<param>
HTML tag.
Parameter Meaning Default addRemoveHatomsEnabled
Add/Remove -> Explicit Hydrogens is enabled or disabled in the Edit menu. It will be disabled if this parameter is false. true
autoTabScale
Automatically change scale when component size changed. Only applicable to the MViewPane bean. false
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 confirmTransfer
Displays a confirmation dialog window upon closing the structure editor window in case the structure has been altered. 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
dispQuality
Display quality.
0
- low quality, faster rendering1
- high quality (antialiasing), slower rendering1
molbg
Molecule background color in hexa. To set different colors for some specified cells, use a comma separated list of "i :#
rrggbb" settings, where i is the cell index. For example, to set the default color to white and the color of cell 2 to red, use "#ffffff,2:#ff0000
". See also: backgroundselectedIndex
Select the specified cell. tabScale
Magnification in the molecule table. Each cell has the specified magnification if positive. The scaling is automatic if negative (-1). -1
transferButtonIcon
Sets the location of a custom icon for the Transfer action.   transferButtonText
Sets custom text for the Transfer action.   transferButtonVisible
Makes the Transfer button visible on the General Toolbar. true
winScale
Magnification in the zoom window. A 1.54 Å long C-C bond is magnified to winScale pixels. 26.4
Simple viewer applet example:
<applet code="MView" width=100 height=100> <param name="molbg" value="#a0ffa0"> <param name="escapeChar" value="\"> <param name="mol" value="Pyrrole\n ... M END\n"></applet>
Parameter Meaning Default atomFont
Atom symbol/label font: Serif
,SansSerif
orMonospaced
SansSerif
atomMappingVisible
Show (true) or hide (false) atom mapping true
atomNumbersVisible
Show (true) or hide (false) atom numbers false
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
atomSymbolsVisible
Show (true) or hide (false) atom symbols in 3D view true
bondLengthVisible
Show (true) or hide (false) bond length labels false
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
chiralitySupport
When to show atom chirality (R/S).
off
- neverselected
- if the chiral flag is set for the molecule or the atom's enhanced stereo type is absoluteall
- alwaysoff
colorScheme
Color scheme.
mono
- monochromecpk
- Corey-Pauling-Kultunshapely
- shapely (residue types)group
- residue sequence numberscpk
downWedge
Wedge bond display convention. Down wedge points downward in MDL's convention ( mdl
), upward (at the chiral center) in Daylight's (daylight
).mdl
explicitH
Show (true) or hide (false) explicit hydrogens. true
ezVisible
Show (true) or hide (false) E/Z labels. false
grinv
Show (true) or hide (false) graph invariants false
implicitH
How to display H labels.
off
hetero
- on heteroatomsheteroterm
- on hetero or terminal atomsall
- all atomsfalse
lonePairsVisible
Show (true) or hide (false) lone pairs false
rgroupsVisible
Show (true) or hide (false) R-group definitions 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,selection
n corresponds to molecule cell n.showSets
Show the specified atom sets only. Comma separated list of set sequence numbers (0, ..., 63). heteroterm
sketchAnyBond
Display type of the Any bond in the sketcher:
auto
- displayed as dashed line in most cases, solid line only when all bonds are generated from atom coordinates (e.g. XYZ and PDB files).dashed
- displayed as dashed linesolid
- displayed as solid lineauto
valenceErrorVisibleInView
Show (true) or hide (false) valence errors true
viewAnyBond
Display type of the Any bond in the viewer:
auto
- displayed as dashed line in most cases, solid line only when all bonds are generated from atom coordinates (e.g. XYZ and PDB files).dashed
- displayed as dashed linesolid
- displayed as solid lineauto
viewCarbonVisibility
Display the label of carbon atoms in structures.
on
- Always show the atom labels of carbon atoms.off
- Never show the atom labels of carbon atoms.inChain
- Show the atom labels of carbon atoms at straight angles and at implicit Hydrogens.inChain
Parameter Meaning Default 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
...
atomSetColor63Atom 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
...
bondSetColor63Bond set color in hexa. 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. See also: cleanOpts, importConv.
2
- two-dimensional cleaning3
- three-dimensional cleaning2
cleanOpts
Options for 2D or 3D cleaning.
cleanOpts
accepts the same parameter values as clean2dOpts or clean3dOpts depending on the cleaning dimension (cleanDim).
