def exercise_02(prefix="tst_mi_test_02"):
# Same as 01, but with SS annotations in PDB file
h_records = """\
HELIX 1 1 PRO A 3 ALA A 21 1 19
HELIX 2 2 ARG A 23 GLN A 44 1 22
"""
pdb_file = open("%s_start.pdb" % prefix, "w")
pdb_file.write(h_records)
pdb_file.write(tst_01_start_lines)
pdb_file.close()
cmd = " ".join([
"phenix.model_idealization",
"%s_start.pdb" % prefix,
errpipe,
"%s.log" % prefix,
errpipe2])
print cmd
easy_run.call(cmd)
res_log = open("%s.log" % prefix, "r")
log_lines = res_log.readlines()
for l in ["Replacing ss-elements with ideal ones:\n"]:
assert l in log_lines, "'%s' not in log file." % l
res_log.close()
assert os.path.isfile("%s_start.pdb_idealized.pdb" % prefix)
res_pdb = open("%s_start.pdb_idealized.pdb" % prefix, "r")
res_pdb_lines = res_pdb.readlines()
res_pdb.close()
for l in [
"HELIX 1 1 PRO A 3 ALA A 21 1 19\n",
"HELIX 2 2 ARG A 23 GLN A 44 1 22\n",
]:
assert l in res_pdb_lines, "'%s' not in pdb file." % l
def OnDisplayLog(self, event):
if (self._result.log_file_name is not None):
if (sys.platform == "darwin"):
easy_run.call("open -a TextEdit %s" %
self._result.log_file_name)
else:
pass
def run():
if (not libtbx.env.has_module("phenix")):
print "phenix not configured, skipping"
return
elif (not libtbx.env.find_in_repositories("chem_data")):
print "chem_data not configured, skipping"
return
f = file("l1r.pdb", "wb")
f.write(l1r_pdb)
f.close()
f = file("l1r.cif", "wb")
f.write(l1r_cif)
f.close()
cmd = 'phenix.geometry_minimization'
cmd += " l1r.pdb l1r.cif use_neutron_distances=False"
cmd += ' selection="element H or element D" write_geo_file=False'
cmd += ' correct_hydrogens=True'
print cmd
ero = easy_run.fully_buffered(command=cmd)
err = StringIO.StringIO()
ero.show_stdout(out=err)
cmd = "phenix.fmodel high_res=4.5 format=mtz label=FOBS type=real r_free=0.1 l1r.pdb generate_fake_p1_symmetry=1"
easy_run.call(cmd)
cmd = 'phenix.refine'
cmd += " l1r.pdb l1r.pdb.mtz l1r.cif"
cmd += " main.number_of_macro_cycles=1"
cmd += ' correct_hydrogens=True'
print cmd
ero = easy_run.fully_buffered(command=cmd)
err = StringIO.StringIO()
ero.show_stdout(out=err)
print "OK"
def run(prefix="tst_model_map"):
"""
Exercise phenix.model_map
"""
# original (zero-origin) map and model
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
pdb_inp.write_pdb_file(file_name="%s.pdb"%prefix)
ph = pdb_inp.construct_hierarchy()
xrs = pdb_inp.xray_structure_simple()
fc0 = xrs.structure_factors(d_min=3.0).f_calc()
#
easy_run.call("phenix.model_map %s.pdb output_file_name_prefix=%s"%(
prefix, prefix))
m1 = iotbx.ccp4_map.map_reader(file_name="%s.ccp4"%prefix).data.as_double()
m2 = iotbx.xplor.map.reader(file_name="%s.xplor"%prefix).data
#
fc1 = fc0.structure_factors_from_map(
map = m1,
use_scale = True,
anomalous_flag = False,
use_sg = False)
fc2 = fc0.structure_factors_from_map(
map = m2,
use_scale = True,
anomalous_flag = False,
use_sg = False)
cc1 = flex.linear_correlation(
x=abs(fc0).data(), y=abs(fc1).data()).coefficient()
cc2 = flex.linear_correlation(
x=abs(fc0).data(), y=abs(fc2).data()).coefficient()
print cc1, cc2
assert cc1>0.9999
assert cc2>0.97 # WHY?
def run(prefix="tst_step_5"):
"""
Exercise phenix.cryo_fit step_5 with all defaults
"""
assert (os.path.isfile("data/input_for_all/1AKE.density.mrc") == True)
assert (
os.path.isfile("data/input_for_all/regression_Adenylate.pdb") == True)
cmd = " ".join([
"phenix.cryo_fit", "data/input_for_all/regression_Adenylate.pdb",
"step_1=False", "step_2=False", "step_3=False", "step_4=False",
"step_6=False", "step_7=False", "step_8=False",
"data/input_for_all/1AKE.density.mrc"
])
print cmd
easy_run.call(cmd)
starting_dir = os.getcwd()
new_path = starting_dir + "/steps/5_make_restraints"
os.chdir(new_path)
#the_step_was_successfully_ran = check_whether_the_step_was_successfully_ran("Step 5", "disre2.itp")
# disre2.itp is easier file to make
the_step_was_successfully_ran = check_whether_the_step_was_successfully_ran(
"Step 5",
"minimized_c_term_renamed_by_resnum_oc_including_disre2_itp.top")
if (the_step_was_successfully_ran != 1):
print "failed, sleep for 10,000 seconds"
time.sleep(10000) # so that it is recognized instantly
assert (the_step_was_successfully_ran != 0)
os.chdir(starting_dir)
shutil.rmtree("steps")
def run(prefix="tst_step_2"):
"""
Exercise phenix.cryo_fit step_2 with all defaults with
"""
assert (os.path.isfile("data/input_for_all/1AKE.density.mrc") == True)
assert (
os.path.isfile("data/input_for_all/regression_Adenylate.pdb") == True)
cmd = " ".join([
"phenix.cryo_fit", "data/input_for_all/regression_Adenylate.pdb",
"step_1=False", "step_3=False", "step_4=False", "step_5=False",
"step_6=False", "step_7=False", "step_8=False",
"data/input_for_all/1AKE.density.mrc"
])
print cmd
easy_run.call(cmd)
starting_dir = os.getcwd()
new_path = starting_dir + "/steps/2_clean_gro"
os.chdir(new_path)
the_step_was_successfully_ran = 0
for check_this_file in glob.glob(
"*.gro"): # there will be only "will_be_minimized_cleaned.gro"
the_step_was_successfully_ran = check_whether_the_step_was_successfully_ran(
"Step 2", check_this_file)
print "the_step_was_successfully_ran:", the_step_was_successfully_ran
if (the_step_was_successfully_ran != 1):
print "failed, sleep for 10,000 seconds"
time.sleep(10000) # so that it is recognized instantly
assert (the_step_was_successfully_ran != 0)
os.chdir(starting_dir)
shutil.rmtree("steps")
def fetch_pdb(code):
if not os.path.exists("%s.pdb" % code):
cmd = "phenix.fetch_pdb --mtz %s" % code
easy_run.call(cmd)
if not os.path.exists("%s.pdb" % code):
return None
return "%s.pdb" % code
def run(args):
assert len(args)==1
mode = args[0]
assert mode in ["cctbx", "xtb", "terachem", "mopac"]
#
if( mode=="cctbx"): cmd = cmd_cctbx
elif(mode=="xtb"): cmd = cmd_xtb
elif(mode=="terachem"): cmd = cmd_terachem
elif(mode=="mopac"): cmd = cmd_mopac
else: assert 0
#
results_prefix = "./%s_opt"%mode
perturbed_prefix = "./perturbed/"
rmsd_dirs = ["0.3/","0.6/","0.9/","1.2/","1.5/"]
base_names = ["0","1","2","3","4","5","6","7","8","9"]
easy_run.call("rm -rf %s_opt"%mode)
os.makedirs(results_prefix)
os.chdir(results_prefix)
for rmsd_dir in rmsd_dirs:
print rmsd_dir
os.makedirs(rmsd_dir)
for bn in base_names:
file_name = "../"+perturbed_prefix+rmsd_dir+bn+".pdb"
if(not os.path.exists(file_name)): assert 0
cmd_full = cmd%(file_name,bn)
print "running command:\n%s"%(cmd_full)
easy_run.call(cmd_full)
easy_run.call("cp pdb/%s_refined.pdb %s/%s.pdb"%(bn,rmsd_dir,bn))
easy_run.call("mv %s.log %s"%(bn,rmsd_dir))
easy_run.call("mv pdb %s/%s_pdb"%(rmsd_dir,bn))
def run(sf_file_name,pdb_file_name):
# check if files exist
if not isfile(sf_file_name): raise Sorry('{} is not a file'.format(sf_file_name))
