Bell: 1 revision

2014-03-28T03:49:38Z

1 revision

New page

[[selInside]] selects all atoms of a certain type that are located within the bounding box defined by some selection. See examples.

= Usage =
<source lang="python">
# find all atoms inside the box spanned by (0,0,0) and (10,10,10)
# for the example PDB, 1hpv
fetch 1hpv
pseudoatom b1, pos=[0,0,0]
pseudoatom b2, pos=[10,10,10]
selInside b1 or b2
</source>

= The Code =
<source lang="python">
import pymol
from pymol import cmd, stored
from random import randint

def selInside(bounding_object, target="*", radius=None):
"""
Selects all atoms of a given target type inside some selection that acts like a bounding box.

PARAMS:
bounding_object -- [PyMOL object/selection] the object/selection inside of which we want to choose atoms
target -- [PyMOL selection] that defines the atoms to select. Use "solvent" to select
only solvent atoms inside the selection
radius -- [float] expand the box by this many angstroms on all sides

RETURNS:
(string) name of the selection created

NOTES:
assumes a single-state setup; for multi-state you must modify this script
"""

# get the extents of the bounding object into two arrays
(bMin, bMax) = cmd.get_extent(bounding_object)

# if the user supplied a size by which we need to expand the box, we do that here
if radius!=None:
try:
# try to convert a string to a float
radius = float(str(radius))
except ValueError:
print "ERROR: Invalid radius declared. Please make sure the radius is a number or left blank"
return
# add/subtract the radius to the bounds
bMin = map( lambda f: f-radius, bMin)
bMax = map( lambda f: f+radius, bMax)

# initialize a selection; selections starting with underscores are hidden by PyMOL
cmd.select("__toRemove", "None")

# for each atom in the target selection, if it's inside the box, add it to the selection
for at in cmd.get_model(target).atom:
if at.coord[0] > bMin[0] and at.coord[0] < bMax[0] and at.coord[1] > bMin[1] and at.coord[1] < bMax[1] and at.coord[2] > bMin[2] and at.coord[2] < bMax[2] :
cmd.select("__toRemove", "__toRemove or index %d" % at.index)

# prepare the return values
rName = "insideBoundingObj"
cmd.set_name("__toRemove", rName)

return rName

cmd.extend("selInside", selInside)
</source>

[[Category:Script_Library]] [[Category:ObjSel_Scripts]]

SelInside - Revision history

Bell: 1 revision