All Classes and Interfaces
Class
Description
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
Detects molecules in which all asymmetric centers have absolute stereo configuration
Abstract base class of atrop stereo descriptors.
Abstract base class of axial stereo descriptors.
Abstract base class of double-bond stereo descriptors.
Abstract superclass for clustering methods.
Abstract base class of all structural search classes.
Abstract class for standardizer actions modifying S-groups.
Abstract implementation of the
StandardizerAction.Abstract base class of all functions checking and repairing chemical
structures.
This class is the default abstract implementation of
StructureFixer interfaceAbstract base class of tetrahedral stereo descriptors.
Absent chiral flag fixer.
Standardizer action that adds explicit hydrogens to the molecule.
CheckerRunner implementation with advanced fixing capabilities.A descendant of
AbstractStructureChecker detecting atoms with alias
labels.Standardizer action that converts atom aliases to actual atoms.
Standardizer action that converts atom aliases to abbreviated groups.
3D Alignment aligns two or more 3D molecules onto each other.
Settings for the representation of a molecular shape.
Base class for the alignment algorithms.
Exception thrown when an error occurs during molecular alignment operations.
Represents a molecule in the context of 3D molecular alignment with its coordinates and transformation state.
Creates an
AlignmentMolecule form a
Molecule based on the settings.Interface for providing progress feedback during alignment operations.
Calculator plugin for aligning molecule onto each other in 2D and 3D.
Predefined configurations for 3D molecular alignment.
Enumeration of degree of freedom types defining how molecules can move and flex during alignment operations.
Conformational flexibility treatment during the alignment for a pair of a molecule.
Represents the result of a molecular alignment operation.
Overlays two molecules using the user defined atom pairs.
Aligns pairs of molecules by translating and rotating one of them and leave
the one called the reference molecule intact.
Amino acid S-groups.
Holds the values for the possible rendering styles for Any bonds.
A descendant of
DefaultStructureCheckerResult for identifying aromaticity problems,
thus errorType property is StructureCheckerErrorType.AROMATICITYA descendant of
AbstractStructureChecker detecting aromatization problems.Standardizer action that aromatizes the molecule.
Type of aromatization
Callback interface for asynchronous service calls
Descendants of the abstract
ComponentChecker 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.
Stores a list of atom labels to be used for certain structure checkers.
A descendant of
AtomChecker detecting atoms with atom map numbers.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.A descendant of
AtomChecker detecting atoms with atom values (labels).Deprecated.
This checker is no longer supported.
Molecular mechanics based atropisomer detection.
Sampling accuracy levels used in atrop bond detection, controlling the number of dihedral rotation steps.
Atrop stereo center implementation.
Descriptor representing atrop stereo information.
Descriptor representing atrop stereo information.
Data object which contains a name and a data (String).
A descendant of
AbstractStructureChecker detecting attached data in the molecule.A list of Strings to be excluded by
AttachedDataChecker.Attachment Point class for the Superatom S-group.
AutoMapper is a tool that performs automated chemical reaction mapping.Configuration options for automated reaction mapping when using static mapping methods.
Auto-closeable result iterator for
AutoMapper.Axial stereo center implementation.
Axial type stereo descriptor.
Axial type stereo descriptor.
Deprecated.
Don't use this class directly, use
AdvancedCheckerRunner instead.Specific exception class that collects possible internal exceptions from the batch actions defined on the following
IDocumentWriter,
IDocumentReader
IDocumentConverter interfaces.BBB score calculator.
Simple result class that contains the predicted value, its BBB score, and the BBB score multiplied by
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.
Bond Angle Checker detects non-preferred 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.
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 pairs of atoms in a molecule graph.
Checker detects bonds with reacting center bond marks.
General chemical bond types.
Detects brackets (generic S-groups) in molecules.
Implements a heuristic MCS algorithm using the build-up method of Takeshi Kawabata.
Utility class for cache registration.
Generic calculator interface
Builder interface for
Calculator.An error that might occur when a calculator is initialized.
Simple interface of classes that are used by calculators to check if they can process an input molecule.
