MarvinView: parameters and events

Version 4.1.12

Contents

1. Parameters
   1. Applet only parameters
   2. 3D and animation
   3. Molecule tables
      1. layout
      2. param
      3. celli
2. 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. Sets the background color of the components (like menubar, toolbar, labels and buttons), excluding the molecule canvas. See also: molbg
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
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 applicable to the MViewPane bean.	false
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, where scale is the current magnification.	0.4
bondSpacing	Double bond spacing in C-C bond length units: spacing*1.54 Å = spacing*scale pixels, where scale is the current magnification.	0.18
molFormat	Default file format: mol, csmol, smiles, cxsmiles, 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"     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
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
bondLengthVisible	Shows bond length labels true - display false - do not display	false
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
lonePairsVisible	Show lone pairs true - display false - do not display	false
grinv	Display graph invariants true - display false - do not display	false
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
addRemoveHatomsEnabled	Add/Remove -> Explicit Hydrogens is enabled or disabled in the Edit menu. It will be disabled if this parameter is false.	true
copyOpts	Enabled output formats at 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
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
selectedIndex	Select the specified cell.
draggable	Allows (true) or denies (false) mouse dragged events in cells.	true

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 file itself (inline) in MDL mol, compressed mol, SMILES or SMARTS 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".
molChanged0 molChanged1 molChanged2 ...	Evaluates a JavaScript code when the molecule is loaded or changed in the specified cell. The number in the parameter name determines the cell index. If no molecule table, use molChanged0 to refer to the molecule. The parameter value should be a JavaScript code. E.g.: <param name="molChanged0" value="alert('First molecule is modified')">
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

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
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
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|action0|action1	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.

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">

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.