def run(args, command_name="iotbx.pdb.superpose_centers_of_mass"):
if len(args) == 0:
args = ["--help"]
command_line = (
option_parser(usage="%s [options] [reference_file] [other_file] [parameter_file]" % command_name)
.enable_show_defaults()
.enable_symmetry_comprehensive()
).process(args=args)
if command_line.expert_level is not None:
master_params.show(expert_level=command_line.expert_level, attributes_level=command_line.attributes_level)
sys.exit(0)
#
# Loop over command-line arguments.
#
parameter_interpreter = master_params.command_line_argument_interpreter()
parsed_params = []
pdb_file_names = []
command_line_params = []
for arg in command_line.args:
arg_is_processed = False
if os.path.isfile(arg):
params = None
try:
params = iotbx.phil.parse(file_name=arg)
except KeyboardInterrupt:
raise
except RuntimeError:
pass
else:
if len(params.objects) == 0:
params = None
if params is not None:
parsed_params.append(params)
arg_is_processed = True
elif pdb.is_pdb_file(file_name=arg):
pdb_file_names.append(arg)
arg_is_processed = True
if not arg_is_processed:
try:
params = parameter_interpreter.process(arg=arg)
except Sorry, e:
if not os.path.isfile(arg):
raise
raise Sorry("Unknown file format: %s" % arg)
else:
command_line_params.append(params)
def run(args, command_name="iotbx.pdb.superpose_centers_of_mass"):
if (len(args) == 0): args = ["--help"]
command_line = (option_parser(
usage=
"%s [options] [reference_file] [other_file] [parameter_file]" %
command_name)
.enable_show_defaults()
.enable_symmetry_comprehensive()
).process(args=args)
if (command_line.expert_level is not None):
master_params.show(
expert_level=command_line.expert_level,
attributes_level=command_line.attributes_level)
sys.exit(0)
#
# Loop over command-line arguments.
#
parameter_interpreter = master_params.command_line_argument_interpreter()
parsed_params = []
pdb_file_names = []
command_line_params = []
for arg in command_line.args:
arg_is_processed = False
if (os.path.isfile(arg)):
params = None
try: params = iotbx.phil.parse(file_name=arg)
except KeyboardInterrupt: raise
except RuntimeError: pass
else:
if (len(params.objects) == 0):
params = None
if (params is not None):
parsed_params.append(params)
arg_is_processed = True
elif (pdb.is_pdb_file(file_name=arg)):
pdb_file_names.append(arg)
arg_is_processed = True
if (not arg_is_processed):
try:
params = parameter_interpreter.process(arg=arg)
except Sorry, e:
if (not os.path.isfile(arg)): raise
raise Sorry("Unknown file format: %s" % arg)
else:
command_line_params.append(params)
def exercise_format_fasta(regression_pdb, coverage=0.1):
import random
looking_for = ["1ee3_stripped.pdb", "jcm.pdb", "pdb1zff.ent"]
for node in os.listdir(regression_pdb):
if (not (node.endswith(".pdb") or node.endswith(".ent"))): continue
if (node not in looking_for and random.random() > coverage):
continue
file_name = op.join(regression_pdb, node)
assert pdb.is_pdb_file(file_name=file_name)
pdb_inp = pdb.input(file_name=file_name)
hierarchy = pdb_inp.construct_hierarchy()
fasta = []
is_protein = []
is_na = []
for model in hierarchy.models():
for chain in model.chains():
for conformer in chain.conformers():
fasta.append(conformer.format_fasta())
is_protein.append(conformer.is_protein())
is_na.append(conformer.is_na())
if (node == "pdb1zff.ent"):
assert fasta == [
['> chain " A" conformer ""', "CCGAATTCGG"]]
assert is_protein == [False] and is_na == [True]
looking_for.remove(node)
assert (hierarchy.models()[0].chains()[0].is_na())
elif (node == "1ee3_stripped.pdb"):
assert fasta == [
['> chain " P" conformer "A"', 'IMEHTV'],
['> chain " P" conformer "B"', 'IMEHTV'],
None,
None]
assert is_protein == [True, True, False, False]
