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
run_program(program_class=pdb_as_cif.Program, args=[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_emringer_residue_scan():
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/mmtbx/em_ringer/tst_emringer_model.pdb",
test=os.path.isfile)
map_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/mmtbx/em_ringer/tst_emringer_map.ccp4",
test=os.path.isfile)
assert (not None in [pdb_file, map_file])
emringer_results = run_program(program_class=emringer.Program, args=[pdb_file, map_file, 'quiet=True'])
results = emringer_results.ringer_result
scoring = emringer_results.scoring_result
rolling = emringer_results.rolling_result
#results, scoring, rolling = emringer.run([pdb_file, map_file], out=null_out())
# Make sure the right number of residues (22 out of 28) get scanned
assert len(results)==22
modelled_list = [290.742121792,192.844056257,45.4781110306,294.247825632,303.618891108,58.7694040824,331.70068496,46.7136045049,290.167261226,304.261231829,282.651244586,268.729721112,195.972333785,305.321933311,314.81066224,286.028424514,311.180807466,313.004918133,296.67781565,296.949191638,169.644245088,192.496265164]
peak_list = [270,180,260,75,305,30,310,90,265,270,270,240,280,260,310,285,295,100,260,165,155,200]
peak_rhos = [0.175600306502,0.351591946536,0.206238983746,0.3269057296,0.68375562882,0.251143527693,0.29106077218,0.199922124642,0.298461589197,0.563313760047,0.412696803251,0.511080434089,0.310001828446,0.228239176285,0.563148497472,0.490755919184,0.200978032127,0.274929619102,0.299229846335,0.179215798655,0.150783734124,0.210869945593]
for i in range(22):
# Make sure the modelled angle is correctly read
assert approx_equal(results[i]._angles[1].angle_current, modelled_list[i])
# Make sure the peak is chosen correctly
assert approx_equal(results[i]._angles[1].peak_chi, peak_list[i])
# Make sure the peak rhos are correct
assert approx_equal(results[i]._angles[1].peak_rho, peak_rhos[i])
emringer_results2 = run_program(program_class=emringer.Program, args=[pdb_file, map_file, "rolling_window_threshold=0.5", 'quiet=True'])
#results, scoring2, rolling2 = emringer.run([pdb_file, map_file, "rolling_window_threshold=0.5"], out=null_out())
results2 = emringer_results2.ringer_result
scoring2 = emringer_results2.scoring_result
rolling2 = emringer_results2.rolling_result
assert rolling.threshold == 0
assert rolling2.threshold == 0.5
def exercise_02():
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
""")
run_program(
program_class=pdb_as_cif.Program,
args=["tst_pdb_as_cif_2.pdb"],
logger=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():
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
""")
run_program(
program_class=pdb_as_cif.Program,
args=["tst_pdb_as_cif_1.pdb"],
logger=null_out(),
)
assert os.path.isfile("tst_pdb_as_cif_1.cif")
cif_in = iotbx.pdb.input("tst_pdb_as_cif_1.cif")
hierarchy = cif_in.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()
try:
run_program(
program_class=pdb_as_cif.Program,
args=["tst_pdb_as_cif_2.pdb"],
logger=out,
)
except Exception, e:
pass
def exercise_cryo_fit2(): #Checks that cryo_fit2 runs well
pdb_file = libtbx.env.find_in_repositories(
relative_path=
"cryo_fit2/regression/input/tst_cryo_fit2_tRNA_EFTU_within_10.pdb",
test=os.path.isfile)
##### <begin> This copy operation seems odd, but needed to test CRYST1 header addition test
pdb_file_no_CRYST1 = pdb_file[:-4] + "_no_CRYST1.pdb"
command_string = "cp " + pdb_file_no_CRYST1 + " " + pdb_file
libtbx.easy_run.call(command=command_string)
##### <end> This copy operation seems odd, but needed to test CRYST1 header addition test
pdb_file = libtbx.env.find_in_repositories(
relative_path=
"cryo_fit2/regression/input/tst_cryo_fit2_tRNA_EFTU_within_10.pdb",
test=os.path.isfile)
map_file = libtbx.env.find_in_repositories(
relative_path=
"cryo_fit2/regression/input/tst_cryo_fit2_tRNA_EFTU_within_10_assume_reso_4.ccp4",
test=os.path.isfile)
resolution = "resolution=4"
max_steps_for_exploration = "max_steps_for_exploration=20"
max_steps_for_final_MD = "max_steps_for_final_MD=20"
assert (not None in [pdb_file, map_file])
cryo_fit2_results = run_program(program_class=cryo_fit2_program.Program, \
