pass
else:
ns_new.basepairs.append(ni)
add1 = False
add2 = False
# BaseStacks
add1 = False
add2 = False
for ni in ns.basestacks:
if ni.iunit1 == target:
if ni.imp1un in aln:
ni.imp1un = aln[ni.imp1un]
add1 = True
if ni.iunit2 == target:
if ni.imp2un in aln:
ni.imp2un = aln[ni.imp2un]
add2 = True
if ((ni.iunit1 == target and not add1)
or (ni.iunit2 == target and not add2)):
pass
else:
ns_new.basestacks.append(ni)
add1 = False
add2 = False
out_ninfo = NinfoFile(sys.argv[5])
out_ninfo.open_to_write()
out_ninfo.write_all(ns_new)
out_ninfo.close()
#!/usr/bin/env python
import sys
from cafysis.file_io.ninfo import NinfoFile
from cafysis.elements.ninfo import NinfoSet
if len(sys.argv) != 3:
print ('Usage: SCRIPT [input ninfo] [output ninfo]')
sys.exit(2)
ninfo = NinfoFile(sys.argv[1])
ninfo.open_to_read()
ns = NinfoSet()
ninfo.read_all(ns)
ninfo.close()
ns.update_info()
ns.sort_by_mp()
ns.reassign_id()
ninfo = NinfoFile(sys.argv[-1])
ninfo.open_to_write()
ninfo.write_all(ns)
ninfo.close()
dih2_iunit2=seq_2,
dih2_imp1un=imp_1_un,
dih2_imp2un=imp_2_un,
dih2_imp3un=imp_4_un,
dih2_imp4un=imp_6_un,
dih2_native=dih2_native,
dih2_coef=CHT18.HB_DIH_CHAIN,
)
ns.hbondDTs.append(hb)
###########################
## Generate ninfo file ##
###########################
nf = NinfoFile(args.outfile)
nf.open_to_write()
nf.write_all(ns)
nf.close()
###################################
## Generate exv file (optional) ##
###################################
if args.exvfile:
n_sep_nlocal_P = 3
n_sep_nlocal_S = 3
n_sep_nlocal_B = 2
if args.end5 == 'P':
nmp = 3 * n_nt
else:
nmp = 3 * n_nt - 1
if len(sys.argv) != 10:
print(
'Usage: SCRIPT [ninfo (one-by-one)] [unit] [dist] [side] [unit] [dist] [side] [edc (post_edc.out)] [out]'
)
print('')
sys.exit(2)
fninfo_in = NinfoFile(sys.argv[1])
fninfo_in.open_to_read()
ns = NinfoSet()
fninfo_in.read_all(ns)
ns.update_info()
fninfo_in.close()
fninfo_out = NinfoFile(sys.argv[-1])
fninfo_out.open_to_write()
unit_aln1 = int(sys.argv[2])
aln1 = {}
side = int(sys.argv[4])
for line in open(sys.argv[3]):
linesp = line.split()
res1 = int(linesp[0]) # Dunkle res
mp1 = int(linesp[1]) # Dunkle mp
res2 = int(linesp[2]) # Jenner res
mp2 = int(linesp[3]) # Jenner mp
#linesp[4] # dist
if side == 1:
aln1[mp1] = mp2
elif side == 2:
aln1[mp2] = mp1
'Usage: SCRIPT [ninfo file] [edc file] [dist(aln) file] [factor] [output ninfo file]'
)
sys.exit(2)
f_ninfo = NinfoFile(sys.argv[1])
f_edc = open(sys.argv[2], 'r')
f_dist = open(sys.argv[3], 'r')
factor = float(sys.argv[4])
f_out_ninfo = NinfoFile(sys.argv[-1])
f_ninfo.open_to_read()
ninfo = NinfoSet()
f_ninfo.read_all(ninfo)
f_ninfo.close()
f_out_ninfo.open_to_write()
f_out_ninfo._file.write('#0: ' + sys.argv[0] + '\n')
f_out_ninfo._file.write('#1: ' + sys.argv[1] + '\n')
f_out_ninfo._file.write('#2: ' + sys.argv[2] + '\n')
f_out_ninfo._file.write('#3: ' + sys.argv[3] + '\n')
f_out_ninfo._file.write('#4: ' + sys.argv[4] + '\n')
f_out_ninfo._file.write('#5: ' + sys.argv[5] + '\n')
aln = {}
# Read from dist file
'''
# Jenner Dunkle
# res mp res mp dist
1 1 4 11 1.55
1 2 4 12 8.02
2 3 5 13 0.93
imp2_offset += c2.num_res()
imp1_offset += c1.num_res()
return
if __name__ == '__main__':
import sys
if len(sys.argv) != 3:
print ('Usage: %SCRIPT [input PDB] [output ninfo]')
sys.exit(2)
from cafysis.file_io.pdb import PdbFile
from cafysis.file_io.ninfo import NinfoFile
from cafysis.elements.ninfo import NinfoSet
f = PdbFile(sys.argv[1])
f.open_to_read()
chains = f.read_all()
f.close()
ns = NinfoSet()
generate_FENEs(chains, ns)
generate_LJs(chains, ns)
f_ninfo = NinfoFile(sys.argv[-1])
f_ninfo.open_to_write()
f_ninfo.write_all(ns)
f_ninfo.close()
@author: Naoto Hori
'''
import sys
from cafysis.file_io.ninfo import NinfoFile
from cafysis.elements.ninfo import NinfoSet
if __name__ == '__main__':
if len(sys.argv) != 3:
print('Usage: %SCRIPT [input ninfo file] [output prefix]')
sys.exit(2)
file_ninfo = NinfoFile(sys.argv[1])
file_ninfo.open_to_read()
ns = NinfoSet()
file_ninfo.read_all(ns)
ns.update_info()
file_ninfo.close()
prefix = sys.argv[2]
ndi = ns.dict_of_ninfoset_by_unit()
for i in range(1, ns.max_unit + 1):
for j in range(i, ns.max_unit + 1):
if ndi[(i, j)].max_unit != 0:
file_out = NinfoFile(prefix + '%03i_%03i.ninfo' % (i, j))
file_out.open_to_write()
file_out.write_all(ndi[(i, j)])
#file_out.write_unit(ns, i, j)
file_out.close()