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.
use
SetAbsoluteStereoAction or
RemoveAbsoluteStereoAction insteadType 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.
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 interfaceAn implementation of
ConfigurationReader for parsing action stringsAbsent 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
AlignmentAPIConformational flexibility treatment during the alignment for a pair of a molecule.
Overlays two molecules using the user defined atom pairs
Example:
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.AROMATICITYA 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.
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.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.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 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.
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.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 based meta data for
StructureChecker
implementationsThe descendant of CheckerRunner interface has to provide the functionality to run
on the given molecule and fix the problems with the associated
Example:
CheckerRunner can be used directly with the
StructureChecker instances automaticallyon 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
implementationsInterface 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
2dUtility 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!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.
Descendants of the abstract ComponentChecker class implement detect problems related to
disconnected components (fragments).
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.
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 contracting s-groups of the target molecule
A descendant of
AbstractStructureFixer which converts the aliases to
contracted abbreviated groups in the moleculeThis 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 moleculeA descendant of
AbstractStructureFixer which converts the aliases to
atom with atom number contained in the alias informationA descendant of
AbstractStructureFixer which converts pseudo atoms to
carbon atomsA descendant of
AbstractStructureFixer which sets wiggly bond to
crossed double bondA descendant of
AbstractStructureFixer which converts the isotopes to non isotope atomsConvert 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 wigglyDetects 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.
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
StructureCheckerResultSimple class for generating molecular descriptors (fingerprints).
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
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.
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
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.
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.
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 moleculeStandardizer 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.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
implementationsComparator 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 fixerThis annotation is used to annotate the
StructureFixer implementations which
error codes (identified by a unqie String) can be fixed by the current fixerfix mode options
Flips wedge bonds.
Molecular formula generation settings.
Chemical formula based search class.
Abstract class to handle common export options.
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.
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.
Calculates hydrophilic-lipophilic balance (HLB) of a molecule.
Builder class for HlbPlugin.
Option type describing the scope of homology matching.
HTTP Request based
ServiceDescriptor implementation
for HTTP POST/GET based servicesServiceHandler implementation for HTTP ServicesPlugin class for Huckel Analysis calculation.
Hybridization state constants.
Addition and removal of explicit hydrogens or lone pairs.
Extends
ImageExportBaseUtil with additional methods.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.
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.
Manages parameters for the
LogD scalar descriptor class.Service Descriptor for java based local services.
ServiceHandler implementation for LocalServiceDescriptorImplements 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.
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 incrementallyProvides support for mapping parts of <T> instances by finding the matching parts and mark them with the same
identifier.
Available mapping styles by
MapperMap 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.
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.
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:
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.Base class for all kinds of
MolecularDescriptor generators.Exception definition for the
MolecularDescriptor.generate()
interface.Molfile compression.
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.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.
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.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.
Moved to
MolecularFormulas.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.
As of Marvin 6.0, replaced by
MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions) and
ValenceCheckOptions.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.
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.Neutralization standardizer action
A descendant of
AbstractStructureFixer which neutralize the charge of the atoms of the moleculeClass 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 (
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 (
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
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 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 persistedThe
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.Plugin class for macro/micro pKa calculation.
PKa training result object.
Exception thrown in case of plugin processing or calculation errors.
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.Work unit performing plugin calculation.
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.Observer for reporting the progress of long running tasks.
A descendant of
AtomChecker detecting pseudo atoms.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.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.
ReactionFingerprint class.A descendant of
Reaction components should contain at least two mapped atoms, otherwise they are considered incorrectly mapped.
ReactionChecker detecting reactions with invalid mapping.Reaction components should contain at least two mapped atoms, otherwise they are considered incorrectly mapped.
A descendant of
AbstractStructureFixer which rearomatize the moleculeRearranges stereo wedge bonds according to IUPAC recommendations.
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.
A descendant of
AbstractStructureChecker detecting molecules having
multiple stereogenic center groupsDate 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 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 moleculeRemove 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 resultFixer 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 moleculeRemove 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 moleculeFixer 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
ServiceDescriptorProvides
ServiceDescriptorEditor instances based on ServiceDescriptor classes.Reader for
ServiceDescriptorsWriter for
ServiceDescriptorsProvides
Dialog instances to provide argument editor and result view for ServiceDescriptorException for failure indication for services.Manages service calls.
ServiceHandler keeps track of the previous call and if it is not yet finished cancels it.
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.
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.
Search interface for different Molecule-Molecule search types.
Factory for creating
SimpleSearcher instances.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
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:
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.
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
See the documentation for details: User's Guide Configuration Developer's Guide
Interface of standardizer actions.
Descriptor of
Contains all needed interface informations.
StandardizerAction objects.Contains all needed interface informations.
Factory of
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
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
This annotation is responsible for adding user interface related meta data for
StandardizerAction
implementationsThe descendant of
As standardizer configuration may contain actions in groups, using
By default, in case of the provided configuration containing error(s) the runner throws
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
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
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\{'"})*
StandardizerConfigurationReader for parsing
action stringsIf 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
Contains a list of
StandardizerAction instances.This interface is provided for classes which can read the configuration of
Configuration error
There are 2 kinds of configuration errors for execution configuration.
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.
Functionalities of old standardizer can be simulated using this class.
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:
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
StructureCheckerEnum containing possible error types for structure checkers.
Deprecated.
use
CheckerFixerFactory insteadAn instance of
StructureCheckerResult identifies a molecule problemUtility 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.
Descriptor class for
StructureFixer classes.Deprecated.
use
CheckerFixerFactory insteadDenotes 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.
Viewer table support class.
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.
Transformation standardizer action
Exception thrown during transformation.
Transformer.
Creates
Molecule Transformer objects.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 un-groups s-groups of the target molecule
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.An interface for providing upper bound calculation for
MaxCommonSubstructure (MCS) search.Represents the settings of the MarvinSketch and MarvinView applications.
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 chargeA 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
The parameters of the JMView applet can be set using the
<param> HTML tag.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.