args=[pdb_file, map_file, resolution, \
max_steps_for_exploration, max_steps_for_final_MD])
def exercise_cryo_fit2(): #Checks that cryo_fit2 runs well
pdb_file = libtbx.env.find_in_repositories(
relative_path="cryo_fit2/regression/input/tst_cryo_fit2_helix_1_8.pdb",
test=os.path.isfile)
##### <begin> This copy operation seems odd, but needed to test CRYST1 header addition test
pdb_file_no_CRYST1 = pdb_file[:-4] + "_no_CRYST1.pdb"
command_string = "cp " + pdb_file_no_CRYST1 + " " + pdb_file
libtbx.easy_run.call(command=command_string)
##### <end> This copy operation seems odd, but needed to test CRYST1 header addition test
map_file = libtbx.env.find_in_repositories(
relative_path="cryo_fit2/regression/input/tst_cryo_fit2_helix_1_8_reso_20.ccp4",
test=os.path.isfile)
explore = "explore=False"
resolution = "resolution=20"
stronger_ss = "stronger_ss=False"
max_steps_for_exploration = "max_steps_for_exploration=50"
max_steps_for_final_MD = "max_steps_for_final_MD=50"
start_temperature = "start_temperature=300"
final_temperature = "final_temperature=280"
MD_in_each_cycle = "MD_in_each_cycle=2"
number_of_steps = "number_of_steps=50"
assert (not None in [pdb_file, map_file])
cryo_fit2_results = run_program(program_class=cryo_fit2_program.Program, \
args=[pdb_file, map_file, resolution, start_temperature, final_temperature, \
MD_in_each_cycle, number_of_steps, stronger_ss, explore, \
max_steps_for_final_MD, max_steps_for_exploration])
def exercise_cryo_fit2(): #Checks that cryo_fit2 runs well
pdb_file = libtbx.env.find_in_repositories(
relative_path="cryo_fit2/regression/input/tst_cryo_fit2_helix_1_8.pdb",
test=os.path.isfile)
pdb_file_no_CRYST1 = pdb_file[:-4] + "_no_CRYST1.pdb"
command_string = "cp " + pdb_file_no_CRYST1 + " " + pdb_file
libtbx.easy_run.call(command=command_string)
pdb_file = libtbx.env.find_in_repositories(
relative_path="cryo_fit2/regression/input/tst_cryo_fit2_helix_1_8.pdb",
test=os.path.isfile)
map_file = libtbx.env.find_in_repositories(
relative_path=
"cryo_fit2/regression/input/tst_cryo_fit2_helix_1_8_reso_20.ccp4",
test=os.path.isfile)
resolution = "resolution=20"
stronger_ss = "stronger_ss=False"
map_weight = "map_weight=0.001" # for faster regression test
explore = "explore=False"
start_temperature = "start_temperature=300"
final_temperature = "final_temperature=280"
MD_in_each_cycle = "MD_in_each_cycle=2"
number_of_steps = "number_of_steps=1"
assert (not None in [pdb_file, map_file])
cryo_fit2_results = run_program(program_class=cryo_fit2_program.Program, \
args=[pdb_file, map_file, resolution, start_temperature, final_temperature, \
MD_in_each_cycle, number_of_steps, map_weight, explore])
def exercise_cryo_fit2(): #Checks that cryo_fit2 runs well
pdb_file = libtbx.env.find_in_repositories(
relative_path="cryo_fit2/regression/input/tst_cryo_fit2_helix_1_8.pdb",
test=os.path.isfile)
pdb_file_no_CRYST1 = pdb_file[:-4] + "_no_CRYST1.pdb"
command_string = "cp " + pdb_file_no_CRYST1 + " " + pdb_file
libtbx.easy_run.call(command=command_string)
pdb_file = libtbx.env.find_in_repositories(
relative_path="cryo_fit2/regression/input/tst_cryo_fit2_helix_1_8.pdb",
test=os.path.isfile)
map_file = libtbx.env.find_in_repositories(
relative_path=
"cryo_fit2/regression/input/tst_cryo_fit2_helix_1_8_reso_20.ccp4",
test=os.path.isfile)
resolution = "resolution=20"
stronger_ss = "stronger_ss=True"
explore = "explore=True"
max_steps_for_exploration = "max_steps_for_exploration=20"
max_steps_for_final_MD = "max_steps_for_final_MD=20"
assert (not None in [pdb_file, map_file])
cryo_fit2_results = run_program(program_class=cryo_fit2_program.Program, \
args=[pdb_file, map_file, resolution, stronger_ss, explore,\
max_steps_for_exploration, max_steps_for_final_MD])
def test_dry_run():
class testProgram(ProgramTemplate):
def validate(self):
raise Sorry('This is a test')
try:
run_program(program_class=testProgram, args=['--dry-run', '--quiet'])
except Sorry:
pass
else:
raise Exception_expected
class testProgram(ProgramTemplate):
def validate(self):
pass
try:
run_program(program_class=testProgram, args=['--dry-run', '--quiet'])
except Exception:
raise Exception_not_expected
def exercise_emringer_insertion_codes():
"""
Checks that emringer doesn't crash when there are insertion codes.
