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Download the script from [http://www.vertrees.org/~tree/pymol/index.php this page], sans line-numbers.
{{Infobox script-repo
|type      = script
|filename  = perp_maker.py
|author    = [[User:Inchoate|Jason Vertrees]]
|license  = MIT
}}


<source lang="python">
The '''perp_maker.py''' script creates perpendicular planes.
#
# $Id$
#


#
Nothing to do with cops.  Given a simple PyMol scene, attempts to create a CGO background triangle perpendicular to the vector created - which is parallel to the line segment drawn through the camera point and current center of mass - as obtained by "get_position," or "get_view."
# perp_maker.py: Nothing to do with cops.  Given a simple PyMol scene, attempts to
# create a CGO background triangle perpendicular to the vector created - which is
# parallel to the line segment drawn through the camera point and current center of
# mass - as obtained by "get_position," or "get_view."
#


#
== Usage ==
# To use: Load your scene.  Orient the scene as you wish.  Run the script.
# Could it be any simpler?!
#


# The TTT Matrix has to be the identity, do achieve this result.  So,
* Load your scene
# run the following:
* Orient the scene as you wish
#  -- 'reset'
* [[Running Scripts|Run]] the script
#  -- then orient your molecule as desired using the EDITING features!
#    -- before running this script, make sure 'get_view' shows the identity
#    -- matrix for the first 9 elements.
#  -- then run the script
#


import pymol
Could it be any simpler?
import math
import sys
import random
from pymol.cgo import *
from pymol.vfont import plain
 
############################################################
#
# Methods
#
############################################################
 
#
# Given the viewVector and center, creates a random sized plane
# perpendicular to the viewVector through the origin.  It is then
# the next step's responsibility to move the plane back some so
# it dosen't cut the molecule/scene in half.
#
def getPPlane( viewVector, center, side_length=100 ):
        """Returns a 3-tuple of 3D points representing the perp. plane."""
 
        # for reproduceable testing
        #random.seed(10)
        #
        # The formula for a plane with our chacteristics is defined by
        #
        # A(x - x') + B(y - y') + C(y - y') + D = 0, where
        # A, B and C are not all zero coefficients in the vector
        # Ai + Bj + Ck such that the plane is perpendicular to this
        # vector; x, y, and z are points on the plane; x', y', and z'
        # are the coordiates through which the plane shall run.
        #
 
        # This is fool-ass.  Gotta' be a better way to do this.
        # Declaring that rVal is a 3-Tuple.
        rVal = [ [], [], [], [], [], [] ]
 
        # Compose two triangles into a square.
        # Never learned any GFX coding, so I'm sure there's something
        # better than this; but, this works.
        for i in range(0, 6):
                if ( i == 0 ) or ( i == 5 ):
                        x = -side_length + center[0]
                        y = -side_length + center[1]
                elif (i == 1):
                        x = -side_length + center[0]
                        y =  side_length + center[1]
                elif ( i == 2 ) or ( i == 3 ):
                        x = side_length + center[0]
                        y = side_length + center[1]
                elif ( i == 4):
                        x = side_length + center[0]
                        y = -side_length + center[1]
 
                if ( viewVector[2] != 0 ):
                        z = -(((viewVector[0]*(x - center[0])) - (viewVector[1]*(y - center[1]))) /
viewVector[2]) + center[2]
 
                else:
                        print "Z-component of viewVector is zero.  Now, I need a nonzero value here
so I'm just making one up. :)"
                        z = random.randint(-200, 200)
 
                rVal[i] = [x, y, z]
 
        return rVal
 
############################################################
#
# End methods
#
############################################################
#
# First, get the center and camera locations
#
view = cmd.get_view()
camera = [ view[9], view[10], view[11] ]
center = [ view[12], view[13], view[14] ]
 
#
# Sanity check
 
#
print "Camera is: " + str(camera)
print "Center is: " + str(center)
 
 
#
# Create the vector through the two points directed
# from the camera to the center - the viewVector
#
viewVector = [ center[0] - camera[0],
                          center[1] - camera[1],
                          center[2] - camera[2] ]
 
print "ViewVector is: " + str(viewVector)
 
#
# Create the plane perpendicular to the viewVector
# running through the origin
#
 
 
pPlane = getPPlane( viewVector, center, side_length=100 )
print "Plane points calculated as: " + str(pPlane)
 
#
# Now translate the plane down away from the camera along the viewVector axis
#
 
 
# now create the CGO and load from the points
obj = [
        BEGIN, TRIANGLES,
        COLOR, 0.2, 0.4, 1,
 
        VERTEX, pPlane[0][0], pPlane[0][1], pPlane[0][2],
        VERTEX, pPlane[1][0], pPlane[1][1], pPlane[1][2],
        VERTEX, pPlane[2][0], pPlane[2][1], pPlane[2][2],
 
        VERTEX, pPlane[3][0], pPlane[3][1], pPlane[3][2],
        VERTEX, pPlane[4][0], pPlane[4][1], pPlane[4][2],
        VERTEX, pPlane[5][0], pPlane[5][1], pPlane[5][2],
 
        END
        ]
 
 
cmd.load_cgo( obj, 'pPlane')
cmd.set_view( view )
</source>


You can rotate and move the plane using the editing features (A > drag, Shift+Drag with right, middle or left mouse button).


[[Category:Script_Library]]
[[Category:Script_Library]]
[[Category:Math_Scripts]]
[[Category:Pymol-script-repo]]

Latest revision as of 17:06, 9 December 2013

Type Python Script
Download perp_maker.py
Author(s) Jason Vertrees
License MIT
This code has been put under version control in the project Pymol-script-repo

The perp_maker.py script creates perpendicular planes.

Nothing to do with cops. Given a simple PyMol scene, attempts to create a CGO background triangle perpendicular to the vector created - which is parallel to the line segment drawn through the camera point and current center of mass - as obtained by "get_position," or "get_view."

Usage

  • Load your scene
  • Orient the scene as you wish
  • Run the script

Could it be any simpler?

You can rotate and move the plane using the editing features (A > drag, Shift+Drag with right, middle or left mouse button).

Retrieved from "https://pymolwiki.org/index.php?title=Perp_maker&oldid=11486"