This is a read-only mirror of pymolwiki.org

Difference between revisions of "DrawBoundingBox"

From PyMOL Wiki
Jump to navigation Jump to search
(Added the padding option and some useful print statements. Change the name to drawBoundingBox, plus some code alterations)
 
m (11 revisions)
 
(8 intermediate revisions by 3 users not shown)
Line 4: Line 4:
 
<gallery>
 
<gallery>
 
Image:DrawMinBB.png|Example of a bounding box
 
Image:DrawMinBB.png|Example of a bounding box
 +
Image:bb_with_padding.png|Two bounding boxes, one with 0 padding, the other with 10 Ang padding.
 
</gallery>
 
</gallery>
  
Line 11: Line 12:
 
fetch 1jsd
 
fetch 1jsd
 
drawBoundingBox 1jsd, r=0.33, g=0.80
 
drawBoundingBox 1jsd, r=0.33, g=0.80
 +
 +
# example from above w/padding, draw it light blue
 +
drawBoundingBox padding=10, r=0.5, g=0.8, b=1.0
 
</source>
 
</source>
  
 
= Installation =
 
= Installation =
Just copy the source to your computer. Then run
+
Copy the source code to your computer, and execute it by issuing the command "run /path/to/drawBoundingBox.py" in PyMOL.
<source lang="python">
 
run /path/to/drawBoundingBox.py
 
</source>
 
  
 
<source lang="python">
 
<source lang="python">
Line 24: Line 25:
 
from pymol import cmd                                                                                       
 
from pymol import cmd                                                                                       
 
from random import randint                                                                                   
 
from random import randint                                                                                   
from string import split                                                                                   
 
  
 
#############################################################################
 
#############################################################################
Line 70: Line 70:
 
         """                                                                                                     
 
         """                                                                                                     
  
         ([minX, minY, minZ],[maxX, maxY, maxZ]) = cmd.get_extent(sel)
+
         ([minX, minY, minZ],[maxX, maxY, maxZ]) = cmd.get_extent(selection)
  
 
         print "Box dimensions (%.2f, %.2f, %.2f)" % (maxX-minX, maxY-minY, maxZ-minZ)
 
         print "Box dimensions (%.2f, %.2f, %.2f)" % (maxX-minX, maxY-minY, maxZ-minZ)
Line 81: Line 81:
 
         maxZ = maxZ + float(padding)
 
         maxZ = maxZ + float(padding)
  
      if padding != 0:
+
        if padding != 0:
 
                 print "Box dimensions + padding (%.2f, %.2f, %.2f)" % (maxX-minX, maxY-minY, maxZ-minZ)
 
                 print "Box dimensions + padding (%.2f, %.2f, %.2f)" % (maxX-minX, maxY-minY, maxZ-minZ)
  
Line 137: Line 137:
 
         cmd.load_cgo(boundingBox,boxName)
 
         cmd.load_cgo(boundingBox,boxName)
 
         return boxName
 
         return boxName
 +
 +
cmd.extend ("drawBoundingBox", drawBoundingBox)
 
</source>
 
</source>
  
Line 144: Line 146:
  
 
[[Category:Script_Library|DrawMinBoundingBox]]
 
[[Category:Script_Library|DrawMinBoundingBox]]
 +
[[Category:Math_Scripts]]
 
[[Category:CGO]]
 
[[Category:CGO]]

Latest revision as of 01:43, 28 March 2014

Overview

Draws a bounding box around a given selection.

Example

run ~/drawBoundingBox.py
fetch 1jsd
drawBoundingBox 1jsd, r=0.33, g=0.80

# example from above w/padding, draw it light blue
drawBoundingBox padding=10, r=0.5, g=0.8, b=1.0

Installation

Copy the source code to your computer, and execute it by issuing the command "run /path/to/drawBoundingBox.py" in PyMOL.

