DrawBoundingBox - Revision history

Pyadmin: 11 revisions

2014-03-28T01:43:48Z

11 revisions

Mretegan: separated the run command from the python code

2013-01-16T12:36:29Z

separated the run command from the python code

Newacct at 08:03, 27 November 2009

2009-11-27T08:03:07Z

New page

= Overview =
Draws a bounding box around a given selection.

<gallery>
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>

= Example =
<source lang="python">
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
</source>

= Installation =
Just copy the source to your computer. Then run
<source lang="python">
run /path/to/drawBoundingBox.py
</source>

<source lang="python">
# -*- 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)
</source>

= See Also =
[[Bounding_Box]]

[[Category:Script_Library|DrawMinBoundingBox]]
[[Category:Math_Scripts]]
[[Category:CGO]]

Slaw at 16:21, 27 May 2009

2009-05-27T16:21:30Z

New page

= Overview =
Draws a bounding box around a given selection.

<gallery>
Image:DrawMinBB.png|Example of a bounding box
</gallery>

= Example =
<source lang="python">
run ~/drawBoundingBox.py
fetch 1jsd
drawBoundingBox 1jsd, r=0.33, g=0.80
</source>

= Installation =
Just copy the source to your computer. Then run
<source lang="python">
run /path/to/drawBoundingBox.py
</source>

<source lang="python">
# -*- coding: utf-8 -*-
from pymol.cgo import *
from pymol import cmd
from random import randint
from string import split

#############################################################################
#
# 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)
</source>

= See Also =
[[Bounding_Box]]

[[Category:Script_Library|DrawMinBoundingBox]]
[[Category:Math_Scripts]]
[[Category:CGO]]

Mretegan: /* Installation */

2009-03-30T19:14:58Z

Installation

Mretegan at 19:13, 30 March 2009

2009-03-30T19:13:42Z

Mretegan: DrawMinBoundingBox moved to DrawBoundingBox: Now it can use padding, so it's not only min.

2009-03-30T19:09:30Z

DrawMinBoundingBox moved to DrawBoundingBox: Now it can use padding, so it's not only min.

Mretegan: Added the padding option and some useful print statements. Change the name to drawBoundingBox, plus some code alterations

2009-03-30T19:08:36Z

Added the padding option and some useful print statements. Change the name to drawBoundingBox, plus some code alterations

New page

= Overview =
Draws a bounding box around a given selection.

<gallery>
Image:DrawMinBB.png|Example of a bounding box
</gallery>

= Example =
<source lang="python">
run ~/drawBoundingBox.py
fetch 1jsd
drawBoundingBox 1jsd, r=0.33, g=0.80
</source>

= Installation =
Just copy the source to your computer. Then run
<source lang="python">
run /path/to/drawBoundingBox.py
</source>

<source lang="python">
# -*- coding: utf-8 -*-
from pymol.cgo import *
from pymol import cmd
from random import randint
from string import split

#############################################################################
#
# 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(sel)

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
</source>

= See Also =
[[Bounding_Box]]

[[Category:Script_Library|DrawMinBoundingBox]]
[[Category:CGO]]

← Older revision	Revision as of 01:43, 28 March 2014
(No difference)

@@ Line 18: / Line 18: @@
 = 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">

@@ Line 137: / Line 137: @@
          cmd.load_cgo(boundingBox,boxName)
          return boxName
-cmd.extend ("getBox", getBox)
 </source>

← Older revision	Revision as of 19:09, 30 March 2009
(No difference)