def run(prefix):
fn = 'test_remove_hg_from_zn_cys.pdb'
f = open(fn, 'w')
f.write(pdb_lines)
f.close()
cmd = 'qr.finalise %s action="capping"' % (fn)
if 0: print(cmd)
rc = easy_run.go(cmd)
os.remove(fn)
fnc = '%s_capping.pdb' % fn.replace('.pdb', '')
f = open(fnc, 'r')
lines = f.read()
f.close()
for line in [
' HG CYS A 3',
' HG CYS A 8',
' HG CYS A 21',
' HG CYS A 25',
' HG CYS A 33',
' HG CYS A 48',
]:
assert line not in lines, 'found %s' % line
assert ' HE ARG A 10' in lines, 'not found HE ARG A 10'
cmd = 'qr.charges %s verbose=1' % (fnc)
if 0: print(cmd)
rc = easy_run.go(cmd)
assert 'Charge: -1' in rc.stdout_lines
os.remove(fnc)
return rc
def run(prefix):
fn = 'test_remove_hg_from_zn_cys.pdb'
f = file(fn, 'wb')
f.write(pdb_lines)
f.close()
cmd = 'qr.finalise %s action="capping"' % (fn)
if 0: print cmd
rc = easy_run.go(cmd)
os.remove(fn)
fnc = '%s_capping.pdb' % fn.replace('.pdb', '')
f = file(fnc, 'rb')
lines = f.read()
f.close()
assert ' HG CYS A 3' not in lines
assert ' HG CYS A 8' not in lines
assert ' HG CYS A 21' not in lines
assert ' HG CYS A 25' not in lines
assert ' HG CYS A 33' not in lines
assert ' HG CYS A 48' not in lines
assert ' HE ARG A 10' in lines
cmd = 'qr.charges %s verbose=1' % (fnc)
if 0: print cmd
rc = easy_run.go(cmd)
assert 'Charge: -1' in rc.stdout_lines
os.remove(fnc)
return rc
def main():
tf = 'test_cis_127.pdb'
f = file(tf, 'wb')
f.write(pdb_lines)
del f
cmd = 'phenix.pdb_interpretation write_geo=True %s' % tf
print(cmd)
easy_run.go(cmd)
f = file('%s.geo' % tf, 'rb')
lines = f.read()
del f
find = '''angle pdb=" C GLY A 73 "
pdb=" N PRO A 74 "
pdb=" CA PRO A 74 "
ideal model delta sigma weight residual
122.60 124.91 -2.31 5.00e+00 4.00e-02 2.14e-01'''
assert lines.find(find) > -1
cmd = 'phenix.pdb_interpretation write_geo=True cis_pro_eh99=True %s' % tf
print(cmd)
easy_run.go(cmd)
f = file('%s.geo' % tf, 'rb')
lines = f.read()
del f
find = '''angle pdb=" C GLY A 73 "
pdb=" N PRO A 74 "
pdb=" CA PRO A 74 "
ideal model delta sigma weight residual
127.00 124.91 2.09 2.40e+00 1.74e-01 7.57e-01'''
assert lines.find(find) > -1
def tst_adding_disulfur_hydrogen_atoms(switch):
element = 'H'
if switch.endswith('_D'): element = 'D'
fn = 'tst_ready_hydrogens_%s.pdb' % (switch)
f = file(fn, 'wb')
f.write(pdb_strings[switch])
del f
pdb_inp = pdb_input(fn)
hierarchy = pdb_inp.construct_hierarchy()
from mmtbx.conformation_dependent_library.testing_utils import get_geometry_restraints_manager
grm = get_geometry_restraints_manager(pdb_filename=fn)
add_disulfur_hydrogen_atoms(grm, hierarchy, element=element)
hierarchy.write_pdb_file(fn.replace('.pdb', '_updated.pdb'))
if switch == 'CYS_1':
f = file(fn.replace('.pdb', '_updated.pdb'), 'rb')
lines = f.read()
del f
assert lines.find('HG') == -1
else:
cmd = 'phenix.pdb_interpretation %s write_geo=True' % fn.replace(
'.pdb', '_updated.pdb')
print(cmd)
easy_run.go(cmd)
assert_lines_in_file(file_name='%s.geo' %
fn.replace('.pdb', '_updated.pdb'),
lines=geo_strings[switch])
def run(args, log=sys.stdout):
if (len(args) == 0):
parsed = defaults(log=log)
parsed.show(prefix=" ", out=log)
return
parsed = defaults(log=log)
processed_args = mmtbx.utils.process_command_line_args(
args=args, log=sys.stdout, master_params=parsed)
processed_args.params.show()
params = processed_args.params.extract()
if (len(processed_args.pdb_file_names) == 0):
raise Sorry("No PDB file found.")
if (len(processed_args.pdb_file_names) > 1):
raise Sorry("More than one PDB file found.")
