Plane Wizard

2010-10-04T18:16:32Z

Sunhwan:

This wizard has a simple purpose - to draw a cgo plane that passes through three points picked by the user. Most of the wizard itself was copied from the measure wizard.

To use, put it in the same directory as the other wizards. This is not quality code, and there may be bugs, but it seems to work okay.

<source lang="python">
import pymol
from pymol import cmd
from pymol.wizard import Wizard
from chempy import cpv
from pymol.cgo import *

def makePrimitive(cgo, name):
cmd.set('auto_zoom', 0, quiet=1)
cmd.load_cgo(cgo, name)
cmd.set('auto_zoom', 1, quiet=1)

def point(p):
x, y, z = p
return [COLOR, 1, 1, 1, SPHERE, float(x), float(y), float(z), 0.5]

def line(p1, p2):
x1, y1, z1 = p1
x2, y2, z2 = p2
return [CYLINDER, float(x1), float(y1), float(z1), float(x2), float(y2), float(z2), 0.25, 1, 1, 1, 1, 1, 1]

def plane(corner1, corner2, corner3, corner4, normal):
planeObj = []
planeObj.extend(point(corner1))
planeObj.extend(point(corner2))
planeObj.extend(point(corner3))
planeObj.extend(point(corner4))
planeObj.extend(line(corner1, corner2))
planeObj.extend(line(corner2, corner3))
planeObj.extend(line(corner3, corner4))
planeObj.extend(line(corner4, corner1))

planeObj.extend([COLOR, 0.8, 0.8, 0.8])
planeObj.extend([BEGIN, TRIANGLE_STRIP])
planeObj.append(NORMAL)
planeObj.extend(normal)
for corner in [corner1, corner2, corner3, corner4, corner1]:
planeObj.append(VERTEX)
planeObj.extend(corner)
planeObj.append(END)
return planeObj

def planeFromPoints(point1, point2, point3, facetSize):
v1 = cpv.normalize(cpv.sub(point2, point1))
v2 = cpv.normalize(cpv.sub(point3, point1))
normal = cpv.cross_product(v1, v2)
v2 = cpv.cross_product(normal, v1)
x = cpv.scale(v1, facetSize)
y = cpv.scale(v2, facetSize)
center = point2
corner1 = cpv.add(cpv.add(center, x), y)
corner2 = cpv.sub(cpv.add(center, x), y)
corner3 = cpv.sub(cpv.sub(center, x), y)
corner4 = cpv.add(cpv.sub(center, x), y)
return plane(corner1, corner2, corner3, corner4, normal)

class PlaneWizard(Wizard):

def __init__(self):
Wizard.__init__(self)

# some attributes to do with picking
self.pick_count = 0
self.object_count = 0
self.object_prefix = "pw"

# the plane facet size (the 'radius' of the section of plane we show)
self.facetSize = 5

self.selection_mode = cmd.get_setting_legacy("mouse_selection_mode")
cmd.set("mouse_selection_mode",0) # set selection mode to atomic
cmd.deselect()

def reset(self):
cmd.delete(self.object_prefix + "*")
cmd.delete("sele*")
cmd.delete("_indicate*")
cmd.unpick()
cmd.refresh_wizard()

def delete_all(self):
cmd.delete("plane*")

def cleanup(self):
cmd.set("mouse_selection_mode",self.selection_mode) # restore selection mode
self.reset()
self.delete_all()

def get_prompt(self):
self.prompt = None
if self.pick_count == 0:
self.prompt = [ 'Please click on the first atom...']
elif self.pick_count == 1:
self.prompt = [ 'Please click on the second atom...' ]
elif self.pick_count == 2:
self.prompt = [ 'Please click on the third atom...' ]
return self.prompt

def do_select(self, name):
# "edit" only this atom, and not others with the object prefix
try:
cmd.edit("%s and not %s*" % (name, self.object_prefix))
self.do_pick(0)
except pymol.CmdException, pmce:
print pmce

def pickNextAtom(self, atom_name):
# transfer the click selection to a named selection
cmd.select(atom_name, "(pk1)")

# delete the click selection
cmd.unpick()

# using the magic of indicate, highlight stuff
indicate_selection = "_indicate" + self.object_prefix
cmd.select(indicate_selection, atom_name)
cmd.enable(indicate_selection)

self.pick_count += 1
self.error = None

# necessary to force update of the prompt
cmd.refresh_wizard()

def do_pick(self, picked_bond):

# this shouldn't actually happen if going through the "do_select"
if picked_bond:
self.error = "Error: please select bonds, not atoms"
print self.error
return

atom_name = self.object_prefix + str(self.pick_count)
if self.pick_count < 2:
self.pickNextAtom(atom_name)
else:
self.pickNextAtom(atom_name)

point1 = cmd.get_atom_coords("(%s%s)" % (self.object_prefix, "0"))
point2 = cmd.get_atom_coords("(%s%s)" % (self.object_prefix, "1"))
point3 = cmd.get_atom_coords("(%s%s)" % (self.object_prefix, "2"))
plane = planeFromPoints(point1, point2, point3, self.facetSize)

planeName = "plane-%02d" % self.object_count
self.object_count += 1
makePrimitive(plane, planeName)
cmd.show("cgo", "plane*")

self.pick_count = 0
self.reset()

def get_panel(self):
return [
[ 1, 'Plane Wizard',''],
[ 2, 'Reset','cmd.get_wizard().reset()'],
[ 2, 'Delete All Planes' , 'cmd.get_wizard().delete_all()'],
[ 2, 'Done','cmd.set_wizard()'],
]

# create an instance

wiz = PlaneWizard()

# make this the active wizard

cmd.set_wizard(wiz)
</source>
[[Category:Script_Library|Plane Wizard]]
[[Category:Math_Scripts]]

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Plane Wizard