if not isfile(pdb_file_name): raise Sorry('{} is not a file'.format(pdb_file_name))
# start processing file
# convert cif to mtz and process mtz file
file_name_mtz = sf_file_name + '.mtz'
# creates file in current folder
easy_run.call("phenix.cif_as_mtz %s"%sf_file_name)
mtz_object = mtz.object(file_name=file_name_mtz)
# Process the mtz_object
miller_arrays_dict = mtz_object.as_miller_arrays_dict()
miller_arrays = mtz_object.as_miller_arrays()
for x in miller_arrays_dict:
print x
print '+'*60
#print miller_arrays_dict[x].show_array()
print '='*60
# read pdb info
pdb_inp = pdb.input(file_name=pdb_file_name) # read the pdb file data
structure = pdb_inp.xray_structure_simple()
xray_structure_simple = pdb_inp.xray_structures_simple() # a list of structure factors
f_miller = xray_structure_simple[0].structure_factors(d_min=2.85).f_calc()
# delete file
os.remove(file_name_mtz)
#
print 'wait here'
def run(filename=None):
assert filename is None
hpdl_database = get_hpdl_database()
if 0:
print "HPDL"
print hpdl_database
for aa in sorted(hpdl_database):
print " %s" % aa
for key, value in sorted(hpdl_database[aa].items()):
print " %s : %s" % (key, value)
assert 0
#
for pdb, lines in pdbs.items():
print pdb
filename="hpdl_%s.pdb" % pdb
f=file(filename, "wb")
f.write(lines)
f.close()
cmd = "phenix.pdb_interpretation %s write_geo=1 hpdl=%s" % (filename, True)
print cmd
easy_run.call(cmd)
if filename.find("his_double")>-1: key="ND1 and NE2 protonated"
elif filename.find("his_nd1")>-1: key="Only ND1 protonated"
elif filename.find("his_ne2")>-1: key="Only NE2 protonated"
if refine_geo_parser:
check_ideals("%s.geo" % filename, hpdl_database[key])
print "OK"
def call_refine(self,
pdb_file,
mtz_file,
output_file_name,
number_of_macro_cycles=3,
pdb_file_symmetry_target=None):
"""
Run refinement and produce refined pdb file in current directory
To set the number of refinement cycles change main.number_of_macro_cycles
Argument:
---------
pdb_file : pdb file to be refined
mtz_file : mtz file from the target experiment f_obs
output_file_name : the output file prefix
pdb_file_symmetry_target : use if you want to force symmetry of a pdb file
Output:
-------
writing out refined model, complete refinement statistics and
electron density maps in various formats.
"""
cmd = " ".join([
"phenix.refine",
"{0} {1}".format(pdb_file,mtz_file),
"strategy=individual_sites",
"main.number_of_macro_cycles={}".format(number_of_macro_cycles),
"output.prefix={}".format(output_file_name),
"--overwrite",
"--quiet"])
if pdb_file_symmetry_target:
cmd = ' '.join([cmd,"--symmetry={}".format(pdb_file_symmetry_target)])
easy_run.call(cmd)
def run(prefix="tst_step_1"):
"""
Exercise phenix.cryo_fit step_1 with all defaults
"""
assert (os.path.isfile("data/input/GTPase_activation_center.map") == True)
assert (os.path.isfile("data/input/regression_GAC.pdb") == True)
cmd = " ".join([
"phenix.cryo_fit", "data/input/regression_GAC.pdb", "step_2=False",
"step_3=False", "step_4=False", "step_5=False", "step_6=False",
"step_7=False", "step_8=False",
"data/input/GTPase_activation_center.map"
])
print cmd
easy_run.call(cmd)
starting_dir = os.getcwd()
new_path = starting_dir + "/steps/1_make_gro"
os.chdir(new_path)
this_step_was_successfully_ran = check_whether_the_step_was_successfully_ran(
"Step 1", "regression_GAC_cleaned_for_gromacs_by_pdb2gmx.gro")
if (this_step_was_successfully_ran != 1):
print "failed, sleep for 10,000 seconds"
time.sleep(10000) # so that it is recognized instantly
assert (this_step_was_successfully_ran != 0)
os.chdir(starting_dir)
shutil.rmtree("steps")
def exercise () :
params = runtime_utils.process_master_phil.extract()
i = 0
while True :
output_dir = os.path.join(os.getcwd(), "simple_run%d" % i)
if os.path.exists(output_dir) :
i += 1
else :
os.makedirs(output_dir)
break
run = runtime_utils.simple_run(output_dir)
params.output_dir = output_dir
params.buffer_stdout = False
params.tmp_dir = output_dir
# driver = runtime_utils.detached_process_driver(output_dir, run)
params.run_file = os.path.join(output_dir, "run.pkl")
eff_file = os.path.join(output_dir, "run.eff")
working_phil = runtime_utils.process_master_phil.format(python_object=params)
working_phil.show(out=open(eff_file, "w"))
easy_pickle.dump(params.run_file, run)
easy_run.call("libtbx.start_process %s &" % eff_file) #params.run_file)
client = runtime_utils.simple_client(params)
client.run()
assert (client.out.getvalue() == """\
current is 44444.444444
current is 50000.000000
current is 57142.857143
current is 66666.666667
""")
assert client.n_cb >= 5 # this is variable!
assert ([ cb.message for cb in client._accumulated_callbacks ] ==
['run 0', 'run 1', 'run 2', 'run 3'])
def fetch_pdb(code):
if not os.path.exists("%s.pdb" % code):
cmd = "phenix.fetch_pdb --mtz %s" % code
easy_run.call(cmd)
if not os.path.exists("%s.pdb" % code):
return None
return "%s.pdb" % code
def exercise():
pdb_file_names = raw_input("pdb file name here:")
p_f = pdb_file_names.split(' ')
for pdb_file_name in p_f:
easy_run.call("phenix.fetch_pdb {0}".format(pdb_file_name[0:4]))
easy_run.call("phenix.ready_set {0}".format(pdb_file_name))
print(pdb_file_name, "-" * 50)
cif_file_name = pdb_file_name[0:4] + ".ligands.cif"
model = get_model(pdb_file_name=pdb_file_name,
cif_file_name=cif_file_name)
results = get_CNCO_bond_angle(model)
for r in results:
'''print dir(r.atom_1.chain())
MTN = {"id":["CSN values"],"O-N":[1.272],"C(L)-N":[1.482],
"C(R)R-N":[1.482],"C-N-C":[115.232],"C(L)-N-O":[122.384],
"C(R)-N-O":[122.384]}
df = pd.DataFrame(MTN,columns = ["id","O-N","C(L)-N",
"C(R)R-N","C-N-C","C(L)-N-O","C(R)-N-O"],index=["one"])
Series = pd.Series({"O-N":r.d23,"C(L)-N":r.d12,
"C(R)R-N":r.d24,"C-N-C":r.a124,"C(L)-N-O":r.a123,
"C(R)-N-O":r.a324})
data = pd.DataFrame()
Series = [[r.d12, r.d23, r.d24, r.a123, r.a124, r.a324]]
df = data.append(Series,ignore_index=True)
print df
'''
print("%s" % r.atom_1.id_str(), r.atom_2.id_str(),
r.atom_3.id_str(), r.atom_4.id_str(), r.d_O_N, r.d_C_L_N,
r.d_C_R_N, r.a_C_N_C, r.a_C_L_N_O, r.a_C_R_N_O)
def run_one_cmd(cmd_info):
t0 = time.time()
from libtbx import easy_run
if (cmd_info.index == 0):
print "command:", cmd_info.cmd
sys.stdout.flush()
try:
easy_run.call(command=cmd_info.cmd)
except: # intentional
show_traceback(file=sys.stdout)
print fmt_time(t0)
print
else:
sys.stdout.flush()
sio = None
try:
buffers = easy_run.fully_buffered(
command=cmd_info.cmd,
join_stdout_stderr=True,
stdout_splitlines=False)
except: # intentional
from cStringIO import StringIO
sio = StringIO()
show_traceback(file=sio)
buffers = None
f = open(cmd_info.log, "w")
if (buffers is not None):
f.write(buffers.stdout_buffer)
if (sio is not None):
f.write(sio.getvalue())
print >> f, fmt_time(t0)
del f
sys.stdout.flush()