pdb_file_name = processed_args.pdb_file_names[0]
if (params.f_obs.f_calc.atomic_model.add_hydrogens):
pdb_file_name_r = os.path.basename(pdb_file_name) + "_reduce"
easy_run.go("phenix.reduce %s > %s" % (pdb_file_name, pdb_file_name_r))
pdb_file_name = pdb_file_name_r
pdb_inp = iotbx.pdb.input(file_name=pdb_file_name)
pdbi_params = mmtbx.monomer_library.pdb_interpretation.master_params.extract(
)
if (params.f_obs.f_calc.atomic_model.use_ramachandran_plot_restraints):
pdbi_params.peptide_link.ramachandran_restraints = True
processed_pdb_file = monomer_library.pdb_interpretation.process(
pdb_inp=pdb_inp,
mon_lib_srv=monomer_library.server.server(),
ener_lib=monomer_library.server.ener_lib(),
params=pdbi_params)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_hierarchy.atoms().reset_i_seq()
xray_structure = processed_pdb_file.xray_structure()
mmtbx.utils.assert_xray_structures_equal(
x1=xray_structure, x2=pdb_inp.xray_structure_simple())
sctr_keys = xray_structure.scattering_type_registry().type_count_dict(
).keys()
has_hd = "H" in sctr_keys or "D" in sctr_keys
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies=False,
plain_pairs_radius=5,
assume_hydrogens_all_missing=not has_hd)
restraints_manager = mmtbx.restraints.manager(geometry=geometry,
normalization=True)
root = iotbx.pdb.hierarchy.root()
loop_1(params=params,
root=root,
xray_structure=xray_structure,
pdb_hierarchy=pdb_hierarchy,
restraints_manager=restraints_manager)
root.write_pdb_file(
file_name=params.f_obs.f_calc.atomic_model.output_file_name,
crystal_symmetry=xray_structure.crystal_symmetry())
simulate_f_obs(root=root,
crystal_symmetry=xray_structure.crystal_symmetry(),
params=params)
def run(args, log = sys.stdout):
if(len(args)==0):
parsed = defaults(log=log)
parsed.show(prefix=" ", out=log)
return
parsed = defaults(log=log)
processed_args = mmtbx.utils.process_command_line_args(args = args,
log = sys.stdout, master_params = parsed)
processed_args.params.show()
params = processed_args.params.extract()
if(len(processed_args.pdb_file_names)==0):
raise Sorry("No PDB file found.")
if(len(processed_args.pdb_file_names)>1):
raise Sorry("More than one PDB file found.")
pdb_file_name = processed_args.pdb_file_names[0]
if(params.f_obs.f_calc.atomic_model.add_hydrogens):
pdb_file_name_r = os.path.basename(pdb_file_name)+"_reduce"
easy_run.go("phenix.reduce %s > %s"% (pdb_file_name, pdb_file_name_r))
pdb_file_name = pdb_file_name_r
pdb_inp = iotbx.pdb.input(file_name = pdb_file_name)
pdbi_params = mmtbx.monomer_library.pdb_interpretation.master_params.extract()
if(params.f_obs.f_calc.atomic_model.use_ramachandran_plot_restraints):
pdbi_params.peptide_link.ramachandran_restraints=True
processed_pdb_file = monomer_library.pdb_interpretation.process(
pdb_inp = pdb_inp,
mon_lib_srv = monomer_library.server.server(),
ener_lib = monomer_library.server.ener_lib(),
params = pdbi_params)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_hierarchy.atoms().reset_i_seq()
xray_structure = processed_pdb_file.xray_structure()
mmtbx.utils.assert_xray_structures_equal(x1 = xray_structure,
x2 = pdb_inp.xray_structure_simple())
sctr_keys=xray_structure.scattering_type_registry().type_count_dict().keys()
has_hd = "H" in sctr_keys or "D" in sctr_keys
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies = False,
plain_pairs_radius = 5,
assume_hydrogens_all_missing = not has_hd)
restraints_manager = mmtbx.restraints.manager(
geometry = geometry,
normalization = True)
root = iotbx.pdb.hierarchy.root()
loop_1(
params = params,
root = root,
xray_structure = xray_structure,
pdb_hierarchy = pdb_hierarchy,
restraints_manager = restraints_manager)
root.write_pdb_file(
file_name = params.f_obs.f_calc.atomic_model.output_file_name,
crystal_symmetry = xray_structure.crystal_symmetry())
simulate_f_obs(root=root, crystal_symmetry=xray_structure.crystal_symmetry(),
params = params)
def main():
for code, item in pdbs.items():
print(code)
pf = 'tst_fe_s_%s.pdb' % code
with open(pf, 'w') as f:
f.write(item[0])
cmd = 'phenix.pdb_interpretation %(pf)s > %(pf)s.log' % locals()
print(cmd)
easy_run.go(cmd)
print(item[1])
for line in item[1].split('\n'):
print(line)
assert_lines_in_file(file_name='%s.log' % pf, lines=line)
def get_miller_arrays(pdb,cif,mtz_folder):
