Explicit values
Explicit values such as numbers, colours and 3D vectors are used as
part of commands or state changes. The specifications described here
are therefore just syntax fragments, not complete commands.
on off
The logical (or boolean) explicit values are used to set some
parameters and in a few commands.
" string-contents "
String values are used in the label
command, the read command and a
few others. A string value is enclosed by double-quote '"'
characters. It cannot contain the newline character (line breaks),
which means that a string cannot be split into more than one line in
the input file. The maximum length of a string is currently 2047
characters. The double-quote character '"' itself may be included
in a string by escaping it with the backslash character: '\"'.
identifier
As a special case, a string which contains no blank characters, such
as tabs or spaces, may be used without the double-quotes. This
kind of string is called an identifier. There are several restrictions
on it: there must be no blank characters in it, it must not contain
characters that are special in a MolScript input file (semi-colon ';',
curly brackets '{' '}'), and it cannot be equal to a command
keyword. Typically, file names are identifiers.
Any item that is a valid numerical value for the standard library
routines in the C programming language is also a valid number in
MolScript. Some examples:
1.2
0.3e1
-1.44E1
-1000
Some invalid numbers:
.2
1E2
Note that in contrast to previous versions of
MolScript (v1.4 and older), it is now allowed to give an integer value
when a floating-point value is expected. The integer is automatically
converted into a floating-point value. However, when an integer is
expected, a floating point value is invalid.
A vector (or coordinate) can be specified either by an explicit
triplet of numbers, or by the keyword position given with
an atom selection.
A vector specified by explicit x, y and z values, is given by three
numbers without separating commas. The values in a
vector must be valid numbers. For example, the
labeloffset parameter is a vector
parameter, so to change it give the following command:
set labeloffset 0 0.5 -0.8;
A vector may be specified by giving an atom selection after the
keyword position. This will compute the geometrical
centre-of-gravity of the atoms as the vector value. All atoms in the
selection have the same weight. Note that in the
transform command, this
computation is done before any of the transformations
have been applied.
Note that the atom selection must contain at least
one atom, or an error will result.
Colours can be specified by a name, by greyscale, by the
RGB (red, green, blue) system, or by the HSB (hue, saturation,
brightness) system.
The colour system within MolScript unfortunately cannot
guarantee that the appearance of a given colour specification will be
the same in different output formats when displayed on different
hardware.
The value in the greyscale specification ranges from 0.0 (black) to
1.0 (white), inclusive.
The values in the RGB specification denote the amount of red, green
and blue, respectively, colour components to use in the colour. Each
value ranges from 0.0 to 1.0, inclusive.
The values in the HSB specification denote the hue, saturation and
brightness values for a colour. These values must all be within the
range from 0.0 to 1.0, inclusive.
- The hue is defined in a circular fashion from
0.0 = red, 0.2 = yellow, 0.333 = green, 0.667 = blue, 0.8 = violet,
1.0 = red again.
- The saturation can be described as the whiteness of
the colour, where 0.0 is completely white and 1.0 is full colour.
- The brightness (loosely, intensity) goes from 0.0 = black to 1.0 =
full intensity.
There are a total of 164 colour names defined in MolScript. They are
just symbolic constants for ordinary colour specifications in the
greyscale (white and black) or RGB systems (all others).
An alphabetical list of defined colour
names is given here
.
Note: the colour purple is no longer the same as magenta.
A colour ramp defines a continuously changing scale of colours. Colour
ramps are used for the
atomcolour and
residuecolour parameters.
The ramp is defined by the two end-point colours. The actual result is
crucially dependent on the colour space in which the ramp is
defined. This is determined by the
colourramp parameter.
The reason for this is that the ramp is computed by linear
interpolation of each colour component in the end-point
colours. When the interpolation is done using the red, green and blue
components (RGB), the result will be different
compared to an interpolation using the hue, saturation, brightness
components (HSB) even though the two end-point
colours have the same visual appearance.
The HSB colour space is conceptually a
colour-wheel. It is therefore possible to interpolate in two opposite
directions in the HSB colour space. The
hsbreverseramp parameter
determines which direction is used. If the two end-point colours are
hsb 0 1 1 (red) and hsb 0.667 1
1 (blue), then interpolation with hsbreverseramp
off (the default) will be in the forward direction, and will go
through hsb 0.333 1 1 (green). If the parameter is
on, then the interpolation will instead go through
hsb 0.8 1 1 (purple).
Note that it does not matter which colour space is
used in the specifications for the ramp end-point colours. The
interpolation is determined by the
colourramp and
hsbreverseramp parameters,
not by how the end-point colours are specified.
Defines the colour ramp by two explicit end-point colour
values. The lower end of the colour ramp is given by the first
colour. The interpolation calculation is affected by the
colourramp parameter, and if this
parameter is hsb, then the
hsbreverseramp parameter also
comes into play.
rainbow
This defines a colour ramp in the HSB colour space from blue to red
via cyan, green, and yellow, i.e. in the reverse direction.
Note that, currently, this colour ramp specification
will automatically set the
colourramp parameter to
hsb and the
hsbreverseramp parameter to
on. This is really a bug.
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