def run(prefix="tst_step_6"):
"""
Exercise phenix.cryo_fit step_6 with all defaults
"""
assert (os.path.isfile("data/input_for_all/1AKE.density.mrc") == True)
assert (
os.path.isfile("data/input_for_all/regression_Adenylate.pdb") == True)
cmd = " ".join([
"phenix.cryo_fit", "data/input_for_all/regression_Adenylate.pdb",
"step_1=False", "step_2=False", "step_3=False", "step_4=False",
"step_5=False", "step_7=False", "step_8=False",
"data/input_for_all/1AKE.density.mrc"
])
print cmd
easy_run.call(cmd)
starting_dir = os.getcwd()
new_path = starting_dir + "/steps/6_make_0_charge"
os.chdir(new_path)
the_step_was_successfully_ran = ''
for check_this_file in glob.glob(
"*_0_charge.top"): # there will be only one file like this
the_step_was_successfully_ran = check_whether_the_step_was_successfully_ran(
"Step 6", check_this_file)
if (the_step_was_successfully_ran != 1):
print "failed, sleep for 10,000 seconds"
time.sleep(10000) # so that it is recognized instantly
assert (the_step_was_successfully_ran != 0)
os.chdir(starting_dir)
shutil.rmtree("steps")
def run_and_check(cmd, pdbs_file, expected_out):
abs_paths = []
for rel_path in open(op.join(dd, pdbs_file)).read().splitlines():
abs_paths.append(op.normpath(op.join(dd, rel_path)))
list_of_pdbs = "list_of_pdbs_%d" % run_serial.next()
print >> open(list_of_pdbs, "w"), "\n".join(abs_paths)
cmd = cmd % list_of_pdbs
if (valgrind):
cmd = "valgrind " + cmd
print cmd
remove_files("out")
if (not valgrind):
buffers = easy_run.fully_buffered(command=cmd).raise_if_errors()
if (expected_out is None):
return buffers.stdout_lines
else:
easy_run.call(command=cmd)
if (expected_out is None):
return None
filtered_lines = []
for line in open("out").read().splitlines():
sw = line.startswith
if (sw("pole") or sw("members") or sw("min: ") or sw("max: ")):
filtered_lines.append(line)
assert not show_diff("\n".join(filtered_lines)+"\n", expected_out)
print "OK"
def exercise () :
params = runtime_utils.process_master_phil.extract()
i = 0
while True :
output_dir = os.path.join(os.getcwd(), "simple_run%d" % i)
if os.path.exists(output_dir) :
i += 1
else :
os.makedirs(output_dir)
break
run = runtime_utils.simple_run(output_dir)
params.output_dir = output_dir
params.buffer_stdout = False
params.tmp_dir = output_dir
# driver = runtime_utils.detached_process_driver(output_dir, run)
params.run_file = os.path.join(output_dir, "run.pkl")
eff_file = os.path.join(output_dir, "run.eff")
working_phil = runtime_utils.process_master_phil.format(python_object=params)
working_phil.show(out=open(eff_file, "w"))
easy_pickle.dump(params.run_file, run)
easy_run.call("libtbx.start_process %s &" % eff_file) #params.run_file)
client = runtime_utils.simple_client(params)
client.run()
assert (client.out.getvalue() == """\
current is 44444.444444
current is 50000.000000
current is 57142.857143
current is 66666.666667
""")
assert client.n_cb >= 5 # this is variable!
assert ([ cb.message for cb in client._accumulated_callbacks ] ==
['run 0', 'run 1', 'run 2', 'run 3'])
def run(prefix="tst_step_7"):
"""
Exercise phenix.cryo_fit step_7 with all defaults
"""
assert (os.path.isfile("data/input_for_all/1AKE.density.mrc") == True)
assert (
os.path.isfile("data/input_for_all/regression_Adenylate.pdb") == True)
cmd = " ".join([
"phenix.cryo_fit", "data/input_for_all/regression_Adenylate.pdb",
"step_1=False", "step_2=False", "step_3=False", "step_4=False",
"step_5=False", "step_6=False", "step_8=False",
"data/input_for_all/1AKE.density.mrc"
])
print cmd
easy_run.call(cmd)
starting_dir = os.getcwd()
new_path = starting_dir + "/steps/7_make_tpr_with_disre2"
os.chdir(new_path)
the_step_was_successfully_ran = check_whether_the_step_was_successfully_ran(
"Step 7", "for_cryo_fit.tpr")
if (the_step_was_successfully_ran != 1):
print "failed, sleep for 10,000 seconds"
time.sleep(10000) # so that it is recognized instantly
assert (the_step_was_successfully_ran != 0)
os.chdir(starting_dir)
shutil.rmtree("steps")
def run(prefix="tst_step_1"):
"""
Exercise phenix.cryo_fit step_1 with all defaults
"""
assert (
os.path.isfile("data/input_for_all/tRNA_EFTU_within_10.ccp4") == True)
assert (os.path.isfile(
"data/input_for_all/regression_tRNA_EFTU_within_10.pdb") == True)
cmd = " ".join([
"phenix.cryo_fit",
"data/input_for_all/regression_tRNA_EFTU_within_10.pdb",
"data/input_for_all/tRNA_EFTU_within_10.ccp4", "step_2=False",
"step_3=False", "step_4=False", "step_5=False", "step_6=False",
"step_7=False", "step_8=False"
])
print cmd
easy_run.call(cmd)
starting_dir = os.getcwd()
new_path = starting_dir + "/steps/1_make_gro"
os.chdir(new_path)
for check_this_file in glob.glob(
"*_by_pdb2gmx.gro"
): # there will be only one *_by_pdb2gmx.gro file
this_step_was_successfully_ran = check_whether_the_step_was_successfully_ran(
"Step 1", check_this_file)
if (this_step_was_successfully_ran != 1):
print "failed, sleep for 10,000 seconds"
time.sleep(10000) # so that it is recognized instantly
assert (this_step_was_successfully_ran != 0)
os.chdir(starting_dir)
shutil.rmtree("steps")
def run(prefix="tst_step_4"):
"""
Exercise phenix.cryo_fit step_4 with all defaults with "few_RNAs.pdb"
"""
assert (os.path.isfile("data/input/GTPase_activation_center.map") == True)
assert (os.path.isfile("data/input/regression_GAC.pdb") == True)
cmd = " ".join([
"phenix.cryo_fit", "data/input/regression_GAC.pdb", "step_1=False",
"step_2=False", "step_3=False", "step_5=False", "step_6=False",
"step_7=False", "step_8=False",
"data/input/GTPase_activation_center.map"
])
print cmd
easy_run.call(cmd)
starting_dir = os.getcwd()
new_path = starting_dir + "/steps/4_minimize"
os.chdir(new_path)
the_step_was_successfully_ran = 0
for check_this_file in glob.glob(
"*.gro"): # there will be only "will_be_minimized_cleaned.gro"
the_step_was_successfully_ran = check_whether_the_step_was_successfully_ran(
"Step 4", check_this_file)
assert (the_step_was_successfully_ran != 0)
if (the_step_was_successfully_ran != 1):
print "failed, sleep for 10,000 seconds"
time.sleep(10000) # so that it is recognized instantly
os.chdir(starting_dir)
shutil.rmtree("steps")
def run(file_name="a87_99_h.pdb"):
path = "../"
shutil.rmtree("perturbed") # BAD AND DANGEROUS
os.mkdir("perturbed")
os.chdir("perturbed")
for p_size in [0.3, 0.6, 0.9, 1.2, 1.5]:
p_size = str(p_size)
os.mkdir(p_size)
os.chdir(p_size)
for trial in xrange(10):
rs = random.randrange(1111111, 9999999)
cmd = " ".join([
"phenix.dynamics",
"../../%s"%file_name,
"stop_at_diff=%s"%p_size,
"number_of_steps=20000",
"temperature=1000",
"write_geo_file=False",
"random_seed=%s"%str(rs),
"use_neutron_distances=true",
"output_file_name_prefix=%s"%str(trial),
"> %s.log"%str(trial)])
easy_run.call(cmd)
easy_run.call("rm -rf *.log")
os.chdir("..")
