MarvinSketch: parameters and events

Contents

1. Parameters
   1. Applet only parameters
2. Events fired by the JavaBean
   1. Action events
   2. Property change events

1   Parameters

Parameter	Meaning	Default
autoscale	How to display a loaded molecule: "true" - fit to the applet's window "false" - use default scaling	false
viewonly	Visualization mode: hide editing buttons; "true" or "false".	false
verticalbar	Enable vertical button bar and move atom, bond and edit buttons from the horizontal bar to the vertical; "true" or "false".	false
dispQuality	Display quality. 0 - low quality, faster rendering 1 - high quality (antialiasing), slower rendering	1
implicitH	How to display H labels. off hetero - on heteroatoms heteroterm - on hetero or terminal atoms all - all atoms	heteroterm
explicitH	Show explicit hydrogens.	true
chiralitySupport	When to show atom chirality (R/S). off - never selected - if chiral flag is set for the molecule or the atom's enhanced stereo type is absolute all - always	off
ezVisible	Show (true) or hide (false) E/Z labels.	false
background	Background color in hexa.
molbg	Molecule background color in hexa.
colorScheme	Color scheme. mono - monochrome cpk - Corey-Pauling-Kultun shapely - shapely (residue types) group - residue sequence numbers	cpk
rendering	Rendering style. wireframe - wireframe wireknobs - wireframe with knobs sticks - 3D sticks ballstick - ball & stick spacefill - balls	wireframe
stickThickness	3D stick diameter for "sticks" and "ballstick" rendering modes, in Angstroms.	0.1
ballRadius	Ball radius for "ballstick" rendering mode, in units of covalent radius.	0.5
scale	Magnification. A 1.54 Å long C-C bond is magnified to scale pixels.	26.4
atomsize	Atom label font size in C-C bond length units: atomsize*1.54 Å = atomsize*scale points	0.4
bondWidth	Width of double bond in C-C bond length units: width*1.54 Å = width*scale pixels	0.18
stickdst	Stick distance of atoms in C-C bond length units.	0.3
mergedst	Merge distance of atoms in C-C bond length units.	0.1
downWedge	Wedge bond display convention. Down wedge points downward in MDL's convention (mdl), upward (at the chiral center) in Daylight's (daylight).	mdl
importConv	Conversion(s) after molecule loading. Currently the following options are implemented: "a" or "+a"     aromatization "-a" dearomatization "H" or "+H"     add explicit H atoms "-H" remove explicit H atoms "c" automatic cleaning
cleanOpts	Options for cleaning (2D or 3D, depending on cleanDim)
clean2dOpts	Options for 2D cleaning (0D->2D) O0 - no optimization O1 - optimize if needed O2 - optimize	O1
clean3dOpts	Options for 3D cleaning (0D->3D) O0 - lightweight optimization OD - Dreiding optimization	O0
cleanDim	Number of space dimensions for cleaning. 2 - two-dimensional cleaning 3 - three-dimensional cleaning See also: cleanOpts, importConv.	2
showSets	Show the specified atom sets only. Comma separated list of set sequence numbers (0, ..., 63).
setColoringEnabled	Atom/bond set coloring.	true
atomSetColor0 atomSetColor1 ... atomSetColor63	Atom set color in hexa.
bondSetColor1 ... bondSetColor63	Bond set color in hexa.
undo	Maximum number of undo operations.	50
moreEnabled	Enable/disable the More button.	true
elements	Comma-separated list of allowed elements (H, He, Li, ...). All elements in an atomic number interval can be specified with the short X-Y notation. Example: "B-F,P-Cl". Here B-F is equivalent to B,C,N,O,F.	H-Ha
