def generate_pairs(match,system):
print system.seq
print system.ss
print system.sse
os.chdir('TEMPLATES')
#want to keep in order of importance: c0+c0 is more important than c0+c3. Have to do fair for all
#pairings that lead to this Fragment (123 --> 1+23 and 12+3 --> the c0+c0 has to be first for both
k = 0
for i in range(numb_cl):
for j in range(numb_cl):
for (f1,f2) in match:
print i,j,f1,f2
s1 = 'h%s.cluster%i' % (f1,i)
s2 = 'h%s.cluster%i' % (f2,j)
print s1,s2
(tmp1,end,ty) = system.sse[int(str(f1)[-1])-1]
if int(str(f1)[0]) == 1:
tmp1 = 0
else:
tmp1 = tmp1-2
(start,tmp2,ty) = system.sse[int(str(f2)[0])-1]
print tmp1,end,ty,start,tmp2,ty
#The numbering is amber like, starts at 1. For beggining of loop (end of first fragment)
#we would do -1 and +1 to select the first "." instead of "H" or "E", so keep same number
#For the end of loop, we should do -1 and -1; since the [ini:fin] is a [:) f(x), only do -1
loop = str(system.seq)[end:start-1]
print loop
renumb = str(system.seq)[tmp1:start-1]
print renumb
#Since there is overlap of one residue to superimpose, correct by 1
offset = len(renumb) - 1
print "offset: ",offset
assemble.make_assembly(first_sse=s1,sec_sse=s2,loop_aa=loop,output_name='template_%i.pdb' % k)
fo = open('template_%i.restraints' % k,'w')
create_constraints.main(fi=s1,fo=fo,offset=0)
create_constraints.main(fi=s2,fo=fo,offset=offset)
k += 1
os.chdir('..')
#! /usr/bin/env python
import assemble
st_1 = ['h1h2.rep.c1','h1h2.rep.c3','h1h2.rep.c4']
st_2 = ['h3.rep.c1','h3.rep.c2','h3.rep.c4']
i = 0
for s1 in st_1:
for s2 in st_2:
assemble.make_assembly(first_sse=s1,sec_sse=s2,loop_aa='DGLDEDG',output_name='template_%i.pdb' % i)
i += 1
