

(18 intermediate revisions by 5 users not shown) 
Line 1: 
Line 1: 
−  <source lang="python">
 +  {{Infobox scriptrepo 
 +  type = script 
 +  filename = perp_maker.py 
 +  author = [[User:InchoateJason Vertrees]] 
 +  license = MIT 
 +  }} 
   
−  #
 +  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 ScriptsRun]] 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
 
−  #
 
   
 +  Could it be any simpler? 
   
−  import pymol
 +  You can rotate and move the plane using the editing features (A > drag, Shift+Drag with right, middle or left mouse button). 
−  import math
 
−  import sys
 
−  import random
 
−  from pymol.cgo import *
 
−  from pymol.vfont import plain
 
   
−  ############################################################
 +  [[Category:Script_Library]] 
−  #
 +  [[Category:Math_Scripts]] 
−  # Methods
 +  [[Category:Pymolscriptrepo]] 
−  #
 
−  ############################################################
 
−   
−  #
 
−  # 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 3tuple 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 foolass. Gotta' be a better way to do this.
 
−  # Declaring that rVal is a 3Tuple.
 
−  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 "Zcomponent 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>
 
−   
−   
−  [[Category:Scripting_Script_Library]]
 