def __init__(self, pdb_file, pdb_hierarchy=None):
for name in self.__slots__:
setattr(self, name, None)
if (pdb_file is not None):
import iotbx.pdb.hierarchy
from iotbx.pdb import extract_rfactors_resolutions_sigma
pdb_in = iotbx.pdb.hierarchy.input(file_name=pdb_file)
published_results = extract_rfactors_resolutions_sigma.extract(
file_lines=pdb_in.input.remark_section(), file_name=None)
if (published_results is not None):
self.r_work = published_results.r_work
self.r_free = published_results.r_free
self.d_min = published_results.high
self.d_max = published_results.low
self.refinement_program = pdb_in.input.get_program_name()
# XXX phenix.refine hack, won't work for other programs
lines = open(pdb_file).readlines()
for line in lines:
if (line.startswith("REMARK Final:")):
fields = line.strip().split()
self.rms_bonds = float(fields[-4])
self.rms_angles = float(fields[-1])
break
if (pdb_hierarchy is not None):
tls_groups = pdb_in.input.extract_tls_params(
pdb_hierarchy).tls_params
if (tls_groups is not None):
self.n_tls_groups = len(tls_groups)
def __init__ (self, pdb_file, pdb_hierarchy=None) :
for name in self.__slots__ :
setattr(self, name, None)
if (pdb_file is not None) :
import iotbx.pdb.hierarchy
from iotbx.pdb import extract_rfactors_resolutions_sigma
pdb_in = iotbx.pdb.hierarchy.input(file_name=pdb_file)
published_results = extract_rfactors_resolutions_sigma.extract(
file_lines=pdb_in.input.remark_section(), file_name=None)
if (published_results is not None) :
self.r_work = published_results.r_work
self.r_free = published_results.r_free
self.d_min = published_results.high
self.d_max = published_results.low
self.refinement_program = pdb_in.input.get_program_name()
# XXX phenix.refine hack, won't work for other programs
lines = open(pdb_file).readlines()
for line in lines :
if (line.startswith("REMARK Final:")) :
fields = line.strip().split()
self.rms_bonds = float(fields[-4])
self.rms_angles = float(fields[-1])
break
if (pdb_hierarchy is not None) :
tls_groups = pdb_in.input.extract_tls_params(pdb_hierarchy).tls_params
if (tls_groups is not None) :
self.n_tls_groups = len(tls_groups)
def run():
result = extract_rfactors_resolutions_sigma.get_r_rfree_sigma(
remark_2_and_3_records = example_cns.splitlines(), file_name = None)
assert approx_equal(result.r_work , 0.171)
assert approx_equal(result.r_free , 0.221)
assert approx_equal(result.high , 2.2 )
assert approx_equal(result.low , 99.0 )
assert approx_equal(result.resolution , 2.2 )
assert approx_equal(result.sigma , 2.0 )
#
result = extract_rfactors_resolutions_sigma.get_r_rfree_sigma(
remark_2_and_3_records = example_refmac.splitlines(), file_name = None)
assert approx_equal(result.r_work , 0.198 )
assert approx_equal(result.r_free , 0.248 )
assert approx_equal(result.high , 1.55 )
assert approx_equal(result.low , 18.0 )
assert approx_equal(result.resolution , 1.55 )
assert approx_equal(result.sigma , 0.0 )
#
result = extract_rfactors_resolutions_sigma.get_r_rfree_sigma(
remark_2_and_3_records = example_shelx.splitlines(), file_name = None)
assert approx_equal(result.r_work , 0.140 )
assert approx_equal(result.r_free , 0.166 )
assert approx_equal(result.high , 1.05 )
assert approx_equal(result.low , 20.0 )
assert approx_equal(result.resolution , 1.05 )
assert approx_equal(result.sigma , 0.0 )
result = extract_rfactors_resolutions_sigma.extract(
file_lines=example_shelx.splitlines(), file_name=None)
assert approx_equal(result.r_work , 0.140 )
def run():
result = extract_rfactors_resolutions_sigma.get_r_rfree_sigma(
remark_2_and_3_records=example_cns.splitlines(), file_name=None)
assert approx_equal(result.r_work, 0.171)
assert approx_equal(result.r_free, 0.221)
assert approx_equal(result.high, 2.2)
assert approx_equal(result.low, 99.0)
assert approx_equal(result.resolution, 2.2)
assert approx_equal(result.sigma, 2.0)
#
result = extract_rfactors_resolutions_sigma.get_r_rfree_sigma(
remark_2_and_3_records=example_refmac.splitlines(), file_name=None)
assert approx_equal(result.r_work, 0.198)
assert approx_equal(result.r_free, 0.248)
assert approx_equal(result.high, 1.55)
assert approx_equal(result.low, 18.0)
assert approx_equal(result.resolution, 1.55)
assert approx_equal(result.sigma, 0.0)
#
result = extract_rfactors_resolutions_sigma.get_r_rfree_sigma(
remark_2_and_3_records=example_shelx.splitlines(), file_name=None)
assert approx_equal(result.r_work, 0.140)
assert approx_equal(result.r_free, 0.166)
assert approx_equal(result.high, 1.05)
assert approx_equal(result.low, 20.0)
assert approx_equal(result.resolution, 1.05)
assert approx_equal(result.sigma, 0.0)
result = extract_rfactors_resolutions_sigma.extract(
file_lines=example_shelx.splitlines(), file_name=None)
assert approx_equal(result.r_work, 0.140)
