Marvin modules

Modules are class files that are not packaged in the applet's JAR file (marvin.jar, jmarvin.jar or sjmarvin.jar) but downloaded at runtime, only as needed.

Common modules in chemaxon/marvin/modules and chemaxon/marvin/common/modules:

Module name Description
AbbrevGroupExport Abbreviated group export. Uses SmilesExport.
AbbrevGroupImport Abbreviated group import. Uses SmilesImport.
Aromata Aromatization. Can be used by any export module (except XYZ, PDB, GZIP) if option "a" is specified.
AtomTypeAssign Used by SybylExport.
BondsFromCoords Used by XyzImport.
Clean2D 2D cleaning.
Clean3D 3D cleaning. (Uses Optimization, Opt3D, DistanceMatrixCalculator.)
CmlExport CML export.
CmlImport CML import. (Uses XmlImport)
CreateImage Off screen image creation support. Currently not used by the applets, only by MolConverter, through ImageExport.
Dearomata Dearomatization. Can be used by any export module (except XYZ, PDB, GZIP) if option "A" is specified.
DiGraphElement Used by Parity.
DistanceMatrixCalculator Used by Clean3D.
FindAllRing Search rings in the graph. Used by Aromata.
GraphInvariants Graph invariant calculation for SmilesExport and Parity.
GzipImport GZIP import.
GzipExport GZIP export.
Hydrogenize Creates explicit H atoms from implicit ones.
ImageExport Creates an Image object from a molecule. Base class of image export modules.
JpegEncoder JPEG encoder, © James R. Weeks and BioElectroMech, Independent JPEG Group. Used by JpegExport.
JpegExport JPEG export.
MolExport MDL molfile and compressed molfile export.
MolImport MDL molfile and compressed molfile import.
MolSelection2 Drags a molecule in a desktop shortcut. Used by MolSelection.
MrvExport Marvin Document export.
MrvImport Marvin Document import. (Uses CmlImport).
Opt3D Used by Clean3D.
Optimization Used by Clean3D.
Parity Stereo parity calculation for SmilesExport and MolExport.
PdbExport PDB export.
PdbImport PDB import.
PngEncoder PNG encoder by J. David Eisenberg. Used by PngExport.

You can freely modify and recompile the source of this module, then replace the binary class file in Marvin with your own version, according to the requirements of the GNU Lesser General Public License.

PngExport PNG export.
PovExport POVRay export.
PpmEncoder PPM encoder, © Jef Poskanzer. Used by PpmExport.
PpmExport PPM export.
ResidueInfo PDB residue information is stored here. Used by PdbImport, PdbExport, CmlImport and CmlExport.
SmilesExport SMILES/SMARTS export.
SmilesImport SMILES/SMARTS import.
Spacefill Spacefill rendering.
SSSR Search SSSR rings in the graph.
SuperatomSgroupCoords Recalculates atom coordinates for residue contraction or expansion.
SvgExport Scalable Vector Graphics export.
SybylExport Sybyl molfile export.
SybylImport Sybyl molfile import.
Threedim 3D utility functions.
XmlImport Base class of XML import modules. Used by CmlImport and MrvImport.
XyzExport XYZ export.
XyzImport XYZ import.

Common GUI modules in chemaxon/marvin/common/awt/modules and chemaxon/marvin/common/swing/modules:

Module name Description
common.awt.About The "About Marvin" window.
The "About Java VM" window.
Molfile source viewer/editor window.
Error message dialog box.
common.swing.Export2dImage Export the molecule in a 2D bitmap or vector graphics format.
common.swing.ExportImage Save Image dialog box. Used by Export2dImage.
common.swing.Help Help window.
common.swing.ImageExportOptsDialog Image export options dialog box (base class).
common.swing.ImageFileFilter Used by ExportImage.
common.swing.JpegExportOptsDialog JPEG export options dialog box.
common.swing.LoadSave File open/save dialog box.
common.swing.MolFileFilter Used by LoadSave.
common.swing.MolSelection Molecule selection object for copy & paste to/from system clipboard, and drag & drop.
common.swing.MolSelectionSmi Used by common.swing.EditMolfileFrame.
common.swing.PngExportOptsDialog PNG export options dialog box.
common.swing.Print Printing.
common.swing.RegenBonds Dialog box with bond generation options. Selecting Edit/Bonds/Regenerate in the menu brings up this dialog.
common.swing.RenderingOptions 3D display options dialog box.
common.swing.SvgExportOptsDialog SVG export options dialog box.

Sketcher modules in chemaxon/marvin/sketch/modules, chemaxon/marvin/sketch/awt/modules and chemaxon/marvin/sketch/swing/modules:

Module name Description
sketch.StringTree String tree. Used for the automatic generation of the Groups menu by PeriodicFrame.
Window of periodic table of elements and extra atom/bond types.
R-logic dialog box.
S-group creation dialog box.
sketch.swing.SketchDnD Drag & drop support for the sketcher.
sketch.swing.TemplateButtonDnD Drag & drop support for the templates.
Window of template molecules.
sketch.swing.TemplatePropertiesDialog Dialog box for setting options of custom templates

Viewer modules in chemaxon/marvin/view/modules, chemaxon/marvin/view/awt/modules and chemaxon/marvin/view/swing/modules:

Module name Description
view.JavaScripter Executes a JavaScript expression with the browser's interpreter.
view.NetscapeJavaScripter Used by JavaScripter.
view.RasMolScripter Interprets RASMol-like scripts.
view.swing.CleanTable Molecule table cleaning thread. Shows a progress monitor when running.
Image viewer component in ImageViewFrame.
Image viewer window.
Animation player. Runs the thread that plays XYZ movie(s) or spins the molecule(s).
Viewer window.
Runs the sketcher from the viewer.
view.swing.PrintView Printing.
view.swing.ViewDnD Drag & drop support for the viewer.