Coloring

`flat.coloring`

Module of adding a little color to your life.

Palettes

Available color palettes in Flat:

class flat.coloring.Color(color=None)

Converts and manipulates common PyMOL color representation: colorname, RGB, or HEX. PyMOL API only.

static hex(string: str)

HEX color constructor method :param string: Hex color string [0, 255] :type string: str

Returns:: Color class.
Return type:: Color

Example

>>> Color.hex("64C8B0")
>>> Color.hex("3F7")

invert() → None

Inverts color :returns: None

Examples

>>> Color.rgb(100, 200, 176).invert()
(155, 55, 79)

static rgb(r: int | float, g: int | float, b: int | float)

RGB color constructor method :param r: Red color fraction between [0, 255] :type r: int, float :param g: Green color fraction between [0, 255] :type g: int, float :param b: Blue color fraction between [0, 255] :type b: int, float

Returns:: Color class.
Return type:: Color

Example

>>> Color.rgb(100, 200, 176)
>>> Color.rgb(0.39, 0.78, 0.69)

to_hex() → str

Return color in HEX format :returns: Color HEX string. :rtype: str

Example

>>> Color.rgb(100, 200, 176).to_hex()
'0x64c8b0'

to_hsl() → tuple[float, float, float]

Return color in HSL format :returns: List of HSL values. :rtype: tuple

Example

>>> Color.rgb(100, 200, 176).to_hsl()
(0.4600, 0.4762, 0.5882)

to_rgb() → tuple[int, int, int]

Return color in RGB format :returns: List of HSL values. :rtype: tuple

Example

>>> Color.hex('64c8b0').to_rgb()
(100, 200, 176)

class flat.coloring.Palette(*args)

Class for better color palette handling. Behaves same as Python list. PyMOL API only.

append(object: str | tuple) → None: Append object to the end of the list

extend(iterable: Iterable) → None: Extend list by appending elements from the iterable

insert(index: int, item: str | tuple) → None: Insert object before index

interp(frac: float) → Color

Computes the linear interpolation between all colors in palette, if the parameter frac is inside [0, 1). :param frac: Value between [0, 1] at which to evaluate the interpolated values color :type frac: float

Returns:: Interpolated Color object
Return type:: result (Color)

Examples

>>> plt = Palette('F00', '0F0', '00F')
>>> plt.interp(0.25).to_hex()
'808000'
>>> nsteps = 10
>>> for i in range(nsteps + 1):
...     plt.interp(i / nsteps).to_hex()

sort(*, key: None = None, reverse: bool = False) → None

Sort the list in ascending order and return None.

The sort is in-place (i.e. the list itself is modified) and stable (i.e. the order of two equal elements is maintained).

If a key function is given, apply it once to each list item and sort them, ascending or descending, according to their function values.

The reverse flag can be set to sort in descending order.

Read more about [color sorting](https://www.alanzucconi.com/2015/09/30/colour-sorting).

Parameters:

key (expr) – A function to specify the sorting criteria(s)
reverse (bool) – Will sort the list in descending order

Example

>>> plt = Palette('0F0', 'F00', 'F0F', '00F', 'FF0', '0FF')
>>> plt.sort(key=lambda x: colorsys.rgb_to_hls(*x))
>>> print([c.to_hex() for c in plt])
['ff0000', 'ffff00', '00ff00', '00ffff', '0000ff', 'ff00ff']

flat.coloring.cbalpha(selection='all', *, _self=cmd)

DESCRIPTION

Color residues by C-alpha atom.

USAGE

cbalpha [ selection ]

ARGUMENTS

selectionstr, optional: Atom selection.

flat.coloring.cbattr(selection='all', attributes=None, *, _self=cmd)

DESCRIPTION

Color by residue by attributes: negative (red), positive (blue), polar (green), nonpolar (yellow), and/or special (gray).

USAGE

cbattr [ selection [, attributes ]]

ARGUMENTS

selectionstr, optional: Atom selection.
attributesstr or list, default = None: Attributes to color, where None colors all.

EXAMPLE

>>> cbattr('all', ['negative', 'positive'])

flat.coloring.cbc(selection='all', *, _self=cmd)

DESCRIPTION

Color by chains.

USAGE

cbc [ selection ]

ARGUMENTS

selectionstr, optional: Atom selection.

flat.coloring.cbe(selection='all', *, _self=cmd, **kwargs)

DESCRIPTION

Color by elements. By default skips coloring carbons.

USAGE

cbe [ selection [, … ]]

ARGUMENTS

selectionstr, optional: Atom selection.
kwargsAny: Define color for each element.

EXAMPLE

>>> cbe('all', 'C'='green', 'oxygen'='red')

flat.coloring.cbi(selection='all', palette='rainbow2', *, _self=cmd)

DESCRIPTION

Color each chain in selection by residue index.

USAGE

cbi [ selection [, palette ]]

ARGUMENTS

selectionstr, optional: Atom selection.
palettestr, default = ‘rainbow2’: Palette name or space separated list of colors.

flat.coloring.cbo(selection='all', *, _self=cmd)

DESCRIPTION

Color by objects.

USAGE

cbo [ selection ]

ARGUMENTS

selectionstr, optional: Atom selection.

flat.coloring.cbs(selection='all', palette='rainbow', repr='ribbon', *, _self=cmd)

DESCRIPTION

Color object by state. Experimental and very finicky.

USAGE

cbs [ selection [, palette [, repr ]]]

ARGUMENTS

selectionstr, optional: Atom selection.
palettestr, default = ‘rainbow’: Palette name or space separated list of colors.
reprstr, default = ‘ribbon’: Molecule representation to color.

EXAMPLE

>>> set all_states, 1
>>> show_as ribbon
>>> cbs all
>>> cbs all, red blue
>>> cbs all, repr=cartoon
>>> cbs all, undo

NOTES

Due to how PyMol handles states only one representation can be colored at the time. To undo the coloring use undo as palette.

flat.coloring.get_colors(selection='all', *, quiet=1, _self=cmd)

DESCRIPTION

Get color of atoms in selection. Returns list of indices and RGB tuples.

USAGE

get_colors [ selection ]

ARGUMENTS

selectionstr, optional: Atom selection.

RETURNS

: List(Tuple(int, Tuple(int, int, int))): List of tuples containing atom indices and RGB color tuple.

flat.coloring.set_color_palette(scheme, *, _self=cmd)

DESCRIPTION

Set elements color palette. Supported palettes:

jmol
[more coming soon]

USAGE

set_colors scheme

ARGUMENTS

schemestr: Available color scheme.

Coloring

flat.coloring

Palettes

`flat.coloring`