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 setColoringEnabled
Atom/bond set coloring. true
Parameter Meaning Default 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
animDelay
Delay (seconds) before repeating the animation. 0
animFPS
Number of frames per second in 3D animation. 10
animSync
Whether the animations in different cells should be synchronized. false
ballRadius
Ball radius for "ballstick" rendering mode, in units of covalent radius. 0.5
rendering
Rendering style.
wireframe
- wireframewireknobs
- wireframe with knobssticks
- 3D sticksballstick
- ball & stickspacefill
- ballswireframe
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">
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
stickThickness
3D stick diameter for "sticks" and "ballstick" rendering modes, in Angstroms. 0.1
wireThickness
line thickness for "wireframe" and "wireknobs" rendering modes, in Angstroms. 0.064
The cells in the multi-cell molecule table mode of MarvinView can be divided further
and they can have they own layout, which however is uniform for all cells in the table.
The parameters described here are used to define the structure of such a cell.
Example of using molecule tables: MarvinView Table View Example
A utility class is also available to generate parameter values: MViewParam
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 themol
parameter.border
Border width in pixels. Default: 0 (no border between cells).
Increases the total appletWIDTH
by border*(cols-1), and theHEIGHT
by border*(rows-1).
layout
parameterlayout
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).c
(center), n
(north), s
(south),
e
(east), w
(west), ne
(northeast), etc.
n
(none), h
(horizontal),
v
(vertical) or b
(both).
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">
param
parameterparam
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:
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".
:M:
width:
heightwidth and height are in pixel units. :L:
fontpropsfontprops: font properties. :B:
fontprops::
:B:
fontprops:
description:
:B:
fontprops:
description:
framefontprops: 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:
descriptionfontprops: font properties,
description: description string.
You may specify the checkbox group number in the type field, by writingg
n next to the type-specifying characterC
, 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:
editablefontprops: 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">
celli
and celli_j
parameterscell
i
parameter, or by assignments for each component separately, using
cell
i_j, where i = 0, 1, ..., rows*cols-1 is the cell index and j = 0, 1,
2, ... is the component index inside the cell.
The contents of cell
i_j parameters are listed
in the following table for the different component types:
Since newlines are usually neglected in applet parameters by the browsers, each newline should be replaced or preceded by
Component Parameters Description M
molfile
molfile: the molecule URL or the molecule itself (inline) in a molecule file format (MDL mol, compressed mol, MRV etc.) L
label
label: the label string. B
|
label|
spec|
actionlabel: the button label,
spec: the special character (%
from now),
action: the action string.C
|||||
|||
state||
|||
state|-|-
...
|
label0|
label1|
state|
action0|
action1label0: 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|
titleiconfile: GIF or JPEG file containing the icon,
action: image file orjs:
JavaScript code
title: window title, only used if action is an image file.
\n
, where
\
is an escape character defined using the escapeChar parameter. If it is defined,
then occurrences of this character must also be escaped as "\\
".
The parameter lists of the B
, C
and
I
components should start with "E\|
" or
"|
", where \
is an escape character which overrides
the escapeChar setting and |
is the separator character (can also be colon, comma or anything else). If
the separator occurs inside the parameter string of a component, then it must
be escaped: "|
" should be replaced by "\|
".Note that specifying the applet parameters in JavaScript (instead of directly inside an HTML applet tag) requires backslash to be escaped once more, except in case of the newline (\n) which does not need without extra escaping.
The action string for the B
, C
and I
components 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="escapeChar" value="\"> <param name="cell2_0" value="\n MSketch 04169816382D\n \n 66 72 0 0 0 0 0 0 0 0999 V2000\n mcIWFRwV60\n ... M END\n"> <param name="cell2_1" value="1002"> <param name="cell2_2" value="not bad"> <param name="cell2_3" value="|||1|js:cbx(1002,'not selected')|js:cbx(1002,'selected')"> <param name="cell2_4" value="| Include | Include ||js:cbx(1002,'no include')|js:cbx(1002,'include')"> <param name="cell2_5" value="| Exclude | Exclude ||js:cbx(1002,'no exclude')|js:cbx(1002,'exclude')"> <param name="cell2_6" value="| Search |%|js:searchmore(1002)">
A cell
i parameter contains the parameter values for
all components in a single list. The list starts either with
"E\|
" or "|
", where \
and |
are the escape and separator characters. (Not necessarily backslash and
vertical line.)