Logger for calculators.
Logging levels controlling the verbosity of calculator log output.
Common base class for calculator plugins.
Data structure holding information about hydrogen atoms in molecules.
Common base class for calculator plugin displays.
Exception thrown in case of plugin processing or calculation errors.
Exception that is thrown when an input molecule of
CalculatorPlugin is rejected.Class providing plugin output in table form.
Interface providing plugin output access.
Base class for types that implement a functionality related to a specific
CalculatorPlugin.List of optional tags that can be reported by a
TaggedCalculator.Available card layout alignments.
Manages parameters the
CustomDescriptor class.Cell types in molecule tables.
The
CFGenerator class generates topological fingerprints
of molecular graphs.Manages fingerprint parameters.
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-related metadata for
StructureChecker implementations.Interface for structure checker runner implementations.
This enum defines the constants which represent the severity of the
StructureChecker
implementationsThe
ChemicalFingerprint class implements topological fingerprints as a
type of MolecularDescriptors.Plugin for generating chemical names and identifiers.
Interface of expression evaluation contexts.
Repeatable annotation used on
ChemTermsContext implementations to declare the context functions
supported by the ChemTermsContext.callContextFunction(String, List) method.Container for the repeatable
ChemTermsContext.ProvidesFunction annotation.Evaluates Chemical Terms expressions.
Exception thrown during the compilation or evaluation of Chemical Terms expressions.
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 (CIP) priority rules.
Wrapper for the calculated descriptor with timeout information.
Cahn-Ingold-Prelog (CIP) stereodescriptor interface.
Detection of Cahn-Ingold-Prelog (CIP) stereo descriptors: tetrahedral, axial,
cis/trans and atrop stereo features.
CIP stereo type.
CIP stereo value.
Atrop stereo value, conforms to IUPAC.
Atrop stereo value.
Axial stereo value, conforms to IUPAC.
Axial stereo value.
Double-bond stereo value, conforms to IUPAC.
Double-bond stereo value.
Tetrahedral stereo value, conforms to IUPAC.
Tetrahedral stereo value.
A descendant of
AbstractStructureChecker detecting circular R-group
references.Cis-trans stereo center implementation.
Double-bond stereo descriptor.
Double-bond stereo descriptor.
Standardizer action that cleans the molecule graph in 2D.
Type of clean action (partial, full, template based or convert 3D to 2D)
Standardizer action that cleans the molecule graph in 3D.
Class to clean MoleculeGraphs, Molecules, SelectionMolecules and S-groups.
Listener interface to be notified on atom changes during partial clean.
A descendant of
AbstractStructureFixer which cleans the molecule in
2dUtility methods for cleaning.
Standardizer action that clears isotope information (mass numbers) from atoms.
Standardizer action that clears stereo information from the molecule.
Clears wedges.
Cluster represents a group of structures.
Exception thrown when an error occurs during molecular clustering operations.
Clustering related utility methods.
ASCII scatter plot.
CNS MPO score calculator.
Simple result class that contains the predicted value and its CNS MPO score.
Base phys-chem property calculators and its score functions for CNS MPO calculation.
Helper class to generate and read base64 encoded string from molstring.
A final class which provides a static access to a color distant color creator class.
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.
All comparison operators for evaluating a conditional rule.
Conditional rule settings to evaluate data entries for conditional formatting.
Deprecated, for removal: This API element is subject to removal in a future version.
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 moleculeStandardizer action that contracts S-groups of the molecule.
This class contains constants for converting atoms, bonds and S-groups in checker results.
ConversionOptions class is the default/basic implementations of the conversion options interface.
A descendant of
AbstractStructureFixer which converts the aliases to
contracted abbreviated groups in the moleculeStandardizer action that converts double bonds to wiggly bonds.
Type of conversion
Standardizer action that converts Pi-metal single bonds to standard coordinate bonds.