queryAtoms	Comma-separated list of query atoms and properties. any - any atom ("A" in molfile, "*" in SMARTS), arom - aliphatic and aromatic, ("a" and "A" in SMARTS), conn - total number of connections, ("X" in SMARTS), H - total number of hydrogens, ("H" in SMARTS), hetero - heteroatom ("Q" in molfile, "[!C!H]" in SMARTS), list - atom list, notlist - atom 'NOT' list, Rgroup - Rgroups, rings - "R" in SMARTS, srs - smallest ring size, "r" in SMARTS, val - valence, "v" in SMARTS, Example: "list,notlist". See also: Query properties in file formats.
atomStrings	Comma-separated list of string type atom properties. alias - atom alias, used in molfiles smarts - SMARTS query atom string Example: "smarts".
extraBonds	Comma-separated list of extra bond types. arom - Aromatic bond, any - Any bond, 1or2 - "Single or Double" query bond, aromany - "Single or Aromatic" and "Double or Aromatic" query bond types, topology - "Chain" and "Ring" bonds (in molfiles), wedge - Up and Down stereo wedge bonds, either - "Up or Down" and "Cis or Trans", ctu - "Cis or Unspecified" and "Trans or Unspecified". Example: "arom,wedge". See also: Query properties in file formats.
reactionSupport	Enables/disables reaction arrow drawing.	true
tmpls0 tmpls1 tmpls2 ...	The format of this parameter is :name:file, where name is the template group name, and file is the sdf or cssdf file containing the template structures. The file can be optionally compressed with GZIP (Java >= 1.1). A button can be rotatable if the rotation.unit fields are specified in the SDfile (the unit rotation angle in degrees). For template tables, the endrow fields must be specified for templates that are last in a row. Template tables are shown in their own window. Template buttons may have a title if the abbreviation fields are specified in the SDfile.	click here
xtmpls	File containing extra templates. Extra templates are left to the normal templates (see tmpls) in the template panel.
abbrevgroups	File containing the abbreviated groups.	chemaxon/marvin /templates /default.abbrevgroup
molFormat	Default file format: mol, csmol, smiles, cml, pdb, pov, sybyl, or xyz.	mol
simpView	Switches on/off "visual fragment placement". 0 - show all 1 - hide bonds 2 - hide bonds and templates This option can also be set from the View/Misc/Object in hand menu.	0
debug	Debug mode. Possible values: 0, 1, 2.	0
atomSymbolsVisible	Shows atom symbols true - display false - do not display	true
atomNumbersVisible	Show atom numbers true - display false - do not display	false
atomMappingVisible	Show atom mapping true - display false - do not display	true
valenceErrorVisible	Highlight (by underlining) the labels of those atoms with valence errors. This option can also be set from the View/Misc/Valence Errors menu. true - display errors false - do not display errors	true
reactionErrorVisible	Highlight invalid reactions with a red rectangle around the reaction arrow. You can also change its value from View/Misc/Reaction Errors menu. true - display rectangle false - do not display rectangle	true
grinv	Set visibility of graph invariants. true - show graph invariants false - hide them	false
skin	Change the component's Look & Feel (only in SWING). If you do not specify this parameter, Marvin will use the default LookAndFeel style. This parameter value is the name of the new LookAndFeel class.	javax.swing.plaf .metal .MetalLookAndFeel
sketchHelp	Sketcher help contents.	chemaxon/marvin/help /sketch-index.html
sketchQuickHelp	Sketcher quick help.	chemaxon/marvin/help /sketch.html
viewHelp	Viewer help contents.	chemaxon/marvin/help /view-index.html
viewQuickHelp	Viewer quick help.	chemaxon/marvin/help /view.html

