def run (args=(), params=None, out=sys.stdout) :
assert (params.convert.file_name is not None)
file_name = params.convert.file_name
error_message = 'Unable to parse %s. ' % file_name
error_message += 'Please make sure that the file exists and is a valid model in PDB or CIF format.'
if (not os.path.exists(file_name)):
raise Sorry(error_message)
try:
model = pdb_input_from_any(file_name=file_name)
except Exception:
raise Sorry(error_message)
output_file = os.path.splitext(os.path.basename(file_name))[0]
if (model.file_format == "pdb"):
print >> out, "Converting %s to mmCIF format." % file_name
pdb_as_cif.run([file_name])
output_file += '.cif'
elif (model.file_format == 'cif'):
print >> out, "Converting %s to PDB format." % file_name
cif_as_pdb.run([file_name])
output_file += '.pdb'
else:
raise Sorry(error_message)
if (not os.path.exists(output_file)):
raise Sorry('Could not find output file. Please check that %s exists'
% output_file)
return output_file
def exercise_02():
from iotbx.command_line import pdb_as_cif
if (os.path.isfile("tst_pdb_as_cif_2.cif")):
os.remove("tst_pdb_as_cif_2.cif")
open("tst_pdb_as_cif_2.pdb", "w").write("""\
CRYST1 209.050 447.220 608.960 90.00 90.00 90.00 P 21 21 21
ATOM 99999 N3 U 367 -23.562 29.366 106.688 1.00135.52 A16S N
ANISOU99999 N3 U 367 20423 14326 16741 -1922 -2828 -1650 A16S N
ATOM A0000 C4 U 367 -23.357 30.626 106.161 1.00133.22 A16S C
ANISOUA0000 C4 U 367 20015 14160 16442 -1873 -2801 -1645 A16S C
""")
pdb_as_cif.run(["tst_pdb_as_cif_2.pdb"], out=null_out())
assert os.path.isfile("tst_pdb_as_cif_2.cif")
inp = open("tst_pdb_as_cif_2.cif", "r")
cntr = 0
for l in inp.readlines():
l = l.strip()
# These are for align_columns=True in iotbx.cif.write_whole_cif_file()
# if(l.startswith("ATOM 99999 N3 . U . 367 ?")): cntr+=1
# if(l.startswith("ATOM 100000 C4 . U . 367 ?")): cntr+=1
# if(l.startswith("99999 N3 . U . 367 ?")): cntr+=1
# if(l.startswith("100000 C4 . U . 367 ?")): cntr+=1
# These are for align_columns=False in iotbx.cif.write_whole_cif_file()
if (l.startswith("ATOM 1 N3 . U A16S 367 ? ")): cntr += 1
if (l.startswith("ATOM 2 C4 . U A16S 367 ?")): cntr += 1
if (l.startswith("1 N3 . U A16S 367 ? ")): cntr += 1
if (l.startswith("2 C4 . U A16S 367 ?")): cntr += 1
assert cntr == 4, cntr
def exercise_01():
from iotbx.command_line import pdb_as_cif
from iotbx.file_reader import any_file
if (os.path.isfile("tst_pdb_as_cif_1.cif")):
os.remove("tst_pdb_as_cif_1.cif")
open("tst_pdb_as_cif_1.pdb", "w").write("""\
CRYST1 97.470 113.870 196.190 90.00 90.00 90.00 P 21 21 21 16
SCALE1 0.010260 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008782 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005097 0.00000
ATOM 1 N MET A 43 8.153 31.407 59.548 1.00182.68 N
ATOM 2 CA MET A 43 8.561 30.228 58.722 1.00182.68 C
ATOM 3 C MET A 43 9.997 29.817 59.022 1.00182.68 C
ATOM 4 O MET A 43 10.910 30.123 58.254 1.00182.68 O
ATOM 5 CB MET A 43 8.435 30.557 57.229 1.00182.68 C
ATOM 6 CG MET A 43 7.111 30.162 56.605 1.00182.68 C
ATOM 7 SD MET A 43 6.779 28.394 56.836 1.00182.68 S
ATOM 8 CE MET A 43 7.824 27.649 55.560 1.00182.68 C
ATOM 9 N LEU A 44 10.187 29.092 60.119 1.00182.68 N
ATOM 10 CA LEU A 44 11.515 28.652 60.526 1.00182.68 C
ATOM 11 C LEU A 44 12.314 27.929 59.481 1.00182.68 C
ATOM 12 O LEU A 44 11.991 26.807 59.098 1.00182.68 O
ATOM 13 CB LEU A 44 11.428 27.808 61.775 1.00182.68 C
ATOM 14 CG LEU A 44 11.367 28.820 62.893 1.00182.68 C
ATOM 15 CD1 LEU A 44 10.820 28.175 64.124 1.00182.68 C
ATOM 16 CD2 LEU A 44 12.755 29.420 63.073 1.00182.68 C
""")
pdb_as_cif.run(["tst_pdb_as_cif_1.pdb"], out=null_out())
assert os.path.isfile("tst_pdb_as_cif_1.cif")
cif_in = any_file("tst_pdb_as_cif_1.cif")
hierarchy = cif_in.file_object.construct_hierarchy()
open("tst_pdb_as_cif_2.pdb", "w").write("""\
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
ATOM 1 N ALA 1 26.216 26.069 22.329 1.00 4.70
ATOM 2 CA ALA 1 25.368 26.545 21.218 1.00 6.09
ATOM 3 C ALA 1 26.005 26.154 19.885 1.00 11.13
ATOM 4 O ALA 1 27.207 25.902 19.835 1.00 16.15
ATOM 5 CB ALA 1 25.434 28.079 21.272 1.00 4.53
ATOM 6 N GLY 2 25.198 26.203 18.856 1.00 8.14
ATOM 7 CA GLY 2 25.677 25.977 17.535 1.00 10.65
ATOM 8 C GLY 2 26.113 24.580 17.267 1.00 9.83
ATOM 9 O GLY 2 26.154 23.705 18.108 1.00 9.22
""")
out = StringIO()
pdb_as_cif.run(["tst_pdb_as_cif_2.pdb"], out=out)
assert (out.getvalue() == """\
Converting tst_pdb_as_cif_2.pdb to mmCIF format.