A descendant of
AbstractStructureFixer which converts the pseudo
informations to contracted abbreviated groups in the moleculeA descendant of
AbstractStructureFixer which converts the aliases to
atoms with atom numbers originally contained in the alias information.A descendant of
AbstractStructureFixer which converts pseudo and query atoms to
carbon atoms.A descendant of
AbstractStructureFixer which sets wiggly bond to
crossed double bondA descendant of
AbstractStructureFixer which converts the isotopes to non isotope atomsStandardizer action that converts stereo information to enhanced stereo representation.
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 wigglyHolds the values for the possible rendering styles for Coordinate bonds connected to Multicenter atoms.
Holds the values for the possible rendering styles for Coordinate bonds.
Detects errors of multicenter coordination systems.
A descendant of
AbstractStructureChecker detecting covalently bonded counterions
(alkaline alcoholates, carboxylates and thio analogs).Standardizer action that searches for groups in the molecule and contracts them.
A descendant of
BondChecker for the detection of unspecified double bonds
represented by crossed bond type.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.
Tools that can be applied in the development of applications
accessing databases.
Class for upgrading JChem database structure.
Class describing the nature of an update.
Data S-group.
A descendant of
DefaultStructureCheckerResult for identifying Sgroup problems.Type of data stored in a cell (structure or text).
Standardizer action that dearomatizes the molecule.
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.Default solubility categories.
This class is the default implementation of
StructureCheckerResultSimple class for generating molecular descriptors (fingerprints).
Rotates a dihedral in a 3D molecule
Results of a dihedral scan.
Encapsulates bond info.
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.
Standardizer action that disconnects metal atoms from other atoms of the molecule.
Display option masks and offsets.
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.
The DocumentHandlerFactory class is the entry point to instantiate classes
which implement the
IDocumentWriter,
IDocumentReader
IDocumentConverter interfaces.A convenience class for dealing with String-based documents, such as TXT, HTML, or XML files.
Available document types.
Utilities for document handling
Detects invalid either double bonds.
ServiceArguments implementing this interface
should support automatic evaluation of arguments before service call
based on context.The
ECFP class implements Extended-Connectivity Fingerprints (ECFPs)
as a type of MolecularDescriptors.Class for representing the substructural features of ECFP fingerprints.
Class for retrieving the substructural features of
ECFP
fingerprints.
The
ECFPGenerator class generates ECFP fingerprints of molecular graphs.Manages ECFP fingerprint parameters.
Calculates molecular formula, mass, MS mass and composition.
Provides static factory methods for creating
ElementalAnalysis instances from various input types.Calculates molecular formula, mass, MS mass and composition.
Represents the different result types of the elemental analysis 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.
Enhanced stereo flags.
An abstract ancestor of JavaBeans that enable exception handling in
different environments.
Error processing interface.
Error reporting class.
Expandable interface for S-groups.
Standardizer action that expands stoichiometry coefficients.
A descendant of
AbstractStructureFixer which expands all abbreviated groups in the moleculeStandardizer action that expands S-groups of the molecule.
A descendant of
AtomChecker detecting explicit hydrogens.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.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.Mode type how the file name is generated from the source molecule.
Interface for fingerprint generators used in Chemical Terms match functions.
This annotation is responsible for adding GUI-related metadata for
StructureFixer implementations.This annotation is used to annotate the
StructureFixer implementations which
StructureCheckerErrorType can be fixed by the current fixerThis annotation is used to annotate the
StructureFixer implementations which
error codes (identified by a unique String) can be fixed by the current fixerFix mode options
Flips wedge bonds.
Available font alignments.
Available font styles.
Represents an atom in an
ElementalAnalysis.Molecular formula generation settings.
Chemical formula based search class.
Results of a framework based clustering.
Provides a high-level API with comprehensive functionality for the generation of various
Molecular Descriptors.
Default implementation of generic quality-related options for document writers and converters.
Plugin class for geometric properties calculations.
Pattern of a group.
Implements hydrogen bond acceptor atom count as a scalar descriptor.
Option type describing the error handling behaviour.
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.
An input checker that only accepts molecules with at most a certain number of heavy atoms.
The results of a hERG activity prediction.
hERG activity predictor.
The possible values of hERG class prediction.
