def __init__ (self, pdb_hierarchy, params=None, outliers_only=True) :
if (params is None) :
params = rna_sugar_pucker_analysis.master_phil.extract()
self.pucker_states = []
self.pucker_perp_xyz = {}
self.pucker_dist = {}
rna_geometry.__init__(self)
from iotbx.pdb.rna_dna_detection import residue_analysis
for model in pdb_hierarchy.models():
for chain in model.chains():
for conformer in chain.conformers():
altloc = conformer.altloc
if altloc == "":
altloc = " "
residues = conformer.residues()
for i_residue,residue in enumerate(residues):
def _get_next_residue():
j = i_residue + 1
if (j == len(residues)): return None
return residues[j]
ra1 = residue_analysis(
residue_atoms=residue.atoms(),
distance_tolerance=params.bond_detection_distance_tolerance)
if (ra1.problems is not None): continue
if (not ra1.is_rna): continue
residue_2_p_atom = None
next_pdb_residue = _get_next_residue()
if (next_pdb_residue is not None):
residue_2_p_atom = next_pdb_residue.find_atom_by(name=" P ")
if (get_res_class(residue.resname) != "common_rna_dna") :
continue
ana = rna_sugar_pucker_analysis.evaluate(
params=params,
residue_1_deoxy_ribo_atom_dict=ra1.deoxy_ribo_atom_dict,
residue_1_c1p_outbound_atom=ra1.c1p_outbound_atom,
residue_2_p_atom=residue_2_p_atom)
self.pucker_states.append(ana)
self.n_total += 1
is_outlier = ana.is_delta_outlier or ana.is_epsilon_outlier
if (is_outlier) :
self.n_outliers += 1
if (is_outlier or not outliers_only) :
pucker = rna_pucker(
chain_id=chain.id,
resseq=residue.resseq,
icode=residue.icode,
altloc=conformer.altloc,
resname=residue.resname,
delta_angle=ana.delta,
is_delta_outlier=ana.is_delta_outlier,
epsilon_angle=ana.epsilon,
is_epsilon_outlier=ana.is_epsilon_outlier,
outlier=is_outlier)
self.results.append(pucker)
key = pucker.id_str() #[8:-1]
self.pucker_perp_xyz[key] = [ana.p_perp_xyz, ana.o3p_perp_xyz]
self.pucker_dist[key] = [ana.p_distance_c1p_outbound_line,
ana.o3p_distance_c1p_outbound_line]
def __init__ (self, pdb_hierarchy, params=None, outliers_only=True) :
if (params is None) :
params = rna_sugar_pucker_analysis.master_phil.extract()
self.pucker_states = []
self.pucker_perp_xyz = {}
self.pucker_dist = {}
rna_geometry.__init__(self)
from iotbx.pdb.rna_dna_detection import residue_analysis
for model in pdb_hierarchy.models():
for chain in model.chains():
for conformer in chain.conformers():
altloc = conformer.altloc
if altloc == "":
altloc = " "
residues = conformer.residues()
for i_residue,residue in enumerate(residues):
def _get_next_residue():
j = i_residue + 1
if (j == len(residues)): return None
return residues[j]
ra1 = residue_analysis(
residue_atoms=residue.atoms(),
distance_tolerance=params.bond_detection_distance_tolerance)
if (ra1.problems is not None): continue
if (not ra1.is_rna): continue
residue_2_p_atom = None
next_pdb_residue = _get_next_residue()
if (next_pdb_residue is not None):
residue_2_p_atom = next_pdb_residue.find_atom_by(name=" P ")
if (get_res_class(residue.resname) != "common_rna_dna") :
continue
ana = rna_sugar_pucker_analysis.evaluate(
params=params,
residue_1_deoxy_ribo_atom_dict=ra1.deoxy_ribo_atom_dict,
residue_1_c1p_outbound_atom=ra1.c1p_outbound_atom,
residue_2_p_atom=residue_2_p_atom)
self.pucker_states.append(ana)
self.n_total += 1
is_outlier = ana.is_delta_outlier or ana.is_epsilon_outlier
if (is_outlier) :
self.n_outliers += 1
if (is_outlier or not outliers_only) :
pucker = rna_pucker(
chain_id=chain.id,
resseq=residue.resseq,
icode=residue.icode,
altloc=conformer.altloc,
resname=residue.resname,
delta_angle=ana.delta,
is_delta_outlier=ana.is_delta_outlier,
epsilon_angle=ana.epsilon,
is_epsilon_outlier=ana.is_epsilon_outlier,
outlier=is_outlier)
self.results.append(pucker)
key = pucker.id_str() #[8:-1]