def exercise_03(fobs_2, flags_2, prefix):
mtz = fobs_2.as_mtz_dataset(column_root_label="FP1")
mtz.mtz_object().write(prefix+"_3.mtz")
flags_2.export_as_cns_hkl(
file_object=open(prefix+"_3.cns", "w"),
file_name=prefix+"_3.cns",
info=["R-free-flags for FP1"])
#
selection = "chain E and resseq 7"
cmd = " ".join([
"phenix.polder",
"tst_polder_1.cif",
"%s_3.mtz" % prefix,
"%s_3.cns" % prefix,
"sphere_radius=5",
"output_file_name_prefix=tst_polder_1_3",
'solvent_exclusion_mask_selection="%s"' % selection,
"> %s_3.log" % prefix
])
print cmd
easy_run.call(cmd)
check(
tuple_calc=[13.7, 20.3, 18.4],
selection=selection,
prefix = prefix + '_3_')
def exercise_02(fobs_1, flags_1, prefix):
fobs_1.export_as_cns_hkl(
file_object=open(prefix+"_2.cns", "w"),
file_name=prefix+"_2.cns",
info=["calculated structure factors FP1"])
#
flags_1.export_as_cns_hkl(
file_object=open(prefix+"_2_free"+".cns", "w"),
file_name=prefix+"_2_free"+".cns",
info=["R-free-flags for FP1"])
#
selection = "chain E and resseq 14"
cmd = " ".join([
"phenix.polder",
"tst_polder_1.pdb",
"%s_2.cns" % prefix,
"%s_2_free.cns" % prefix,
"sphere_radius=5",
"output_file_name_prefix=tst_polder_1_2",
'solvent_exclusion_mask_selection="%s"' % selection,
"> %s_2.log" % prefix
])
print cmd
easy_run.call(cmd)
check(
tuple_calc=[10.7, 15.1, 13.4],
selection=selection,
prefix = prefix + '_2_')
def exercise_01(fobs_1, fobs_2, flags_1, flags_2, prefix):
mtz = fobs_1.as_mtz_dataset(column_root_label="FP1")
mtz.add_miller_array(fobs_2, column_root_label="FP2")
mtz.add_miller_array(flags_1, column_root_label="R-free-flags-1")
mtz.add_miller_array(flags_2, column_root_label="R-free-flags-2")
mtz.mtz_object().write(prefix+"_1.mtz")
#
selection = "chain A"
cmd = " ".join([
"phenix.polder",
"tst_polder_1.pdb",
"%s_1.mtz" % prefix,
"sphere_radius=3",
'solvent_exclusion_mask_selection="%s"' % selection,
"data_labels=FP1",
"output_file_name_prefix=tst_polder_1_1",
"r_free_flags_labels=R-free-flags-1",
"> %s_1.log" % prefix
])
print cmd
easy_run.call(cmd)
#
check(
tuple_calc=[10.6, 16.0, 13.5],
selection=selection,
prefix = prefix + '_1_')
def exercise():
pdb_file_names = raw_input(
"pdb file name here,space interval,such as : 2ona.pdb 2whb.pdb")
p_f = pdb_file_names.split(' ')
for pdb_file_name in p_f:
easy_run.call("phenix.fetch_pdb {0}".format(pdb_file_name[0:4]))
easy_run.call("phenix.ready_set {0}".format(pdb_file_name))
print(pdb_file_name, "-" * 50)
cif_file_name = pdb_file_name[0:4] + ".ligands.cif"
if os.path.exists(cif_file_name):
cif_file_names = cif_file_name
else:
cif_file_names = None
model = get_model(pdb_file_name=pdb_file_name,
cif_file_name=cif_file_names)
resnames = raw_input(
'list of resnames ,comma interval,such as: resname PHE,resname HIS'
)
resn = resnames.split(',')
ss = " or ".join(resn)
m_sel = model.selection(ss)
new_model = model.select(m_sel)
hierarchy = new_model.get_hierarchy()
crystal_symmetry = new_model.crystal_symmetry()
hierarchy.write_pdb_file(file_name=pdb_file_name[0:4] + "new.pdb",
crystal_symmetry=crystal_symmetry)
def exercise_003(file_name="tst_mtrix_biomt_cmdl_003.pdb"):
"""
Make sure SS is fine when expanding without BIOMT
"""
of = open(file_name, "w")
print(pdb_str_2b, file=of)
of.close()
easy_run.call("phenix.pdb.biomt_reconstruction %s" % file_name)
pdb_inp = iotbx.pdb.input(
file_name="tst_mtrix_biomt_cmdl_003_BIOMT_expanded.pdb")
a = pdb_inp.extract_secondary_structure()
assert a.get_n_helices() == 1, a.get_n_helices()
assert a.get_n_sheets() == 1, "%d" % a.get_n_sheets()
# checking chain ids. If this part is failing, then something is changed in
# chain expanding which made chain ids in hierarchy.py:join_roots()
# not compatible with those used in secondary_structure.py:multiply_to_asu
chain_ids = [h.start_chain_id for h in a.helices]
assert chain_ids == ['A'], chain_ids
# checking sheets
for i, sh in enumerate(a.sheets):
assert sh.n_strands == 2
assert sh.registrations[0] == None
assert sh.registrations[1].cur_chain_id == 'B'
assert sh.registrations[1].prev_chain_id == 'A'
assert sh.strands[0].start_chain_id == 'A'
assert sh.strands[0].end_chain_id == 'A'
assert sh.strands[1].start_chain_id == 'B'
assert sh.strands[1].end_chain_id == 'B'
def run(file_name="tst_tls_as_xyz.pdb"):
of = open(file_name, "w")
print(pdb_str, file=of)
of.close()
uc = iotbx.pdb.input(file_name=file_name).crystal_symmetry().unit_cell()
#for n in range(10,100,10)+range(100,1000,100)+range(1000,10001,1000)+[15000,20000]:
for n in [
1000,
]:
easy_run.call("phenix.tls_as_xyz %s n_models=%s > tst_tls_as_xyz.log" %
(file_name, str(n)))
for i in [0, 1]:
u1 = iotbx.pdb.input(
file_name="tst_tls_as_xyz_u_from_ensemble_%s.pdb" %
str(i)).xray_structure_simple().scatterers().extract_u_cart(uc)
u2 = iotbx.pdb.input(
file_name="tst_tls_as_xyz_u_from_tls_%s.pdb" %
str(i)).xray_structure_simple().scatterers().extract_u_cart(uc)
u1, u2 = u1.as_double(), u2.as_double()
cc = flex.linear_correlation(x=u1, y=u2).coefficient()
r = flex.sum(flex.abs(flex.abs(u1)-flex.abs(u2)))/\
flex.sum(flex.abs(flex.abs(u1)+flex.abs(u2)))*2
print("%5d %6.4f %6.4f" % (n, cc, r))
assert cc > 0.99, cc
assert r < 0.06, r
def run(args):
if (len(args) == 0):
n_iterations = 1000
elif (len(args) == 1):
n_iterations = int(args[0])
assert n_iterations > 0
else:
from libtbx.utils import Usage
raise Usage("scitbx.show_exp_times [n_iterations]")
evar = "LIBTBX_NO_LD_PRELOAD"
evar_set = evar in os.environ
if (evar_set):
print("%s set:" % evar)
else:
print("%s not set:" % evar)
from scitbx.math.tests.tst_exp_functions import \
exercise_with_random_arguments as exercise
exercise(n_arguments=10000, n_iterations=n_iterations)
print()
sys.stdout.flush()
if (not evar_set):
if ("LD_PRELOAD" in os.environ):
del os.environ["LD_PRELOAD"]
os.environ[evar] = "1"
from libtbx import easy_run
easy_run.call(command="scitbx.show_exp_times %d" % n_iterations)
def run_one_cmd(cmd_info):
t0 = time.time()
from libtbx import easy_run
if (cmd_info.index == 0):
print("command:", cmd_info.cmd)
sys.stdout.flush()
try:
easy_run.call(command=cmd_info.cmd)
except: # intentional
show_traceback(file=sys.stdout)
print(fmt_time(t0))
print()
else:
sys.stdout.flush()
sio = None
try:
buffers = easy_run.fully_buffered(command=cmd_info.cmd,
join_stdout_stderr=True,
stdout_splitlines=False)
except: # intentional
from six.moves import cStringIO as StringIO
sio = StringIO()
show_traceback(file=sio)
buffers = None
f = open(cmd_info.log, "w")
if (buffers is not None):
f.write(buffers.stdout_buffer)
if (sio is not None):
f.write(sio.getvalue())