The results of a 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.
Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated, use the constructor of
HLBPlugin class directly instead.Option type describing the scope of homology matching.
HTTP Request based
ServiceDescriptor implementation
for HTTP POST/GET based servicesServiceHandler implementation that invokes remote services over HTTP.Plugin class for Huckel Analysis calculation.
Hybridization state constants.
Addition and removal of explicit hydrogens or lone pairs.
Specific settings for arrangement of structures and properties,
which is like the one structure per page when the structure is placed separate from the property table.
ICellData interface provides functionality to read/write cell data
ICellFormat interface gives functionality to read/write the formatting
options of a table cell.
Interface for generating rendering code for JChem Office integration.
IConversionOptions interface gives read/write information about the different
settings during document conversion.
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.The IDocumentConverter interface offers the functionality to convert the
structures in the given document to a new format.
The IDocumentReader interface gives the functionality to read the Chemical
Structures from a given document.
The IDocumentTemplateWriter interface offers the functionality to report chemical information in a predefined template.
The IDocumentWriter interface gives the functionality to write/update
documents with Chemical Structures.
IGenericOption interface gives read/write information about generic quality related options.
Interface for accessing and modifying cell location in a workbook.
Extends
ImageExportBaseUtil with additional methods.Available Image Generation Types {ImageWriter, FormattingString}.
IMoleculeData interface contains Molecule class and related data.
Interface for accessing molecule data and its location in a workbook.
Interface for a generic renderer that can be registered in a renderer container.
Incorrect Tetrahedral Stereo Checker detects stereo wedge configurations around chiral atoms which are not possible.
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.
Defines cell format specifications for property table rendering in JChem Office.
Interface for configuring molecule rendering and positioning settings in documents.
Plugin class for isoelectric point and pH - charge distribution calculation.
IsotopeChecker detects isotopes (non-elemental atoms).
Interface for accessing and modifying table cell data and formatting.
ITableModel interface gives basic information about the table.
ITemplateWriterOptions interface gives read/write information about the different
settings during document reporting based on templates.
Deprecated, for removal: This API element is subject to removal in a future version.
This class is deprecated and subject to removal in a future release.
To instanciate an implementation of the IWorkbookreader interface use the
WorkbookHandlerFactory.createWorkbookReader method.
Performs variable-length Jarvis-Patrick clustering based on binary
fingerprints (bits strings) and/or other data stored in a database table
or a file.
Low-level API to create JChem For Excel files.
JavaBean for structure searching in structure tables of relational databases.
Class for presenting the available dissimilarity metrics for similarity
search.
Error occurred during structural search in database.
Class to encapsulate search parameters used by
JChemSearch.Provides version information of JChem products.
Service descriptor of JSON type requests.
HTTP methods used for JSON RPC requests.
Service handler for JSON type requests.
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.API adapter to use
LibraryMcs clustering with the new clustering API.Parameters for
LibraryMcs clustering implementation.Assigns levels for clusters and leaves.
Compares two compound libraries using diversity and dissimilarity calculations.
The
LibraryMCS class computes the maximum common substructure (MCS)
of a set of compounds.The common interface of license-protected classes of Chemaxon.
Thrown when the product is not properly licensed.
Service Descriptor for java based local services.
ServiceHandler implementation for LocalServiceDescriptor.Represents a position in a document with page number and coordinates.
Implements logD value as a scalar descriptor.
Plugin class for logD calculation.
Implements LogP value as a scalar descriptor.
Enumeration of logP calculation methods.
Plugin class for logP calculation.
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.
A special text box containing analysis results.
Represents a term in
MAnalysisBox.Formatter interface for
MAnalysisBoxTerm.Standardizer action that adds atom map numbers to the molecule.
A descendant of
AbstractStructureFixer which maps the atoms of the molecule incrementallyStandardizer action that adds atom-atom mapping to the reaction.
A descendant of
AbstractStructureFixer which maps the reaction with AutoMapper.A descendant of
AbstractStructureFixer which adds an attached data to
the bond: "STEREO = M"A descendant of
AbstractStructureFixer which adds an attached data to
the bond: "STEREO = U"Option type describing the way aromaticity is handled in Markush structures.
