| |
Marvin unsigned
applets |
Marvin signed
applets1 |
Marvin Beans and
applications |
| Cut/Copy/Paste |
inside Marvin |
yes |
yes |
| Drag & Drop |
no |
yes2 |
yes |
1: You can find more info about signed Marvin applets in the
following documents:
Applet platforms,
Signed applets
2: Drag & Drop works only when the sketcher is in its own window.
When the applet is in the browser window, drop events are received by the
browser instead of the applet.
Copy, Copy as Smiles
Marvin has two commands to place objects on the clipboard: Copy
and Copy as Smiles.
- Using the Copy command, the structure is copied to the clipboard in
a couple of formats. The molecule always will be there in mrv,
MDL Molfile and DayLight SMILES formats. The other formats (like
Plain Text or Bitmap Image) are optional.
See the table in the Clipboard formats
section about supported options and default settings.
- Using the Copy as Smiles command, the Smiles string of the structure
is copied to the clipboard in
String and Plain Text
formats.
Note:Any file format of
Marvin can be copied to the clipboard as a string or as
plain text. From the
Edit menu choose Source then
Edit/Copy to place the desired format on
the clipboard as plain text.
Clipboard formats
Marvin can place more than one clipboard object on the clipboard, each
represents the same molecule in different format.
Copy from Marvin supports the following representations:
- Marvin Document (mrv): Marvin's own format. Only
Marvin can paste it.
- MDL Molfile: a popular molecule description format.
A lot of chemical drawing tool can paste it like Marvin, ChemDraw, etc.
- Daylight SMILES: wide range molecule format. Several chemical editor
can paste it. In a few editor, SMILES can not be pasted directly. E.g.
ChemDraw uses the "Paste Special/SMILES" option to copy SMILES from the
clipboard.
- Plain Text (molecule in SMILES): To be able to copy
the molecule source into text editors or into other application that do not
support chemical formats.
- Bitmap Image: To paste molecule image into presentations
or into documents.
- Vector Graphical Image (EMF): The vector graphics is
scalable unlike bitmap image. It can be pasted into MS-Office
documents or into other applications that support Enhanced MetaFile format.
A couple of formats are not available on a few platforms.
Furthermore, you can also apply or deny the
accessibility of one or more copy formats. You can set it by the following ways:
| Format |
Windows |
Mac OS X |
Linux |
| Java 1.3.x |
Java 1.4
and aboves |
Java 1.3.x |
Java 1.4
and aboves |
Java 1.3.x |
Java 1.4
and aboves |
| Marvin Document (mrv) |
+D | +D |
+D | - |
+D | +D |
| MDL Molfile |
+D | +D |
+D | - |
+D | +D |
| Daylight SMILES |
+D | +D |
+D | - |
+D | +D |
| Plain Text (molecule in SMILES) |
+D | + |
+D | + |
+D | +D |
| Bitmap Image |
- | + |
- | + |
- | +D |
| Vector Graphical Image (EMF) |
- | +D |
- | - |
- | - |
|
|
| + | supported |
|---|
| - | not supported |
|---|
| D | selected as default |
|---|
|
When the content of the clipboard is pasted into an application (and
its available in more than one format), the
application retrieves data in the most descriptive format.
Most versions of Microsoft Office prefer pasting image instead of
text if the content of the clipboard is available in both formats.
But there are a few ones that paste text as default. In that case, you should
use "Paste As Special" option in MS-Office to paste it as image but it can be
unconfortable to someone.
The workaround can be the restriction of the text copy from Marvin.
That is the reason why text copy is disabled in the default settings of Marvin
(on a couple of platforms).
In that case, we recommend Copy as SMILES to paste text into MS-Word and
in other editors.
Another solution can be the changing the default options of the Copy
command (see above howto do it).
If we compare Bitmap and Vector Graphical Image formats, the
situation is the same than in the previous case (text vs. image). Most of the
applications prefer bitmap image although they can accept vector graphical
images as an Enhanced MetaFile (EMF), like MS-Word. Since vector graphics
are scalable unlike bitmap images, we have chosen EMF as default from image
formats (where it is supported).
Data transfer between Marvin and other chemical drawing tools
| |
Windows1 |
Macintosh OS X |
| Java 1.3.x | Java 1.4.x4 |
| ISISDraw2 |
Copy & Paste |
Copy & Paste |
Copy & Paste |
| ChemDraw |
Copy & Paste |
Copy & Paste |
Copy & Paste |
| ChemDraw Plugin |
Copy & Paste |
Paste 3 |
Paste |
|
|
Copy: copy a structure from the application into Marvin
Paste: copy a structure from Marvin into the application
|
1: On windows in Java 1.2-1.3.1, the
<Java home directory>/jre/lib/flavormap.properties file must be edited:
MDLCT=chemical/x-mdl-Molfile
2: In case of ISISDraw the following option must be
checked: Option -> Settings -> General -> Copy Mol/Rxnfile to the
Clipboard
3: Copy as SMILES works
4: In OS X, since Java 1.4, data transfer in chemical formats does
not work. In that case, molecule can be pasted only as image or text into
chemical drawing tools.
Copy from an application to Marvin works if the application can place data
as Plain Text to the clipboard.
Data transfer between Marvin and other applications
Marvin can paste SMILES strings, MDL MolFiles, etc. from a text editor
as molecules.
X Window System: most text editors (xedit, emacs, gvim, etc.) do not
transfer data to the X clipboard, so Marvin is unable to communicate with them.
Copy & Paste works with the following editors and other programs:
- GNOME programs: gedit, gnotepad+ (gnp), gxedit, etc.
- Motif programs: asWedit, nedit, Netscape, etc.
Note: With the xclipboard program, you can test
whether your favorite editor uses the X clipboard or not.
|