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<source lang="python">
{{Infobox script-repo
####################################################################################
|type      = script
#
|filename  = perp_maker.py
# perp_maker.py:  Creates perpendicular planes.
|author    = [[User:Inchoate|Jason Vertrees]]
# =============
|license  = MIT
#
}}
# 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."
#
# @COPYRIGHT: Jason Vertrees (C), 2005-2007
# @LICENSE: Released under GPL:
# This program is free software; you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation; either version 2 of the License, or
#    (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with
# this program; if not, write to the Free Software Foundation, Inc., 51 Franklin
# Street, Fifth Floor, Boston, MA 02110-1301, USA
#
#
#


#
The '''perp_maker.py''' script creates perpendicular planes.
# 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,
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."
# run the following:
#  -- 'reset'
#  -- 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
== Usage ==
import math
import sys
import random
from pymol.cgo import *
from pymol.vfont import plain


############################################################
* Load your scene
#
* Orient the scene as you wish
# Methods
* [[Running Scripts|Run]] the script
#
############################################################


#
Could it be any simpler?
# 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: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).

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