Python NinfoFile.close Examples

Example #1

File: ninfo_sort_mp.py Project: naotohori/life-of-py

#!/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()

Example #2

        #    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
            if ni.imp2un in aln:

Example #3

#!/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)

Example #4

File: edc_post_aln.py Project: naotohori/life-of-py

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
        #linesp[4] # dist
        if side == 1:

Example #5

File: ninfo_split.py Project: naotohori/life-of-py

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:
    ninfo_out[(ba.iunit1, ba.iunit2)].bondangles.append(ba)

Example #6

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')
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

Example #7

File: pdb_ninfo.py Project: naotohori/life-of-py

    
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)
    
print(("## Confirmation: number of atoms = %i" % len(xyz)))
        
f_out = open(sys.argv[-1],'w')

f_out.write('#Contacts\n')

Example #8

File: ninfo_divide.py Project: naotohori/life-of-py

@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()