"""
convert cif to mtz and write it in the mtz_folder
convert cif of the format 'r_name_sf.ent.gz' to mtz file
creates mtz file with crystal symmetry in current folder
Returns:
"""
if not (os.path.isfile(pdb) and os.path.isfile(cif)):
return None
pdb_id = get_4_letters_pdb_id(cif)
mtz_fn = os.path.join(mtz_folder, pdb_id + '.mtz')
cmd_list = []
cmd_list.append('phenix.cif_as_mtz')
cmd_list.append(cif)
cmd_list.append('--output-file-name={}'.format(mtz_fn))
cmd_list.append("--merge")
cmd_list.append("--remove-systematic-absences")
cmd_list.append("--map-to-asu")
cmd_list.append("--ignore-bad-sigmas")
cmd_list.append("--extend-flags")
cmd = ' '.join(cmd_list)
r = easy_run.go(cmd)
# NOTE !!! in windows r does not returns the errors as expected
tmp = [x for x in r.stdout_lines if '--' in x]
tmp2 = ''.join(tmp)
run_cmd_again = False
if '--incompatible_flags_to_work_set' in tmp2:
cmd_list.append('--incompatible_flags_to_work_set')
run_cmd_again = True
if '--symmetry' in tmp2:
cmd_list.append('--symmetry={}'.format(pdb))
run_cmd_again = True
if run_cmd_again:
cmd = ' '.join(cmd_list)
easy_run.go(cmd)
try:
# Get miller arrays from mtz file
mtz_object = iotbx.mtz.object(file_name=mtz_fn)
miller_arrays = mtz_object.as_miller_arrays()
except:
miller_arrays = None
# cleanup
os.remove(cif)
if not miller_arrays:
return None
return miller_arrays
def main():
i=0
filename = 'cdl_nucleotide.pdb'
f=open(filename, 'w')
f.write(pdb)
del f
for param1 in range(2):
if param1 and not restraintlib_installed: break
for param2 in ['phenix', 'csd']:
cmd = 'phenix.pdb_interpretation %s write_geo=True cdl_nucleotides=%s cdl_nucleotides_esd=%s' % (
filename,
param1,
param2,
)
print(i, param1, param2, cmd)
rc = easy_run.go(cmd)
lines=[]
for line in rc.stdout_lines:
lines.append(line.strip())
for line in std_asserts[i]:
assert line in lines, 'missing %s' % line
f=open('%s.geo' % filename, 'r')
lines=f.read()
del f
for line in geo_asserts[i]:
assert lines.find(line)>-1, 'missing %s' % line
i+=1
print('OK')
print('OK')
def main():
with open('tst_mcl_02.pdb', 'w') as f:
f.write(pdb_string)
cmd = 'phenix.pdb_interpretation tst_mcl_02.pdb write_geo=1'
print(cmd)
rc = easy_run.go(cmd)
assert os.path.exists('tst_mcl_02.pdb.geo')
return rc.return_code
def run_cmd(prefix, args, pdb_name="m00_poor.pdb", mtz_name="m00_good.mtz"):
test_folder_name = prefix
cmd = ["qr.refine", mtz_name, os.path.join(qr_unit_tests_data, pdb_name)]
for arg in args:
cmd.append(arg)
cmd.append("output_folder_name=%s" % test_folder_name)
cmd.append("> %s.log" % prefix)
if (0): print " ".join(cmd)
return easy_run.go(" ".join(cmd))
def main():
input_model_filename = 'carbo_linking_output.pdb'
with open(input_model_filename, 'w') as f:
f.write(input_model)
cmd = 'phenix.pdb_interpretation %s' % input_model_filename
rc = easy_run.go(cmd)
lines = '\n'.join(rc.stdout_lines)
assert lines.find(result) > -1
print('OK')
def run(prefix):
"""
Make sure 'qr.charges tst_22.pdb' runs without errors (finishes successfully).
"""
pdb_name = os.path.join(qr_unit_tests_data, "tst_22.pdb")
cmd = "qr.charges %s verbose=False" % pdb_name
if (0): print cmd
r = easy_run.go(cmd)
# Make sure no
assert len(r.stderr_lines) == 0, r.stderr_lines
assert len(r.stdout_lines) == 0, r.stdout_lines
def run(prefix):
fn = 'test_zn_his_charge.pdb'
f = open(fn, 'w')
f.write(pdb_lines)
f.close()
cmd = 'qr.charges %s verbose=1' % (fn)
if 0: print(cmd)
rc = easy_run.go(cmd)
assert 'Charge: 0' in rc.stdout_lines
os.remove(fn)
return rc
def main():
for i, pdb_str in enumerate([pdb_str_1, pdb_str_2]):
print(i)
fn = 'tst_mcl_%d.pdb' % i
with open(fn, 'w') as f:
f.write(pdb_str)
cmd = 'phenix.pdb_interpretation %s write_geo=true' % fn
print(cmd)
rc = easy_run.go(cmd)
assert os.path.exists('%s.geo' % fn)
assert not rc.return_code
def run(prefix):
fn = 'test_cu_cys.pdb'
f = open(fn, 'w')
f.write(pdb_lines)
f.close()
cmd = 'qr.finalise %s action="capping"' % (fn)
if 0: print(cmd)
rc = easy_run.go(cmd)
os.remove(fn)
fnc = '%s_capping.pdb' % fn.replace('.pdb', '')
f = open(fnc, 'r')
lines = f.read()
f.close()
assert ' HG CYS A 78' not in lines
cmd = 'qr.charges %s verbose=1' % (fnc)
if 0: print(cmd)
rc = easy_run.go(cmd)
assert 'Charge: 0' in rc.stdout_lines
os.remove(fnc)
return rc
def tst_adding_side_chain_acid_hydrogen_atoms(switch):