self.pucker_perp_xyz[key] = [ana.p_perp_xyz, ana.o3p_perp_xyz]
self.pucker_dist[key] = [ana.p_distance_c1p_outbound_line,
ana.o3p_distance_c1p_outbound_line]
def exercise(args):
assert len(args) == 0
params = rna_sugar_pucker_analysis.master_phil.fetch().extract()
for i_pass, some_x in enumerate([31.101, 21.101]):
analysis = rna_sugar_pucker_analysis.evaluate(
params=params,
residue_1_deoxy_ribo_atom_dict=atom_dict([(some_x, 30.048, 33.325),
(22.184, 28.704, 36.539),
(21.527, 28.782, 35.281),
(22.379, 28.287, 34.119),
(22.676, 26.795, 34.032)
]),
residue_1_c1p_outbound_atom=atom((19.628, 30.157, 32.953)),
residue_2_p_atom=atom((33.058, 33.903, 32.613)))
assert analysis.epsilon is None
if (i_pass == 0):
assert analysis.delta is None
else:
assert approx_equal(analysis.delta, 69.6819176834)
assert analysis.p_distance_c1p_outbound_line is None
assert analysis.is_epsilon_outlier is None
if (i_pass == 0):
assert analysis.is_2p_delta is None
assert analysis.is_2p_p_distance_c1p_outbound_line is None
assert analysis.is_2p_o3p_distance_c1p_outbound_line is None
assert analysis.is_2p is None
else:
assert not analysis.is_2p_delta
assert analysis.is_2p_p_distance_c1p_outbound_line is None
assert not analysis.is_2p_o3p_distance_c1p_outbound_line
assert not analysis.is_2p
analysis = rna_sugar_pucker_analysis.evaluate(
params=params,
residue_1_deoxy_ribo_atom_dict=atom_dict([(50.473, 9.942, 36.204),
(48.952, 10.236, 33.644),
(49.474, 11.213, 34.497),
(50.978, 11.174, 34.278),
(51.710, 12.501, 34.095)]),
residue_1_c1p_outbound_atom=atom((50.926, 10.084, 37.569)),
residue_2_p_atom=atom((48.114, 10.641, 32.347)))
assert approx_equal(analysis.epsilon, 250.715932662)
assert approx_equal(analysis.delta, 133.811229901)
assert approx_equal(analysis.p_distance_c1p_outbound_line, 1.52374220064)
assert approx_equal(analysis.o3p_distance_c1p_outbound_line,
0.860583842822)
assert not analysis.is_epsilon_outlier
assert analysis.is_2p_delta
assert analysis.is_2p_p_distance_c1p_outbound_line
assert analysis.is_2p_o3p_distance_c1p_outbound_line
assert analysis.is_2p
for residue_2_p_atom in [atom((41.856, 17.581, 31.191)), None]:
analysis = rna_sugar_pucker_analysis.evaluate(
params=params,
residue_1_deoxy_ribo_atom_dict=atom_dict([(42.736, 12.998, 31.661),
(42.922, 16.529, 31.706),
(42.428, 15.271, 31.984),
(43.132, 14.710, 33.185),
(42.545, 15.146, 34.511)
]),
residue_1_c1p_outbound_atom=atom((41.433, 12.332, 31.466)),
residue_2_p_atom=residue_2_p_atom)
assert not analysis.is_epsilon_outlier
assert not analysis.is_2p_delta
if (residue_2_p_atom is not None):
assert not analysis.is_2p_p_distance_c1p_outbound_line
else:
assert analysis.is_2p_p_distance_c1p_outbound_line is None
assert not analysis.is_2p_o3p_distance_c1p_outbound_line
assert not analysis.is_2p
#
params.epsilon_range_min = None
params.epsilon_range_max = None
params.delta_range_2p_min = None
params.delta_range_2p_max = None
params.delta_range_3p_min = None
params.delta_range_3p_max = None
params.p_distance_c1p_outbound_line_2p_max = None
params.o3p_distance_c1p_outbound_line_2p_max = None
analysis = rna_sugar_pucker_analysis.evaluate(
params=params,
residue_1_deoxy_ribo_atom_dict=atom_dict([(50.473, 9.942, 36.204),
(48.952, 10.236, 33.644),
(49.474, 11.213, 34.497),
(50.978, 11.174, 34.278),
(51.710, 12.501, 34.095)]),
residue_1_c1p_outbound_atom=atom((50.926, 10.084, 37.569)),
residue_2_p_atom=atom((48.114, 10.641, 32.347)))
assert approx_equal(analysis.epsilon, 250.715932662)
assert approx_equal(analysis.delta, 133.811229901)
assert approx_equal(analysis.p_distance_c1p_outbound_line, 1.52374220064)
assert analysis.is_epsilon_outlier is None
assert analysis.is_2p_delta is None
assert analysis.is_2p_p_distance_c1p_outbound_line is None
