cui_pymol.py

#!/usr/bin/python2.7 -i

import sys, os

### autocompletion
import readline
import rlcompleter
readline.parse_and_bind('tab: complete')

### pymol environment
moddir='/opt/pymol-svn/modules'
sys.path.insert(0, moddir)
os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')

### pymol launching
# PyMOL captures sys.stdout and sys.stderr, to control it with it's own feedback mechanism.
# To prevent that, save and restore both streams,
stdout = sys.stdout  
stderr = sys.stderr
import pymol
pymol.pymol_argv = ['pymol','-qc'] + sys.argv[1:]
pymol.finish_launching()
sys.stdout = stdout
sys.stderr = stderr
cmd = pymol.cmd

### read pdb
r = cmd.fetch("4m61","obj1")
print r
#cmd.iterate_state(1, "obj1", "print x,y,z")

from pymol import stored #MUST!!!
stored.alphaCarbons = []
cmd.iterate_state(1, pymol.selector.process("all"), "stored.alphaCarbons.append([x,y,z])")
print stored.alphaCarbons[0]
#for i in stored.alphaCarbons:
#    print "{x:8.3f} {y:>8.3f} {z:>8.3f}".format(x=i[0],y=i[1],z=i[2])
#    print "{0:8.3f} {1:>8.3f} {2:>8.3f}".format(i[0],i[1],i[2])

### alter coordinates
#print stored.alphaCarbons[123]
#f = lambda a:[round(a[0],3),round(a[1],3),round(a[2],3)]
f = lambda a:[round(a[0],3) -1000,round(a[1],3) -1000,round(a[2],3) -1000]
stored.rCord1 = map(f,stored.alphaCarbons)
print stored.rCord1[0]

#for i in stored.rCord1:
#    print "{x:8.3f} {y:>8.3f} {z:>8.3f}".format(x=i[0],y=i[1],z=i[2])
cmd.alter_state(1,"obj1","(x,y,z)=stored.rCord1.pop(0)")
cmd.iterate_state(1, "obj1", "print x,y,z")