print(fmt_time(t0), file=f)
del f
sys.stdout.flush()
def exercise_02(fobs_1, flags_1, prefix):
with open(prefix + "_2.cns", "w") as file_object:
fobs_1.export_as_cns_hkl(file_object=file_object,
file_name=prefix + "_2.cns",
info=["calculated structure factors FP1"])
#
with open(prefix + "_2_free" + ".cns", "w") as file_object:
flags_1.export_as_cns_hkl(file_object=file_object,
file_name=prefix + "_2_free" + ".cns",
info=["R-free-flags for FP1"])
#
selection = "chain E and resseq 14"
cmd = " ".join([
"phenix.polder", "tst_polder_1.pdb",
"%s_2.cns" % prefix,
"%s_2_free.cns" % prefix, "sphere_radius=5",
"output_file_name_prefix=tst_polder_1_2",
'solvent_exclusion_mask_selection="%s"' % selection,
"> %s_2.log" % prefix
])
print(cmd)
easy_run.call(cmd)
check(tuple_calc=[10.7, 15.1, 13.4],
selection=selection,
prefix=prefix + '_2_')
def run(prefix="tst_step_final"):
"""
Exercise phenix.cryo_fit step_final with all defaults
"""
assert (os.path.isfile("data/input_for_all/1AKE.density.mrc") == True)
assert (
os.path.isfile("data/input_for_all/regression_Adenylate.pdb") == True)
cmd = " ".join([
"phenix.cryo_fit", "data/input_for_all/regression_Adenylate.pdb",
"step_1=False", "step_2=False", "step_3=False", "step_4=False",
"step_5=False", "step_6=False", "step_7=False", "step_8=False",
"data/input_for_all/1AKE.density.mrc"
])
print cmd
easy_run.call(cmd)
starting_dir = os.getcwd()
new_path = starting_dir + "/output"
os.chdir(new_path)
#the_step_was_successfully_ran = check_whether_the_step_was_successfully_ran("Step final", "user_provided_cleaned_for_real_space_refine_molprobity.pdb")
the_step_was_successfully_ran = check_whether_the_step_was_successfully_ran(
"Step final",
"extracted_0_target_step_0.0_target_ps_cleaned_for_real_space_refine_molprobity.pdb"
)
if (the_step_was_successfully_ran != 1):
print "failed, sleep for 10,000 seconds"
time.sleep(10000) # so that it is recognized instantly
assert (the_step_was_successfully_ran != 0)
os.chdir(starting_dir)
shutil.rmtree("steps")
shutil.rmtree("output")
def run():
path = "../01d_fixSplit_GFA/"
for i_f, f in enumerate(os.listdir(path)):
if(f.endswith(".pdb")):
prefix = f[:-4]
os.mkdir(prefix)
os.chdir(prefix)
for p_size in [0.3, 0.6, 0.9, 1.2, 1.5]:
p_size = str(p_size)
os.mkdir(p_size)
os.chdir(p_size)
file_name = "../../"+path+f
print i_f, file_name
for trial in xrange(10):
rs = random.randrange(1111111, 9999999)
cmd = " ".join([
"phenix.dynamics",
"%s"%file_name,
"stop_at_diff=%s"%p_size,
"number_of_steps=20000",
"temperature=1000",
"write_geo_file=False",
"random_seed=%s"%str(rs),
"output_file_name_prefix=%s"%str(trial),
"> %s.log"%prefix])
easy_run.call(cmd)
easy_run.call("rm -rf *.log")
os.chdir("..")
os.chdir("..")
def exercise(prefix="tst_models_to_from_chains"):
# inputs
expected_n = 5
xrs = iotbx.pdb.input(source_info=None, lines=pdb_str).xray_structure_simple()
input_file_name = "%s.pdb"%prefix
of = open(input_file_name,"w")
print >> of, pdb_str
of.close()
mi = flex.miller_index(((0,0,1), ))
ms = miller.set(xrs.crystal_symmetry(), mi, anomalous_flag=False)
complete_set = ms.complete_set(d_min=3)
fc = complete_set.structure_factors_from_scatterers(
xray_structure=xrs).f_calc()
# models -> chains
easy_run.call("phenix.models_as_chains %s"%input_file_name)
pdb_inp = iotbx.pdb.input(file_name="chains_"+input_file_name)
h = pdb_inp.construct_hierarchy()
assert len(list(h.chains()))==expected_n
assert len(list(h.models()))==1
xrs_c = pdb_inp.xray_structure_simple()
fc_c = complete_set.structure_factors_from_scatterers(
xray_structure=xrs_c).f_calc()
#
easy_run.call("phenix.chains_as_models chains_%s"%input_file_name)
pdb_inp = iotbx.pdb.input(file_name="models_chains_"+input_file_name)
h = pdb_inp.construct_hierarchy()
assert len(list(h.chains()))==expected_n
assert len(list(h.models()))==expected_n
xrs_m = pdb_inp.xray_structure_simple()
fc_m = complete_set.structure_factors_from_scatterers(
xray_structure=xrs_m).f_calc()
#
assert approx_equal(0, r(fc, fc_c) )
assert approx_equal(0, r(fc, fc_m) )
assert approx_equal(0, r(fc_c, fc_m))
def run(only_i=None,
chunk_n=1,
chunk_size=len(pdb_paths)
):
try: only_i = int(only_i)
except ValueError: only_i=None
try: chunk_n = int(chunk_n)
except ValueError: chunk_n=1
try: chunk_size = int(chunk_size)
except ValueError: chunk_size=len(pdb_paths)
assert chunk_size==len(pdb_paths) or chunk_n==1
assert chunk_n>0
assert chunk_size>0
if chunk_n!=1:
chunk_size = (len(pdb_paths)-1)//chunk_n+1
elif chunk_size!=1:
chunk_n = len(pdb_paths)%chunk_size+1
for i, pdb_path in enumerate(pdb_paths):
pdb_code = get_pdb_code(pdb_path)
#pdb_code = pdb_path
cmd = get_cmd(pdb_path)
if only_i is None:
print i, cmd
continue
else:
if chunk_n!=1 or chunk_size!=len(pdb_paths):
if only_i!=i//chunk_size+1: continue
else:
if only_i!=i+1: continue
print 'Running', i+1
print 'Command', cmd
easy_run.call(cmd)
def run(prefix="tst_step_3"):
"""
Exercise phenix.cryo_fit step_3 with all defaults
"""
assert (
os.path.isfile("data/input_for_all/tRNA_EFTU_within_10.ccp4") == True)
assert (os.path.isfile(
"data/input_for_all/regression_tRNA_EFTU_within_10.pdb") == True)
cmd = " ".join([
"phenix.cryo_fit",
"data/input_for_all/regression_tRNA_EFTU_within_10.pdb",
"data/input_for_all/tRNA_EFTU_within_10.ccp4", "step_1=False",
"step_2=False", "step_4=False", "step_5=False", "step_6=False",
"step_7=False", "step_8=False"
])
print cmd
easy_run.call(cmd)
starting_dir = os.getcwd()
new_path = starting_dir + "/steps/3_make_tpr_to_minimize"
os.chdir(new_path)
the_step_was_successfully_ran = check_whether_the_step_was_successfully_ran(
"Step 3", "to_minimize.tpr")
if (the_step_was_successfully_ran != 1):
print "failed, sleep for 10,000 seconds"
time.sleep(10000) # so that it is recognized instantly
assert (the_step_was_successfully_ran != 0)
os.chdir(starting_dir)
shutil.rmtree("steps")
def exercise_001(file_name="tst_mtrix_biomt_cmdl_001.pdb"):
"""
Make sure SS gets populated by MTRIX
"""
of = open(file_name,"w")
print >> of, pdb_str_2b
of.close()
easy_run.call("phenix.pdb.mtrix_reconstruction %s"%file_name)
pdb_inp = iotbx.pdb.input(
file_name="tst_mtrix_biomt_cmdl_001_MTRIX_expanded.pdb")
a = pdb_inp.extract_secondary_structure()
assert a.get_n_helices() == 3, a.get_n_helices()
assert a.get_n_sheets() == 3, "%d" % a.get_n_sheets()
# checking chain ids. If this part is failing, then something is changed in
# chain expanding which made chain ids in hierarchy.py:join_roots()
# not compatible with those used in secondary_structure.py:multiply_to_asu
chain_ids = [h.start_chain_id for h in a.helices]
