Plane Wizard

Introduction

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.

Original

import pymol
from pymol import cmd
from pymol.wizard import Wizard
from chempy import cpv
from pymol.cgo import *

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

Modification

Small modifications to the same code as above.

Gallery

• Plane img1

  Drawing a plane in a protein

• Plane img2

  Drawing 6 planes in a box

• Plane img3

  Drawing 6 planes in a box