assert is_na == [False, False, False, False]
looking_for.remove(node)
elif (node == "jcm.pdb"):
assert fasta == [
['> chain " A" conformer ""',
'MSSIFINREYLLPDYIPDELPHREDQIRKIASILAPLYREEKPNNIFIY'
'GLTGTGKTAVVKFVLSKLHKKFLGKFKHVY',
'INTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQV'
'VIVLDEIDAFVKKYNDDILYKLSRINSISF',
'IGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAFK'
'PGVLPDNVIKLCAALAAREHGDARRALDLL',
'RVSGEIAERMKDTKVKEEYVYMAKEEIERDRVRDIILTLPFHSKLVLMA'
'VVSISSEENVVSTTGAVYETYLNICKKLGV',
'EAVTQRRVSDIINELDMVGILTVVNRGRYGKTKEIGLAVDKNIIVRSLIESDS'],
['> chain " B" conformer ""',
'KNPKVFIDPLSVFKEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTG'
'TGKTFVSKYIFNEIEEVKKEDEEYKDVKQA',
'YVNCREVGGTPQAVLSSLAGKLAGFSVPKHGINLGEYIDKIKNGTRNIR'
'AIIYLDEVDTLVKRRGGDIVLYQLLRSDAN',
'ISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYG'
'LIKGTYDDEILSYIAAISAKEHGDARKAVN',
'LLFRAAQLASGGGIIRKEHVDKAIVDYEQERLIEAVKALPFHYKLALRS'
'LIESEDVMSAHKMYTDLCNKFKQKPLSYRR',
'FSDIISELDMFGIVKIRIINRGRAGGVKKYALVEDKEKVLRALNET'],
['> chain " C" conformer ""',
'TGTAAATTTCCTACGTTTCATCTGAAAATCTAGAGATTTTCAGATGAAACGTAGGAAATTTACATC'],
None]
assert is_protein == [True, True, False, False]
assert is_na == [False, False, True, False]
looking_for.remove(node)
if (len(looking_for) != 0):
print "WARNING: exercise_format_fasta(): some input files missing:", \
looking_for
def run(args, command_name="iotbx.pdb.superpose_centers_of_mass"):
if (len(args) == 0): args = ["--help"]
command_line = (option_parser(
usage="%s [options] [reference_file] [other_file] [parameter_file]" %
command_name).enable_show_defaults().enable_symmetry_comprehensive()
).process(args=args)
if (command_line.expert_level is not None):
master_params.show(expert_level=command_line.expert_level,
attributes_level=command_line.attributes_level)
sys.exit(0)
#
# Loop over command-line arguments.
#
parameter_interpreter = master_params.command_line_argument_interpreter()
parsed_params = []
pdb_file_names = []
command_line_params = []
for arg in command_line.args:
arg_is_processed = False
if (os.path.isfile(arg)):
params = None
try:
params = iotbx.phil.parse(file_name=arg)
except KeyboardInterrupt:
raise
except RuntimeError:
pass
else:
if (len(params.objects) == 0):
params = None
if (params is not None):
parsed_params.append(params)
arg_is_processed = True
elif (pdb.is_pdb_file(file_name=arg)):
pdb_file_names.append(arg)
arg_is_processed = True
if (not arg_is_processed):
try:
params = parameter_interpreter.process(arg=arg)
except Sorry as e:
if (not os.path.isfile(arg)): raise
raise Sorry("Unknown file format: %s" % arg)
else:
command_line_params.append(params)
#
# Consolidation of inputs, resulting in effective phil_params.
#
phil_params = master_params.fetch(sources=parsed_params +
command_line_params)
params = phil_params.extract()
for param_group in [params.reference, params.other, params.output]:
if (param_group.file_name is None and len(pdb_file_names) > 0):
param_group.file_name = pdb_file_names[0]
pdb_file_names = pdb_file_names[1:]
if (len(pdb_file_names) > 0):
raise Sorry("Too many PDB file names: %s" %
", ".join([show_string(s) for s in pdb_file_names]))
if (params.output.file_name is None
and params.other.file_name is not None):
name = os.path.basename(params.other.file_name)
if (name.lower().endswith(".pdb")): name = name[:-4]
name += "_superposed.pdb"
params.output.file_name = name
if (params.crystal_symmetry.unit_cell is None):
params.crystal_symmetry.unit_cell = \
command_line.symmetry.unit_cell()
if (params.crystal_symmetry.space_group is None):
params.crystal_symmetry.space_group = \
command_line.symmetry.space_group_info()
phil_params = master_params.format(python_object=params)
phil_params.show()
print("#phil __OFF__")