assert chain_ids == ['A1', 'A2', 'A3'], chain_ids
# checking sheets
for i, sh in enumerate(a.sheets):
assert sh.n_strands == 2
assert sh.registrations[0] == None
assert sh.registrations[1].cur_chain_id == 'B%d' % (i+1)
assert sh.registrations[1].prev_chain_id == 'A%d' % (i+1)
assert sh.strands[0].start_chain_id == 'A%d' % (i+1), sh.strands[0].start_chain_id
assert sh.strands[0].end_chain_id == 'A%d' % (i+1)
assert sh.strands[1].start_chain_id == 'B%d' % (i+1), sh.strands[1].start_chain_id
assert sh.strands[1].end_chain_id == 'B%d' % (i+1)
def exercise_001(file_name="tst_mtrix_biomt_cmdl_001.pdb"):
"""
Make sure SS gets populated by MTRIX
"""
of = open(file_name, "w")
print(pdb_str_2b, file=of)
of.close()
easy_run.call("phenix.pdb.mtrix_reconstruction %s" % file_name)
pdb_inp = iotbx.pdb.input(
file_name="tst_mtrix_biomt_cmdl_001_MTRIX_expanded.pdb")
a = pdb_inp.extract_secondary_structure()
assert a.get_n_helices() == 3, a.get_n_helices()
assert a.get_n_sheets() == 3, "%d" % a.get_n_sheets()
# checking chain ids. If this part is failing, then something is changed in
# chain expanding which made chain ids in hierarchy.py:join_roots()
# not compatible with those used in secondary_structure.py:multiply_to_asu
chain_ids = [h.start_chain_id for h in a.helices]
assert chain_ids == ['A', 'C', 'E'], chain_ids
# checking sheets
assert not show_diff(
a.as_pdb_str(), """\
HELIX 1 1 THR A 1 THR A 2 1 6
HELIX 2 2 THR C 1 THR C 2 1 6
HELIX 3 3 THR E 1 THR E 2 1 6
SHEET 1 1 2 THR A 1 THR A 3 0
SHEET 2 1 2 THR B 4 THR B 5 -1 O THR B 4 N THR A 2
SHEET 1 2 2 THR C 1 THR C 3 0
SHEET 2 2 2 THR D 4 THR D 5 -1 O THR D 4 N THR C 2
SHEET 1 3 2 THR E 1 THR E 3 0
SHEET 2 3 2 THR F 4 THR F 5 -1 O THR F 4 N THR E 2""")
def run():
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
model = mmtbx.model.manager(model_input=pdb_inp, log=null_out())
model.process(make_restraints=True)
a = aev.AEV(model=model)
print('forward AEVs')
print(a.BAEVs)
print('backward AEVs')
print(a.EAEVs)
gv = a.get_values()
for key in gv:
outl = key
for cc in gv[key]:
outl += ' %0.3f' % cc
print(outl)
# print('backward AEVs')
# print(a.EAEVs)
# print('middle AEVs')
# print(a.MAEVs)
b = aev.compare(a)
print(b)
assert b['GLY A 1']['E'] is None
print(b['GLY A 5'])
assert b['GLY A 5']['E'] > 0.99
assert b['GLY A 5']['M'] > 0.99
assert b['GLY A 5']['B'] > 0.99
assert b['GLY A 10']['B'] is None
recs = aev.format_HELIX_records_from_AEV(b, 0.9)
assert len(recs) == 1
r = "HELIX 1 1 GLY A 2 GLY A 9 8"
assert r == recs[0]
#
with open("development.aev.pdb", "w") as fo:
fo.write(pdb_str)
easy_run.call("mmtbx.development.aev development.aev.pdb 0.9")
def exercise_set_seg_id () :
input_pdb = """\
ATOM 1 O GLY A 3 1.434 1.460 2.496 1.00 6.04 O
ATOM 2 O CYS A 7 2.196 4.467 3.911 1.00 4.51 O
ATOM 3 O CYS A 1 -1.433 4.734 5.405 1.00 7.85 O
TER
ATOM 4 O SER B 4 0.297 0.843 7.226 1.00 7.65 O
ATOM 5 OG ASER B 4 -2.625 1.057 4.064 0.50 5.46 O
ATOM 6 OG BSER B 4 -0.885 0.189 3.843 0.50 11.74 O
TER
ATOM 7 O LEU 0 5.613 12.448 6.864 1.00 7.32 O
TER
END
"""
open("tmp_seg_id.pdb", "w").write(input_pdb)
easy_run.call("phenix.pdbtools tmp_seg_id.pdb set_seg_id_to_chain_id=True --quiet")
pdb_out_1 = open("tmp_seg_id.pdb_modified.pdb").read()
assert not show_diff(pdb_out_1, """\
ATOM 1 O GLY A 3 1.434 1.460 2.496 1.00 6.04 A O
ATOM 2 O CYS A 7 2.196 4.467 3.911 1.00 4.51 A O
ATOM 3 O CYS A 1 -1.433 4.734 5.405 1.00 7.85 A O
TER
ATOM 4 O SER B 4 0.297 0.843 7.226 1.00 7.65 B O
ATOM 5 OG ASER B 4 -2.625 1.057 4.064 0.50 5.46 B O
ATOM 6 OG BSER B 4 -0.885 0.189 3.843 0.50 11.74 B O
TER
ATOM 7 O LEU 0 5.613 12.448 6.864 1.00 7.32 O
TER
END
""")
easy_run.call("phenix.pdbtools tmp_seg_id.pdb_modified.pdb clear_seg_id=True --quiet")
pdb_out_2 = open("tmp_seg_id.pdb_modified.pdb_modified.pdb").read()
assert (pdb_out_2 == input_pdb)
def run(args):
if (len(args) == 0):
n_iterations = 1000
elif (len(args) == 1):
n_iterations = int(args[0])
assert n_iterations > 0
else:
from libtbx.utils import Usage
raise Usage("scitbx.show_exp_times [n_iterations]")
evar = "LIBTBX_NO_LD_PRELOAD"
evar_set = os.environ.has_key(evar)
if (evar_set):
print "%s set:" % evar
else:
print "%s not set:" % evar
from scitbx.math.tests.tst_exp_functions import \
exercise_with_random_arguments as exercise
exercise(n_arguments=10000, n_iterations=n_iterations)
print
sys.stdout.flush()
if (not evar_set):
if (os.environ.has_key("LD_PRELOAD")):
del os.environ["LD_PRELOAD"]
os.environ[evar] = "1"
from libtbx import easy_run
easy_run.call(command="scitbx.show_exp_times %d" % n_iterations)
def run(prefix="tst_step_8"):
"""
Exercise phenix.cryo_fit step_8 with all defaults with "partial_GTPase_activation_center.pdb"
"""
assert (os.path.isfile("data/input/GTPase_activation_center.map") == True)
assert (os.path.isfile("data/input/regression_GAC.pdb") == True)
cmd = " ".join([
"phenix.cryo_fit", "data/input/regression_GAC.pdb",
"data/input/GTPase_activation_center.map", "step_1=False",
"step_2=False", "step_3=False", "step_4=False", "step_5=False",
"step_6=False", "step_7=False"
])
print cmd
easy_run.call(cmd)
starting_dir = os.getcwd()
new_path = starting_dir + "/steps/8_cryo_fit"
os.chdir(new_path)
cc = check_cc("cc_record")
assert (cc != 0.004804)
the_step_was_successfully_ran = check_whether_the_step_was_successfully_ran(
"Step 8", "cc_record")
if ((cc == 0.004804) or (the_step_was_successfully_ran != 1)):
print "failed step 8 for GAC, sleep for 10,000 seconds"
time.sleep(10000) # so that it is recognized instantly
assert (the_step_was_successfully_ran != 0)
os.chdir(starting_dir)
shutil.rmtree("steps")
def run():
phenix_dir = libtbx.env.dist_path("phenix")
print '\n Phenix modules found :',phenix_dir
amberhome = os.environ.get("AMBERHOME", None)
if amberhome is None:
raise Sorry("$AMBERHOME not set")
print "\n $AMBERHOME set :",amberhome
print "\n Linking AMBERHOME to Phenix modules"
assert os.path.exists(amberhome)
target = os.path.join(os.path.dirname(phenix_dir), "amber")
if os.path.exists(target):
if os.path.samefile(target, amberhome):
print '''
Not linking $AMBERHOME into Phenix modules directory because there is
already a link and it points to the same directory as $AMBERHOME.
$AMBERHOME : %s
Phenix link: %s
''' % (amberhome, target)
else:
print '''
Not linking $AMBERHOME into Phenix modules directory because there is
already a link and it does not point to the same directory as $AMBERHOME.
$AMBERHOME : %s
Phenix link: %s
Consider removing the Phenix link to update to a new $AMBERHOME.
