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. |
AutoMapper | Maps reactant side atoms to product side atoms of a reaction. |
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. |
CxsmilesExport | ChemAxon Extended SMILES/SMARTS export. Uses SmilesExport. |
CxsmilesImport | ChemAxon Extended SMILES/SMARTS import. Uses SmilesImport. |
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. |
MolImportX | Loaded by MolImport if reaction, RGfile or extended (V3) molfile is imported. |
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. |
SmilesImportX | Loaded by SmilesImport if reaction, extra fields or enhanced stereo information is imported. |
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. |
common.swing.AboutJVM common.awt.AboutJVM |
The "About Java VM" window. |
common.swing.EditMolfileFrame common.awt.EditMolfileFrame |
Molfile source viewer/editor window. |
common.swing.ExceptionFrame common.awt.ExceptionFrame |
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.MultiMoleculeSave | |
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. |
sketch.swing.PeriodicFrame sketch.awt.PeriodicFrame |
Window of periodic table of elements and extra atom/bond types. |
sketch.swing.RlogicDialog sketch.awt.RlogicDialog |
R-logic dialog box. |
sketch.swing.SgroupCreationDialog
sketch.awt.SgroupCreationDialog |
S-group creation dialog box. |
sketch.swing.SketchDnD | Drag & drop support for the sketcher. |
sketch.swing.TemplateButtonDnD | Drag & drop support for the templates. |
sketch.swing.TemplateFrame sketch.awt.TemplateFrame |
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. |
view.swing.ImageViewCanvas view.awt.ImageViewCanvas |
Image viewer component in ImageViewFrame. |
view.swing.ImageViewFrame view.awt.ImageViewFrame |
Image viewer window. |
view.swing.MViewAnimator view.awt.MViewAnimator |
Animation player. Runs the thread that plays XYZ movie(s) or spins the molecule(s). |
view.swing.MViewFrame view.awt.MViewFrame |
Viewer window. |
view.swing.MViewSketch view.awt.MViewSketch |
Runs the sketcher from the viewer. |
view.swing.PrintView | Printing. |
view.swing.ViewDnD | Drag & drop support for the viewer. |