MarvinView: parameters and events

Version 5.0.0

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

Parameters of the MView and JMView applets can be set using the <param> HTML tag.

ParameterMeaningDefault
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

ParameterMeaningDefault
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 Deprecated  
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')">
 
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

1.2   3D and animation

ParameterMeaningDefault
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

The layout and layoutH parameters are in the following format: ":rows:cols:type:k:l:h:w:anchor:fill:[weighty:[weightx:]]type:k:l:...", where : is the field separator, rows is the number of rows in the cell, cols is the number of columns, type is the type of the component in row k, column l of the current cell, h is the height of the component (rows), w is the width (columns).
The anchor parameter determines where to place the component if its size is smaller than its display area. It the component size is larger than the size of its text label, then anchor also sets the label alignment. Possible values: c (center), n (north), s (south), e (east), w (west), ne (northeast), etc.
The fill parameter determines how to resize the component if its size is smaller then its display area. Possible values: n (none), h (horizontal), v (vertical) or b (both).
The weights are nonnegative integers, zero by default. They determine how to distribute space. If all the weights are zero, all the components clump together in the center of the applet.

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

In a param or paramH parameter, the first character is the field separator (`:' here). The first field is the type of the first component (M, L, B, C or T), followed by its n parameters in the forthcoming n fields. Then the same for the second component, etc. Component parameters:
: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 for the URL ("_self" = show in the window and frame that contain the applet, "_parent" = show in the applet's parent frame, "_top" = show in the top-level frame of the applet's window, "_blank" = show in new window).
: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).
The fontprops field usually contains only one number, the font size. Additional properties are "b" (bold font) and "i" (italic). A 12pt bold italic font is specified as "12bi".

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

In a celli parameter, the first character is the field separator (`|' here). The fields contain the component parameters in order.

ComponentParametersDescription
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.

The action string can be an URL for buttons, a JPEG, PNG or GIF file for images, or js:javascript expression for buttons, checkboxes and images. The button action string may contain %C (where % is the special character), which is substituted with the checkbox states represented as a hexadecimal number. The nth bit in this number is the state of the nth checkbox.

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