| reactionquerydrawing | Draw reaction query |
| importexport | Core classes for import / export modules |
| license | License manager |
| drawing | Drawable components |
| util | Frequently used utility classes |
| concurrent | Concurrent processing |
| logging | Extra classes for logging |
| view | MarvinView GUI core classes |
| sketchstart | Core classes that are called by MarvinSketch startup |
| lwsketchmenu | Classes to load menu in MarvinSketch from file |
| sketchmenu | Classes to load menu in MarvinSketch without file |
| sketchmenubg | Extra classes for menu in MarvinSketch |
| sketchbackground | Menu actions and other resources that are not required immediately by MarvinSketch startup |
| sketch | Core MarvinSketch classe |
| smarts | Smarts module |
| nullexport | Dummy Null export module |
| smilesimport | SMILES import |
| molimport | MDL mol format import |
| sybylexport | Tripos Sybyl export |
| sybylimport | Tripos Sybyl import |
| mol2export | Tripos Mol2 export |
| mol2import | Tripos Mol2 import |
| mrvexport | MRV export |
| cmlexport | CML export |
| cdximportexport | CDX import/export |
| gzipexport | Gzip export |
| gzipimport | Gzip import |
| base64export | Base64 export |
| base64import | Base64 import |
| xyzexport | XYZ export |
| inchi | IUPAC InChi import/export |
| hydrogenize | Hydrogenize module |
| pdbexport | PDB export |
| spacefill | Spacefill module |
| atomlabellers | Module for drawing atom labels |
| superatomsgroupcoords | Superatom Sgroup Coordinates module |
| threedim | 3D utility functions |
| xyzimport | XYZ import |
| goutimport | Gout import |
| gjfexport | Gjf export |
| charmmimport | CharmmGrid import |
| pdbimport | PDB import |
| jpegexport | Jpeg export |
| msbmpexport | MS BMP image export |
| pngexport | PNG image export |
| ppmexport | PPM image export |
| povexport | POV image export |
| svgexport | SVG graphics export |
| vectgraphicsexport | PDF grapics export and old EMF graphics export |
| imageexport | common classes for various image export modules |
| documenthandling | Document handling |
| mchart | MChart module |
| abbrevgroups | Abbreviation groups dialog |
| reaxysgenerics | Generic groups dialog |
| abbrevgroupexport | Abbreviationgroup export |
| clean2d | Clean 2D |
| clean3d | Clean 3D |
| modelling | Modelling package |
| atommapper | Mapping atoms |
| singlelinerecordreader | SingleLine record reader |
| nameexport | IUPAC name export |
| nameimport | IUPAC name import |
| peptidevmnimport | Peptide and VMN import |
| peptideexport | Peptide export |
| skc | Skc file format import/export |
| common.swing.aboutjvm | About dialog |
| common.swing.editmolfileframe | EditMolfile frame |
| common.swing.exceptionframe | Exception frame |
| common.swing.help | Help dialog |
| common.swing.loadsave | Load/save dialog |
| common.swing.print | Print module |
| common.swing.regenbonds | Regenerate bonds |
| common.swing.preferences | Preferences dialog |
| common.swing.fontediting | Font attributes panel |
| sketch.edit | Utility for S-groups |
| sketch.linesm | Polyline drawing mode |
| sketch.boxsm | Rectangle drawing |
| sketch.bracketsm | Bracket drawing |
| sketch.swing.periodicdialog | Periodic system dialog |
| sketch.swing.rlogicdialog | Rlogic dialog |
| sketch.swing.groupcreationdialog | Create group dialog |
| sketch.swing.attachdatadialog | Attach data dialog |
| sketch.swing.textboxeditor | Text box editor |
| sketch.swing.templates | Handling templates |
| sketch.swing.mobjectpropertiesdialog | Graphical object properties dialog |
| sketch.swing.guiconfigurationdialog | Menu configuration dialog |
| view.scripter | Helper class for handling JavaScript invokes |
| view.swing.viewdnd | Drag and drop in MarvinView |
| view.swing.imageviewframe | Image viewer frame |
| view.swing.mviewanimator | Molecule rotation in MarvinView |
| view.swing.mviewframe | Popup MarvinView frame |
| view.swing.mviewsketch | Popup MarvinSketch frame from MarvinView |
| view.swing.printview | Additional resource for print in MarvinView |
| view.swing.molsframe | Display multiple molecules in a separate frame |
| view.swing.tableview | Spreadsheet table renderer |
| view.swing.gridbagview | Moleculematrix table renderer |
| view.swing.find | Find dialog |
| view.swing.showconformers | Display conformers |
| Plugin | Core and GUI classes for calculator plugins |
| plugins.Alignment | Alignment plugin |
| plugins.CalculationsCore | Core classes needed for calculator plugins |
| plugins.Protonation | Protonations plugins |
| plugins.Partitioning | Partitioning plugins |
| plugins.Tautomers | Tautomer plugins |
| plugins.Analysers | Analyser plugins |
| plugins.MolecularModelling | Plugins for molecular modelling |
| plugins.MarkushEnumeration | Markush enumeration plugin |
| plugins.Other | Other plugins |
| checkers | Various structure checkers |
| propertyeditor | Classes for editing atom/bond/molecule properties |
| jep | jep package |
| icons | Icons mainly for the menus |