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Property Colors in MarvinView

The Property List

It is possible to color molecules in MarvinView by certain properties of their atoms. These properties are stored in an additional data field in an SDfile as a property list. The name of the data field can be specified for MarvinView by the -t parameter. The property list contains one or more property symbols for each atom, by the order of the atoms. The properties of different atoms are separated by a semicolon. The number of specified atoms must match the number of atoms in the molecule. If an atom has two or more properties, they are separated by a slash.

An example describing the atomic properties of a molecule containing 5 atoms:

;;a;b/c;

  • the first two atoms have no properties.
  • the third atom has property denoted by symbol "a"
  • the fourth atom has both property b and c
  • the fifth atom has no properties.

The Color Configuration File

The color profile for each data field label is stored in a configuration file in a "symbol = value" format. The file name of the color profile is an input parameter of MarvinView (-p).

Example:

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a = red
b = blue
c = green
d = black
e = navy
f = maroon
a/d = purple
b/d = lime
a/c = aqua
empty = #808080
other = fuchsia

All property symbols and their combinations (separated by slash character) can have their colors assigned. There are two special symbols: empty and other . Atoms not having any property will be displayed with the color of empty . The rest of the atoms are displayed with the color of other (undefined combinations). MarvinView supports the 16 color names of the HTML standard (see below), but it is allowed to assign any valid RGB color value to symbols.

Supported color names:

Name Code
Black #000000
Green #008000
Silver #C0C0C0
Lime #00FF00
Gray #808080
Olive #808000
White #FFFFFF
Yellow #FFFF00
Maroon #808080
Navy #000080
Red #FF0000
Blue #0000FF
Purple #800080
Teal #008080
Fuchsia #FF00FF
Aqua #00FFFF