def find_sec_str(self, pdb_hierarchy):
if self.params.secondary_structure.protein.search_method == "ksdssp":
pdb_str = pdb_hierarchy.as_pdb_string()
print >> self.log, " running ksdssp..."
(records, stderr) = run_ksdssp_direct(pdb_str)
return iotbx.pdb.secondary_structure.annotation.from_records(
records=records,
log=self.log)
elif self.params.secondary_structure.protein.search_method == "mmtbx_dssp":
from mmtbx.secondary_structure import dssp
print >> self.log, " running mmtbx.dssp..."
return dssp.dssp(
pdb_hierarchy=pdb_hierarchy,
pdb_atoms=self.pdb_atoms,
out=null_out()).get_annotation()
elif self.params.secondary_structure.protein.search_method == "from_ca":
from mmtbx.secondary_structure import find_ss_from_ca
print >> self.log, " running find_ss_from_ca..."
fss = find_ss_from_ca.find_secondary_structure(
hierarchy=pdb_hierarchy,
out=null_out())
return fss.get_annotation()
elif self.params.secondary_structure.protein.search_method == "cablam":
from mmtbx.validation import cablam
print >> self.log, " running cablam..."
cablam_results = cablam.cablamalyze(
pdb_hierarchy = pdb_hierarchy,
outliers_only=False,
out=null_out(),
quiet=False)
return cablam_results.as_secondary_structure()
else:
print >> self.log, " WARNING: Unknown search method for SS. No SS found."
return iotbx.pdb.secondary_structure.annotation.from_records()
def run(args, out=sys.stdout):
from mmtbx.secondary_structure import dssp
from iotbx.file_reader import any_file
import iotbx.phil
cmdline = iotbx.phil.process_command_line_with_files(
args=args, master_phil=dssp.master_phil, pdb_file_def="file_name")
params = cmdline.work.extract()
if (params.file_name is None):
raise Sorry("Please specify a PDB file.")
f = any_file(params.file_name, force_type="pdb")
pdb_hierarchy = f.file_object.hierarchy
xray_structure = f.file_object.xray_structure_simple()
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
t1 = time.time()
SS = dssp.dssp(pdb_hierarchy=pdb_hierarchy,
pdb_atoms=pdb_atoms,
xray_structure=xray_structure,
params=params,
out=out,
log=sys.stderr)
if (params.atom_output):
out.write(pdb_hierarchy.as_pdb_string(crystal_symmetry=xray_structure))
t2 = time.time()
if (params.verbosity >= 1):
print >> sys.stderr, "total DSSP runtime: %.3fs" % (t2 - t1)
return SS
def run (args, out=sys.stdout) :
from mmtbx.secondary_structure import dssp
from iotbx.file_reader import any_file
import iotbx.phil
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=dssp.master_phil,
pdb_file_def="file_name")
params = cmdline.work.extract()
if (params.file_name is None) :
raise Sorry("Please specify a PDB file.")
