MarvinView: parameters and events

Contents

1. Parameters
   1. Applet only parameters
   2. 3D and animation
   3. Molecule tables
      1. layout
      2. param
      3. celli
2. Events fired by the JavaBean
3. Troubleshooting - MView and JMView tables

1   Parameters

Parameter	Meaning	Default
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 the 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
navmode	Mouse drag action. translate - move the structure zoom - change magnification rotZ - rotate in the screen's plane rot3d - 3D rotation	rotZ
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
winScale	Magnification in the zoom window. A 1.54 Å long C-C bond is magnified to winScale pixels.	26.4
tabScale	Magnification in the molecule table. Each cell has the specified magnification if positive. The scaling is automatic if negative (-1).	-1
autoTabScale	Automatically change scale when component size changed. Only in the swing version, only applicable to the MViewPane bean.	false
atomsize	Atom label font size in C-C bond length units: atomsize*1.54 Å = atomsize*scale points, where scale is the current magnification.	0.4
bondWidth	Width of double bond in C-C bond length units: width*1.54 Å = width*scale pixels, where scale is the current magnification.	0.18
molFormat	Default file format: mol, csmol, smiles, cml, pdb, pov, sybyl, or xyz.	mol
debug	Debug mode. Possible values: 0, 1, 2.	0
selectable	Use selectable=false to forbid molecule selection with mouse click.	true
selection0 selection1 selection2 ...	Comma-separated list of atom numbers (0, ..., n-1). Selected atoms are highlighted. In a simple one-molecule viewer, selection0 must be used. In a molecule table, selectionn corresponds to molecule cell n.
editable	Modes: display only (0) or editable (1, 2). If editable=2, then doubleclick launches MarvinSketch (instead of a viewer window).	0
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
atomSet0.1 ... atomSet0.63 atomSet1.1 ... atomSet1.63 ...	Atom sets. Comma separated list of atom indices (0, ..., n-1). An atom in molecule cell number N will be in set M if its number appears in the atomSetN.M list. By default, all atoms are in set 0.
atomSetColor0 ... atomSetColor63	Atom set color in hexa.
bondSet0.1 ... bondSet0.63 bondSet1.1 ... bondSet1.63 ...	Bond sets. Comma separated list of atom index pairs in i-j format, where i, j = 0, ..., n-1. A bond in molecule cell number N will be in set M if the corresponding atom pair appears in the bondSetN.M list. By default, all bonds are in set 0.
bondSetColor1 ... bondSetColor63	Bond set color in hexa.
showSets	Show the specified atom sets only. Comma separated list of set sequence numbers (0, ..., 63).
setColoringEnabled	Atom/bond set coloring.	true
atomSymbolsVisible	Show 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
grinv	Display graph invariants true - display false - do not display	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
detachable	Enable or disable popping up detached viewer window. If this parameter is true, the selected molecule can be displayed in separate window by selecting "Window" menu item in the popup menu or by doubleclicking on the canvas. Viewer is not detachable if detachable parameter is false. (See also editable.)	true
importEnabled	Allow or forbid molecule import. If this parameter is false, paste function is disabled in MarvinView, also Import option is disabled in the Molecule Source window. (Use editable parameter to forbid the editing of the molecules.)	true
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

Simple viewer applet example:

<applet CODE=MView WIDTH=100 HEIGHT=100>
<param NAME="molbg" VALUE="#a0ffa0">
<param NAME="mol" VALUE="Pyrrole\
...
M  END\
"></applet>

1.1   Applet only parameters

Parameter	Meaning
mol	The URL of the molecule file or the molfile itself (inline) in MDL mol or compressed mol format. If you specify the molfile inline in an HTML file (as an applet parameter), then you must end all 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 getM() 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 getM from JavaScript in a buggy browser/JVM combination. Without preloading, getM 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).
loadMols	Comma-separated list of molfiles to preload. Useful for caching molecules in JavaScript "slideshows".

1.2   3D and animation

Parameter	Meaning	Default
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
animate	Start an XYZ animation sequence, or starts rotating the specified 3D molecule(s). Possible values: off, all, or a comma-separated list of molecule indices (0...n-1). Note: This parameter does not apply to beans, only to applet.	off
animFPS	Number of frames per second in 3D animation.	10
animDelay	Delay (seconds) before repeating the animation.	0
animSync	Whether the animations in different cells should be synchronized.	false
spin spin0 spin1 spin2 ...	Spinning rate and axis for animated molecules. Spinning rate is specified in degrees per second, the axis is specified with a 3D vector. Numbers are separated by commas. Note: XYZ animations do not spin by default, only if this parameter is set.	36,0,1,0
script script0 script1 script2 ...	Script containing a subset of RasMol commands delimited by semicolons. If this applet parameter is specified, then the mol parameter is neglected. The molecule(s) must be loaded using the load command in the script. Note: To load the script from a file, use the script command: <param NAME="script" VALUE="script myscript.spt">

1.3   Molecule tables

rows	Number of "molecule rows", including the optional header row.
cols	Number of "molecule columns".
visibleRows	Number of visible rows. The table is scrollable if less than rows. Default value: visibleRows = rows.
visibleCols	Number of visible columns. The table is scrollable if less than cols. Default value: visibleCols = cols.
layout	Layout of molecule, label, button and checkbox components in a cell.
layoutH	Layout for the header row.
param	Parameters of the components.
paramH	Parameters for the header row.
cell0 cell1 cell2 ...	Contents of the cells. Use these instead of the mol parameter.
border	Border width in pixels. Default: 0 (no border between cells). Increases the total applet WIDTH by border*(cols-1), and the HEIGHT by border*(rows-1).

