility methods.
Molecule filter.
Something's wrong with a molecule file format.
Class for handling molecules for systems based on ChemAxon's programming interface.
Imports MDL Molfile, SDfile, RGfile, RDfile, Rxnfile and (Chemaxon) compressed molfile.
Molecule file importer.
Base class of Molecule import modules.
 
Factory interface for MolImportModules.
Input producer wrapping a MolImporter object.
Molecule input stream that has the ability to determine the input file format.
Molecule renderer that can draw a molecule to a graphics context using various display settings.
MolRenderer is a simple TableCellRenderer component based on MolPrinter that can be used to render Molecule objects in JTables.
Atom-by-atom structure search.
Class to encapsulate search parameters used by Search implementations(ex: MolSearch).
Point object.
Polyline object.
Progress monitor interface.
Property base class.
Property container.
Property factory.
Reaction arrow object.
Special MTextBox desdendant for displaying Reaction signs.
Record in a multi-molecule file.
Marvin molecule file reader.
Record reading exception.
Marvin record reader.
Position in the input file.
Factory interface for MRecordReaders.
Rectangle object.
Rectangle point object.
Fixed rectangle point that can be a point of a polyline.
Rounded rectangle object.
Plugin class for molecular surface area calculation.
Selection document.
Java independent serialization of the sketcher bean.
The MarvinSketch Bean.
MarvinSketch bean information.
String property.
Text attributes.
Text box object.
 
Text document consisting of sections with different attributes.
Plain text section with uniform attributes.
The interface of Marvin transferable implementations.
Interface for 3D transformable classes.
MultiCenterChecker detects structures containing multicenter atoms.
Multicenter S-group to represent complexes like markush ring structures, ferrocenes, metallocenes...
MultiComponentChecker detects structures containing disconnected components/fragments.
Multiple S-group.
A descendant of AbstractStructureChecker detecting molecules containing multiple stereocenters.
Class for NMR multiplets.
Java independent serialization of the viewer bean.
MViewEditor is an implementation of AbstractCellEditor and TableCellEditor that can be used to assign a cell editor to Molecule objects in JTables.
The MarvinView Bean.
MarvinView bean information.
MViewParams is a helper tool to generate parameter string to MViewPane.
MViewRenderer is a TableCellRenderer component that can be used to render Molecule objects in JTables.
The interface of a converter from names to structures.
Maintains the list of custom and built-in name-to-structures converters.
A failure to convert a name to a structure.
Exception signaling that the given input name should not be converted.
This exception should be thrown by a NameConverter to indicate that even though a name cannot be converted to a structure, it is the prefix of a valid name.
Compares two sets of objects (like compound libraries) using diversity and dissimilarity calculations.
Neutralization standardizer action
A descendant of AbstractStructureFixer which neutralize the charge of the atoms of the molecule
Class for NMR spectrum calculation.
Builder class for NMRCalculator.
Class for NMR spectrum export.
Class for the representation of NMR spectra.
Nucleus enumeration type.
Unit enumeration type.
Non-standard Wedge Scheme Checker detects wedge configurations not following the IUPAC recommendations.
Non-stereo Wedge Bond Checker detects wedge bonds connected to non-stereo atoms.
This class represents NoStructure labels.
OCRErrorChecker detects structures which do not look like chemical structures.
General option descriptor class.
Displays plugin parameter tabbed panes.
Plugin class for orbital electronegativity calculation.
OverlappingAtomsChecker detects atoms that are too close to each other.

This checker checks 2D structures only.

Two atoms considered as overlapping when their euclidean distance is less than the half of the Chemaxon standard bond length ( MolBond.CCLENGTH ).
OverlappingBondsChecker detects bonds that are too close to each other.

This checker checks two dimensional structures only.

