Spectrumbar
From PyMOLWiki
| 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
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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)
