def _print_seqalign(self, alignment, quiet=False):
"""Print a sequence alignment details."""
matches = alignment.matches()
self.log("Alignment details:")
self.log("\tmatches after alignment: %s" %
(matches.count("|") + matches.count("*")))
self.log("\tsequence alignment:")
# Since this prints directly, check if quiet.
if not (quiet or self._quiet):
# Change the labels to target.desc
alignment.pretty_print(matches=matches,
block_size=50,
n_block=1,
top_name="moving",
bottom_name="fixed")
def _print_seqalign(self, alignment, quiet=False):
"""Print a sequence alignment details."""
matches = alignment.matches()
self.log("Alignment details:")
self.log("\tmatches after alignment: %s"%(matches.count("|") + matches.count("*")))
self.log("\tsequence alignment:")
# Since this prints directly, check if quiet.
if not (quiet or self._quiet):
# Change the labels to target.desc
alignment.pretty_print(
matches = matches,
block_size = 50,
n_block = 1,
top_name = "moving",
bottom_name = "fixed")
def align_chains_rigid(mov_chain, ref_chain):
"""Takes two chains and aligns them - return rt_mx"""
mov_seq, mov_sites, mov_flags = extract_sites_for_alignment(mov_chain)
ref_seq, ref_sites, ref_flags = extract_sites_for_alignment(ref_chain)
align_obj = mmtbx.alignment.align(
seq_a=ref_seq,
seq_b=mov_seq,
gap_opening_penalty = 20,
gap_extension_penalty = 2,
similarity_function = 'blosum50',
style = 'local')
# Extract the alignment
alignment = align_obj.extract_alignment()
# List of matches - '|' for exact match, '*' for good match
matches = alignment.matches()
equal = matches.count("|")
similar = matches.count("*")
total = len(alignment.a) - alignment.a.count("-")
alignment.pretty_print(
matches=matches,
block_size=50,
n_block=1,
top_name="fixed",
bottom_name="moving")
# Create list of selected sites
ref_sites_sel = flex.vec3_double()
mov_sites_sel = flex.vec3_double()
for ia,ib,m in zip(alignment.i_seqs_a, alignment.i_seqs_b, matches):
if (m not in ["|", "*"]): continue
# Check that the sites are flagged to be used
if (ref_flags[ia] and mov_flags[ib]):
# Append sites to list to align
ref_sites_sel.append(ref_sites[ia])
mov_sites_sel.append(mov_sites[ib])
if (ref_sites_sel.size() == 0):
raise Exception("No matching C-alpha atoms.")
lsq_rt = superpose.least_squares_fit(reference_sites=ref_sites_sel, other_sites=mov_sites_sel).rt()
return lsq_rt, mov_sites_sel, ref_sites_sel
def run(args, command_name="mmtbx.super"):
if (len(args) == 0):
print "usage: %s fixed.pdb moving.pdb [parameter=value ...]" % command_name
return
print "#"
print "# ", command_name
print "#"
print "# A lightweight sequence-based structure superposition tool."
print "#"
print "#"
phil_objects = []
argument_interpreter = master_params.command_line_argument_interpreter(
home_scope="super")
fixed_pdb_file_name = None
moving_pdb_file_name = None
for arg in args:
if (os.path.isfile(arg)):
if (fixed_pdb_file_name is None): fixed_pdb_file_name = arg
elif (moving_pdb_file_name is None): moving_pdb_file_name = arg
else: raise Sorry("Too many file names.")