Plugin class for enumerating Markush molecules.
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.
String property.
Bracket object.
Byte array property.
Wrapper for the EasyChart module.
Molecule graph object.
Collection of properties.
Align molecules using the maximum common substructure (MCS) of the given molecules.
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.Enum type for search modes of
MaxCommonSubstructure (MCS) algorithms.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.
Optimization of metric parameters for dissimilarity based screening.
Marvin document source.
Sparse dynamic document storage and reader.
Document production listener.
Marvin document.
Provides information for Structure Checker highlight.
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.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.
Base class definitions for
MDSet output streams.Exception definition for the
MDWriter class.Electron flow arrow.
Electron flow arrow base point.
Represents an electron associated with a molecular atom.
Container for managing electrons and radicals in a molecular structure.
Ellipse object.
Standardizer action that generates the canonical mesomeric form of the molecule.
Structure checker result for metallocene-related issues.
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.The
Metrics class implements dissimilarity metrics for
MolecularDescriptors.Enumeration of similarity metric types (Tanimoto, Tversky, Dice, Euclidean, etc.) used for molecular descriptor
comparison.
File format descriptor class.
File format related utility functions.
Font wrapper class that does not require an X server.
Font property.
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 atoms without atom map numbers.
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 of a Marvin document.
Property that stores any object.
Tool for aligning a target molecule to a pattern molecule.
Atom object in a molecule.
Bond object in a molecule.
Interface for comparing atoms, bonds, etc.
Expression evaluation context containing a single molecule.
Converts between molecule file formats.
MolConverter builder.
Generic definition of molecular descriptors.
Molecular Dynamics plugin.
Represents a molecule (a chemical structure).
MoleculeChargeChecker detects molecules where the sum of the formal atom
charges is not zero.
Default implementation of IMoleculeData containing molecule structure and related metadata.
Molecule importer.
Molecule iterator interface.
Molecule iterator factory.
MoleculeMap class stores the Molecule related information.
Container class that collects renderer (more pieces of renderer in the future).
Molecule exporter class.
Molecule export exception.
Abstract base class of molecule export modules.
Molecule filter interface.
Something's wrong with a molecule file format.
Class for handling molecules for systems based on Chemaxon's programming interface.
Molecule file importer.
Interface for molecule importer classes.
Base class of Molecule import modules.
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 options used by molecule search implementations.
Point object in Marvin documents.
Polyline object.
Deprecated, for removal: This API element is subject to removal in a future version.
Use
ProgressMonitor instead.Property base class.
Property container.
Property factory.
Reaction arrow object.
Special MTextBox desdendant for displaying Reaction signs.
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.
Handles affine transformation of text boxes in molecular graphics.
Text document consisting of sections with different attributes.
Plain text section with uniform attributes.
The interface of Marvin transferable implementations.
Interface for classes that are transformable in 3D.
MultiCenterChecker detects structures containing multicenter atoms.
Multicenter S-group to represent complexes like metallocenes and position variation in
Markush structures.
MultiComponentChecker detects structures containing disconnected components/fragments.
Multiple S-group.
A descendant of
AbstractStructureChecker detecting molecules
containing multiple stereocenters.Java independent serialization of the viewer bean.
Implementation of AbstractCellEditor and TableCellEditor that can be used to
assign a cell editor to Molecule objects in JTables.
MViewCellRenderer is a TableCellRenderer component that can be used to render Molecule objects in JTables.
The MarvinView Bean.
MarvinView bean information.
MViewParams is a helper tool to generate parameter string to MViewPane.
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.
Standardizer action that neutralizes charged atoms in the molecule.
A descendant of
AbstractStructureFixer which neutralize the charge of the atoms of the moleculeClass for NMR spectrum calculation.
Builder class for NMRCalculator.
Error classification categories for shifts.
Class for NMR spectrum export.
Class for NMR multiplets.
NMR chemical shift class.