''' % (amberhome, target)
raise Sorry("$AMBERHOME and Phenix link mismatch")
else:
os.symlink(amberhome, target)
build_dir = os.path.dirname(os.path.dirname(phenix_dir))
build_dir = os.path.join(build_dir, "build")
if 0: # don't do this as the python version can change
dispatcher_include = os.path.join(os.path.dirname(phenix_dir),
"amber_adaptbx",
"dispatcher_include_amber.sh",
)
shutil.copyfile(dispatcher_include,
os.path.join(build_dir,
"dispatcher_include_amber.sh",
)
)
else:
os.chdir(build_dir)
for filename in os.listdir(os.path.join(amberhome, "lib")):
if filename.startswith("python"):
break
f=file("dispatcher_include_amber.sh", "wb")
f.write(dispatcher_include_str % (filename, filename) )
f.close()
print "Building amber_adaptbx"
cmd = "libtbx.configure amber"
print "\n ~> %s\n" % cmd
easy_run.call(cmd)
os.chdir(build_dir)
def run(prefix="tst_map_model_cc"):
"""
Make sure it works with map having origin != (0,0,0)
"""
# original (zero-origin) map and model
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
pdb_inp.write_pdb_file(file_name="%s_%s"%(prefix,"orig.pdb"))
ph = pdb_inp.construct_hierarchy()
xrs = pdb_inp.xray_structure_simple()
fc = xrs.structure_factors(d_min=1.5).f_calc()
fft_map = fc.fft_map(resolution_factor = 0.25)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
assert map_data.all() == (40, 45, 54)
assert map_data.origin() == (0, 0, 0)
assert map_data.focus() == (40, 45, 54)
write_ccp4_map(map_data=map_data, cs=xrs.crystal_symmetry(),
file_name="%s_%s"%(prefix,"orig.ccp4"))
# shift origin of the map
g = flex.grid((-20,-25,-27), (20,20,27))
map_data.reshape(g)
assert map_data.all() == (40, 45, 54)
assert map_data.origin() == (-20, -25, -27)
assert map_data.focus() == (20, 20, 27)
write_ccp4_map(map_data=map_data, cs=xrs.crystal_symmetry(),
file_name="%s_%s"%(prefix,"shifted.ccp4"))
# apply same shift to the model
a,b,c = xrs.crystal_symmetry().unit_cell().parameters()[:3]
N = map_data.all()
O=map_data.origin()
sites_cart = ph.atoms().extract_xyz()
sx,sy,sz = a/N[0]*O[0], b/N[1]*O[1], c/N[2]*O[2]
sites_cart_shifted = sites_cart+\
flex.vec3_double(sites_cart.size(), [sx,sy,sz])
ph.atoms().set_xyz(sites_cart_shifted)
ph.write_pdb_file(file_name="%s_%s"%(prefix,"shifted.pdb"))
# run phenix.real_space_refine
checked = 0
for opt in ["","resolution=1.5"]:
cmd = " ".join([
"phenix.map_model_cc",
"%s_shifted.pdb"%prefix,
"%s_shifted.ccp4"%prefix,
"%s"%opt,
"> %s.zlog"%prefix
])
print cmd
easy_run.call(cmd)
# check results
fo = open("%s.zlog"%prefix,"r")
for l in fo.readlines():
if(l.startswith("around atoms:")):
cc = float(l.split()[2])
assert cc>0.989
checked+=1
fo.close()
assert checked==2
def run(args):
sit_reldir = os.environ.get("SIT_RELDIR")
sit_release = os.environ.get("SIT_RELEASE")
sit_arch = os.environ.get("SIT_ARCH")
assert [sit_reldir, sit_release, sit_arch].count(None) == 0
pyana_path = os.path.join(sit_reldir,sit_release,"arch",sit_arch,"bin","psana")
cmd = " ".join([pyana_path] + args)
print cmd
easy_run.call(cmd)
def run_multi(cmd):
from libtbx import easy_run
import traceback
print cmd
try:
easy_run.call(command=cmd)
except: # intentional
sys.stdout.flush()
print >> sys.stderr, "CAUGHT EXCEPTION: run_multi(%s)" % cmd
traceback.print_exc()
sys.stderr.flush()
def run(filename):
print filename
if 0:
print "RDL"
for aa in sorted(rdl_database):
print " %s" % aa
for key, value in rdl_database[aa].items():
print " %s" % key
for names, values in rdl_database[aa][key].items():
print " %s : %s" % (names, values)
assert 0
#
if filename=="3sgs.pdb":
from libtbx import easy_run
f=file("mse.pdb", "wb")
f.write(pdbs["mse.pdb"])
f.close()
f=file("met.pdb", "wb")
f.write(pdbs["met.pdb"])
f.close()
cmd="phenix.pdb_interpretation rdl=True write_geo=1 mse.pdb"
print cmd
easy_run.call(cmd)
cmd="phenix.pdb_interpretation rdl=True write_geo=1 met.pdb"
print cmd
easy_run.call(cmd)
#
pdb_inp = pdb.input(filename)
pdb_hierarchy = pdb_inp.construct_hierarchy()
geometry_restraints_manager = get_geometry_restraints_manager(filename)
pdb_hierarchy.reset_i_seq_if_necessary()
rdl.update_restraints(pdb_hierarchy,
geometry_restraints_manager,
assert_rotamer_found=True,
verbose=True,
)
print "OK"
mmtbx_dir = libtbx.env.dist_path("mmtbx")
props = os.path.join(mmtbx_dir,"rotamer","rotamer_names.props")
f=file(props, "rb")
props = f.readlines()
f.close()
for prop in props:
print prop
key = prop.split("=")[0]
residue, rotamer_name = key.split()
residue = residue.upper()
if residue in ["MSE"]: continue
assert residue in rdl_database
assert rotamer_name in rdl_database[residue]
def exercise_set_charge () :
from iotbx import file_reader
input_pdb = """
ATOM 1 CL CL X 1 0.000 0.000 0.000 1.00 20.00 CL
END
"""
open("tmp_cl.pdb", "w").write(input_pdb)
easy_run.call('phenix.pdbtools tmp_cl.pdb charge_selection="element Cl" charge=-1 --quiet')
pdb_in = file_reader.any_file("tmp_cl.pdb_modified.pdb").file_object
hierarchy = pdb_in.hierarchy
xrs = pdb_in.xray_structure_simple()
assert (xrs.scatterers()[0].scattering_type == 'Cl1-')
assert (hierarchy.atoms()[0].charge == '1-')
def run_function_as_detached_process_in_dialog (
parent,
thread_function,
title,
message,
tmp_dir,
callback=None,
project_id=None,
job_id=None) :
if (tmp_dir is None) :
tmp_dir = os.getcwd()
params = runtime_utils.process_master_phil.extract()
params.tmp_dir = tmp_dir
if (job_id is None) :
job_id = str(os.getpid()) + "_" + str(int(random.random() * 1000))
params.prefix = str(job_id)
target = runtime_utils.detached_process_driver(target=thread_function)
run_file = os.path.join(tmp_dir, "libtbx_run_%s.pkl" % job_id)
easy_pickle.dump(run_file, target)
params.run_file = run_file
eff_file = os.path.join(tmp_dir, "libtbx_run_%s.eff" % job_id)
runtime_utils.write_params(params, eff_file)
dlg = ProcessDialog(
parent=parent,
message=message,
caption=title,
callback=callback)
setup_process_gui_events(
window=dlg,
OnExcept=dlg.OnError,
OnAbort=dlg.OnAbort,
OnComplete=dlg.OnComplete)
agent = event_agent(
window=dlg,
project_id=project_id,
job_id=job_id)
process = detached_process(params, proxy=agent)
cb = event_agent(dlg, project_id=project_id, job_id=job_id)
easy_run.call("libtbx.start_process \"%s\" &" % eff_file)
result = None
abort = False
if (dlg.run(process) == wx.ID_OK) :
result = dlg.get_result()
elif dlg.exception_raised() :
dlg.handle_error()
elif (dlg.was_aborted()) :
abort = True
wx.CallAfter(dlg.Destroy)
if (abort) :
raise Abort()
return result
def exercise () :
pdb_file_name_1 = libtbx.env.find_in_repositories(
relative_path="phenix_regression/misc/1l3r_no_ligand.pdb",
test=os.path.isfile)
pdb_in_1 = iotbx.pdb.input(file_name = pdb_file_name_1)
xrs1 = pdb_in_1.xray_structure_simple()
ofn = "1l3r_rt.pdb"
cmd = " ".join([
"phenix.pdbtools",
"%s"%pdb_file_name_1,
"rotate='90 10 20' translate='10 10 10'",
"output.file_name=%s"%ofn,
"--quiet"])
easy_run.call(cmd)
pdb_in_rt = iotbx.pdb.input(file_name = ofn)
xrs_rt = pdb_in_rt.xray_structure_simple()
fft_map_1 = xrs1.structure_factors(d_min=1.5).f_calc().fft_map(
resolution_factor = 1./3)
fft_map_1.apply_sigma_scaling()
map_data_1 = fft_map_1.real_map_unpadded()
mmtbx.maps.utils.write_xplor_map(sites_cart = xrs1.sites_cart(),
unit_cell = xrs1.unit_cell(),
map_data = map_data_1,
n_real = fft_map_1.n_real(),
file_name = "1l3r.xplor")
lsq_fit_obj = superpose.least_squares_fit(
reference_sites=xrs_rt.sites_cart(),
other_sites=xrs1.sites_cart().deep_copy())
f_o_r = common_frame_of_reference(
all_sites_cart=[xrs1.sites_cart(),xrs_rt.sites_cart()],
lsq_fits=[None, lsq_fit_obj])
hierarchy_rt = pdb_in_rt.construct_hierarchy()
lsq_fit_obj = f_o_r.transformation_matrices[1]
hierarchy_rt.atoms().set_xyz(f_o_r.shifted_sites[1])
open("1l3r_rt.pdb", "w").write(hierarchy_rt.as_pdb_string())
xrs_rt, map_data_rt = transform_map_by_lsq_fit(
fft_map=fft_map_1,
unit_cell=xrs1.unit_cell(),
lsq_fit_obj=lsq_fit_obj.inverse(),
pdb_hierarchy=hierarchy_rt,
d_min=1.5,
file_name="1l3r_rt.xplor",
log=null_out())
f_o_r.inverse_transform_hierarchy(1, hierarchy_rt)
open("1l3r.pdb", "w").write(hierarchy_rt.as_pdb_string())
#for sf1, sf2 in zip(xrs1.sites_frac(), xrs_rt.sites_frac()):
