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# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
import os, sys
seq = 'gattaca'
n = len(seq)
strands = 2
# NAMOT seems broken for one strand? Am I using it wrong?
#########################################################
#
# We will need to ask Paul R to help us understand these distortions.
# I can see what a few of them are doing, but not all.
#
# There is also a probable confusion bug between the "bu" and "pt"
# parameters. See src/input.c lines 1086 and 1102, and notice that
# they appear to be reversed, judging by the names of the fields they
# are changing.
#
# Base parameters
bu = 0.0 # twists the bases perpendicular to helical axis
op = 0.0
pt = 0.0 # makes the inner part of each base dip by that angle
# Unit parameters
# These are applied to the bases and sugars, but NOT to the phosphates??
dx = 0.0
dy = 0.0
dz = 0.0 # additional space between bases, unlike x and y, this is cumulative
twist = 0.0
tilt = 0.0 # does some kind of A-DNA-like twist that I don't get
roll = 10.0
###################################################
def use_pynamot():
"""NAMOT includes a Python interface (pynamot.so, pynamot.dll).
We can use this (assuming NE-1 is able to find it), but there are
possible license implications to doing it this way.
"""
sys.path += ['/usr/local/libexec', '/usr/local/lib']
import pynamot
pynamot.Cmd('generate %s d b %s' % (" sd"[strands], seq))
if True:
pynamot.Cmd('modify unit dx g 1:1 1:%d %f' % (n, dx))
pynamot.Cmd('modify unit dy g 1:1 1:%d %f' % (n, dy))
pynamot.Cmd('modify unit dz g 1:1 1:%d %f' % (n, dz))
pynamot.Cmd('modify unit twist g 1:1 1:%d %f' % (n, twist))
pynamot.Cmd('modify unit tilt g 1:1 1:%d %f' % (n, tilt))
pynamot.Cmd('modify unit roll g 1:1 1:%d %f' % (n, roll))
pynamot.Cmd('write pdb foo.pdb')
def use_cmd_line():
# The '-nogui' option comes from our special version of main.c.
namot = os.popen('namot -nogui', 'w')
namot.write('generate %s d b %s\n' % (" sd"[strands], seq))
if False:
namot.write('modify base bu 1:1:1 1:%d:%d %f\n' % (n, strands, bu))
namot.write('modify base op 1:1:1 1:%d:%d %f\n' % (n, strands, op))
namot.write('modify base pt 1:1:1 1:%d:%d %f\n' % (n, strands, pt))
if True:
namot.write('modify unit dx l 1:1 1:%d %f\n' % (n, dx))
namot.write('modify unit dy l 1:1 1:%d %f\n' % (n, dy))
namot.write('modify unit dz l 1:1 1:%d %f\n' % (n, dz))
namot.write('modify unit twist l 1:1 1:%d %f\n' % (n, twist))
namot.write('modify unit tilt l 1:1 1:%d %f\n' % (n, tilt))
namot.write('modify unit roll l 1:1 1:%d %f\n' % (n, roll))
namot.write('write pdb foo.pdb\n')
namot.write('quit\n')
namot.close()
use_cmd_line()
#use_pynamot()
#os.system('babel foo.pdb foo.mmp')
os.system('rasmol foo.pdb')
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