Class for the representation of NMR spectra.
Nucleus enumeration type.
Unit enumeration type.
Defines the coloring of the nodes in the alignment graph.
Exception thrown when a superatom method fails due to running out of free
attachment points.
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.
Interface for search option enum types that provide option strings.
Plugin class for orbital electronegativity calculation.
An arbitrary element of an ordered collection.
OverlappingAtomsChecker detects atoms that are too close to each other.
OverlappingBondsChecker detects bonds that are too close to each other.
Page Settings of multipage molecular documents.
Align pairs of molecules (query and the target) using the shape
AlignmentThis 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
Similarity3DParameters of Marvin components.
Plugin parameter panel handler interface.
This exception is thrown when parse errors are encountered.
Partial clean
Periodic table of the elements.
This annotation signs if a property of a
StructureChecker should be persisted.This annotation signs if a property of a
StandardizerAction should be persisted.The
PFGenerator class generates 2-dimensional pharmacophore
fingerprints for molecular graphs.Manages 2D pharmacophore fingerprint parameters.
3D Pharmacophore representation for 3D alignments.
The
PharmacophoreFingerprint class implements 2D pharmacophoric fingerprints.Observer for reporting the progress of long-running tasks.
Plugin class for macro/micro pKa calculation.
Represents pKa training result.
Enumeration of pKa group types representing different acidic and basic functional groups in molecules.
Plugin factory: responsible for plugin parameter panel
and plugin creation and central management.
Class representing the pharmacophore properties found for the atoms of
a target molecule.
Class for searching for pharmacophore properties in a molecule.
Point in three-dimensional space.
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.
Function passed for DFS post order traversal.
An abstract calculator implementation which supports progress notification and cancellation.
Simple progress monitor interface.
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.
Conditional formatting descriptor for property tables (card layout).
Available property table relative position to the structure in the document section.
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.Bond object with query features.
A descendant of
BondChecker detecting query bonds.A descendant of
AtomChecker detecting asymmetric tetrahedral atoms without
specific stereochemistry.Enumeration of the supported radicals.
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.Checker detects bonds with reacting center bond marks.
Descendants of ReactionChecker detect reaction scheme problems.
Expression evaluation context to evaluate reaction conditions.
Reaction Exception class.
ReactionFingerprint class.A descendant of
ReactionChecker detecting reactions with invalid mapping.Interface of reaction mappers that identify the corresponding parts of reactants and products and mark them
with the same identifier.
Available mapping styles for
ReactionMapper.Executes a chemical reaction: creates products from reactants with
reaction center data.
A descendant of
AbstractStructureFixer which rearomatize the moleculeStandardizer action that rearranges reaction components.
Rearranges stereo wedge bonds according to IUPAC recommendations.
Exception indicating errors during recalculation.
File format recognizer.
Represents the result of a format recognition attempt.
Plugin class for refractivity calculation.
Contains the constants of the regeneration checker.
A descendant of
AbstractStructureChecker detecting molecules having
multiple stereogenic center groupsDate values accepted by the
SubjectToRemoval annotation.Standardizer action that removes the absolute stereo flag from the molecule.
A descendant of
AbstractStructureFixer which removes the alias information from
the atoms of the moleculeA descendant of
AbstractStructureFixer which removes the atoms of the
molecule signed in the resultA descendant of
AbstractStructureFixer which removes the atom maps from the moleculeA descendant of
AbstractStructureFixer which removes query properties
from the given atoms.A descendant of
AbstractStructureFixer which removes the atom value from the moleculeStandardizer action that removes atom values from the molecule.
Standardizer action that removes attached data from the molecule.
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 resultFixer removes reactiong center bond marks from bonds.
Removes brackets from molecule by ungrouping S-groups surrounded by brackets.
A
StructureFixer implementation that removes the chiral flag ("absolute stereo" flag) from the molecule.A descendant of
AbstractStructureFixer which implicitize the
hydrogens in the moleculeStandardizer action that removes explicit hydrogens from the molecule.
Standardizer action that removes fragments from the molecule.