Two bonds considered as overlapping when they crossing each other, or their distance is smaller then the 80% of the standard Chemaxon bond length ( MolBond.CCLENGTH ).
Page Settings of multipage molecular documents.
Align pairs of molecules (query and the target) using the shape Alignment
This interface designed for comparing two molecules in 3D by various overlay methodologies.
Align pairs of molecules (query and the target) using the atom/atom matcher Similarity3D
This interface represents a builder.
Parameters of Marvin Applets and Beans.
A configurable implementation of the plugin specific parameter setting panel.
Plugin parameter panel handler interface.
Represents a parameter tab.
Partial clean
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
Periodic System of the Elements.
This annotation signs if a property of a StructureChecker should be persisted
Comparator for PharmacophoreFP descriptor representation.
Generates 2D pharmacophore fingerprints.
The PFGenerator class generates 2-dimensional pharmacophore fingerprints for molecular graphs.
Pharmacophore FP parameters class.
Manages 2D pharmacophore fingerprint parameters.
Builder class for the immutable parameter object.
Interface representing PF generator constructor.
MDTable reader for 2D pharmacophore fingerprints.
Factory class.
3D Pharmacophore representation for 3D alignments.
The PharmacophoreFingerprint class implements 2D pharmacophoric fingerprints.
2D pharmacophore fingerprint representation.
Observer for reporting the progress of long-running tasks.
Plugin class for macro/micro pKa calculation.
PKa training result object.
 
Exception thrown in case of plugin processing or calculation errors.
Exception wrapping a cause Throwable and the plugin object which has thrown the Throwable.
Plugin factroy: responsible for plugin parameter panel and plugin creation and central management.
Exception thrown when a CalculatorInputChecker rejects an input molecule of a CalculatorPlugin.
Multimolecular result source object based on result MDocument Iterator.
Work unit performing plugin calculation.
Class representing the pharmacophore properties found for the atoms of a target molecule.
Class for searching for pharmacophore properties in a molecule.
Plugin class for atom polarizability calculation.
Positioned input stream that has the ability to set / get the stream position as well as put back some parts already read.
Deprecated, for removal: This API element is subject to removal in a future version.
This interface will be removed, use CustomFunction instead.
Function passed for DFS post order traversal.
Observer for reporting the progress of long running tasks.
Class to display the progress of some operation.
Interface for retrieving messages for events (especially errors) which were suppressed during execution.
A descendant of AtomChecker detecting pseudo atoms.
Class storing and sorting pharmacophore symbols.
Marks types that are part of the Chemaxon public API.
A descendant of AtomChecker detecting generic atoms or ones having query properties.
Chemical bond.
A descendant of BondChecker detecting query bonds.
A descendant of AtomChecker detecting asymmetric tetrahedral atoms without specific stereochemistry.
Filter for racemic tetrahedral centers.
A descendant of AtomChecker detecting radical atoms.
A descendant of AtomTypeChecker detecting structures containing elements which are usually rare in organic/drug molecules.
A descendant of AbstractStructureChecker detecting R-atoms.
Deprecated, for removal: This API element is subject to removal in a future version.
Checker detects bonds with reacting center bond marks.
Descendants of ReactionChecker detect reaction scheme problems.
Deprecated, for removal: This API element is subject to removal in a future version. 
Expression evaluation context to evaluate reaction conditions.
Reaction Exception class.
ReactionFingerprint class.
A descendant of ReactionChecker detecting reactions with invalid mapping.

Reaction components should contain at least two mapped atoms, otherwise they are considered incorrectly mapped.
Executes a chemical reaction: creates products from reactants with reaction center data.
A descendant of AbstractStructureFixer which rearomatize the molecule
 
