Latest revision as of 03:55, 28 March 2014

Coloring with a gradient of different green shades

This script works similar to the spectrum command, but instead of predefined palettes, any color sequence can be used.

The color sequence is given by a space separated list of colors, so palette "red_white_blue" is the same as color sequence "red white blue".

Example

	Included in psico; This command or function is available from psico, which is a PyMOL extension.
Module	psico.viewing

Type	Python Module
Download	spectrumany.py
Author(s)	Thomas Holder
License	BSD-2-Clause
	This code has been put under version control in the project Pymol-script-repo

fetch 2x19

# these two produce the same result
spectrum count, red_white_blue, chain B
spectrumany count, red white blue, chain B

# gradient of different green colors
spectrumany count, smudge palegreen limegreen limon green forest, chain B

@@ Line 1: / Line 1: @@
+{{Infobox script-repo
+|type      = module
+|filename  = spectrumany.py
+|author    = [[User:Speleo3|Thomas Holder]]
+|license   = BSD-2-Clause
+}}
+{{Infobox psico
+|module    =  psico.viewing
+}}
 [[File:SpectrumanyExample.png|300px|thumb|right|Coloring with a gradient of different green shades]]
@@ Line 18: / Line 29: @@
 </source>
-= The Script =
+[[Category:Script_Library]]
-<source lang="python">
-'''
-(c) 2010 Thomas Holder
-'''
-from pymol import cmd, stored
-def spectrumany(expression, color_list, selection='(all)', minimum=None, maximum=None):
-    '''
-DESCRIPTION
-    Define a color spectrum with as many color-stops as you like (at least 2).
-USAGE
-    spectrumany expression, color_list [, selection [, minimum [, maximum ]]]
-ARGUMENTS
-    expression = count, resi, b, q, or pc: respectively, atom count, residue
-    index, temperature factor, occupancy, or partial charge {default: count}
-    color_list = string: Space separated list of colors
-    ... all other arguments like with `spectrum` command
-EXAMPLE
-    spectrumany count, forest green yellow white
-    spectrumany b, red yellow white, (polymer), maximum=100.0
-SEE ALSO
-    spectrum
-    '''
-    colors = color_list.split()
-    if len(colors) < 2:
-        print 'failed! please provide at least 2 colors'
-        return
-    colvec = [cmd.get_color_tuple(i) for i in colors]
-    parts = len(colvec) - 1
-    count_expr = 'index'
-    expression = {'pc': 'partial_charge', 'fc': 'formal_charge',
-            'count': count_expr}.get(expression, expression)
-    minmax_expr = {'resi': 'resv'}.get(expression, expression)
-    discrete_expr = ['index', 'resi']
-    if cmd.count_atoms(selection) == 0:
-        print 'empty selection'
-        return
-    if None in [minimum, maximum]:
-        stored.e = list()
-        cmd.iterate(selection, 'stored.e.append(%s)' % (minmax_expr))
-        if minimum is None:
-            minimum = min(stored.e)
-        if maximum is None:
-            maximum = max(stored.e)
-    minimum, maximum = float(minimum), float(maximum)
-    print ' Spectrum: range (%.5f to %.5f)' % (minimum, maximum)
-    if maximum == minimum:
-        print 'no spectrum possible, only equal %s values' % (expression)
-        return
-    if expression in discrete_expr:
-        val_range = int(maximum - minimum + 1)
-    else:
-        val_range = maximum - minimum
-        cmd.color(colors[0], selection)
-    steps = 60 / parts
-    steps_total = steps * parts
-    val_start = minimum
-    for p in range(parts):
-        for i in range(steps):
-            ii = float(i)/steps
-            col_list = [colvec[p+1][j] * ii + colvec[p][j] * (1.0 - ii) for j in range(3)]
-            col_name = '0x%02x%02x%02x' % (col_list[0] * 255, col_list[1] * 255, col_list[2] * 255)
-            val_end = val_range * (i + 1 + p * steps) / steps_total + minimum
-            if expression in discrete_expr:
-                cmd.color(col_name, '(%s) and %s %d-%d' % (selection, expression, val_start, val_end))
-            else:
-                cmd.color(col_name, '(%s) and %s > %f' % (selection, expression, val_start))
-            val_start = val_end
-cmd.extend('spectrumany', spectrumany)
-</source>
-[[Category:Plugins]]
 [[Category:Coloring]]
+[[Category:Pymol-script-repo]]

Difference between revisions of "Spectrumany"

Latest revision as of 03:55, 28 March 2014

Example

Navigation menu

Search

Included in psico This command or function is available from psico, which is a PyMOL extension.
Module	psico.viewing