def __init__ (self,
fmodel,
pdb_hierarchy,
params=None,
processed_pdb_file=None,
geometry_restraints_manager=None,
cif_objects=(),
cif_files=(), # XXX bug
debug=None,
verbose=True,
out=sys.stdout) :
adopt_init_args(self, locals())
if (self.params is None) :
self.params = master_phil.extract().alt_confs
self.extract_selection()
self.refine_cycle = 1
self.map_file = None
self.r_work_start = fmodel.r_work()
self.r_free_start = fmodel.r_free()
t_start = time.time()
for i_cycle in range(params.macro_cycles) :
n_alts = self.build_residue_conformers(stop_if_none=(i_cycle==0))
if (n_alts == 0) :
if (i_cycle == 0) :
raise Sorry("No alternate conformations found.")
else :
self.refine(constrain_occupancies=False)
refine_again = self.params.refinement.constrain_correlated_occupancies
if (self.rejoin()) :
refine_again = True
self.refine(title="Refining final model")
make_header("Finished", out=out)
from mmtbx.validation import molprobity
validation = molprobity.molprobity(
pdb_hierarchy=self.pdb_hierarchy,
outliers_only=False)
print >> self.out, ""
validation.show_summary(out=self.out, prefix=" ")
make_sub_header("Analyzing final model", out=out)
analyze_model.process_pdb_hierarchy(
pdb_hierarchy=self.pdb_hierarchy,
validation=validation,
log=self.out).show(out=out, verbose=self.verbose)
print >> self.out, ""
print >> self.out, "Start: r_work=%6.4f r_free=%6.4f" % \
(self.r_work_start, self.r_free_start)
print >> self.out, "Final: r_work=%6.4f r_free=%6.4f" % \
(self.fmodel.r_work(), self.fmodel.r_free())
t_end = time.time()
print >> self.out, ""
print >> self.out, "Total runtime: %d s" % int(t_end - t_start)
print >> self.out, ""
def analyze_fragment(pdb_str):
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_str)
model = mmtbx.model.manager(pdb_in.input)
validation = molprobity.molprobity(model, outliers_only=False)
result = analyze_model.process_pdb_hierarchy(
pdb_hierarchy=model.get_hierarchy(),
validation=validation,
log=null_out())
return result
def analyze_fragment(pdb_str):
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_str)
hierarchy = pdb_in.hierarchy
validation = molprobity.molprobity(pdb_hierarchy=hierarchy,
outliers_only=False)
result = analyze_model.process_pdb_hierarchy(pdb_hierarchy=hierarchy,
validation=validation,
log=null_out())
return result
def analyze_fragment (pdb_str) :
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_str)
hierarchy = pdb_in.hierarchy
validation = molprobity.molprobity(pdb_hierarchy=hierarchy,
outliers_only=False)
result = analyze_model.process_pdb_hierarchy(
pdb_hierarchy=hierarchy,
validation=validation,
log=null_out())
return result
def run(args, out=sys.stdout):
from mmtbx.disorder import analyze_model
import mmtbx.validation.molprobity
import mmtbx.command_line
cmdline = mmtbx.command_line.load_model_and_data(
args=args,
master_phil=master_phil(),
require_data=False,
create_fmodel=True,
process_pdb_file=True,
usage_string="mmtbx.analyze_static_disorder model.pdb",
out=out)
hierarchy = cmdline.pdb_hierarchy
params = cmdline.params
validation = mmtbx.validation.molprobity.molprobity(
pdb_hierarchy=hierarchy,
xray_structure=cmdline.xray_structure,
fmodel=cmdline.fmodel,
crystal_symmetry=cmdline.crystal_symmetry,
geometry_restraints_manager=cmdline.geometry,
header_info=None,
keep_hydrogens=False,
outliers_only=False,
nuclear=False)
segments = []
make_header("Analyzing model", out=out)
if (params.ignore_inconsistent_occupancy):
print("Discontinuous occupancies will be ignored.", file=out)
process = analyze_model.process_pdb_hierarchy(
pdb_hierarchy=hierarchy,
validation=validation,
ignore_inconsistent_occupancy=params.ignore_inconsistent_occupancy,
log=out)
make_sub_header("MolProbity validation", out=out)
validation.show_summary(out=out)
make_sub_header("Disorder analysis", out=out)
if (process.n_disordered == 0):
print("No alternate conformations found.", file=out)
else:
process.show(out=out, verbose=params.verbose)
if (params.pickle):
file_name = os.path.basename(
os.path.splitext(params.input.pdb.file_name[0])[0]) + ".pkl"
easy_pickle.dump(file_name, process)
return process
def run (args, out=sys.stdout) :
from mmtbx.disorder import analyze_model
import mmtbx.validation.molprobity
import mmtbx.command_line
cmdline = mmtbx.command_line.load_model_and_data(
args=args,
master_phil=master_phil(),
require_data=False,
create_fmodel=True,
process_pdb_file=True,
usage_string="mmtbx.analyze_static_disorder model.pdb",
out=out)
hierarchy = cmdline.pdb_hierarchy
params = cmdline.params
validation = mmtbx.validation.molprobity.molprobity(
pdb_hierarchy=hierarchy,
xray_structure=cmdline.xray_structure,
fmodel=cmdline.fmodel,
crystal_symmetry=cmdline.crystal_symmetry,
geometry_restraints_manager=cmdline.geometry,
header_info=None,
keep_hydrogens=False,
outliers_only=False,
nuclear=False)
segments = []
make_header("Analyzing model", out=out)
if (params.ignore_inconsistent_occupancy) :
print >> out, "Discontinuous occupancies will be ignored."
process = analyze_model.process_pdb_hierarchy(
pdb_hierarchy=hierarchy,
validation=validation,
ignore_inconsistent_occupancy=params.ignore_inconsistent_occupancy,
log=out)
make_sub_header("MolProbity validation", out=out)
validation.show_summary(out=out)
make_sub_header("Disorder analysis", out=out)
if (process.n_disordered == 0) :
print >> out, "No alternate conformations found."
else :
process.show(out=out, verbose=params.verbose)
if (params.pickle) :
file_name = os.path.basename(
os.path.splitext(params.input.pdb.file_name[0])[0]) + ".pkl"
easy_pickle.dump(file_name, process)
return process