Type of measurement
Type of removal methods
A descendant of
AbstractStructureFixer which removes the radicals from the
atoms of the moleculeFixer removes reactiong center bond marks from bonds.
Standardizer action that removes R-group definitions from the molecule.
Standardizer action that removes common solvents from the molecule.
Standardizer action that removes the stereo care boxes from the bonds in the molecule.
Fixer for molecules containing Stereo-Care Boxes.
Removes stereo inversion retention marks from atoms.
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.Enum representing the available molecular rendering styles.
Source-based and structure-based representation of repeating unit groups (polymers and
repeating units with repetition ranges).
Standardizer action that replaces specified atoms in the molecule.
ReportSettings class can be instantiated and used in writer functionalities.
Plugin class for finding resonant structures.
Generator class for the
ReactionFingerprint descriptor.Manages reaction fingerprint parameters.
A molecule or reaction containing R-groups.
R-group container interface.
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.
A descendant of
DefaultStructureCheckerResult providing information of R-group issues.R-group decomposition.
Convenience class for generating, storing and returning results of a search
in different forms: as r-group decomposition or Markush molecule.
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.
Detects rotatable bonds in a molecule, used for conformer generation and flexible alignment.
Chemical reaction structure.
Base class for all scalar descriptors.
Manages
ScalarDescriptor parameters.Constants for structure searching
Expression evaluation context containing search hit data:
the target, the query and the hit.
Exception denoting errors during the search process.
Search hit object.
Class to encapsulate common search options.
Exceptions indicating timeout during the search process.
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
Reader for
ServiceDescriptorsHelper class for accessing
ServiceDescriptorReader and ServiceDescriptorWriter
implementations and various configuration data for services.Writer for
ServiceDescriptorsException thrown when a service invocation fails.
Manages service calls.
Standardizer action that sets the absolute stereo flag on the molecule.
Standardizer action that sets hydrogen isotope symbols to be used in the molecule (D/T or 2H/3H).
Hydrogen isotope representation type
Option type describing the supported smallest set of rings
used for property calculations.
Represents a structural group (S-group) in a molecule.
Superatom of
SuperatomSgroup.A descendant of
DefaultStructureCheckerResult for identifying Sgroup problems.A factory class to create different types of S-groups.
Enum of possible S-group types.
Holds the shape representation data of a molecule used for shape-based alignment and similarity calculations.
Shape descriptor implements a 3D alignment based similarity calculation.
Generates
ShapeDescriptor data from a molecule using 3D shape analysis.Configuration parameters for shape-based molecular descriptor generation and comparison.
Descriptor similarity calculation can be performed using SimilarityCalculator.
This factory creates a similarity calculator object according to the user defined parameters.
Exception class for similarity calculator tools.
Calculates the similarity of two bit strings.
Simple DFS traversal visitor.
A grouping of structures into disjunct groups.
Single linkage similarity clustering algorithm.
Parameters of
MSketchPane.Solubility calculator.
Stores the array of solubility categories.
Undefined category.
Interface for solubility categories.
Solubility prediction result.
Solubility unit.
SolventChecker detects common solvents in multi-fragment molecules.
Implements sphere exclusion clustering for grouping molecules based on dissimilarity thresholds.
MolSearch subclass that standardizes query and target structures by default before searching.
Performs the standardization determined by the XML configuration file, or
simple action string configuration.
Interface of standardizer actions.
Descriptor of
StandardizerAction objects.Factory of
StandardizerAction objects.Builder class for
StandardizerActionFactory.Descriptor of a standardizer class
Standardizer action info annotation.
Standardizer configuration reader for parsing action strings.
Standardizer configuration writer for action strings.
Standardizer configuration class.
Configuration reader interface of Standardizer.
Configuration writer interface of Standardizer.
Standardizer configuration reader for parsing XML configuration files.
Standardizer configuration writer for XML configuration files.
Utility class for standardizer.
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.
Checker to find molecules containing Stereo-Care Boxes.
Interface for stereo centers.
Visitor interface for stereo centers.
Central class for accessing functions analyzing the topology of a molecule.
