Spectrumbar

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Type Python Script
Download spectrumbar.py
Author(s) Sean M. Law
License -
This code has been put under version control in the project Pymol-script-repo

Contents

Description

Often times one may color their structure based upon some predefined color spectrum. However, this alone is not helpful when dealing with publication images. The purpose of this script is to allow the user to draw their own custom spectrum bar to accompany their structural images.

Further work will be done to improve the functionality of this script. Please feel free to contact the author for function requests.

USAGE

load the script using the run command

spectrumbar (RGB_Colors,radius=1.0,name=spectrumbar,head=(0.0,0.0,0.0),tail=(10.0,0.0,0.0),length=10.0, ends=square)

Please see the script comments for further custom options. Once the script completes, it will generate a new object called "spectrumbar" (which can be changed through the options) which is a cylinder colored according to the user-specified colors.

Note: It is strongly recommended to turn off the specular reflections before ray tracing

EXAMPLES

Fig.1 - spectrumbar red
Fig.2 - spectrumbar 1,0,0
Fig.3 - spectrumbar red, orange, yellow
Fig.4 - spectrumbar red,orange,yellow,green,blue,purple
Fig.5 - spectrumbar 1,0,0, orange, yellow, 0,1,0, 0,0,1, purple
Fig.6 - spectrum red,radius=2
Fig 7 - spectrumbar red, red, red, orange, yellow, yellow
Fig 8 - spectrumbar red, radius=2, ends=rounded

Script

load the script using the run command

from pymol.cgo import *
from math import *
from pymol import cmd
from re import *
 
def spectrumbar (*args, **kwargs):
 
    """
    Author Sean M. Law
    University of Michigan
    seanlaw_(at)_umich_dot_edu
 
    USAGE
 
    While in PyMOL
 
    run spectrumbar.py
 
    spectrumbar (RGB_Colors,radius=1.0,name=spectrumbar,head=(0.0,0.0,0.0),tail=(10.0,0.0,0.0),length=10.0, ends=square)
 
    Parameter     Preset         Type     Description
    RGB_Colors    [1.0,1.0,1.0]  N/A      RGB colors can be specified as a
                                          triplet RGB value or as PyMOL
                                          internal color name (i.e. red)
    radius        1.0            float    Radius of cylindrical spectrum bar
    name          spectrumbar    string   CGO object name for spectrum bar
    head          (0.0,0.0,0.0)  float    Starting coordinate for spectrum bar
    tail          (10.0,0.0,0.0) float    Ending coordinate for spectrum bar
    length        10.0           float    Length of spectrum bar
    ends          square         string   For rounded ends use ends=rounded
 
    Examples:
 
    spectrumbar red, green, blue
    spectrumbar 1.0,0.0,0.0, 0.0,1.0,0.0, 0.0,0.0,1.0
 
    The above two examples produce the same spectrumbar!
 
    spectrumbar radius=5.0
    spectrumbar length=20.0
 
    """
 
    rgb=[1.0, 1.0, 1.0]
    name="spectrumbar"
    radius=1.0
    ends="square"
    x1=0
    y1=0
    z1=0
    x2=10
    y2=0
    z2=0
    num=re.compile('[0-9]')
    abc=re.compile('[a-z]')
 
    for key in kwargs:
        if (key == "radius"):
            radius = float(kwargs["radius"])
        elif (key == "name"):
            name=kwargs["name"]
        elif (key == "head"):
            head=kwargs["head"]
            head=head.strip('" []()')
            x1,y1,z1=map(float,head.split(','))
        elif (key == "tail"):
            tail=kwargs["tail"]
            tail=tail.strip('" []()')
            x2,y2,z2=map(float,tail.split(','))
        elif (key == "length"):
            if (abc.search(kwargs["length"])):
                print "Error: The length must be a value"
                return
            else:
                x2=float(kwargs["length"]);
        elif (key == "ends"):
            ends=kwargs["ends"]
        elif (key != "_self"):
            print "Ignoring unknown option \""+key+"\""
        else:
            continue
 
    args=list(args)
    if (len(args)>=1):
        rgb=[]
    while (len(args)>=1):
        if (num.search(args[0]) and abc.search(args[0])):
            if (str(cmd.get_color_tuple(args[0])) != "None"):
                rgb.extend(cmd.get_color_tuple(args.pop(0)))
            else:
                return
        elif (num.search(args[0])):
            rgb.extend([float(args.pop(0))])
        elif (abc.search(args[0])):
            if (str(cmd.get_color_tuple(args[0])) != "None"):
                rgb.extend(cmd.get_color_tuple(args.pop(0)))
            else:
                return
        else:
            print "Error: Unrecognized color format \""+args[0]+"\""
            return
 
    if (len(rgb) % 3):
        print "Error: Missing RGB value"
        print "Please double check RGB values"
        return
 
    dx=x2-x1
    dy=y2-y1
    dz=z2-z1
    if (len(rgb) == 3):
        rgb.extend([rgb[0]])
        rgb.extend([rgb[1]])
        rgb.extend([rgb[2]])
    t=1.0/(len(rgb)/3.0-1)
    c=len(rgb)/3-1
    s=0
    bar=[]
 
    while (s < c):
        if (len(rgb) >0):
            r=rgb.pop(0)
            g=rgb.pop(0)
            b=rgb.pop(0)
        if (s == 0 and ends == "rounded"):
            bar.extend([COLOR, float(r), float(g), float(b), SPHERE, x1+(s*t)*dx, y1+(s*t)*dy, z1+(s*t)*dz, radius])
        bar.extend([CYLINDER])
        bar.extend([x1+(s*t)*dx, y1+(s*t)*dy, z1+(s*t)*dz])
        bar.extend([x1+(s+1)*t*dx, y1+(s+1)*t*dy, z1+(s+1)*t*dz])
        bar.extend([radius, float(r), float(g), float(b)])
        if (len(rgb) >= 3):
            bar.extend([float(rgb[0]), float(rgb[1]), float(rgb[2])])
            r=rgb[0]
            g=rgb[1]
            b=rgb[2]
        else:
            bar.extend([float(r), float(g), float(b)])
        if (s == c-1 and ends == "rounded"):
            bar.extend([COLOR, float(r), float(g), float(b), SPHERE, x1+(s+1)*t*dx, y1+(s+1)*t*dy, z1+(s+1)*t*dz, radius])
        s=s+1
 
    cmd.delete(name)
    cmd.load_cgo(bar,name)
 
 
    return
cmd.extend("spectrumbar",spectrumbar)
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