#
# Final checks.
#
if (params.reference.file_name is None):
raise Sorry("Required file name is missing: reference.file_name")
if (params.other.file_name is None):
raise Sorry("Required file name is missing: other.file_name")
if (params.output.file_name is None):
raise Sorry("Required file name is missing: output.file_name")
#
# Processing of input PDB files.
#
pdb_objs = []
sites_carts = []
centers_of_mass = []
for param_group in [params.reference, params.other]:
pdb_obj = pdb.hierarchy.input(file_name=param_group.file_name)
pdb_obj.atoms = pdb_obj.hierarchy.atoms()
pdb_objs.append(pdb_obj)
sites_carts.append(pdb_obj.atoms.extract_xyz())
sites_sel = sites_carts[-1]
if (param_group.atom_selection is not None):
sel = pdb_obj.hierarchy.atom_selection_cache().selection(
param_group.atom_selection)
sites_sel = sites_sel.select(sel)
print("Number of selected sites:", sites_sel.size())
centers_of_mass.append(sites_sel.mean())
#
# Consolidation of crystal symmetries.
#
crystal_symmetry = command_line.symmetry
for pdb_obj in pdb_objs:
crystal_symmetry_from_pdb = pdb_obj.input.crystal_symmetry()
if (crystal_symmetry_from_pdb is not None):
crystal_symmetry = crystal_symmetry.join_symmetry(
other_symmetry=crystal_symmetry_from_pdb, force=False)
if (crystal_symmetry.unit_cell() is None):
raise Sorry(
"Unknown unit cell parameters."
"\n Use --unit_cell or --symmetry to supply unit cell parameters."
)
if (crystal_symmetry.space_group_info() is None):
raise Sorry(
"Unknown space group symmetry."
"\n Use --space_group or --symmetry to supply symmetry information."
)
crystal_symmetry.show_summary()
#
# Obtain transformation to reference setting.
# To ensure all allowed origin shifts are parallel to the basis vectors.
#
cb_op_to_ref = crystal_symmetry.change_of_basis_op_to_reference_setting()
sym_ref = crystal_symmetry.change_basis(cb_op=cb_op_to_ref)
#
# Obtain allowed origin shifts.
# This is the most convenient interface. Essentially we just need
# sgtbx.structure_seminvariants.
#
match_symmetry = euclidean_model_matching.euclidean_match_symmetry(
space_group_info=sym_ref.space_group_info(),
use_k2l=False,
use_l2n=False)
#
# Compute the symmetry operation which maps the center of mass of
# "other" closest to the center of mass of "reference."
#
centers_frac = [
sym_ref.unit_cell().fractionalize(cb_op_to_ref.c() * center_cart)
for center_cart in centers_of_mass
]
dist_info = sgtbx.min_sym_equiv_distance_info(
sym_ref.special_position_settings().sym_equiv_sites(centers_frac[0]),
centers_frac[1], match_symmetry.continuous_shift_flags)
sym_op = cb_op_to_ref.inverse().apply(dist_info.sym_op())
print("Rotation in fractional space:", sym_op.r().as_xyz())
sym_op = sym_op.as_rational().as_float() \
+ matrix.col(dist_info.continuous_shifts())
print("Translation in fractional space: (%s)" %
(", ".join(["%.6g" % t for t in sym_op.t])))
#
centers_frac = [
sym_ref.unit_cell().fractionalize(center_cart)
for center_cart in centers_of_mass
]
sym_center_frac = sym_op * centers_frac[1]
sym_center_cart = crystal_symmetry.unit_cell().orthogonalize(
sym_center_frac)
print("Centers of mass:")
print(" Reference: (%s)" %
", ".join(["%8.2f" % v for v in centers_of_mass[0]]))
print(" Original other: (%s)" %
", ".join(["%8.2f" % v for v in centers_of_mass[1]]))
print(" Symmetry related other: (%s)" %
", ".join(["%8.2f" % v for v in sym_center_cart]))
print("Cartesian distance between centers of mass: %.4f" %
dist_info.dist())
#
# Internal consistency check (in input setting).
#
assert approx_equal(
crystal_symmetry.unit_cell().distance(centers_frac[0],
sym_center_frac),
dist_info.dist())