Rearranges stereo wedge bonds according to IUPAC recommendations.
Exception indicating errors during recalculation.
File format recognizer.
Factory interface for Recognizers.
Deprecated, for removal: This API element is subject to removal in a future version.
Not used, will be removed
Plugin class for refractivity calculation.
Contains the constants of the regeneration checker.
A descendant of AbstractStructureChecker detecting molecules having multiple stereogenic center groups
Date values accepted by the SubjectToRemoval annotation.
Set absolute stereo standardizer action
A descendant of AbstractStructureFixer which removes the alias information from the atoms of the molecule
A descendant of AbstractStructureFixer which removes the atoms of the molecule signed in the result
A descendant of AbstractStructureFixer which removes the atom maps from the molecule
A descendant of AbstractStructureFixer which removes query properties from the given atoms.
A descendant of AbstractStructureFixer which removes the atom value from the molecule
Remove Atom Values standardizer action
Remove Attached Data standardizer action
A descendant of AbstractStructureFixer which removes the attached data from the molecule.
A descendant of AbstractStructureFixer which removes the bonds of the molecule signed by the result
Fixer removes reactiong center bond marks from bonds.
Removes brackets from molecule by ungrouping S-groups surrounded by brackets.
A StructureFixer implementation which removes absolute stereo property from the molecule.
A descendant of AbstractStructureFixer which implicitize the hydrogens in the molecule
Remove explicit H standardizer action
Removal standardizer action
Type of measurement
Type of removal methods
A StructureFixer implementation which removes absolute stereo property from the molecule.
A descendant of AbstractStructureFixer which removes the radicals from the atoms of the molecule
Fixer removes reactiong center bond marks from bonds.
Remove R-group definition standardizer action
Remove solvents standardizer action.
Remove Stereo Care Box standardizer action
Fixer for molecules containing Stereo Care Boxes.
Removes stereo inversion retention marks.
A descendant of AbstractStructureFixer that removes unused R-group definitions.
A descendant of AbstractStructureFixer which removes valence properties from the given atoms.
A descendant of AbstractStructureFixer which sets the z-coordinates of atoms to zero.
Source-based and structure-based representation of repeating unit groups (polymers and repeating units with repetition ranges).
Replace atoms standardizer action
Plugin class for finding resonant structures.
Complex result panel.
Work unit performing plugin calculation.
Generator class for the ReactionFingerprint descriptor.
Manages reaction fingerprint parameters.
Convenience class for generating, storing and returning results of a search in different forms: as r-group decomposition or Markush molecule.
A molecule or reaction containing R-groups.
A descendant of AbstractStructureChecker detecting invalid attachments in R-group definitions.
A descendant of AbstractStructureFixer that can fix attachment errors in R-group definition members.
Identifies an R-group bridge position by storing a pair of R-group IDs.
Checker for R-atoms that form R-group bridges: One R-group can be involved in at most one bridge. Two R-atoms that represent a bridge must be in the scaffold or in the same R-group definition member. The R-group number that represents an R-group bridge cannot represent an ordinary R-group.
A descendant of DefaultStructureCheckerResult providing information of R-group issues.
R-group decomposition.
The ring class provides information of the ring types in a molecule.
Enum type for the ring handling modes of MaxCommonSubstructure (MCS) algorithms.
RingStrainErrorChecker detects triple bonds, trans or cumulated double bonds small rings containing less than 8 atoms.
 
Reaction.
Base class for all scalar descriptors.
Manages ScalarDescriptor parameters.
Abstract base class of all structural search classes.
Constants for structure searching
Exception denoting errors during the search process.
Search hit object.
Enum type for search modes of MaxCommonSubstructure (MCS) algorithms.
Class to encapsulate common search parameters.
A selection object which can contain atoms and bonds without real parent relationship (the real parent of atoms and bonds is another MoleculeGraph ancestor).
Describes an argument passed to services
Descriptor class for marvin services
Provides editor suport for ServiceDescriptor
Provides ServiceDescriptorEditor instances based on ServiceDescriptor classes.
Reader for ServiceDescriptors
Writer for ServiceDescriptors
Provides Dialog instances to provide argument editor and result view for ServiceDescriptor
Exception for failure indication for services.
Manages service calls.
ServiceHandler keeps track of the previous call and if it is not yet finished cancels it.
Set absolute stereo standardizer action
Set hydrogen isotope symbol standardizer action
Hydrogen isotope representation type
Option type describing the supported smallest set of rings used for property calculations.
Structural group representation in the molecule.
S-group superatom.
A descendant of DefaultStructureCheckerResult for identifying Sgroup problems.
Enum of possible sgroup types.
 
 
Flexible alignment based shape descriptor calculation
 
Shape descriptor implements a 3D alignment based similarity calculation.
 
 
 
 
 
 
NMR chemical shift class.
Calculates the similarity of two bit strings.
Descriptor similarity calculation can be performed using SimilarityCalculator.
This factory creates a similarity calculator object according to the user defined parameters.
 