else:
try: command_line_params = argument_interpreter.process(arg=arg)
except KeyboardInterrupt: raise
except Exception: raise Sorry("Unknown file or keyword: %s" % arg)
else: phil_objects.append(command_line_params)
working_params = master_params.fetch(sources=phil_objects)
params = working_params.extract()
def raise_missing(what):
raise Sorry("""\
Missing file name for %(what)s structure:
Please add
%(what)s=file_name
to the command line to specify the %(what)s structure.""" % vars())
if (fixed_pdb_file_name is None):
if (params.super.fixed is None): raise_missing("fixed")
else:
params.super.fixed = fixed_pdb_file_name
if (moving_pdb_file_name is None):
if (params.super.moving is None): raise_missing("moving")
else:
params.super.moving = moving_pdb_file_name
print "#Parameters used:"
print "#phil __ON__"
print
working_params = master_params.format(python_object=params)
working_params.show()
print
print "#phil __OFF__"
print
print "Reading fixed structure:", params.super.fixed
fixed_pdb = iotbx.pdb.input(file_name=params.super.fixed)
print
print "Reading moving structure:", params.super.moving
moving_pdb = iotbx.pdb.input(file_name=params.super.moving)
print
fixed_seq, fixed_sites, fixed_site_flags = extract_sequence_and_sites(
pdb_input=fixed_pdb)
moving_seq, moving_sites, moving_site_flags = extract_sequence_and_sites(
pdb_input=moving_pdb)
print "Computing sequence alignment..."
align_obj = mmtbx.alignment.align(
seq_a=fixed_seq,
seq_b=moving_seq,
gap_opening_penalty=params.super.gap_opening_penalty,
gap_extension_penalty=params.super.gap_extension_penalty,
similarity_function=params.super.similarity_matrix,
style=params.super.alignment_style)
print "done."
print
alignment = align_obj.extract_alignment()
matches = alignment.matches()
equal = matches.count("|")
similar = matches.count("*")
total = len(alignment.a) - alignment.a.count("-")
alignment.pretty_print(
matches=matches,
block_size=50,
n_block=1,
top_name="fixed",
bottom_name="moving",
comment="""\
The alignment used in the superposition is shown below.
The sequence identity (fraction of | symbols) is %4.1f%%
of the aligned length of the fixed molecule sequence.
The sequence similarity (fraction of | and * symbols) is %4.1f%%
of the aligned length of the fixed molecule sequence.
""" % (100.*equal/max(1,total), 100.*(equal+similar)/max(1,total)))
fixed_sites_sel = flex.vec3_double()
moving_sites_sel = flex.vec3_double()
for ia,ib,m in zip(alignment.i_seqs_a, alignment.i_seqs_b, matches):
if (m not in ["|", "*"]): continue
if (fixed_site_flags[ia] and moving_site_flags[ib]):
fixed_sites_sel.append(fixed_sites[ia])
moving_sites_sel.append(moving_sites[ib])
print "Performing least-squares superposition of C-alpha atom pairs:"
print " Number of C-alpha atoms pairs in matching residues"
print " indicated by | or * above:", fixed_sites_sel.size()
if (fixed_sites_sel.size() == 0):
raise Sorry("No matching C-alpha atoms.")
lsq_fit = superpose.least_squares_fit(
reference_sites=fixed_sites_sel,
other_sites=moving_sites_sel)
rmsd = fixed_sites_sel.rms_difference(lsq_fit.other_sites_best_fit())
print " RMSD between the aligned C-alpha atoms: %.3f" % rmsd
print
print "Writing moved pdb to file: %s" % params.super.moved
pdb_hierarchy = moving_pdb.construct_hierarchy()
for atom in pdb_hierarchy.atoms():
atom.xyz = lsq_fit.r * matrix.col(atom.xyz) + lsq_fit.t
pdb_hierarchy.write_pdb_file(file_name=params.super.moved, append_end=True)
print
def run(args, command_name="mmtbx.super"):
if len(args) == 0:
print "usage: %s fixed.pdb moving.pdb [parameter=value ...]" % command_name
return
print "#"
print "# ", command_name
print "#"
print "# A lightweight sequence-based structure superposition tool."
print "#"
print "#"
phil_objects = []
argument_interpreter = master_params.command_line_argument_interpreter(home_scope="super")
fixed_pdb_file_name = None
moving_pdb_file_name = None
for arg in args:
if os.path.isfile(arg):
if fixed_pdb_file_name is None:
fixed_pdb_file_name = arg
elif moving_pdb_file_name is None:
moving_pdb_file_name = arg
else:
raise Sorry("Too many file names.")
else:
try:
command_line_params = argument_interpreter.process(arg=arg)
except KeyboardInterrupt:
raise
except Exception:
raise Sorry("Unknown file or keyword: %s" % arg)
else:
phil_objects.append(command_line_params)
working_params = master_params.fetch(sources=phil_objects)
params = working_params.extract()
def raise_missing(what):
raise Sorry(
"""\
Missing file name for %(what)s structure:
Please add
%(what)s=file_name
to the command line to specify the %(what)s structure."""