element = 'H'
if switch.endswith('_D'): element = 'D'
for i in range(4):
fn = 'tst_ready_hydrogens_%s_%d.pdb' % (switch, i)
with open(fn, 'w') as f:
f.write(pdb_strings[switch])
pdb_inp = pdb_input(fn)
hierarchy = pdb_inp.construct_hierarchy()
add_side_chain_acid_hydrogens(hierarchy,
configuration_index=i,
element=element)
hierarchy.write_pdb_file(fn.replace('.pdb', '_updated.pdb'))
cmd = 'phenix.pdb_interpretation %s flip_sym=0 write_geo=True' % fn.replace(
'.pdb', '_updated.pdb')
print(cmd)
easy_run.go(cmd)
assert_lines_in_file(file_name='%s.geo' %
fn.replace('.pdb', '_updated.pdb'),
lines=geo_strings[switch][i])
def find_majority_blame(full_path):
cmd = 'git blame %s' % full_path
rc = easy_run.go(cmd)
blames = {}
for line in rc.stdout_lines:
key = line[line.find('(') + 1:line.find('(') + 11]
blames.setdefault(key, 0)
blames[key] += 1
m = max(blames.values())
for key, item in blames.items():
if item == m: return key
def run(prefix):
fn = 'test_one_alt_loc.pdb'
f = file(fn, 'wb')
f.write(pdb_lines)
f.close()
cmd = 'qr.charges %s verbose=1' % (fn)
if 0: print cmd
rc = easy_run.go(cmd)
assert 'Charge: -2' in rc.stdout_lines
os.remove(fn)
return rc
def test_running_from_command_line():
'''
Make sure mmtbx.nonbonded_overlaps can run without errors
'''
file_name = 'test_pdb_file.pdb'
if not os.path.isfile(file_name):
open(file_name,'w').write(raw_records_1)
#self.file_to_delete.append(self.file_name)
cmd = 'mmtbx.nonbonded_overlaps {}'
cmd = cmd.format(file_name)
r = easy_run.go(cmd, join_stdout_stderr=False)
assert(not bool(r.stderr_lines))
def run(prefix):
fn = 'expansion.pdb'
f = open(fn, 'w')
f.write(expansion)
f.close()
fn = 'test_alt_loc_original.pdb'
f = open(fn, 'w')
f.write(pdb_lines)
f.close()
cmd = 'phenix.python %s/completion.py %s model_completion=False original_pdb_filename=expansion.pdb' % (
qrefine_path, fn)
if 0: print(cmd)
easy_run.go(cmd)
fnc = '%s_capping.pdb' % fn.replace('.pdb', '')
cmd = 'phenix.pdb_interpretation %s' % fnc
if 0: print(cmd)
rc = easy_run.go(cmd)
assert ' H 47 1.00' in rc.stdout_lines
os.remove(fn)
os.remove(fnc)
return rc
def main():
tf = 'test_cis_127.pdb'
with open(tf, 'w') as f:
f.write(pdb_lines[0])
cmd = 'phenix.pdb_interpretation write_geo=True cis_pro_eh99=False %s' % tf
print(cmd)
easy_run.go(cmd)
with open('%s.geo' % tf, 'r') as f:
lines = f.read()
find = '''angle pdb=" C GLY A 73 "
pdb=" N PRO A 74 "
pdb=" CA PRO A 74 "
ideal model delta sigma weight residual
122.60 124.91 -2.31 5.00e+00 4.00e-02 2.14e-01'''
assert lines.find(find)>-1
cmd = 'phenix.pdb_interpretation write_geo=True cis_pro_eh99=True %s' % tf
print(cmd)
easy_run.go(cmd)
with open('%s.geo' % tf, 'r') as f:
lines = f.read()
find = '''angle pdb=" C GLY A 73 "
pdb=" N PRO A 74 "
pdb=" CA PRO A 74 "
ideal model delta sigma weight residual
127.00 124.91 2.09 2.40e+00 1.74e-01 7.57e-01'''
assert lines.find(find)>-1
tf = 'test_cis_127_1.pdb'
with open(tf, 'w') as f:
f.write(pdb_lines[1])
cmd = 'phenix.pdb_interpretation write_geo=True cis_pro_eh99=True %s' % tf
print(cmd)
easy_run.go(cmd)
assert os.path.exists('%s.geo' % tf), 'command failed due to missing CD'
def run():
print 'test'
f = file('tst_mol_args.pdb', 'wb')
f.write(pdb_str)
f.close()
results = {}
for keep_hydrogen in range(3):
for nuclear in range(2):
cmd = 'phenix.clashscore tst_mol_args.pdb'
if keep_hydrogen != 2:
cmd += ' keep_hydrogen=%(keep_hydrogen)s' % locals()
cmd += ' nuclear=%(nuclear)s' % locals()
print 'CMD', cmd
rc = easy_run.go(cmd)
clashscore1 = get_clashscore(rc.stdout_lines)
print clashscore1
results[cmd] = clashscore1
cmd = 'phenix.molprobity tst_mol_args.pdb'
if keep_hydrogen != 2:
cmd += ' keep_hydrogen=%(keep_hydrogen)s' % locals()
cmd += ' pdb_interpretation.use_neutron_distances=%(nuclear)s' % locals(
)
print 'CMD', cmd
rc = easy_run.go(cmd)
clashscore2 = get_clashscore(rc.stdout_lines)
print clashscore2
results[cmd] = clashscore2
print '-' * 80
for cmd, c in results.items():
print cmd, c
assert clashscore1 == clashscore2, 'molprobity does not match clashscore %s %s: %.f != %.f' % (
keep_hydrogen,
nuclear,
clashscore1,
clashscore2,
)
def run(self):
model = self.data_manager.get_model()
if not model.has_hd():
raise Sorry('Model has no hydrogen atoms! Please add H/D and try again.')