Example:
<param name="cell2" value="E\|\n MSketch 04169816382D\n \n 66 72 0 0 0 0 0 0 0 0999 V2000\n mcIWFRwV60\n ... M END\n |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">
Parameter Meaning Default copyAsFormat
Default clipboard format by Copy As action. platform dependent copyOpts
Enabled output formats at copy command To specify more formats, enumerate them in a comma separated list.
text
- Copy As Textbitmap
- Copy As Bitmap Imageemf
- Copy As Vector Graphical Image (EMF)platform dependent debug
Debug mode. Possible values: 0, 1, 2. 0
defaultSaveFormat
Determines the default chemical file format in the Save As dialog. mrv
draggable
Allows (true) or denies (false) mouse dragged events in cells. true
editable
Modes: display only (0) or editable (1, 2). If editable=2
, then doubleclick launches MarvinSketch (instead of a viewer window).0
escapeChar
Escape character to use for parsing the values of mol and cell parameters. 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
molFormat
Default file format: mol
,csmol
,smiles
,cxsmiles
,cml
,pdb
,pov
,sybyl
, orxyz
.mol
navmode
Mouse drag action.
translate
- move the structurezoom
- change magnificationrotZ
- rotate in the screen's planerot3d
- 3D rotationrotZ
selectable
Use selectable=false
to forbid molecule selection with mouse click.true
sketchHelp
Sketcher help contents. chemaxon/marvin/help
/sketch-index.htmlsketchQuickHelp
Sketcher quick help. chemaxon/marvin/help
/sketch.htmlviewHelp
Viewer help contents. chemaxon/marvin/help
/view-index.htmlviewQuickHelp
Viewer quick help. chemaxon/marvin/help
/view.html
Parameter Meaning Default mol
The URL of the molecule file or the file itself (inline) in any supported structure format such as MDL mol, compressed mol, SMILES, SMARTS, etc format.
For multiline values of this parameter, it is recommended to specify escapeChar="\" and replace or precede each newline occurring in the string with "\n". The escape character should also be escaped as "\\".
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}"
preloadDeprecated cacheMols
Store loaded molecules in an internal cache ( true
orfalse
).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
Enable/disable property change event listener of the applet. If the listener is enabled the applet will call the propertyChange(prop) JavaScript method. The code snippet below demonstrates the handling of property change events in JavaScript. Note: If the MAYSCRIPT option is not specified, JavaScript can not be evaluated from the applet. function propertyChange(prop) { if(document.eventform != null) { var s = document.eventform.txt.value; document.eventform.txt.value = s + "\n" + prop; } } mview_mayscript=true; mview_begin("marvin",400,300); mview_param("listenpropertychange","true"); mview_end();Live applet example: MarvinView Example - Listening for events in applets
If you also specify the "appletid" parameter, its value will appearin the name of the property as prefix (e.g.: "firstapplet.mol").false appletid
Identify applet in property change event notifications to JavaScript. Use this parameter with listenpropertychange when more than one applet are located on the same web page. It helps to identify which applet sent the notification. listenmouseevent
Enable/disable mouse event listener of the applet. If the listener is enabled the applet will call the mouseEvent(evt) JavaScript method.
The code snippet below demonstrates the handling of mouse events in JavaScript. Note: If the MAYSCRIPT option is not specified, JavaScript can not be evaluated from the applet.function mouseEvent(evt) { var s = document.mouseform.txt.value; s = s + evt + "\n"; document.mouseform.txt.value = s; } mview_mayscript=true; mview_begin("marvin",400,300); mview_param("listenmouseevent","true"); mview_end();Live applet example: MarvinView Example - Listening for events in appletsfalse 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
.MetalLookAndFeelsplashScreenImage
Change the component's Splash Screen displayed at startup. If you do not specify this parameter, Marvin will use its default splash screen.
This parameter value is the relative path of the image, specify relatively to the CODEBASE
Note: Animated gif files can be displayed badly(flashing, or too fast animation)null
license
Sets the contents of a pre-read license file to the license manager to read and validate licenses from. licenseFile
Sets the license file location to the license manager to read and validate licenses from.
getC
, setC
,
setActionC
, setActionB
or setM
called with too large argument.