# e1 = map_data_1.eight_point_interpolation(sf1)
# e2 = map_data_rt.eight_point_interpolation(sf2)
# print abs(e1-e2)
# assert abs(e1-e2) < 1.
print "OK"
def exercise(
verbose,
file_names_cpp,
number_of_function_files=None,
separate_files_main_namespace={},
separate_files_separate_namespace={}):
if (verbose): print "next exercise"
import libtbx.load_env
test_valid = libtbx.env.under_dist(
module_name="fable", path="test/valid", test=op.isdir)
import fable.cout
top_cpp = fable.cout.process(
file_names=[op.join(test_valid, "subroutine_3.f")],
top_procedures=["prog"],
namespace="tst_separate_files",
top_cpp_file_name=file_names_cpp[0],
number_of_function_files=number_of_function_files,
separate_files_main_namespace=separate_files_main_namespace,
separate_files_separate_namespace=separate_files_separate_namespace)
from fable import simple_compilation
comp_env = simple_compilation.environment()
from libtbx import easy_run
file_names_obj = []
for file_name_cpp in file_names_cpp:
obj = comp_env.file_name_obj(file_name_cpp=file_name_cpp)
remove_file_if_necessary(file_name=obj)
cmd = comp_env.compilation_command(file_name_cpp=file_name_cpp)
if (verbose): print cmd
easy_run.call(command=cmd)
assert op.exists(obj)
file_names_obj.append(obj)
exe_root = "tst_separate_files"
exe = comp_env.file_name_exe(exe_root=exe_root)
remove_file_if_necessary(file_name=exe)
cmd = comp_env.link_command(file_names_obj=file_names_obj, exe_root=exe_root)
if (verbose): print cmd
easy_run.call(command=cmd)
cmd = op.join(".", exe)
if (verbose): print cmd
assert op.exists(cmd)
stdout = easy_run.fully_buffered(command=cmd).raise_if_errors().stdout_lines
text = "\n".join(stdout)
if (verbose):
print text
from fable.tst_cout_compile import read_file_names_and_expected_cout
info = read_file_names_and_expected_cout(test_valid=test_valid).get(
"subroutine_3.f")[0]
from libtbx.test_utils import show_diff
assert not show_diff(text, "\n".join(info.out_lines))
if (verbose): print
def exercise(prefix="tst_helix_sheet_recs_as_pdb_files"):
of = open(prefix+".pdb", "w")
print >> of, pdb_str
of.close()
xrs1 = iotbx.pdb.input(file_name=prefix+".pdb").xray_structure_simple()
easy_run.call("phenix.helix_sheet_recs_as_pdb_files %s"%(prefix+".pdb"))
xrs2 = iotbx.pdb.input(
file_name="HELIX_1_1_ALA_E_1_ALA_E_16_1_16.pdb").xray_structure_simple(crystal_symmetry=xrs1.crystal_symmetry())
fc1 = xrs1.structure_factors(d_min=3).f_calc()
fc2 = fc1.structure_factors_from_scatterers(
xray_structure=xrs2).f_calc()
fc1=flex.abs(abs(fc1).data())
fc2=flex.abs(abs(fc2).data())
assert flex.sum(flex.abs(fc1-fc2))/flex.sum(flex.abs(fc1+fc2)) < 1.e-3
def run():
if (not libtbx.env.has_module("phenix")) :
print "phenix not configured, skipping"
return
elif (not libtbx.env.find_in_repositories("chem_data")) :
print "chem_data not configured, skipping"
return
f=file("l1r.pdb", "wb")
f.write(l1r_pdb)
f.close()
f=file("l1r.cif", "wb")
f.write(l1r_cif)
f.close()
cmd = 'phenix.geometry_minimization'
cmd += " l1r.pdb l1r.cif use_neutron_distances=False"
cmd += ' selection="element H or element D" write_geo_file=False'
cmd += ' correct_hydrogens=True'
print cmd
ero = easy_run.fully_buffered(command=cmd)
err = StringIO.StringIO()
ero.show_stdout(out=err)
for line in err.getvalue().split("\n"):
if line.find("Number of hydrogens corrected")>-1:
print line
break
else:
assert 0
print "OK"
cmd = "phenix.fmodel high_res=4.5 format=mtz label=FOBS type=real r_free=0.1 l1r.pdb generate_fake_p1_symmetry=1"
easy_run.call(cmd)
cmd = 'phenix.refine'
cmd += " l1r.pdb l1r.pdb.mtz l1r.cif"
cmd += " main.number_of_macro_cycles=1"
cmd += ' correct_hydrogens=True'
print cmd
ero = easy_run.fully_buffered(command=cmd)
err = StringIO.StringIO()
ero.show_stdout(out=err)
for line in err.getvalue().split("\n"):
if line.find("Number of hydrogens corrected")>-1:
print line
break
else:
assert 0
print "OK"
def exercise_00(prefix="tst_molprobity_3_exercise_00"):
for pdb_str in [pdb_str_1, pdb_str_2]:
of = open("%s.pdb"%prefix, "w")
print >> of, pdb_str
of.close()
cmd = " ".join([
"phenix.fmodel",
"%s.pdb"%prefix,
"high_res=10",
"type=real r_free=0.1 label=F-obs",
"output.file_name=%s.mtz"%prefix,
"> %s.zlog"%prefix])
easy_run.call(cmd)
cmd = "phenix.molprobity %s.pdb %s.mtz > %s.zlog"%(prefix,prefix,prefix)
easy_run.call(cmd)
def exercise () :
if (os.path.isfile("tst_fmodel_anomalous.mtz")) :
os.remove("tst_fmodel_anomalous.mtz")
pdb_file = make_fake_anomalous_data.write_pdb_input_cd_cl(
file_base="tst_fmodel_anomalous")
# phenix.fmodel (with wavelength)
args = [
pdb_file,
"high_resolution=1.0",
"wavelength=1.116",
"label=F",
"type=real",
"output.file_name=tst_fmodel_anomalous.mtz",
"r_free_flags_fraction=0.1",
]
fmodel.run(args=args, log=null_out())
assert os.path.isfile("tst_fmodel_anomalous.mtz")
mtz_in = file_reader.any_file("tst_fmodel_anomalous.mtz")
array = mtz_in.file_server.miller_arrays[0]
assert (array.anomalous_flag())
anom_diffs = array.anomalous_differences()
assert approx_equal(flex.max(anom_diffs.data()), 5.72, eps=0.01)
# mmtbx.fmodel_simple
result = easy_run.call(
"mmtbx.fmodel_simple \"%s\" tst_fmodel_anomalous.mtz high_resolution=2.0"
% pdb_file)
print "OK"