Applet example:

<applet CODE=MSketch WIDTH=480 HEIGHT=400>
<param NAME="background" VALUE="#cccccc>
<param NAME="molbg" VALUE="#ffffff">
<param NAME="implicitH" VALUE="hetero">
</applet>

MSketchPane sketchPane = new MSketchPane();
sketchPane.setParams(
    "background=#cccccc\n"+
    "molbg=#ffffff\n"+
    "implicitH=hetero\n");

1.1   Applet only parameters

Parameter	Meaning	Default
menubar	Enable the embedded menubar in the Swing applet.	true
detach	Detachment behavior. The value consists of two optional arguments, show/hide and size . If both arguments are included, they must be separated by a comma. To detach the sketcher from the web page and display it in a window, set "show". To detach the sketcher but do not display the window, set "hide". Both settings make the applet on the web page look like a molecule viewer. The initial size of the sketcher window can be specified with "size=widthxheight" Examples: "show", "size=500x500", "hide,size=500x500".	size=444x350
mol	The molecule file to be loaded at startup, as either a URL or the molfile itself (inline) in MDL mol or compressed mol format. If you specify the molfile inline, then you must end all the molfile lines with "\" (backslash). The file format and/or import options can be specified if one of the following forms is used: "file(options)", "file(MULTISET,options)", "file(format:)", "file(format:options)", or "file(format:MULTISET,options)". If the MULTISET option is specified, then a multi-molecule file is read into one molecule object containing multiple atom sets. Examples: "foo.xyz(f1.4C4)", "foo.xyz.gz(gzip:xyz:MULTISET,f1.4C4)"
preload	Comma-separated list of external modules to preload. External modules are class files in the chemaxon/marvin/modules directory. module argument of getMol() call that requires it MolExport "mol", "csmol" SmilesExport "smiles" CmlExport "cml" Parity "mol", "smiles" (but not "smiles:0") PdbExport "pdb" PovExport "pov" SybylExport "sybyl" XYZExport "xyz" Note. Preloading is required if you call getMol from JavaScript in a buggy browser/JVM combination. Without preloading, getMol might freeze Netscape 6 (Sun Java 1.3) and Netscape 3 would also fail because these browsers cannot call network functions from JavaScript.
cacheMols	Store loaded molecules in an internal cache (true or false).	false
loadMols	Comma-separated list of molfiles to preload. Useful for caching molecules in JavaScript "slideshows".
usedJars	Comma-separated list of additional jar files that can be used by the applet. The additional files have to be defined with their paths relative to the applet's base.
imageSaveURL	The URL of the cgi, jsp or asp file use to save the image posted by the applet to the server. The cgi has to read the image from the standard input into a byte array, save it to a temporary file and send back the absolute path of the file to the applet. A jsp example: saveimage.jsp
imageShowURL	The URL of the cgi, jsp or asp file that either saves the data into a file generated by the applet or shows the generated image that was saved to a temporary file by imageSaveURL. The posted parameters: name description filename If the applet generated an image, it was saved into a temporary file on the server. In this case this parameter contains the absolute path of the temporary file. type Sets the type of the file and its extension. It can be: "mol", "csmol", "pdb", "sybyl", "xyz", "jpeg", "png", "pov", "svg". where Sets the location in which the image will be "shown" Possible values: "file", "browser", null. "file" - the generated data will be saved into a file. "browser" - the data will be displayed in a browser window. data If the applet generated a kind of molecule format file (see: formats), it is posted by this parameter. In this case the text file have to be saved as a file. A jsp example: showimage.jsp

2   Events fired by the JavaBean

2.1   Action events

Source name	Source component type	Meaning
"close"	javax.swing.JMenuItem	File/Close has been chosen, sketcher window should be closed.

Example:

sketchPane.addActionListener(this);
    ...

public void actionPerformed(ActionEvent ev) {
    if(ev.getSource() instanceof JComponent) {
	String name = ((JComponent)ev.getSource()).getName();
	if(name.equals("close")) {
	    dispose();
	}
    }
}

2.2   Property change events

Property name	Type	Meaning
"mol"	Molecule	Molecule changed.
"file"	java.io.File	Molecule file changed from File/Open or File/Save As.
"implicitH"	String	Implicit Hydrogen display style changed.
"explicitH"	Boolean	Explicit Hydrogen display style changed. true: show explicit H atoms false: hide explicit H atoms
"colorScheme"	String	Color scheme changed.
"autoscale"	Boolean	Autoscale changed.
"rendering"	String	Rendering style changed.
"stickThickness"	Double	Sticks diameter changed.
"ballRadius"	Double	Ball radius changed.
"grinv"	Boolean	Graph invariants displayed/not displayed.
"downWedge"	String	Down wedge bond orientation changed.
"objectAtPointer"	Object	The MolAtom or MolBond object at the mouse pointer.
"invisibleSets"	Long	Visibility of atom sets changed.
"atomNumbersVisible"	Boolean	Visibility of atom numbers changed.
"atomMappingVisible"	Boolean	Visibility of atom mapping changed.
"popupMenusEnabled"	Boolean	Popup menus are enabled/disabled.
"valenceErrorVisible"	Boolean	Visibility of valence errors changed.
"reactionErrorVisible"	Boolean	Visibility of reaction errors changed.

Example:

    sketchPane.addPropertyChangeListener(this);
    ...

public void propertyChange(PropertyChangeEvent ev) {
    String name = ev.getPropertyName();
    if(name.equals("file")) {
	File f = (File)ev.getNewValue();
	if(f != null)
	    setTitle("MarvinSketch: "+f.getName());
    }
}