Error converting tst_pdb_as_cif_2.pdb to mmCIF format:
Missing element symbol for 7 atoms.
""")
assert not os.path.isfile("tst_pdb_as_cif_2.cif")
def exercise_01():
from iotbx.command_line import pdb_as_cif
from iotbx.file_reader import any_file
if (os.path.isfile("tst_pdb_as_cif_1.cif")) :
os.remove("tst_pdb_as_cif_1.cif")
open("tst_pdb_as_cif_1.pdb", "w").write("""\
CRYST1 97.470 113.870 196.190 90.00 90.00 90.00 P 21 21 21 16
SCALE1 0.010260 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008782 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005097 0.00000
ATOM 1 N MET A 43 8.153 31.407 59.548 1.00182.68 N
ATOM 2 CA MET A 43 8.561 30.228 58.722 1.00182.68 C
ATOM 3 C MET A 43 9.997 29.817 59.022 1.00182.68 C
ATOM 4 O MET A 43 10.910 30.123 58.254 1.00182.68 O
ATOM 5 CB MET A 43 8.435 30.557 57.229 1.00182.68 C
ATOM 6 CG MET A 43 7.111 30.162 56.605 1.00182.68 C
ATOM 7 SD MET A 43 6.779 28.394 56.836 1.00182.68 S
ATOM 8 CE MET A 43 7.824 27.649 55.560 1.00182.68 C
ATOM 9 N LEU A 44 10.187 29.092 60.119 1.00182.68 N
ATOM 10 CA LEU A 44 11.515 28.652 60.526 1.00182.68 C
ATOM 11 C LEU A 44 12.314 27.929 59.481 1.00182.68 C
ATOM 12 O LEU A 44 11.991 26.807 59.098 1.00182.68 O
ATOM 13 CB LEU A 44 11.428 27.808 61.775 1.00182.68 C
ATOM 14 CG LEU A 44 11.367 28.820 62.893 1.00182.68 C
ATOM 15 CD1 LEU A 44 10.820 28.175 64.124 1.00182.68 C
ATOM 16 CD2 LEU A 44 12.755 29.420 63.073 1.00182.68 C
""")
pdb_as_cif.run(["tst_pdb_as_cif_1.pdb"], out=null_out())
assert os.path.isfile("tst_pdb_as_cif_1.cif")
cif_in = any_file("tst_pdb_as_cif_1.cif")
hierarchy = cif_in.file_object.construct_hierarchy()
open("tst_pdb_as_cif_2.pdb", "w").write("""\
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
ATOM 1 N ALA 1 26.216 26.069 22.329 1.00 4.70
ATOM 2 CA ALA 1 25.368 26.545 21.218 1.00 6.09
ATOM 3 C ALA 1 26.005 26.154 19.885 1.00 11.13
ATOM 4 O ALA 1 27.207 25.902 19.835 1.00 16.15
ATOM 5 CB ALA 1 25.434 28.079 21.272 1.00 4.53
ATOM 6 N GLY 2 25.198 26.203 18.856 1.00 8.14
ATOM 7 CA GLY 2 25.677 25.977 17.535 1.00 10.65
ATOM 8 C GLY 2 26.113 24.580 17.267 1.00 9.83
ATOM 9 O GLY 2 26.154 23.705 18.108 1.00 9.22
""")
out = StringIO()
pdb_as_cif.run(["tst_pdb_as_cif_2.pdb"], out=out)
assert (out.getvalue() == """\
Converting tst_pdb_as_cif_2.pdb to mmCIF format.
Error converting tst_pdb_as_cif_2.pdb to mmCIF format:
Missing element symbol for 7 atoms.
""")
assert not os.path.isfile("tst_pdb_as_cif_2.cif")
def exercise_02():
from iotbx.command_line import pdb_as_cif
from iotbx.file_reader import any_file
if (os.path.isfile("tst_pdb_as_cif_2.cif")) :
os.remove("tst_pdb_as_cif_2.cif")
open("tst_pdb_as_cif_2.pdb", "w").write("""\
CRYST1 209.050 447.220 608.960 90.00 90.00 90.00 P 21 21 21
ATOM 99999 N3 U 367 -23.562 29.366 106.688 1.00135.52 A16S N
ANISOU99999 N3 U 367 20423 14326 16741 -1922 -2828 -1650 A16S N
ATOM A0000 C4 U 367 -23.357 30.626 106.161 1.00133.22 A16S C
ANISOUA0000 C4 U 367 20015 14160 16442 -1873 -2801 -1645 A16S C
""")
pdb_as_cif.run(["tst_pdb_as_cif_2.pdb"], out=null_out())
assert os.path.isfile("tst_pdb_as_cif_2.cif")
inp = open("tst_pdb_as_cif_2.cif", "r")
cntr = 0
for l in inp.readlines():
l = l.strip()
if(l.startswith("ATOM 99999 N3 . U . 367 ?")): cntr+=1
if(l.startswith("ATOM 100000 C4 . U . 367 ?")): cntr+=1
if(l.startswith("99999 N3 . U . 367 ?")): cntr+=1
if(l.startswith("100000 C4 . U . 367 ?")): cntr+=1
assert cntr == 4
