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selInside selects all atoms of a certain type that are located within the bounding box defined by some selection. See examples.
# 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
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 > bMin and at.coord < bMax and at.coord > bMin and at.coord < bMax and at.coord > bMin and at.coord < bMax : 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)