% vars()
)
if fixed_pdb_file_name is None:
if params.super.fixed is None:
raise_missing("fixed")
else:
params.super.fixed = fixed_pdb_file_name
if moving_pdb_file_name is None:
if params.super.moving is None:
raise_missing("moving")
else:
params.super.moving = moving_pdb_file_name
print "#Parameters used:"
print "#phil __ON__"
print
working_params = master_params.format(python_object=params)
working_params.show()
print
print "#phil __OFF__"
print
print "Reading fixed structure:", params.super.fixed
fixed_pdb = iotbx.pdb.input(file_name=params.super.fixed)
print
print "Reading moving structure:", params.super.moving
moving_pdb = iotbx.pdb.input(file_name=params.super.moving)
print
fixed_seq, fixed_sites, fixed_site_flags = extract_sequence_and_sites(pdb_input=fixed_pdb)
moving_seq, moving_sites, moving_site_flags = extract_sequence_and_sites(pdb_input=moving_pdb)
print "Computing sequence alignment..."
align_obj = mmtbx.alignment.align(
seq_a=fixed_seq,
seq_b=moving_seq,
gap_opening_penalty=params.super.gap_opening_penalty,
gap_extension_penalty=params.super.gap_extension_penalty,
similarity_function=params.super.similarity_matrix,
style=params.super.alignment_style,
)
print "done."
print
alignment = align_obj.extract_alignment()
matches = alignment.matches()
equal = matches.count("|")
similar = matches.count("*")
total = len(alignment.a) - alignment.a.count("-")
alignment.pretty_print(
matches=matches,
block_size=50,
n_block=1,
top_name="fixed",
bottom_name="moving",
comment="""\
The alignment used in the superposition is shown below.
The sequence identity (fraction of | symbols) is %4.1f%%
of the aligned length of the fixed molecule sequence.
The sequence similarity (fraction of | and * symbols) is %4.1f%%
of the aligned length of the fixed molecule sequence.
"""
% (100.0 * equal / max(1, total), 100.0 * (equal + similar) / max(1, total)),
)
fixed_sites_sel = flex.vec3_double()
moving_sites_sel = flex.vec3_double()
for ia, ib, m in zip(alignment.i_seqs_a, alignment.i_seqs_b, matches):
if m not in ["|", "*"]:
continue
if fixed_site_flags[ia] and moving_site_flags[ib]:
fixed_sites_sel.append(fixed_sites[ia])
moving_sites_sel.append(moving_sites[ib])
print "Performing least-squares superposition of C-alpha atom pairs:"
print " Number of C-alpha atoms pairs in matching residues"
print " indicated by | or * above:", fixed_sites_sel.size()
if fixed_sites_sel.size() == 0:
raise Sorry("No matching C-alpha atoms.")
lsq_fit = superpose.least_squares_fit(reference_sites=fixed_sites_sel, other_sites=moving_sites_sel)
rmsd = fixed_sites_sel.rms_difference(lsq_fit.other_sites_best_fit())
print " RMSD between the aligned C-alpha atoms: %.3f" % rmsd
print
print "Writing moved pdb to file: %s" % params.super.moved
pdb_hierarchy = moving_pdb.construct_hierarchy()
for atom in pdb_hierarchy.atoms():
atom.xyz = lsq_fit.r * matrix.col(atom.xyz) + lsq_fit.t
pdb_hierarchy.write_pdb_file(file_name=params.super.moved, append_end=True)
print
