Merge branch 'master' into patch-1

Author: jrom99

cgoCircle.py

@@ -0,0 +1,100 @@
+"""
+This script was initially copied from https://pymolwiki.org/index.php/CgoCircle on Sept. 23, 2024. 
+
+The PyMOL Wiki page containing the code that was copied is licensed under GNU Free Documentation License 1.2.
+
+Probable Author: Jason Vertrees.
+"""
+
+import math
+import pymol
+from pymol.cgo import *
+from pymol import cmd
+
+def cgoCircle(x, y, z, r=8.0, cr=1.0, cg=0.4, cb=0.8, w=2.0):
+  """
+  Create a CGO circle
+
+  PARAMS
+        x, y, z
+          X, Y and Z coordinates of the origin
+
+        r
+          Radius of the circle
+
+        cr, cg, cb
+          Color triplet, [r,g,b] where r,g,b are all [0.0,1.0].
+
+        w
+          Line width of the circle
+
+  RETURNS
+        the CGO object (it also loads it into PyMOL, too).
+
+  """
+  x = float(x)
+  y = float(y)
+  z = float(z)
+  r = abs(float(r))
+  cr = abs(float(cr))
+  cg = abs(float(cg))
+  cb = abs(float(cb))
+  w = float(w)
+
+  obj = [ BEGIN, LINES, COLOR, cr, cg, cb ]
+  for i in range(180):
+        obj.append( VERTEX )
+        obj.append(r*math.cos(i) + x )
+        obj.append(r*math.sin(i) + y )
+        obj.append(z)
+        obj.append( VERTEX )
+        obj.append(r*math.cos(i+0.1) + x )
+        obj.append(r*math.sin(i+0.1) + y )
+        obj.append(z)
+  obj.append(END)
+ 
+  cName = cmd.get_unused_name("circle_")
+  cmd.load_cgo( obj, cName )
+  cmd.set("cgo_line_width", w, cName )
+  return obj
+
+
+def circleSelection( selName, r=None, cr=1.0, cg=0.4, cb=0.8, w=2.0 ):
+  """
+  circleSelection -- draws a cgo circle around a given selection or object
+
+  PARAMS
+        selName
+          Name of the thing to encircle.
+
+        r
+          Radius of circle.
+          DEFAULT: This cript automatically defines the radius for you.  If
+          you select one atom and the resultant circle is too small, then
+          you can override the script's calculation of r and specify your own.
+
+        cr, cg, cb
+          red, green and blue coloring, each a value in the range [0.0, 1.0]
+
+  RETURNS
+        The circle object.
+
+  """
+  ((minX, minY, minZ), (maxX, maxY, maxZ)) = cmd.get_extent(selName)
+
+  if r==None:
+        r = max( [maxX-minX, maxY-minY, maxZ-minZ] )
+
+  stored.coords = []
+  cmd.iterate_state(1, selName, "stored.coords.append([x,y,z])")
+  l = len(stored.coords)
+
+  centerX = sum(map(lambda x: x[0], stored.coords)) / l
+  centerY = sum(map(lambda x: x[1], stored.coords)) / l
+  centerZ = sum(map(lambda x: x[2], stored.coords)) / l
+
+  return cgoCircle( centerX, centerY, centerZ, r, cr, cg, cb, w )
+
+
+cmd.extend( "cgoCircle", cgoCircle )
+cmd.extend( "circleSelection", circleSelection )