def generate_smotif(top_entry,csmotif_index,csmotif_subentry,ex1,ex2):
#[8, 9, 'left']
log=top_entry[2]
direction=csmotif_index[2]
if direction=='left':
pss_index=csmotif_index[1]
css_index=csmotif_index[0]
dir_no,s2_struct,domain=log[pss_index][0],log[pss_index][1],log[pss_index][2]
s1_struct=csmotif_subentry
else:
pss_index=csmotif_index[0]
css_index=csmotif_index[1]
dir_no,s1_struct,domain=log[pss_index][0],log[pss_index][1],log[pss_index][2]
s2_struct=csmotif_subentry
# 9_8_1 ['strand', 9, 13, 3, 112, 120] ['strand', 8, 4, 3, 123, 132] ['3po3K00', 'ARG', '70', 'THR', '77', 'PRO', '83', 'LEU', '111']
print s1_struct,s2_struct
start=s1_struct[5]
end=s2_struct[4]
if end-start>1:
smotif = ud.getSmotif(s1_struct, s2_struct)
return dir_no,domain,s1_struct,s2_struct,smotif,direction
else:
create_log_file(ex1,ex2)
sys.exit()
f_ss.close()
f_map = open("map_route.dict", 'r')
map_route = pickle.load(f_map)
f_map.close()
#*********************************
#load in cathdb and extract info
#*********************************
ss_indices = map_route['map_route'][0]
s1_profile = ss_profiles[ss_indices[0]][int(sys.argv[1])]
s2_profile = ss_profiles[ss_indices[1]][int(sys.argv[2])]
smotif = ud.getSmotif(s1_profile, s2_profile)
rdc_file, ss_seq, cathdb = ud.initData()
cath_entries = ud.extractCath(smotif, cathdb)
print sys.argv[1], sys.argv[2], s1_profile, s2_profile
print smotif
print len(cath_entries)
#*********************************
# Search for needles in the haystack
#*********************************
B0 = 18.8
TinK = 298.0
Sorder = 1.0
scal = rf.rdcScal(Sorder, B0, TinK)
csmotif = ud.getNextSmotif(map_route, psmotif)
top_dict, top_list = read_top(psmotif)
top_entry = top_dict[top_list[int(sys.argv[3])]]
profiles = ud.getSSProfile(ss_profiles,csmotif)
sc_profile = profiles[int(sys.argv[4])]
# sort_nchi[sum(temp_nchi)]=[temp_nchi,temp_tensor, log, domain]
log = top_entry[-2]
dir_name, sp_profile, domain, direction = getSx(log, csmotif)
if direction == 'left':
smotif = ud.getSmotif(sc_profile, sp_profile)
else:
smotif = ud.getSmotif(sp_profile, sc_profile)
print csmotif, psmotif, smotif
init_data = ud.testinitData('rdc_file', 'ss_seq', 'cathdb', 'rmsd_cutoff')
rdc_file, ss_seq, cathdb, rmsd_cutoff = init_data[0], init_data[1], init_data[2], init_data[3]
cath_entries = ud.extractCath(smotif, cathdb)
#*********************************
# Search for needles in the haystack
#*********************************
B0 = 18.8
TinK = 298.0
map_route=pickle.load(f_map)
f_map.close()
init_data = ud.testinitData('broker_file', 'ss_seq', 'cathdb')
rdc_file, ss_seq, cathdb = init_data[0], init_data[1], init_data[2]
s1,s2=get_r0(map_route['map_route'])
s1_list,s2_list=get_profiles(s1,s2,ss_profile)
s1_struct=s1_list[int(sys.argv[1])]
s2_struct=s2_list[int(sys.argv[2])]
#smotif= get_smotif(s1_struct,s2_struct)
smotif = ud.getSmotif(s1_struct, s2_struct)
# ss_array has [['helix', 22, 2, 23], ['SStruct', len(SStruct),start_res, end_res]]
print smotif , s1_struct, s2_struct
#cath_entries=extract_cath(smotif,cathdb)
cath_entries = ud.extractCath(smotif,cathdb)
print sys.argv[1],sys.argv[2],len(cath_entries)
# main
nM = 5000 # 1000 pts in each sphere
M = [10,50] # 40 spheres 10-50 Angstrom
npts = (M[1] - M[0]) * nM # 50 spheres * 1000 pts each
rMx = fastT1FM.MakeDvector(npts) #allocate memmory
rMy = fastT1FM.MakeDvector(npts)
rMz = fastT1FM.MakeDvector(npts)
