#!/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 1] [input ninfo 2]")
sys.exit(2)
nf = NinfoFile(sys.argv[1])
nf.open_to_read()
ns1 = NinfoSet()
nf.read_all(ns1)
nf.close()
nf = NinfoFile(sys.argv[2])
nf.open_to_read()
ns2 = NinfoSet()
nf.read_all(ns2)
nf.close()
nhb1 = len(ns1.hbondDTs)
nhb2 = len(ns2.hbondDTs)
# Do not use index 0
flag1 = [False] * (nhb1 + 1)
flag2 = [False] * (nhb2 + 1)
#!/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_iunit1=seq_1,
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:
#if first:
# delta1 = mp1 - 1
# delta2 = mp2 - 1
# first = False
if side == 1:
#aln[mp1 - delta1] = mp2 - delta2
aln[mp1] = mp2
elif side == 2:
#aln[mp2 - delta2] = mp1 - delta1
aln[mp2] = mp1
else:
print('"side" is not acceptable. See usage')
sys.exit(2)
ns = NinfoSet()
file_ninfo = NinfoFile(sys.argv[1])
file_ninfo.open_to_read()
file_ninfo.read_all(ns)
file_ninfo.close()
ns_new = NinfoSet()
# 両方のユニットともターゲットのときは、
# 両方のIDがalnに含まれていないとaddしない
# BondLengths
add1 = False
add2 = False
for ni in ns.bondlengths:
if ni.iunit1 == target:
if ni.imp1un in aln:
import sys
from cafysis.file_io.ninfo import NinfoFile, NinfoSet
def show_usage():
print('')
print(' usage: ninfo_split.py [ninfo file] [prefix (can be dir)]')
print('')
if len(sys.argv) != 3:
show_usage()
sys.exit(2)
f_ninfo = NinfoFile(sys.argv[1])
f_ninfo.open_to_read()
ninfo = NinfoSet()
f_ninfo.read_all(ninfo)
f_ninfo.close()
out_prefix = sys.argv[2]
ninfo.update_info()
nUnit = ninfo.max_unit
print(nUnit)
ninfo_out = {}
for i in range(1, nUnit + 1):
for j in range(i, nUnit + 1):
ninfo_out[(i, j)] = NinfoSet()
for bd in ninfo.bondlengths:
@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) != 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
dih1_imp4=pre_mp_1 + imp_5,
dih1_iunit1=ic_2 + 1,
dih1_iunit2=ic_1 + 1,
dih1_imp1un=imp_2,
dih1_imp2un=imp_1,
dih1_imp3un=imp_3,
dih1_imp4un=imp_5,
dih1_native=dih1_native,
dih1_coef=DT13.HB_DIH_CHAIN,
dih2_imp1=pre_mp_1 + imp_1,
dih2_imp2=pre_mp_2 + imp_2,
dih2_imp3=pre_mp_2 + imp_4,
dih2_imp4=pre_mp_2 + imp_6,
dih2_iunit1=ic_1 + 1,
dih2_iunit2=ic_2 + 1,
dih2_imp1un=imp_1,
dih2_imp2un=imp_2,
dih2_imp3un=imp_4,
dih2_imp4un=imp_6,
dih2_native=dih2_native,
dih2_coef=DT13.HB_DIH_CHAIN,
)
ns.hbondDTs.append(hb)
#nf = NinfoFile('ninfo_RNA13_pdb.ninfo')
nf = NinfoFile(sys.argv[-1])
nf.open_to_write()
nf.write_all(ns)
nf.close()
#!/usr/bin/env python
'''
@author: Naoto Hori
'''
import sys
from cafysis.file_io.ninfo import NinfoFile
from cafysis.elements.ninfo import NinfoSet
if len(sys.argv) != 6:
print(
'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')
'''
if __name__ == '__main__':
pass
import sys
from cafysis.elements.ninfo import NinfoSet
from cafysis.file_io.ninfo import NinfoFile
from cafysis.file_io.pdb import PdbFile
if len(sys.argv) != 4:
print ("Usage: SCRIPT [ninfo file] [pdb file] [output file]")
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()
file_pdb = PdbFile(sys.argv[2])
file_pdb.open_to_read()
chains = file_pdb.read_all()
xyz = []
for c in chains:
for i in range(c.num_atom()):
xyz.append(c.get_atom(i).xyz)
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()
# -*- coding: utf-8 -*-
'''
Created on 2012/01/19
@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)])
dih1_imp4=imp_S2,
dih1_iunit1=1,
dih1_iunit2=1,
dih1_imp1un=imp_P1,
dih1_imp2un=imp_S1,
dih1_imp3un=imp_P2,
dih1_imp4un=imp_S2,
dih1_native=ARNA.DIH_PSPS,
dih1_coef=DT15.ST_DIH,
dih1_type_str='PSPS',
dih2_imp1=imp_S1,
dih2_imp2=imp_P2,
dih2_imp3=imp_S2,
dih2_imp4=imp_P3,
dih2_iunit1=1,
dih2_iunit2=1,
dih2_imp1un=imp_S1,
dih2_imp2un=imp_P2,
dih2_imp3un=imp_S2,
dih2_imp4un=imp_P3,
dih2_native=ARNA.DIH_SPSP,
dih2_coef=DT15.ST_DIH,
dih2_type_str='SPSP')
ns.basestackDTs.append(bs)
from cafysis.file_io.ninfo import NinfoFile
nf = NinfoFile('ninfo_ssRNA15.ninfo')
nf.open_to_write()
nf.write_all(ns)
nf.close()
elif linesp[0] == 'locaxis':
re1 = re.match('^\d+$', linesp[1])
re2 = re.match('^\d+$', linesp[2])
re3 = re.match('^\d+$', linesp[3])
if re1:
linesp[1] = int(linesp[1])
if re2:
linesp[2] = int(linesp[2])
if re3:
linesp[3] = int(linesp[3])
cmds.append(tuple(linesp))
elif linesp[0] == 'def_ninfo':
name = linesp[1]
filename = linesp[2]
nf = NinfoFile(filename)
nf.open_to_read()
ns = NinfoSet()
nf.read_all(ns)
nf.close()
defs[name] = ('ninfo', filename, ns)
elif linesp[0] == 'q':
cmds.append(tuple(linesp))
elif linesp[0] == 'dock':
cmds.append(tuple(linesp))
elif linesp[0] == 'enc':
cmds.append(tuple(linesp))