1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
|
from ost import io, seq
from promod3 import modelling, loop
# setup
tpl = io.LoadPDB('data/gly.pdb')
seq_trg = 'AAAAGGGGGGGGGGGGGGGGGGGGAAAAAA'
seq_tpl = '----GGGGGGGGGGGGGGGGGGGG------'
aln = seq.CreateAlignment(seq.CreateSequence('trg', seq_trg),
seq.CreateSequence('tpl', seq_tpl))
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
# close gaps
print('Number of gaps before: %d' % len(mhandle.gaps))
modelling.ModelTermini(mhandle,
loop.LoadTorsionSamplerCoil())
print('Number of gaps after: %d' % len(mhandle.gaps))
|