 
Simple DFS traversal visitor.
Search interface for different Molecule-Molecule search types.
Factory for creating SimpleSearcher instances.
A grouping of structures into disjunct groups.
Single linkage similarity clustering algorithm.
Deprecated, for removal: This API element is subject to removal in a future version.
Parameters of MarvinSketch Applet and Bean.
The parameters of the JMSketch applet can be set using the <param> HTML tag.
Class for partial interpretation of smarts atoms.
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
Array-based molecule interface.
Service descriptor of SOAP type requests.
Service handler for SOAP type requests.
Solubility calculator.
API usage example:
Array of solubility categories.
Undefined category.
Interface for solubility categories.
Solubility prediction result.
Solubility unit.
SolventChecker detects common solvents in multicomponent structures.
Core functionality related to sphere exclusion clustering.
MolSearch subclass that standardizes (e.g.
Performs the standardization determined by the XML configuration file, or simple action string configuration.
See the documentation for details: User's Guide Configuration Developer's Guide
Interface of standardizer actions.
Descriptor of StandardizerAction objects.
Contains all needed interface informations.
Factory of StandardizerAction objects
Initializes the list of available standardizer action based on the provided factory configuration XML files, defining the factory: Internal list: the factory configuration XML containing the definitions of internal (Chemaxon defined) standardizer actions, that should be available using the factory External list: the factory configuration XML containing the definitions of external (user defined) standardizer actions, that should be available using the factory The schema of the definition XML is defined by the StandardizerActionFactory.DEFAULT_CONFIGURATION_SCHEMA:
Builder class for StandardizerActionFactory.
Descriptor of a standardizer class
Standardizer action info annotation
This annotation is responsible for adding user interface related meta data for StandardizerAction implementations
The descendant of StandardizerActionRunner interface has to provide the functionality to run StandardizerConfiguration instances automatically on the given molecule.
As standardizer configuration may contain actions in groups, using StandardizerActionRunner.setTargetGroup(String) and StandardizerActionRunner.setTargetGroups(String...) methods, the target groups, containing the actions to be executed can be defined.
By default, in case of the provided configuration containing error(s) the runner throws IllegalArgumentException.
An implementation of StandardizerConfigurationReader for parsing action strings
If the configuration contains references to molecules/molecule files not contained by the configuration file, the base path of the configuration must be set by the method StandardizerActionStringReader.setPath(String) before gathering the configuration.
Syntax of action strings:
<actionString>::=<actionStringEntry>(..<actionStringEntry>) *
<actionStringEntry>::=<standardizerAction>|<groupDefinitions& gt;<standardizerAction>
<groupDefinitions>::=<groupDefinition>(,<groupDefinition>)*
<groupDefinition>::=(a-zA-Z0-9)+
<standardizerAction>::=<actionName>|<actionName>< parameters>
<actionName>::=(a-zA-Z0-9)+
<parameters>::=<parameter>(:<parameter>)*
<parameter>::=<key>| '<extendedKey>'|<key>=<value>|<key>='<extendedValu e & g t ; '
<key>::=(a-zA-Z0-9)+
<value>::=(anything\{.':,"})*
<extendedKey>::=(anything\{'" })*
<extendedValue>::=(anything\{'"})*
Standardizer configuration class.
Contains a list of StandardizerAction instances.
This interface is provided for classes which can read the configuration of StandardizerActionRunner
Configuration error
There are 2 kinds of configuration errors for execution configuration.
Result of a standardization process for a molecule
Concurrent executor of the standardizer
Policy for error handling
Utility class for standardizer
Functionalities of old standardizer can be simulated using this class.
Wrap Standardizer for the similarity subsystem.
Provide utility methods for StandardizerWrapper.
XML Configuration reader for standardizer configurations.
This class implements a max-weight matching-based upper bound calculator for the MCS problem.
A descendant of AtomChecker detecting so called star atoms having "*" as atomic symbol.
Stereo active molecule part with stereo active atom index and its ligands which takes part in the stereo description.
The stereo analysis module is able to calculate stereochemical descriptors for a molecule, giving an analysis in terms of the stereochemical properties.
API usage example:
Checker to find molecules containing Stereo Care Boxes.
Interface for stereo centers.
Visitor interface for stereo centers.
Deprecated, for removal: This API element is subject to removal in a future version.
Will be removed from the public API.
Central class for accessing functions analyzing the topology of a molecule.
Constants for atom parity and double bond stereo.
Wrapper interface for stereo constants.
Enhanced stereo flags.
Deprecated, for removal: This API element is subject to removal in a future version.
Check the implementing enums for details.
Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated, for removal: This API element is subject to removal in a future version.
Stereo center type.
Detects reaction inversion/retention marks on atoms.
Enumerates stereoisomers of the specified molecule.
Deprecated.
Settings class for StereoisomerEnumeration.
Types of stereoisomers.
A descendant of AbstractStructureChecker detecting double bonds in molecule which can be either "E" or "Z".
Strip salts standardizer action
Utility class for assembling and parsing structural FP configurations.
Plugin class to calculate Bemis-Murcko and other structural scaffolds of input molecules.
FrameworkTypes represents the available calculations
Verbose printer specification
This class contains the command line interface for running inner StructureChecker and StructureFixer instances.
General interface describing functions that are available for a chemical structure checker.
Descriptor for StructureChecker
Enum containing possible error types for structure checkers.
Deprecated.
An instance of StructureCheckerResult identifies a molecule problem
Utility to handle core features
Options descriptor for structure checker command line interface
The mode of the structure check
Converter for Mode enumeration.
The output type of the structure check
Converter for Type enumeration.
A StructureFixer can fix a Molecule problem identified by a StructureCheckerResult
Descriptor class for StructureFixer classes.
Deprecated.
Class for storing options for structure table creation.
Denotes that an entity has been deprecated and is subject to removal in a release following the specified date.
This descendant of AbstractStructureChecker is responsible for detecting substructures in a Molecule instance.
 
