DrawBoundingBox: Difference between revisions
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(Added the padding option and some useful print statements. Change the name to drawBoundingBox, plus some code alterations) |
m (separated the run command from the python code) |
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| (7 intermediate revisions by 4 users not shown) | |||
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<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 = | ||
Copy the source code to your computer, and execute it by issuing the command "run /path/to/drawBoundingBox.py" in PyMOL. | |||
run /path/to/drawBoundingBox.py | |||
<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 | ||
############################################################################# | ############################################################################# | ||
| Line 70: | Line 70: | ||
""" | """ | ||
([minX, minY, minZ],[maxX, maxY, maxZ]) = cmd.get_extent( | ([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: | |||
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 07:36, 16 January 2013
Overview
Draws a bounding box around a given selection.
Example of a bounding box
Two bounding boxes, one with 0 padding, the other with 10 Ang padding.
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)