Ejemplo n.º 1
0
def create_restraints():
    print os.getcwd()
    os.chdir('TEMPLATES')
    files = glob.glob('template_*.pdb')
    for f in files:
        name = '{}restraints'.format(f[0:-3])
        print name,f
        create_constraints.main(fi=f,fo=name)
    os.chdir('..')
    print os.getcwd()
Ejemplo n.º 2
0
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('..')