MarvinSketch: parameters and events

Version 5.0.0

Contents

  1. Parameters
    1. Applet only parameters
 

1   Parameters

Parameters of the MSketch and JMSketch applets can be set using the <param> HTML tag.

ParameterMeaningDefault
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
statusBar Enable the status bar. 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 Deprecated. No more any effect of this parameter.  
molbg Molecule background color in hexa. Sets the background color of the molecule canvas. See also: background  
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
wireThickness Line thickness for "wireframe" and "wireknobs" rendering modes, in Angstroms. 0.064
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
atomFont Atom symbol/label font: Serif, SansSerif or Monospaced SansSerif
atomsize Atom symbol font size in C-C bond length units:
atomsize*1.54 Å = atomsize*scale points
0.4
bondSpacing Double bond spacing in C-C bond length units:
spacing*1.54 Å = spacing*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"     General aromatization
"a_bas" or "+a_bas"     Basic aromatization
"-a" dearomatization
"H" or "+H"     add explicit H atoms
"-H" remove explicit H atoms
"c" automatic cleaning
  
cleanOpts Options for 2D or 3D cleaning.
cleanOpts accepts the same parameter values as clean2dOpts or clean3dOpts depending on the cleaning dimension (cleanDim). 		 
clean2dOpts Options for 2D cleaning (0D->2D) See base 2D cleaning options  
clean3dOpts Options for 3D cleaning (0D->3D) See base 3D cleaning options  
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 aliases
  • pseudo - pseudoatoms
  • 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 set name, file is the sdf or cssdf file containing the template structures and the option - defines a separator line over the template name in the menu.

The file can be optionally compressed with GZIP (Java >= 1.1). A template molecule is automatically converted to 2D if the mol2dcmd field contains one of the following values:

  • z=0 - for trivial conversion,
  • clean - for sophisticated 2D cleaning.
For automatic 3D conversion, the value of the mol3dcmd field must be
  • clean - for sophisticated 3D cleaning.
Template buttons may have a title if the abbreviation fields are specified. A button is rotatable if the rotation.unit field is specified (the unit rotation angle in degrees). For template tables, endrow=E can be specified for molecules in the last column. If it is not set for any molecule, then the best number of columns and rows are calculated automatically.

click here
ttmpls0
ttmpls1
ttmpls2
... 		Templates for the toolbar. Same as tmpls but these template tables must contain only one row to fit in the toolbar. 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, cxsmiles, cml, pdb, pov, sybyl, or xyz. mol
bondDraggedAlong Bond in hand is visible (true) or not (false). This option can also be set from the Edit/Preferences/Sketching menu. true
debug Debug mode. Possible values: 0, 1, 2. 0
bondLengthVisible Shows bond length labels
  • true - display
  • false - do not display
 false
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
lonePairsVisible Show lone pairs
  • true - display
  • false - do not display
 false
valenceErrorVisible Highlight (by underlining) the labels of those atoms with valence errors. This option can also be set from the Edit/Preferences/Sketching 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 Edit/Preferences/Sketching menu.
  • true - display rectangle
  • false - do not display rectangle
 true
grinvVisible Set visibility of graph invariants.
  • true - show graph invariants
  • false - hide them
 false
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
addRemoveHatomsEnabled Add/Remove -> Explicit Hydrogens is enabled or disabled in the Edit menu. It will be disabled if this parameter is false. true
2dviewerEnabled 2D viewer is allowed or not.
  • true - enabled
  • false - disabled
 true
3dviewerEnabled 3D viewer is allowed or not.
  • true - enabled
  • false - disabled
 true
copyOpts Output formats for the copy command. To specify more formats, enumerate them in a comma separated list.
  • text - Copy As Text
  • bitmap - Copy As Bitmap Image
  • emf - Copy As Vector Graphical Image (EMF)
 platform dependent
defaultSaveFormat Determines the default chemical file format in the Save As dialog. mrv
customizationEnabled Specifies whether an end-user can customize the user interface. Setting this parameter to false disables the View/Customize dialog and the View/Configurations menu. true
menuconfig Specifies an alternative menu customization file location instead of the default .chemaxon/{MarvinSketch_version}/customization.xml (Unix) or chemaxon/{MarvinSketch_version}/customziation.xml (Windows) file under the user's home. Please note that if this parameter is used, the customizationEnabled parameter is defaults to false.  
shortcuts Specifies an alternative shortcut customization file location instead of the default .chemaxon/{MarvinSketch_version}/shortcuts.xml (Unix) or chemaxon/{MarvinSketch_version}/shortcuts.xml (Windows) file under the user's home. Please note that if this parameter is used, the customizationEnabled parameter is defaults to false.  
sketchAnyBond How to draw any bond in sketcher.
  • auto - dashed line in most cases, solid line only when all bonds are generated from atom coordinates (e.g. XYZ and PDB files).
  • dashed - draw dashed line
  • solid - draw solid line
 auto
viewAnyBond How to draw any bond in viewer.
  • auto - dashed line in most cases, solid line only when all bonds are generated from atom coordinates (e.g. XYZ and PDB files).
  • dashed - draw dashed line
  • solid - draw solid line
 auto
rgroupsVisible Show (true) or hide (false) R-group definitions. true

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>

1.1   Applet only parameters

The following parameters are meaningful only for the applets (MSketch, JMSketch) and not for the JavaBean (MSketchPane).

ParameterMeaningDefault
menubar Enable the embedded menubar. true
buttonmenubar Enable menubar in button (/hide) mode if the menubar parameter is true. Combine it with the detach parameter to set the button mode.
True, to allow, false to deny menu bar on the big sketcher button.		 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
undetachByX Sketcher window close (x) behavior.
false: always hide sketcher
true: replace viewer component by sketcher in web browser window if the applet is large enough (>= 400x300) 		true
mol The molecule file to be loaded at startup, as either a URL or the file itself (inline) in MDL mol, compressed mol, SMILES or SMARTS 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 Deprecated  
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 		 
imageSaveFormat The default file format for image saving. png
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:
namedescription
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 		 
molLoaderFinishedEvent Evaluates a JavaScript code after the loading of the molecule into the editor is finished. This "event" is invoked if molecule is loaded-in into the applet in any of the following cases:
  • Automaticaly, at applet starting: (using the mol applet parameter)
  • Calling (J)MSketch.setMol(...) from JavaScript.
Note: If the MAYSCRIPT option is not specified, JavaScript can not be evaluated from the applet. E.g.:
     msketch_mayscript=true;
     msketch_begin("marvin",400,300);
     msketch_param("mol","caffeine.mol");
     msketch_param("molLoaderFinishedEvent","js:alert('Molecule is loaded-in.')");
     msketch_end();
 
listenpropertychange Switch on/off property change event listener to the applet. If listener is active, the applet will call propertyChange(prop) JavaScript method. If you would like to handle property change events in JavaScript, implement this method in your html source. Note: If the MAYSCRIPT option is not specified, JavaScript can not be evaluated from the applet. E.g.:
     function propertyChange(prop) {
        if(document.textform != null) {
            var s = document.textform.txt.value;
            document.textform.txt.value = s + "\n" + prop;
        }
     }

     msketch_mayscript=true;
     msketch_begin("marvin",400,300);
     msketch_param("listenpropertychange","true");
     msketch_end();
false
skin Change the component's Look & Feel (only in SWING applet). 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