cpptraj_exe = os.path.join(amber_dir,
'bin',
'cpptraj'
)
preamble = self.data_manager.get_model_names()[0].split('.')[0]
print('''
Running cpptraj executable
%s
on input
"""
%s
"""
''' % ( cpptraj_exe, input_str % locals()))
rc = easy_run.go(command=cpptraj_exe,
stdin_lines=input_str % locals(),
)
rc.show_stdout()
print(' Writing H-bonds to %(preamble)s.hbond.dat' % locals())
f=file('%(preamble)s.hbond.dat' % locals(), 'rb')
lines = f.read()
f.close()
if self.params.output.list_h_bonds:
print()
print(lines)
nr = get_number_of_residues(model.get_hierarchy())
if self.params.output.show_number_of_h_bonds_per_1000:
h_bonds = len(lines.splitlines())-1
atoms = len(model.get_hierarchy().atoms())
print('_'*80)
print('''
Number of H-bonds found : %7d
Number of atoms : %7d
H-bonds per 1000 atoms : %10.2f
H-bonds per residues : %10.2f
''' % (h_bonds,
atoms,
h_bonds/atoms*1000,
h_bonds/nr,
))
def get_updated_file_name(file_name,out_folder='',use_reduce=True):
"""
When using ready_set or reduce, a new file will be created, one that includes
hydrogens. This function finds the new name and returns it
Args:
file_name: pdb file name including path that should be
processed using ready_set or reduce
use_reduce (bool): When True use phenix.reduce, otherwise phenix.ready_set
out_folder (str): the folder where the updated file will be writen (when
different than the source file location)
Return:
file_name: the file name of the modified pdb file, the one that includes
hydrogens
"""
(path,file_name) = os.path.split(file_name)
pdb_id = get_pdb_id(file_name)
if out_folder:
path = out_folder
tmp = file_name.split('.')
# check that the file is not already an updated file
if not (len(tmp)==3 and tmp[1] == 'updated'):
file_name = get_file_from_rcsb(pdb_id)
# stop processing if file_name was not found
if not os.path.isfile(file_name): return ''
reduce = 'phenix.reduce {0} > {1}.updated.pdb'
ready_set = '{0}.updated.{1}'
if use_reduce:
#file_name = file_name[-8:]
cmd = reduce.format(file_name,pdb_id)
else:
cmd = 'phenix.ready_set {0}'.format(file_name)
#
probe_out = easy_run.go(cmd)
# getting to modified file name
if use_reduce:
file_name = ready_set.format(tmp[0],tmp[-1])
else:
line = [x for x in probe_out.stdout_lines if 'Writing model to' in x]
if line != []:
file_name = line[0].split('Writing model to ')[-1]
else:
collect_sorry = [x for x in probe_out.stdout_lines if 'Sorry:' in x]
for x in collect_sorry:
print x
return file_name
def run():
f = open('tst_pH_gnp.pdb', 'w')
f.write(gnp)
f.close()
cmd = 'phenix.geometry_minimization tst_pH_gnp.pdb'
rc = easy_run.go(cmd)
find = [
'Changed 28 bond restraint(s), added 1 bond restraint(s)',
'Changed 43 angle restraint(s), added 1 angle restraint(s)',
]
for f in find:
for line in rc.stdout_lines:
if line.find(f) > -1:
print(line)
break
else:
assert 0, 'line not found: %s' % f
return rc
def run_qm_cmd(
cmd,
log_filename,
error_lines=None,
redirect_output=True,
log=None,
verbose=False,
):
def loop_over_list(l):
for line in l:
yield l
import time
t0 = time.time()
if verbose: print('run_qm_cmd', cmd, log_filename)
if redirect_output:
cmd += ' >& %s' % log_filename
print(' Starting : %s' % cmd, file=log)
rc = easy_run.go(cmd)
if not os.path.exists(log_filename):
raise Sorry('QM program did not appear to write log file : %s' %
log_filename)
generator = loop_over_file(log_filename)
# if redirect_output:
# generator = loop_over_file(log_filename)
# else:
# generator = loop_over_list(rc.stdout_lines)
status = process_qm_log_file(generator=generator,
error_lines=error_lines,
log=log)
if rc.stderr_lines:
print('stderr')
for line in rc.stderr_lines:
print(line)
print('stdout')
for line in rc.stdout_lines:
print(line)
assert 0
return rc
def process_file(file_name):
""" Get pdb id and pdb file """
_,fn = os.path.split(file_name)
pdb_id = get_pdb_id(fn)
# Get files in pdb format even when at LBL, to avoid issues with phenix.reduce
if ('_mirror' in file_name) or (file_name == pdb_id):
file_name = pdb_id + '.pdb'
file_to_clean = []
if not os.path.isfile(file_name):
# leave file in folder if it was already there
# cmd = 'phenix.fetch_pdb {} --all'.format(pdb_id)
cmd = 'phenix.fetch_pdb {}'.format(pdb_id)
r = easy_run.go(cmd,join_stdout_stderr=False)
for fn in r.stdout_lines:
fn = os.path.split(fn)[-1]
if '.pdb' in fn: file_name = fn
file_to_clean.append(fn)
fn = fn.replace('.pdd','_with_h.pdb')
file_to_clean.append(fn)
return file_name,pdb_id,file_to_clean
def run():
work_dir = '/net/cci-filer2/raid1/home/youval/Work/work/junk'
os.chdir(work_dir)
#
#file_name = '3zzv'
#file_name = '4iw4'
#file_name = '2btv'
files = set(['3m8l', '2btv', '1vcr', '1llc', '3dpr', '3dar',
'2w4y', '2zah', '1tnv', '1dwn', '2w0c', '1w39',
'1x33', '2izw', '1x35', '3nop', '2bny', '1ei7',
'3not', '3nou', '1dzl', '3lob', '3nap', '1vsz'])
for fn in files:
sf_fn = fetch.get_pdb (fn,'xray',mirror='rcsb',log=sys.stdout,format='cif')
cmd = 'phenix.cif_as_mtz {0} --output-file-name=tmp_file.mtz --merge --remove-systematic-absences --map-to-asu --extend-flags'.format(sf_fn)
r = easy_run.go(cmd)
print 'Results for file: {}'.format(fn)
print '-'*60
for x in r.stdout_lines:
print x
print '='*60
def get_new_file_name(file_name):
'''(str) -> str
When using ready_set or reduce, a new file will be created, one that includes
hydrogens. This function finds the new name and returns it
Argument:
file_name: a file name of a pdb file, including the path, that was processed
using ready_set or reduce
Return:
file_name: the file name of the modified pdb file, the one that includes hydrogens
'''
tmp = file_name.split('.')