1.3.1   layout

If you are familiar with Java, you might have noticed that anchor, fill, weightx and weighty have the same names as the fields of the GridBagConstraints class. The reason is that MarvinView uses the GridBagLayout class to determine the places and sizes of the components.

Component types: M (molecule), L (label), B (button), C (checkbox), T (text field) and I (image).

Example:

<param NAME=layout VALUE=":4:3:
M:0:0:4:1:c:n:
L:0:2:1:1:c:n:0:10:
L:1:2:1:1:c:n:0:10:
C:0:1:1:1:c:n:
C:1:1:1:1:c:n:
C:2:1:1:1:c:n:
B:3:1:1:1:c:n:10">

1.3.2   param

:M:width:height	width and height are in pixel units.
:L:fontprops	fontprops: font properties.
:B:fontprops:: :B:fontprops:description: :B:fontprops:description:frame	fontprops: font properties, description: description string, target: target frame.
:C:fontprops: :C:fontprops:description	fontprops: font properties, description: description string. You may specify the checkbox group number in the type field, by writing gn next to the type-specifying character C, where n is the group number. No more than one button in a group can be pressed at the same time.
:T:fontprops :T:fontprops:columns :T:fontprops:columns:editable	fontprops: font properties, columns: number of columns, editable: editable (rw) or read only (r).

Example:

<param NAME=param VALUE=":
M:100:100:
L:10b:
C:10:select this molecule:
Cg0:10:include this structure:
B:10:search for more molecules like this:_self:
T:10:
T:10:15:
T:10:15:rw">

1.3.3   celli

Component	Parameters	Description
M	|molfile	molfile: the molecule URL or the molecule itself (inline) in MDL mol or compressed mol format.
L	|label	label: the label string.
B	|label|spec|action	label: the button label, spec: the special character (% from now), action: the action string.
C	||||| |||state|| |||state|-|- ... |label0|label1|state|action1|action2	label0: label for the unchecked state, label1: label for the checked state, state: default state (0, 1 or nothing), action0: action string for unchecking, action1: action string for checking. For a "real" checkbox, both labels have to be empty string, otherwise the "checkbox" will be buttonlike. If both action strings are empty, then the checkbox is disabled. To make it enabled without specifying JavaScript actions, the action values must be "-". Example: "|||1|-|-"
T	| |string	string: initial value.
I	|iconfile|| |iconfile|action|title	iconfile: GIF or JPEG file containing the icon, action: image file or js:JavaScript code title: window title, only used if action is an image file.

A javascript expression can be used only if you specify the MAYSCRIPT attribute in the applet tag.

It is suggested to use celli parameter in MViewPane JavaBean to create an advanced layout (containing more visual elements than one molecule with a label, such as, checkboxes, buttons, images, etc.). Since Javascript is not supported in MarvinBeans: use ActionListeners and ItemListeners in your code instead of action strings. See marvinbeans/examples/view-checkbox/MViewExampleWithCheckbox.java.

Example:

<param NAME=cell2 VALUE="|\
  MSketch 04169816382D\\ 66 72  0  0  0  0  0  0  0  0999 V2000\mcIWFRwV60\
l0i01\M  END\|
1002|
not bad|
||1|js:cbx(1002,'not selected')|js:cbx(1002,'selected')|
 Include | Include ||js:cbx(1002,'no include')|js:cbx(1002,'include')|
 Exclude | Exclude ||js:cbx(1002,'no exclude')|js:cbx(1002,'exclude')|
 Search |%|searchmore.cgi?mol=1002&n=5&cbx=%C">

2   Events fired by the JavaBean

Property name	Type	Meaning
"mols#"	Molecule[]	Molecule(s) changed in the specified cell (# = 0, ..., n-1).
"implicitH"	String	Implicit Hydrogen display style changed.
"explicitH"	Boolean	Explicit Hydrogen display style changed. true: show explicit H atoms false: hide explicit H atoms
"navmode"	String	Drag action changed. translate: Translate, zoom: Zoom, rotZ: Rotate, rot3d: Rotate in 3D
"colorScheme"	String	Color scheme 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.
"animFPS"	Double	Animation frame rate changed.
"animDelay"	Double	Animation repeat delay changed.
"animSync"	Double	Animation synchronization changed.
"invisibleSets"	Long	Visibility of atom sets changed.
"winScale"	Double	Zoom window magnification changed.
"tabScale"	Double	Magnification for molecule cells changed.
"atomNumbersVisible"	Boolean	Visibility of atom numbers changed.
"atomMappingVisible"	Boolean	Visibility of atom mapping changed.
"popupMenusEnabled"	Boolean	Popup menus are enabled/disabled.
"detachable"	Boolean	Detachability of viewer changed.

Since the behaviour of buttons and checkboxes in molecule cells are similar as AbstractButton objects, they can fire ActionEvents and ItemEvents.

3   Troubleshooting - MView and JMView tables

• JavaScript Error: uncaught Java exception java/lang/ArrayIndexOutOfBoundsException
  Cause: getC, setC, setActionC, setActionB or setM called with too large argument.
• Molecule cells hang out of the applet, some inner rows intertwine.
  Possible causes:
  • Applet size too small.
    
  • There are some rows of labels, buttons or checkboxes in a cell between the molecule, and their total height is bigger than the molecule height you specified.
    Solution: increase molecule height, decrease font size or reduce the number of rows per cell.