#!/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()
# 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:
ni.imp1un = aln[ni.imp1un]
add1 = True
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
mp1 = int(linesp[1]) # Dunkle mp
res2 = int(linesp[2]) # Jenner res
mp2 = int(linesp[3]) # Jenner mp
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:
ninfo_out[(bd.iunit1, bd.iunit2)].bondlengths.append(bd)
for ba in ninfo.bondangles:
#!/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()
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))
elif linesp[0] == 'polar':
cmds.append(tuple(linesp))