def run(args, out=None):
if (out is None): out = sys.stdout
from mmtbx.building.alternate_conformations import single_residue
import mmtbx.command_line
cmdline = mmtbx.command_line.load_model_and_data(args=args,
master_phil=master_phil(),
process_pdb_file=True,
create_fmodel=True,
out=out,
usage_string="""\
mmtbx.build_alt_confs_simple model.pdb data.mtz [options]
Simple tool for building alternate conformations by real-space refinement into
difference density. Not intended for production use - use the program
mmtbx.build_alternate_conformations if you want refinement and post-processing.
""")
params = cmdline.params
validate_params(params)
log = multi_out()
log.register("stdout", out)
log_file_name = os.path.splitext(params.output.file_name)[0] + ".log"
logfile = open(log_file_name, "w")
log.register("logfile", logfile)
pdb_hierarchy, n_alternates = single_residue.build_cycle(
pdb_hierarchy=cmdline.pdb_hierarchy,
fmodel=cmdline.fmodel,
geometry_restraints_manager=cmdline.geometry,
params=params,
cif_objects=cmdline.cif_objects,
selection=params.selection,
nproc=params.nproc,
verbose=params.output.verbose,
debug=params.output.debug,
out=log)
# TODO real-space refinement of multi-conformer model
f = open(params.output.file_name, "w")
f.write(
pdb_hierarchy.as_pdb_string(
crystal_symmetry=cmdline.fmodel.xray_structure))
f.close()
make_header("Building complete", out=out)
print >> log, ""
print >> log, "Wrote %s" % params.output.file_name
print >> log, "You MUST refine this model before using it!"
def run (args, out=None) :
if (out is None) : out = sys.stdout
from mmtbx.building.alternate_conformations import single_residue
import mmtbx.command_line
cmdline = mmtbx.command_line.load_model_and_data(
args=args,
master_phil=master_phil(),
process_pdb_file=True,
create_fmodel=True,
out=out,
usage_string="""\
mmtbx.build_alt_confs_simple model.pdb data.mtz [options]
Simple tool for building alternate conformations by real-space refinement into
difference density. Not intended for production use - use the program
mmtbx.build_alternate_conformations if you want refinement and post-processing.
""")
params = cmdline.params
validate_params(params)
log = multi_out()
log.register("stdout", out)
log_file_name = os.path.splitext(params.output.file_name)[0] + ".log"
logfile = open(log_file_name, "w")
log.register("logfile", logfile)
pdb_hierarchy, n_alternates = single_residue.build_cycle(
pdb_hierarchy = cmdline.pdb_hierarchy,
fmodel = cmdline.fmodel,
geometry_restraints_manager = cmdline.geometry,
params = params,
cif_objects=cmdline.cif_objects,
selection=params.selection,
nproc=params.nproc,
verbose=params.output.verbose,
debug=params.output.debug,
out=log)
# TODO real-space refinement of multi-conformer model
f = open(params.output.file_name, "w")
f.write(pdb_hierarchy.as_pdb_string(
crystal_symmetry=cmdline.fmodel.xray_structure))
f.close()
make_header("Building complete", out=out)
print >> log, ""
print >> log, "Wrote %s" % params.output.file_name
print >> log, "You MUST refine this model before using it!"
def build_residue_conformers (self, stop_if_none=False) :
self.extract_selection()
print >> self.out, ""
#self.fmodel.info().show_targets(out=self.out, text="starting model")
make_sub_header("Fitting individual residues", out=self.out)
t1 = time.time()
params = self.params
self.pdb_hierarchy, n_alternates = single_residue.build_cycle(
pdb_hierarchy = self.pdb_hierarchy,
fmodel = self.fmodel,
geometry_restraints_manager = self.geometry_restraints_manager,
params = params,
cif_objects=self.cif_objects,
selection=params.selection,
nproc=params.nproc,
verbose=self.verbose,
debug=self.debug,
out=self.out)
if (n_alternates == 0) and (stop_if_none) :
raise Sorry("No new conformations generated.")
return n_alternates