if not (len(tmp)==3 and tmp[1] == 'updated'):
file_name = get_pdb_file(file_name,fetch_file=True,print_out=False)
# when using phenix.reduce
#file_name = file_name[-8:]
cmd = 'phenix.reduce {0} > {1}.updated.{2}'.format(file_name,tmp[0],tmp[-1])
# when using ready_set
#cmd = 'phenix.ready_set {0}'.format(file_name)
#
probe_out = easy_run.go(cmd)
# getting to modified file name
# when using phenix.reduce
file_name = '{0}.updated.{1}'.format(tmp[0],tmp[-1])
# when using ready_set
#line = [x for x in probe_out.stdout_lines if 'Writing model to' in x]
#if line != []:
#file_name = line[0].split('Writing model to ')[-1]
#else:
#collect_sorry = [x for x in probe_out.stdout_lines if 'Sorry:' in x]
#for x in collect_sorry:
#print x
return file_name
write_tardy_geo_files = False
.type = bool
include scope mmtbx.monomer_library.pdb_interpretation.grand_master_phil_str
""", process_includes=True)
if __name__=='__main__':
print '*'*80
# set work folder
set_working_path('Clashes\junk')
print 'Current working path {}'.format(os.getcwd())
#file_name = get_pdb_file('3e8k.pdb')
file_name = get_pdb_file('101m_H.pdb')
#cmd = 'phenix.ready_set {}'.format(file_name)
#print 'Running: {}'.format(cmd)
#print '*'*80
#probe_out = easy_run.go(cmd)
## getting to modified file name
#line = [x for x in probe_out.stdout_lines if 'Writing model to' in x]
#file_name = line[0].split('Writing model to ')[-1]
print 'Using the file {}, the file returned from phenix.ready_set'.format(file_name)
#print '*'*80
out = easy_run.go('phenix.clashscore {} keep_hydrogens=True'.format(file_name))
#print 'phenix.{}'.format(out.stdout_lines[-1])
for l in out.stdout_lines:
print l
print '*'*80
# Call the new clashscore
run([file_name])
def run():
fn = '4udx_sf4.pdb'
f = file(fn, 'wb')
f.write(pdbs[fn])
f.close()
for i, superpose in enumerate(['None', 'all']):
cmd = 'phenix.geometry_minimization %s superpose_ideal=%s' % (
fn,
superpose,
)
print cmd
rc = easy_run.go(cmd)
for line in rc.stdout_lines:
#print line
if line.find('bond_residual_sum') > -1:
bond_value = round(float(line.split()[-1]))
if line.find('angle_residual_sum') > -1:
angle_value = round(float(line.split()[-1]))
# in the second iteration bond_value and angle_value are expected to be 0!
# assert bond_value, "%f %f" % (bond_value, results[fn][i][0])
# assert angle_value, angle_value
assert bond_value == results[fn][i][0], 'not matching %s to %s' % (
bond_value,
results[fn][i][0],
)
assert angle_value == results[fn][i][1], 'not matching %s to %s' % (
angle_value,
results[fn][i][1],
)
for i, superpose in enumerate(['None', 'all']):
cmd = 'phenix.pdb_interpretation %s superpose_ideal=%s' % (
fn,
superpose,
)
print cmd
rc = easy_run.go(cmd)
for line in rc.stdout_lines:
#print line
if line.find('bond_residual_sum') > -1:
value = round(float(line.split()[-1]))
print 'value', value
assert value == results[fn][i][2], 'not matching %s to %s' % (
value,
results[fn][i][2],
)
if line.find('angle_residual_sum') > -1:
value = round(float(line.split()[-1]))
print 'value', value
assert value == results[fn][i][3], 'not matching %s to %s' % (
value,
results[fn][i][3],
)
fn = '4udx_sf4_cys.pdb'
f = file(fn, 'wb')
f.write(pdbs[fn])
f.close()
# lines = '''
# SF4/F3S coordination
# SF4 X1001
# pdb="FE1 SF4 X1001 " - pdb=" SG CYS X 51 "
# pdb="FE2 SF4 X1001 " - pdb=" SG CYS X 48 "
# pdb="FE3 SF4 X1001 " - pdb=" SG CYS X 56 "
# pdb="FE4 SF4 X1001 " - pdb=" SG CYS X 70 "'''
from libtbx.test_utils import assert_lines_in_file
lines = [
'SF4/F3S coordination',
'SF4 X1001',
'pdb="FE1 SF4 X1001 " - pdb=" SG CYS X 51 "',
'pdb="FE4 SF4 X1001 " - pdb=" SG CYS X 70 "',
'pdb="FE3 SF4 X1001 " - pdb=" SG CYS X 56 "',
'pdb="FE2 SF4 X1001 " - pdb=" SG CYS X 48 "',
]
cmd = 'phenix.pdb_interpretation %s link_all=True > %s.log' % (fn, fn)
print cmd
assert not easy_run.call(cmd)
for line in lines:
print line
assert_lines_in_file(file_name='%s.log' % fn, lines=line)
return 0
def run():
msg = [
'',
'Welcome to the Q|R interface checker',
'',
]
draw_box_around_text(msg, width=78)
cmd = 'java -version'
rc = easy_run.go(cmd)
for line in rc.stdout_lines:
if line.find('java version') > -1:
version = line.split('"')[1][:3]
if float(version) < 1.8:
print '''
Need at least Java 1.8. Please update your system Java using a JDK bundle
and try again.
