非常感谢!!在用python对modeller 建模绘制打分图脚本如下,运行时一直报错显示
“AttributeError: module 'modeller' has no attribute 'modeller' ”
有谁知道怎么解决吗?谢谢了
脚本
import pylab
import modeller
def r_enumerate(seq):
"Enumerate a sequence in reverse order"
# Note that we don't use reversed() since Python 2.3 doesn't have it
num = len(seq) - 1
while num >= 0:
yield num, seq[num]
num -= 1
def get_profile(profile_file, seq):
"Read profile_file
into a Python array, and add gaps corresponding to
the alignment sequence seq
."
# Read all non-comment and non-blank lines from the file:
f = open(profile_file)
vals = []
for line in f:
if not line.startswith('#') and len(line) > 10:
spl = line.split()
vals.append(float(spl[-1]))
# Insert gaps into the profile corresponding to those in seq:
for n, res in r_enumerate(seq.residues):
for gap in range(res.get_leading_gaps()):
vals.insert(n, None)
# Add a gap at position '0', so that we effectively count from 1:
vals.insert(0, None)
return vals
e = modeller.Environ()
a = modeller.Alignment(e, file='TvLDH-1bdmA.ali')
template = get_profile('1bdmA.profile', a['1bdmA'])
model = get_profile('TvLDH.profile', a['TvLDH'])
pylab.figure(1, figsize=(10,6))
pylab.xlabel('Alignment position')
pylab.ylabel('DOPE per-residue score')
pylab.plot(model, color='red', linewidth=2, label='Model')
pylab.plot(template, color='green', linewidth=2, label='Template')
pylab.legend()
pylab.savefig('dope_profile.png', dpi=65)