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()
if unit_aln1 == iunit1 and unit_aln2 == iunit2:
aln_mp1_u = aln1[con.imp1un]
aln_mp2_u = aln2[con.imp2un]
elif unit_aln1 == iunit2 and unit_aln2 == iunit2:
aln_mp1_u = aln2[con.imp1un]
aln_mp2_u = aln1[con.imp2un]
else:
print('Error:')
print('unit_aln1:', unit_aln1)
print('unit_aln2:', unit_aln2)
print('con.iunit1:', iunit1)
print('con.iunit2:', iunit2)
sys.exit(2)
if (aln_mp1_u, aln_mp2_u) in pairlist:
energy = pairlist[(aln_mp1_u, aln_mp2_u)].energy
elif (aln_mp2_u, aln_mp1_u) in pairlist:
energy = pairlist[(aln_mp2_u, aln_mp1_u)].energy
else:
energy = 0.0
print('caution: pair is not found.')
print('icon=', con.id)
if energy < 0.0:
con.factor = -1.0 * energy
else:
con.factor = 0.0
fninfo_out.write_all(ns)
fninfo_out.close()
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
for bd in ninfo.bondlengths:
ninfo_out[(bd.iunit1, bd.iunit2)].bondlengths.append(bd)
for ba in ninfo.bondangles:
ninfo_out[(ba.iunit1, ba.iunit2)].bondangles.append(ba)
for dih in ninfo.dihedrals:
ninfo_out[(dih.iunit1, dih.iunit2)].dihedrals.append(dih)
for con in ninfo.contacts:
ninfo_out[(con.iunit1, con.iunit2)].contacts.append(con)
for bp in ninfo.basepairs:
ninfo_out[(bp.iunit1, bp.iunit2)].basepairs.append(bp)
for bs in ninfo.basestacks:
ninfo_out[(bs.iunit1, bs.iunit2)].basestacks.append(bs)
for i in range(1, nUnit + 1):
for j in range(i, nUnit + 1):
if (len(ninfo_out[(i, j)].bondlengths) != 0
or len(ninfo_out[(i, j)].bondangles) != 0
or len(ninfo_out[(i, j)].dihedrals) != 0
or len(ninfo_out[(i, j)].contacts) != 0
or len(ninfo_out[(i, j)].basepairs) != 0
or len(ninfo_out[(i, j)].basestacks) != 0):
filename = out_prefix + '%i_%i' % (i, j) + '.ninfo'
nf = NinfoFile(filename)
nf.open_to_write()
nf.write_all(ninfo_out[(i, j)])
# f_out.write('%3i %6i %4s %6i %3s | %3i %6i %4s %6i %3s | %6i %6i | %f\n' % info)
linesp = line.split()
imp1_orig = int(linesp[3])
imp2_orig = int(linesp[9])
if imp1_orig in aln:
imp1_tp = aln[imp1_orig]
else:
continue
if imp2_orig in aln:
imp2_tp = aln[imp2_orig]
else:
continue
for imp1 in imp1_tp:
for imp2 in imp2_tp:
if (imp1, imp2) in energys:
print(('Error: (imp1,imp2) in energys = True', imp1_orig,
imp2_orig, imp1, imp2))
energys[(imp1, imp2)] = float(linesp[15])
f_edc.close()
for con in ninfo.contacts:
if (con.imp1, con.imp2) in energys:
e = energys[(con.imp1, con.imp2)]
if e > 0.0:
con.coef = 0.0
else:
con.coef = factor * (-1.0 * e) * con.coef
f_out_ninfo.write_all(ninfo)
f_out_ninfo.close()
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()
#!/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] [factor] [output ninfo]")
sys.exit(2)
f_ninfo_in = NinfoFile(sys.argv[1])
f_ninfo_in.open_to_read()
ninfo = NinfoSet()
f_ninfo_in.read_all(ninfo)
f_ninfo_in.close()
k_factor = float(sys.argv[2])
f_ninfo_out = NinfoFile(sys.argv[-1])
f_ninfo_out.open_to_write()
for con in ninfo.contacts:
con.coef = con.coef * k_factor * con.factor
con.factor = 1.0
f_ninfo_out.write_all(ninfo)
f_ninfo_out.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()