The correctness of output is not checked.
"""
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/mmtbx/em_ringer/tst_emringer_insertion_codes_model.pdb",
test=os.path.isfile)
map_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/mmtbx/em_ringer/tst_emringer_map.ccp4",
test=os.path.isfile)
assert (not None in [pdb_file, map_file])
emringer_results = run_program(program_class=emringer.Program, args=[pdb_file, map_file, 'quiet=True'])
from __future__ import absolute_import, division, print_function # LIBTBX_SET_DISPATCHER_NAME phenix.evalurama from mmtbx.programs import evalurama from iotbx.cli_parser import run_program run_program(evalurama.Program)
from __future__ import absolute_import, division, print_function # LIBTBX_SET_DISPATCHER_NAME mmtbx.ss_idealization from mmtbx.programs import ss_idealization from iotbx.cli_parser import run_program run_program(ss_idealization.Program)
from __future__ import division, print_function
from iotbx.cli_parser import run_program
from mmtbx.programs import emringer
if __name__ == '__main__':
run_program(program_class=emringer.Program)
# =============================================================================
# old code - maybe necessary until GUI is updated
# LIBTBX_SET_DISPATCHER_NAME phenix.emringer
# LIBTBX_PRE_DISPATCHER_INCLUDE_SH PHENIX_GUI_ENVIRONMENT=1
# LIBTBX_PRE_DISPATCHER_INCLUDE_SH export PHENIX_GUI_ENVIRONMENT
"""
Implementation of the EMRinger method, with plots, for use with the
EMRinger workflow.
References:
Barad BA, Echols N, Wang RYR, Cheng YC, DiMaio F, Adams PD, Fraser JS. (2015)
Side-chain-directed model and map validation for 3D Electron Cryomicroscopy.
Nature Methods, in press.
Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T.
Automated electron-density sampling reveals widespread conformational
polymorphism in proteins. Protein Sci. 2010 Jul;19(7):1420-31. PubMed PMID:
20499387
"""
