Quick dist

quick_dist will quickly find and write out the pairwise distances between two selections in PyMOL. On my machine this will write about 80,000 distance measures/second.

#
# quick_dist.py
#
def quick_dist(s1, s2, inFile=None):
  import math
  m1 = cmd.get_model(s1)
  m2 = cmd.get_model(s2)

  if inFile!=None:
    f = open(inFile, 'w')
    f.write("ATOM1\tATOM2\tDIST\n")

  s=""

  for c1 in range(len(m1.atom)):
    for c2 in range(len(m2.atom)):
      s+="%s/%d\t%s/%d\t%3.2f\n" % (m1.atom[c1].name, m1.atom[c1].index,\
        m2.atom[c2].name, m2.atom[c2].index,\
        math.sqrt(sum(map(lambda f: (f[0]-f[1])**2, zip(a1.coord,a2.coord)))))

  if inFile!=None:
    f.write(s)
    f.close()
  else:
    print s


cmd.extend("quick_dist", quick_dist)