'''
sys.exit()
java_env_vars = {
'JAVA_HOME': 'absolute_path_of_java_home',
'JAVA_LIB_PATH': 'absolute_path_of_java_lib',
'LD_LIBRARY_PATH': '$LD_LIBRARY_PATH:$JAVA_LIB_PATH/server',
}
count = 0
for env_var in java_env_vars:
print ' Set? "%s" "%s"' % (env_var, os.environ.get(env_var, False))
if not os.environ.get(env_var, False):
print '''
The following environment variables need setting.
'''
for env_var, help in java_env_vars.items():
print '%s %s : %s' % (' ' * 10, env_var, help)
if env_var.startswith('JAVA'):
print '''
On OSX use
/usr/libexec/java_home -v 1.8
to find the install directory
'''
elif env_var == 'LD_LIBRARY_PATH':
print '''
The Phenix environment ignores the user set LD_LIBRARY_PATH unless the
environmental variable PHENIX_TRUST_OTHER_ENV is set.
'''
count += 1
break
else:
print '\n Java appears to be installed\n'
if count:
print ' STOPPING'
sys.exit()
qm_engine_env_vars = {
'MOPAC_COMMAND': 'Mopac executable',
'TERACHEM_COMMAND': 'TeraChem directory',
}
count = []
for env_var in qm_engine_env_vars:
if os.environ.get(env_var, False):
print '\n Environmental variable %s set for "%s" to "%s"\n' % (
env_var,
qm_engine_env_vars[env_var],
os.environ[env_var],
)
if not os.path.exists(os.environ[env_var]):
print '''
Environmental variable "%s" : "%s" does not point to anything!
STOPPING
''' % (env_var, os.environ[env_var])
sys.exit()
count.append(env_var)
else:
print ' Environmental variable %s for "%s" not found\n' % (
env_var,
qm_engine_env_vars[env_var],
)
if count:
print '''
QM engines set
'''
for env_var in count:
print '%s %s : %s' % (' ' * 10, env_var, os.environ[env_var])
print
else:
print '''
No QM engines found!
Install and set an environmental variable from the list.
'''
for env_var, help in qm_engine_env_vars.items():
print '%s %s : %s' % (' ' * 10, env_var, help)
print
draw_box_around_text(
['', 'Done!', '', 'Run a Q|R job using qr.refine', ''])
def run(args):
"""
Run one of the following refinements:
-no_ncs
-cartesian_ncs_restraints
-torsion_ncs_restraints
-ncs_constraints_no_operators
-ncs_constraints_all
Args:
args should contain:
pdb_id (str)
one of the refinements types
-again : when this option present, erase previous refinement results
Examples:
>>>pyhton run_refinement_test.py 1vcr -no_ncs
>>>pyhton run_refinement_test.py 1vcr -torsion_ncs_restraints -again
"""
osType = sys.platform
assert not ('win' in osType),'Please run on LBL machine'
delete_existing_results = '-again' in args
if delete_existing_results:
args.pop(args.index('-again'))
assert len(args) == 2, 'Not enough parameters provided'
# collect files and set working directories
pdb_id = args[0]
refine_method = args[1]
c = collect_ncs_files.ncs_paper_data_collection()
pdb = os.path.join(c.asu_dir,pdb_id + '.pdb')
mtz = os.path.join(c.mtz_dir,pdb_id + '.mtz')
cif = os.path.join(c.cif_dir,pdb_id + '.ligands.cif')
if not os.path.isfile(cif): cif = ''
files = '{} {} {} '.format(pdb,mtz,cif)
refinement_dir_list = collect_ncs_files.get_refinement_folders()
# refinement string
s = 'optimize_xyz=true '
s += 'optimize_adp=true strategy=individual_sites+individual_adp'
option_list = [
'-no_ncs',
'-cartesian_ncs_restraints',
'-torsion_ncs_restraints',
'-ncs_constraints_sites_no_operators',
'-ncs_constraints_sites_operators',
'-ncs_constraints_adp_operators',
'-ncs_constraints_all']
# remove limits on ncs distance
dist_limit = ' refinement.ncs.excessive_distance_limit=None '
cmd_option_list = [
s,
'main.ncs=True ncs.type=cartesian ' + s,
'main.ncs=True ' + s,
'ncs_search=true refine_operators=false strategy=individual_sites',
'ncs_search=true refine_operators=true strategy=individual_sites',
'ncs_search=true refine_operators=true strategy=individual_adp',
'ncs_search=true refine_operators=true strategy=individual_adp+individual_sites']
i = option_list.index(refine_method)
cmd_option = cmd_option_list[i]
out_folder = refinement_dir_list[i]
#
cmd = 'phenix.refine {} {} '.format(files,cmd_option) + dist_limit
# Run refinement
current_dir = os.getcwd()
make_new_folder = True
os.chdir(out_folder)
if os.path.isdir(pdb_id):
try:
# remove if empty
os.rmdir(pdb_id)
except OSError:
if delete_existing_results:
shutil.rmtree(pdb_id)
else:
print 'refinement results already exist for:',pdb_id
make_new_folder = False
if make_new_folder:
os.mkdir(pdb_id)
os.chdir(pdb_id)
# r = easy_run.fully_buffered(cmd)
r = easy_run.go(cmd)
os.chdir(current_dir)
print 'Done'
def run():
msg = [
'',
'Welcome to the Q|R interface checker',
'',
'For more information: https://github.com/qrefine/qrefine/wiki/Installation',
]
draw_box_around_text(msg, width=78)
cmd = 'java -version'
rc = easy_run.go(cmd)
for line in rc.stdout_lines:
if line.find('java version') > -1:
version = line.split('"')[1][:3]
if float(version) < 1.8:
print('''
Need at least Java 1.8. Please update your system Java using a JDK bundle
and try again.