#
# Transform atomic coordinates of "other."
#
sites_frac_other = crystal_symmetry.unit_cell().fractionalize(
sites_cart=sites_carts[1])
sites_frac_other_superposed = sym_op * sites_frac_other
sites_cart_other_superposed = crystal_symmetry.unit_cell().orthogonalize(
sites_frac=sites_frac_other_superposed)
#
# Replace original coordinates with transformed coordinates.
#
pdb_objs[1].atoms.set_xyz(new_xyz=sites_cart_other_superposed)
#
# Write (selected) transformed coordinates.
#
pdb_hierarchy = pdb_objs[1].hierarchy
if (params.output.atom_selection is not None):
sel = pdb_hierarchy.atom_selection_cache().selection(
params.output.atom_selection)
pdb_hierarchy = pdb_hierarchy.select(atom_selection=sel)
pdb_hierarchy.write_pdb_file(file_name=params.output.file_name,
crystal_symmetry=crystal_symmetry,
append_end=True,
atoms_reset_serial_first_value=1)
def exercise_format_fasta(regression_pdb, coverage=0.1):
import random
looking_for = ["1ee3_stripped.pdb", "jcm.pdb", "pdb1zff.ent"]
for node in os.listdir(regression_pdb):
if not (node.endswith(".pdb") or node.endswith(".ent")):
continue
if node not in looking_for and random.random() > coverage:
continue
file_name = op.join(regression_pdb, node)
assert pdb.is_pdb_file(file_name=file_name)
pdb_inp = pdb.input(file_name=file_name)
hierarchy = pdb_inp.construct_hierarchy()
fasta = []
is_protein = []
is_na = []
for model in hierarchy.models():
for chain in model.chains():
for conformer in chain.conformers():
fasta.append(conformer.format_fasta())
is_protein.append(conformer.is_protein())
is_na.append(conformer.is_na())
if node == "pdb1zff.ent":
assert fasta == [['> chain " A" conformer ""', "CCGAATTCGG"]]
assert is_protein == [False] and is_na == [True]
looking_for.remove(node)
assert hierarchy.models()[0].chains()[0].is_na()
elif node == "1ee3_stripped.pdb":
assert fasta == [
['> chain " P" conformer "A"', "IMEHTV"],
['> chain " P" conformer "B"', "IMEHTV"],
None,
None,
]
assert is_protein == [True, True, False, False]
assert is_na == [False, False, False, False]
looking_for.remove(node)
elif node == "jcm.pdb":
assert fasta == [
[
'> chain " A" conformer ""',
"MSSIFINREYLLPDYIPDELPHREDQIRKIASILAPLYREEKPNNIFIY" "GLTGTGKTAVVKFVLSKLHKKFLGKFKHVY",
"INTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQV" "VIVLDEIDAFVKKYNDDILYKLSRINSISF",
"IGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAFK" "PGVLPDNVIKLCAALAAREHGDARRALDLL",
"RVSGEIAERMKDTKVKEEYVYMAKEEIERDRVRDIILTLPFHSKLVLMA" "VVSISSEENVVSTTGAVYETYLNICKKLGV",
"EAVTQRRVSDIINELDMVGILTVVNRGRYGKTKEIGLAVDKNIIVRSLIESDS",
],
[
'> chain " B" conformer ""',
"KNPKVFIDPLSVFKEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTG" "TGKTFVSKYIFNEIEEVKKEDEEYKDVKQA",
"YVNCREVGGTPQAVLSSLAGKLAGFSVPKHGINLGEYIDKIKNGTRNIR" "AIIYLDEVDTLVKRRGGDIVLYQLLRSDAN",
"ISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYG" "LIKGTYDDEILSYIAAISAKEHGDARKAVN",
"LLFRAAQLASGGGIIRKEHVDKAIVDYEQERLIEAVKALPFHYKLALRS" "LIESEDVMSAHKMYTDLCNKFKQKPLSYRR",
"FSDIISELDMFGIVKIRIINRGRAGGVKKYALVEDKEKVLRALNET",
],
['> chain " C" conformer ""', "TGTAAATTTCCTACGTTTCATCTGAAAATCTAGAGATTTTCAGATGAAACGTAGGAAATTTACATC"],
None,
]
assert is_protein == [True, True, False, False]
assert is_na == [False, False, True, False]
looking_for.remove(node)
if len(looking_for) != 0:
print "WARNING: exercise_format_fasta(): some input files missing:", looking_for