Constants for atom parity and double bond stereo.
Detects reaction inversion/retention marks on atoms.
Enumerates stereoisomers of a molecule considering all tetrahedral and cis-trans stereocenters.
Deprecated.
Use
StereoisomerEnumeration instead.Settings class for
StereoisomerEnumeration.Types of stereoisomers.
Stereo center type.
A descendant of
AbstractStructureChecker detecting double bonds in molecule which can be either "E" or "Z".Standardizer action that strips salts from the molecule.
Plugin class to calculate Bemis-Murcko and other structural scaffolds of input
molecules.
FrameworkTypes represents the available calculations
Verbose printer specification
Utility class for assembling and parsing structural key configurations.
General interface describing functions that are available for a chemical structure checker.
Structure Checker configuration reader for parsing action strings.
Structure Checker configuration writer for action strings.
Configuration reader interface for Structure Checker.
Configuration writer interface for Structure Checker.
Structure Checker configuration reader for parsing XML configuration files.
Structure Checker configuration writer for XML configuration files.
Descriptor for
StructureCheckerEnum containing possible error types for structure checkers.
Monitor for
CheckerRunner.An instance of
StructureCheckerResult identifies a molecule problemDescriptor class for
StructureFixer classes.Adds molecule/structure data to a JChemExcel workbook.
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.Structure checker result for substructure-based checks.
Fixer to fix substructure issues.
Superatom S-group.
Supported OLE types being converted
Swing utility functions.
This class is a tool for exporting molecules from database tables into an
OutputStream object.
Tool for importing molecules to database tables from a File
or InputStream object.
Class for storing options for structure table creation.
SDF table options for MarvinView.
Class for collecting table statistics.
Viewer table support class.
Constants for importing/exporting structures
Exception indicating errors during import and export.
Interface representing table type related constants.
Provides methods for handling structure tables.
Represents a database row (record).
Error occurred during some update in database.
Base interface for calculator objects that can report a set of optional tags, which are used primarily to identify
the calculator in configuration files.
General interface of classes that are used by calculators to check if they can process an input molecule.
Option to control homology matching on target side.
Tautomer equality mode.
Standardizer action that generates canonical tautomer form of the molecule.
Tautomer form to be used by
TautomerizeAction.Plugin class for generating tautomer structures.
Shows the way tautomer substructure search is handled.
Tautomer transformation mode.
TemplateWriterOptions class is the default/basic implementations of the template writer options interface.
Tetrahedral stereo center implementation.
Tetrahedral stereo descriptor.
Tetrahedral stereo descriptor.
A descendant of
AtomChecker detecting atoms with 3D coordinates (non-zero Z coordinates).Calculates topological data.
Provides functions for analyzing the topology of a molecule.
Implements TPSA (Topological Polar Surface Area) value as a scalar descriptor.
Plugin class for TPSA (topological polar surface area) calculation.
Data object to store lookup information for MTransferable objects.
Transformation matrix in three-dimensional space.
Standardizer action that applies a specified transformation to the molecule.
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 moleculeStandardizer action that ungroups S-groups of the molecule.
Standardizer action that removes atom map numbers from the molecule.
Exception class which helps to differentiate query problems from others.
A descendant of
AbstractStructureChecker detecting unused R-group definitions.Represents the settings of the MarvinSketch and MarvinView applications.
Provides options for valence calculation.
Builder for ValenceCheckOptions.
A descendant of
AtomChecker detecting atoms with invalid valences.Molecule filter that excludes molecules having valence errors.
A descendant of
AbstractStructureFixer which fixes valence problem in the
molecule if it is possible with removing explicit hydrogens or by adding chargeA descendant of
AtomChecker detecting atoms having an
explicitly set valence property.Provides version information of Chemaxon products.
Parameters of
MViewPane.Uses Ward's minimum variance method for clustering molecules based on
molecular fingerprints or other descriptors.
Standardizer action that rearranges the wedge bond representations of the molecule.
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.Factory class for creating workbook reader instances.
This class implements the default conversion from XML to HTML.