Fixer to fix substructure issues.
Superatom S-group.
Swing utility functions.
SDF table options for MarvinView.
Class for collecting table statistics.
Viewer table support class.
Interface representing table type related constants.
Base interface for calculator objects that can report a set of optional tags, which are used primarily to identify the calculator in configuration files.
Instances of this interface are used by calculators to check if they can process an input molecule.
Option to control homology matching on target side.
Generic task scheduler interface.
 
Plugin class for generating tautomer structures.
Tautomerize standardizer action
 
 
Filter for tetrahedral centers.
Tetrahedral stereo center implementation.
 
A descendant of AtomChecker detecting atoms having non-zero Z coordinates.
Central class for accessing functions analysing the topology of a molecule.
Calculates topological data.
Implements TPSA (Topological Polar Surface Area) value as a scalar descriptor.
Plugin class for TPSA (topological polar surface area) calculation.
Filter for TRANS double bonds.
Data object to store lookup information for MTransferable objects.
Exception indicating errors during import and export.
Transformation standardizer action
Exception thrown during transformation.
Transformer.
Creates Molecule Transformer objects.
Parameters for Tversky index.
Builder for parameter object.
A descendant of AtomChecker detecting reaction schemes having more atoms on one side of the reaction arrow than on the other.
A descendant of AbstractStructureFixer which ungroups all abbreviated groups in the molecule
Standardizer action un-groups s-groups of the target molecule
Assigning unit distance based on path length from leaves/roots.
Filter for unknown atrop stereo centers.
Filter for unknown axial centers.
Filter for unknown, resolved tetrahedral centers.
Unmap reaction standardizer action
Filter for unresolved tetrahedral centers.
A descendant of AbstractStructureChecker detecting unused R-group definitions.
Provides methods for handling structure tables, e.g.: creating tables updating and inserting rows dropping tables Both fix columns (the ones which have "cd_" prefix in their names) and additional columns can be set using the class.
Represents a database row (record).
Error occurred during some update in database.
Class for upgrading JChem database structure.
Class describing the nature of an update.
Deprecated, for removal: This API element is subject to removal in a future version.
Will be removed, no replacement.
An interface for providing upper bound calculation for MaxCommonSubstructure (MCS) search.
Represents the settings of the MarvinSketch and MarvinView applications.
Clustering related utility methods.
ASCII scatter plot.
Class created to make valence calculation configurable.
Builder for ValenceCheckOptions.
A descendant of AtomChecker detecting atoms with invalid valences.
A descendant of AbstractStructureFixer which fixes valence problem in the molecule if it is possible with removing explicit hydrogens or by adding charge
A descendant of AtomChecker detecting atoms having an explicitly set valence property.
Provides version information of Chemaxon products.
Parameters of MarvinView Applet and Bean.
The parameters of the JMView applet can be set using the <param> HTML tag.
Uses Ward's minimum variance method for clustering molecules based on molecular fingerprints or other descriptors.
Wedge clean standardizer action
Deprecated.
Deprecated.
A descendant of AbstractStructureChecker detecting wiggly bonds on tetrahedral stereo centers.
A descendant of BondChecker detecting double bonds having wiggly bond ligands representing unspecified double bond stereo configuration.
Deprecated, for removal: This API element is subject to removal in a future version.
A descendant of ConfigurationReader which can read CheckerRunner configuration described Chemaxon's own checker configuration XML format (schema in jar: chemaxon/checkers/runner/configuration /reader/resoruce/checkerconfiguation.xsd)
ServiceDescriptor implementation for XML-RPC services.
ServiceHandler implementation for XML-RPC Services.
This class implements the default conversion from XML to HTML.