''')
sys.exit()
java_env_vars = {
'JAVA_HOME': 'absolute_path_of_java_home',
'JAVA_LIB_PATH': 'absolute_path_of_java_lib',
'LD_LIBRARY_PATH': '$LD_LIBRARY_PATH:$JAVA_LIB_PATH/server',
}
count = 0
for env_var in java_env_vars:
print(' Set? "%s" "%s"' % (env_var, os.environ.get(env_var, False)))
if not os.environ.get(env_var, False):
print('''
The following environment variables need setting.
''')
for env_var, help in java_env_vars.items():
print('%s %s : %s' % (' ' * 10, env_var, help))
if env_var.startswith('JAVA'):
print('''
On OSX use
/usr/libexec/java_home -v 1.8
to find the install directory
''')
elif env_var == 'LD_LIBRARY_PATH':
print('''
The Phenix environment ignores the user set LD_LIBRARY_PATH unless the
environmental variable PHENIX_TRUST_OTHER_ENV is set.
''')
count += 1
break
else:
print('\n Java appears to be installed\n')
if count:
print(' STOPPING')
#sys.exit()
qm_engine_env_vars = {
'MOPAC_COMMAND': 'Mopac executable',
'TERACHEM_COMMAND': 'TeraChem directory',
'Orca_COMMAND': 'Orca directory',
'XTBHOME': 'XTB directory',
'g16root': 'Gaussian 16 directory',
'TURBODIR ': 'Turbomole directory',
}
count = []
for env_var in qm_engine_env_vars:
if os.environ.get(env_var, False):
print('\n Environmental variable %s set for "%s" to "%s"\n' % (
env_var,
qm_engine_env_vars[env_var],
os.environ[env_var],
))
if not os.path.exists(os.environ[env_var]):
print('''
Environmental variable "%s" : "%s" does not point to anything!
STOPPING
''' % (env_var, os.environ[env_var]))
sys.exit()
count.append(env_var)
else:
print(' Environmental variable %s for "%s" not found\n' % (
env_var,
qm_engine_env_vars[env_var],
))
qm_engines_python = {
'PyScf':
' A collection of electronic structure programs powered by Python',
'ANI': 'ANI-1 neural net potential with python interface (ASE)',
'TorchANI': 'Accurate Neural Network Potential on PyTorch'
}
qm_engines_python_installed = {}
for name, description in qm_engines_python.items():
if name == 'PyScf':
try:
import pyscf
print(" PyScf successfully imported")
qm_engines_python_installed[name] = description
except:
print(" PyScf could not be imported")
if name == 'TorchANI':
try:
import torch
import torchani
print(" TorchANI successfully imported")
qm_engines_python_installed[name] = description
except:
print(" TorchANI could not be imported")
if name == 'ANI':
try:
import ani
from ani.ase_interface import aniensloader
from ani.ase_interface import ANIENS
print(" ANI successfully imported")
qm_engines_python_installed[name] = description
except:
print(" ANI could not be imported")
if count:
print('''
QM engines set
''')
for env_var in count:
print('%s %s : %s' % (' ' * 10, env_var, os.environ[env_var]))
for name, description in qm_engines_python_installed.items():
print('%s %s : %s' % (' ' * 10, name, description))
else:
print('''
No QM engines found!
Install and set an environmental variable from the list.
''')
for env_var, help in qm_engine_env_vars.items():
print('%s %s : %s' % (' ' * 10, env_var, help))
print
draw_box_around_text([
'', 'Done!', '', 'Run a Q|R job using qr.refine', '',
'https://github.com/qrefine/qrefine/wiki/Installation'
])
def get_file(fn):
os.chdir('/net/cci-filer2/raid1/home/youval/Work/work/junk')
cmd = "phenix.fetch_pdb {}".format(fn)
r = easy_run.go(cmd)
os.chdir('/net/cci-filer2/raid1/home/youval/Work/work')