# -*- coding: utf-8 -*-                                                                                     
from pymol.cgo import *                                                                                     
from pymol import cmd                                                                                       
from random import randint                                                                                  

#############################################################################
#                                                                            
# drawBoundingBox.py -- Draws a box surrounding a selection 
#
#                                                                            
# AUTHOR: Jason Vertrees                                                   
# DATE  : 2/20/2009                                                          
# NOTES : See comments below.                                                
#                                                                            
#############################################################################
def drawBoundingBox(selection="(all)", padding=0.0, linewidth=2.0, r=1.0, g=1.0, b=1.0):     
        """                                                                  
        DESCRIPTION                                                          
                Given selection, draw the bounding box around it.          

        USAGE:
                drawBoundingBox [selection, [padding, [linewidth, [r, [g, b]]]]]

        PARAMETERS:
                selection,              the selection to enboxen.  :-)
                                        defaults to (all)
   
                padding,                defaults to 0

                linewidth,              width of box lines
                                        defaults to 2.0

                r,                      red color component, valid range is [0.0, 1.0]
                                        defaults to 1.0                               

                g,                      green color component, valid range is [0.0, 1.0]
                                        defaults to 1.0                                 

                b,                      blue color component, valid range is [0.0, 1.0]
                                        defaults to 1.0                                

        RETURNS
                string, the name of the CGO box

        NOTES
                * This function creates a randomly named CGO box that minimally spans the protein. The
                user can specify the width of the lines, the padding and also the color.                            
        """                                                                                                    

        ([minX, minY, minZ],[maxX, maxY, maxZ]) = cmd.get_extent(selection)

        print "Box dimensions (%.2f, %.2f, %.2f)" % (maxX-minX, maxY-minY, maxZ-minZ)

        minX = minX - float(padding)
        minY = minY - float(padding)
        minZ = minZ - float(padding)
        maxX = maxX + float(padding)
        maxY = maxY + float(padding)
        maxZ = maxZ + float(padding)

        if padding != 0:
                 print "Box dimensions + padding (%.2f, %.2f, %.2f)" % (maxX-minX, maxY-minY, maxZ-minZ)

        boundingBox = [
                LINEWIDTH, float(linewidth),

                BEGIN, LINES,
                COLOR, float(r), float(g), float(b),

                VERTEX, minX, minY, minZ,       #1
                VERTEX, minX, minY, maxZ,       #2

                VERTEX, minX, maxY, minZ,       #3
                VERTEX, minX, maxY, maxZ,       #4

                VERTEX, maxX, minY, minZ,       #5
                VERTEX, maxX, minY, maxZ,       #6

                VERTEX, maxX, maxY, minZ,       #7
                VERTEX, maxX, maxY, maxZ,       #8


                VERTEX, minX, minY, minZ,       #1
                VERTEX, maxX, minY, minZ,       #5

                VERTEX, minX, maxY, minZ,       #3
                VERTEX, maxX, maxY, minZ,       #7

                VERTEX, minX, maxY, maxZ,       #4
                VERTEX, maxX, maxY, maxZ,       #8

                VERTEX, minX, minY, maxZ,       #2
                VERTEX, maxX, minY, maxZ,       #6


                VERTEX, minX, minY, minZ,       #1
                VERTEX, minX, maxY, minZ,       #3

                VERTEX, maxX, minY, minZ,       #5
                VERTEX, maxX, maxY, minZ,       #7

                VERTEX, minX, minY, maxZ,       #2
                VERTEX, minX, maxY, maxZ,       #4

                VERTEX, maxX, minY, maxZ,       #6
                VERTEX, maxX, maxY, maxZ,       #8

                END
        ]

        boxName = "box_" + str(randint(0,10000))
        while boxName in cmd.get_names():
                boxName = "box_" + str(randint(0,10000))

        cmd.load_cgo(boundingBox,boxName)
        return boxName

cmd.extend ("drawBoundingBox", drawBoundingBox)

See Also

Bounding_Box