1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
|
# ================================================================
# NOTE: THIS APPROACH IS NOT RECOMMENDED SINCE THE PyMOL LAUNCH
# PROCESS IS SUBJECT TO CHANGE WITHOUT WARNING
#
# The recommended approach is to just use PyMOL as your python
# interpreter:
#
# "pymol -r <script.py>" or
# "pymol -qcr <script.py>" instead of
# "python <script.py>"
#
# However, If must invoke PyMOL from an external interpreter, then
# you willl need to:
#
# (1) prepare the environment first by sourcing "pymol.csh"
# or an equivalent shell script which defines PYMOL_PATH,
# LD_LIBRARY_PATH, TCL_LIBRARY, etc.
#
# (2) include the following code block at the *top* level of your
# program script.
#
# ================================================================
# PyMOL launch code
#
# === Provide arguments to PyMOL (first one must be "pymol")
pymol_argv = [ "pymol", "-q" ]
#
# === Launch the PyMOL thread(s)
import os,threading,__main__,__builtin__
threading.Thread(target=__builtin__.execfile,
args=(os.environ['PYMOL_PATH']+"/modules/launch_pymol.py",
__main__.__dict__,__main__.__dict__)).start()
#
# === Wait until PyMOL is ready to receive commands
e=threading.Event()
while not hasattr(__main__,'pymol'):
e.wait(0.01)
while not pymol._cmd.ready():
e.wait(0.01)
#
# PyMOL is now launched, you can now import "pymol" modules.
# ===============================================================
from pymol import cmd
cmd.load("$PYMOL_PATH/test/dat/pept.pdb")
print " The surface area is: %8.3f"%cmd.get_area()
|
