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 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 updaterdl(self, prefix):
if self.restraints_manager is None: return
from mmtbx.conformation_dependent_library import rotamers
from mmtbx.refinement import print_statistics
print_statistics.make_header(prefix, out=self.log)
self.rdl_proxies = None #rotamers.setup_restraints(result)
rc = rotamers.update_restraints(
self.pdb_hierarchy,
self.restraints_manager.geometry,
current_geometry=self.pdb_hierarchy.extract_xray_structure(),
rdl_proxies=self.rdl_proxies,
log=self.log,
verbose=False,
)
print >> self.log, "=" * 79
return rc
def updaterdl(self, prefix):
if self.restraints_manager is None: return
from mmtbx.conformation_dependent_library import rotamers
from mmtbx.refinement import print_statistics
print_statistics.make_header(prefix, out=self.log)
self.rdl_proxies = None #rotamers.setup_restraints(result)
rc = rotamers.update_restraints(
self.pdb_hierarchy,
self.restraints_manager.geometry,
current_geometry=self.pdb_hierarchy.extract_xray_structure(),
rdl_proxies=self.rdl_proxies,
log=self.log,
verbose=False,
)
print >> self.log, "="*79
return rc