assert analysis.is_2p_o3p_distance_c1p_outbound_line is None
assert analysis.is_2p is None
#
print "OK"
def exercise(args):
assert len(args) == 0
params = rna_sugar_pucker_analysis.master_phil.fetch().extract()
for i_pass,some_x in enumerate([31.101, 21.101]):
analysis = rna_sugar_pucker_analysis.evaluate(
params=params,
residue_1_deoxy_ribo_atom_dict=atom_dict([
(some_x,30.048,33.325), (22.184,28.704,36.539), (21.527,28.782,35.281),
(22.379,28.287,34.119), (22.676,26.795,34.032)]),
residue_1_c1p_outbound_atom=atom((19.628,30.157,32.953)),
residue_2_p_atom=atom((33.058,33.903,32.613)))
assert analysis.epsilon is None
if (i_pass == 0):
assert analysis.delta is None
else:
assert approx_equal(analysis.delta, 69.6819176834)
assert analysis.p_distance_c1p_outbound_line is None
assert analysis.is_epsilon_outlier is None
if (i_pass == 0):
assert analysis.is_2p_delta is None
assert analysis.is_2p_p_distance_c1p_outbound_line is None
assert analysis.is_2p_o3p_distance_c1p_outbound_line is None
assert analysis.is_2p is None
else:
assert not analysis.is_2p_delta
assert analysis.is_2p_p_distance_c1p_outbound_line is None
assert not analysis.is_2p_o3p_distance_c1p_outbound_line
assert not analysis.is_2p
analysis = rna_sugar_pucker_analysis.evaluate(
params=params,
residue_1_deoxy_ribo_atom_dict=atom_dict([
(50.473,9.942,36.204), (48.952,10.236,33.644), (49.474,11.213,34.497),
(50.978,11.174,34.278), (51.710,12.501,34.095)]),
residue_1_c1p_outbound_atom=atom((50.926,10.084,37.569)),
residue_2_p_atom=atom((48.114,10.641,32.347)))
assert approx_equal(analysis.epsilon, 250.715932662)
assert approx_equal(analysis.delta, 133.811229901)
assert approx_equal(analysis.p_distance_c1p_outbound_line, 1.52374220064)
assert approx_equal(analysis.o3p_distance_c1p_outbound_line, 0.860583842822)
assert not analysis.is_epsilon_outlier
assert analysis.is_2p_delta
assert analysis.is_2p_p_distance_c1p_outbound_line
assert analysis.is_2p_o3p_distance_c1p_outbound_line
assert analysis.is_2p
for residue_2_p_atom in [atom((41.856,17.581,31.191)), None]:
analysis = rna_sugar_pucker_analysis.evaluate(
params=params,
residue_1_deoxy_ribo_atom_dict=atom_dict([
(42.736,12.998,31.661), (42.922,16.529,31.706), (42.428,15.271,31.984),
(43.132,14.710,33.185), (42.545,15.146,34.511)]),
residue_1_c1p_outbound_atom=atom((41.433,12.332,31.466)),
residue_2_p_atom=residue_2_p_atom)
assert not analysis.is_epsilon_outlier
assert not analysis.is_2p_delta
if (residue_2_p_atom is not None):
assert not analysis.is_2p_p_distance_c1p_outbound_line
else:
assert analysis.is_2p_p_distance_c1p_outbound_line is None
assert not analysis.is_2p_o3p_distance_c1p_outbound_line
assert not analysis.is_2p
#
params.epsilon_range_min = None
params.epsilon_range_max = None
params.delta_range_2p_min = None
params.delta_range_2p_max = None
params.delta_range_3p_min = None
params.delta_range_3p_max = None
params.p_distance_c1p_outbound_line_2p_max = None
params.o3p_distance_c1p_outbound_line_2p_max = None
analysis = rna_sugar_pucker_analysis.evaluate(
params=params,
residue_1_deoxy_ribo_atom_dict=atom_dict([
(50.473,9.942,36.204), (48.952,10.236,33.644), (49.474,11.213,34.497),
(50.978,11.174,34.278), (51.710,12.501,34.095)]),
residue_1_c1p_outbound_atom=atom((50.926,10.084,37.569)),
residue_2_p_atom=atom((48.114,10.641,32.347)))
assert approx_equal(analysis.epsilon, 250.715932662)
assert approx_equal(analysis.delta, 133.811229901)
assert approx_equal(analysis.p_distance_c1p_outbound_line, 1.52374220064)
assert analysis.is_epsilon_outlier is None
assert analysis.is_2p_delta is None
assert analysis.is_2p_p_distance_c1p_outbound_line is None
assert analysis.is_2p_o3p_distance_c1p_outbound_line is None
assert analysis.is_2p is None
#
print "OK"