# Any software that wants to use the pkl output of this tool
# should import ringer_residue and ringer_chi from it.
from __future__ import absolute_import, division, print_function
from iotbx.cli_parser import run_program
from iotbx.programs import box_around_molecule
if __name__ == '__main__':
run_program(program_class=box_around_molecule.Program)
from __future__ import division, print_function from iotbx.cli_parser import run_program from mmtbx.programs import validate_ligands if __name__ == '__main__': run_program(program_class=validate_ligands.Program) #old stuff #from __future__ import division #from libtbx.str_utils import make_sub_header #from libtbx.utils import Sorry #import os #import sys # #def master_phil () : # from mmtbx.command_line import generate_master_phil_with_inputs # return generate_master_phil_with_inputs( # enable_automatic_twin_detection=True, # phil_string=""" #ligand_code = None # .type = str # .multiple = True #reference_structure = None # .type = path #only_segid = None # .type = str #verbose = False # .type = bool #""")
from __future__ import absolute_import, division, print_function from iotbx.cli_parser import run_program from mmtbx.programs import probe2 run_program(probe2.Program)
from __future__ import division # LIBTBX_SET_DISPATCHER_NAME phenix.cablam_idealization from iotbx.cli_parser import run_program from mmtbx.programs import cablam_idealization run_program(cablam_idealization.Program)
# LIBTBX_SET_DISPATCHER_NAME mmtbx.process_predicted_model
# LIBTBX_SET_DISPATCHER_NAME phenix.process_predicted_model
from __future__ import division, print_function
from iotbx.cli_parser import run_program
from mmtbx.programs import process_predicted_model
if __name__ == '__main__':
run_program(program_class=process_predicted_model.Program)
from __future__ import absolute_import, division, print_function # LIBTBX_SET_DISPATCHER_NAME iotbx.unique_with_biomt # LIBTBX_SET_DISPATCHER_NAME phenix.unique_with_biomt from iotbx.programs import unique_with_biomt from iotbx.cli_parser import run_program result = run_program(unique_with_biomt.Program)
# LIBTBX_SET_DISPATCHER_NAME phenix.polder
from __future__ import absolute_import, division, print_function
from iotbx.cli_parser import run_program
from mmtbx.programs import polder
if __name__ == '__main__':
run_program(program_class=polder.Program)
from __future__ import absolute_import, division, print_function # LIBTBX_SET_DISPATCHER_NAME phenix.pdbtools from iotbx.cli_parser import run_program from mmtbx.programs import pdbtools run_program(pdbtools.Program)
# LIBTBX_SET_DISPATCHER_NAME mmtbx.nonbonded_overlaps
from __future__ import division, print_function
from iotbx.cli_parser import run_program
from mmtbx.programs import nonbonded_overlaps
if __name__ == '__main__':
run_program(program_class=nonbonded_overlaps.Program)
# from __future__ import division
# from __future__ import print_function
# import mmtbx.monomer_library.pdb_interpretation as pdb_inter
# import cctbx.geometry_restraints.nonbonded_overlaps as nbo
# import mmtbx.validation.clashscore as mvc
# from libtbx.utils import null_out
# from libtbx.utils import Sorry
# from libtbx.utils import Usage
# import iotbx.phil
# import sys
# master_phil_str = """
# model = None
# .type = path
# .optional = False
# .help = '''input PDB file'''
# cif = None
# .type = path
# .optional = True
# .help = '''Optional Crystallographic Information File (CIF)'''
from __future__ import absolute_import, division, print_function # LIBTBX_SET_DISPATCHER_NAME phenix.secondary_structure_validation from mmtbx.programs import ss_validation from iotbx.cli_parser import run_program run_program(ss_validation.Program)
# LIBTBX_SET_DISPATCHER_NAME phenix.HKLinfo
# LIBTBX_SET_DISPATCHER_NAME cctbx.HKLinfo
from __future__ import absolute_import, division, print_function
from iotbx.cli_parser import run_program
from crys3d.programs import HKLinfo
if __name__ == '__main__':
run_program(program_class=HKLinfo.Program)
from __future__ import absolute_import, division, print_function # LIBTBX_SET_DISPATCHER_NAME phenix.comparama from mmtbx.programs import comparama from iotbx.cli_parser import run_program run_program(comparama.Program)
from __future__ import absolute_import, division, print_function from iotbx.cli_parser import run_program from mmtbx.programs import hydrogenate run_program(hydrogenate.Program)
# LIBTBX_SET_DISPATCHER_NAME phenix.pdb_as_cif
from __future__ import absolute_import, division, print_function
from iotbx.cli_parser import run_program
from mmtbx.programs import pdb_as_cif
if __name__ == '__main__':
run_program(program_class=pdb_as_cif.Program)
from __future__ import division, print_function from iotbx.cli_parser import run_program from amber_adaptbx.programs import h_bond_information if __name__ == '__main__': run_program(program_class=h_bond_information.Program)
# -*- coding: utf-8 -*- from __future__ import division, print_function # LIBTBX_SET_DISPATCHER_NAME cctbx.development.ntc_validation from iotbx.cli_parser import run_program from mmtbx.programs.ntc_validation import Program # ============================================================================= if (__name__ == '__main__'): results = run_program(program_class=Program)
from __future__ import division # LIBTBX_SET_DISPATCHER_NAME phenix.hbond from mmtbx.programs import hbond from iotbx.cli_parser import run_program run_program(hbond.Program)