f = any_file(params.file_name, force_type="pdb")
pdb_hierarchy = f.file_object.hierarchy
xray_structure = f.file_object.xray_structure_simple()
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
t1 = time.time()
SS = dssp.dssp(
pdb_hierarchy=pdb_hierarchy,
pdb_atoms=pdb_atoms,
xray_structure=xray_structure,
params=params,
out=out,
log=sys.stderr)
if (params.atom_output) :
out.write(pdb_hierarchy.as_pdb_string(crystal_symmetry=xray_structure))
t2 = time.time()
if (params.verbosity >= 1) :
print >> sys.stderr, "total DSSP runtime: %.3fs" % (t2-t1)
return SS
def find_sec_str(self, pdb_hierarchy):
if (pdb_hierarchy.atoms_size() > 99999
and self.params.secondary_structure.protein.search_method
== "ksdssp"):
print("Warning!!! ksdssp method is not applicable for" + \
"structures with more than 99999 atoms!\nSwitching to from_ca.", file=self.log)
self.params.secondary_structure.protein.search_method = "from_ca"
if self.params.secondary_structure.protein.search_method == "ksdssp":
pdb_str = pdb_hierarchy.as_pdb_string()
print(" running ksdssp...", file=self.log)
(records, stderr) = run_ksdssp_direct(pdb_str)
return iotbx.pdb.secondary_structure.annotation.from_records(
records=records, log=self.log)
elif self.params.secondary_structure.protein.search_method == "mmtbx_dssp":
from mmtbx.secondary_structure import dssp
print(" running mmtbx.dssp...", file=self.log)
return dssp.dssp(pdb_hierarchy=pdb_hierarchy,
pdb_atoms=self.pdb_atoms,
out=null_out()).get_annotation()
elif self.params.secondary_structure.protein.search_method == "from_ca":
from mmtbx.secondary_structure import find_ss_from_ca
from_ca_args = []
ca_label = "liberal"
if self.params.secondary_structure.from_ca_conservative:
from_ca_args = [
"alpha.rise_tolerance=0.13",
"beta.rise_tolerance=0.3",
"alpha.dot_min=0.94",
]
ca_label = "conservative"
print(" running find_ss_from_ca %s..." % ca_label, file=self.log)
fss = find_ss_from_ca.find_secondary_structure(
hierarchy=pdb_hierarchy,
args = from_ca_args,
ss_by_chain=self.params.secondary_structure.ss_by_chain,
max_rmsd=self.params.secondary_structure.max_rmsd,
use_representative_chains=\
self.params.secondary_structure.use_representative_chains,
max_representative_chains=\
self.params.secondary_structure.max_representative_chains,
out=null_out())
return fss.get_annotation()
elif self.params.secondary_structure.protein.search_method == "cablam":
from mmtbx.validation import cablam
print(" running cablam...", file=self.log)
cablam_results = cablam.cablamalyze(pdb_hierarchy=pdb_hierarchy,
outliers_only=False,
out=null_out(),
quiet=False)
return cablam_results.as_secondary_structure()
else:
print(" WARNING: Unknown search method for SS. No SS found.",
file=self.log)
return iotbx.pdb.secondary_structure.annotation.from_records()
def find_sec_str(self, pdb_hierarchy):
if (pdb_hierarchy.atoms_size() > 99999
and self.params.secondary_structure.protein.search_method
== "ksdssp"):
print >> self.log, "Warning!!! ksdssp method is not applicable for" + \
"structures with more than 99999 atoms!\nSwitching to from_ca."
self.params.secondary_structure.protein.search_method = "from_ca"
if self.params.secondary_structure.protein.search_method == "ksdssp":
pdb_str = pdb_hierarchy.as_pdb_string()
print >> self.log, " running ksdssp..."
(records, stderr) = run_ksdssp_direct(pdb_str)
return iotbx.pdb.secondary_structure.annotation.from_records(
records=records, log=self.log)
elif self.params.secondary_structure.protein.search_method == "mmtbx_dssp":
from mmtbx.secondary_structure import dssp
print >> self.log, " running mmtbx.dssp..."
return dssp.dssp(pdb_hierarchy=pdb_hierarchy,
pdb_atoms=self.pdb_atoms,
out=null_out()).get_annotation()
elif self.params.secondary_structure.protein.search_method == "from_ca":
from mmtbx.secondary_structure import find_ss_from_ca
print >> self.log, " running find_ss_from_ca..."
fss = find_ss_from_ca.find_secondary_structure(
hierarchy=pdb_hierarchy,
ss_by_chain=self.params.secondary_structure.ss_by_chain,
max_rmsd=self.params.secondary_structure.max_rmsd,
use_representative_chains=\
self.params.secondary_structure.use_representative_chains,
max_representative_chains=\
self.params.secondary_structure.max_representative_chains,
out=null_out())
return fss.get_annotation()
elif self.params.secondary_structure.protein.search_method == "cablam":
from mmtbx.validation import cablam
print >> self.log, " running cablam..."
cablam_results = cablam.cablamalyze(pdb_hierarchy=pdb_hierarchy,
outliers_only=False,
out=null_out(),
quiet=False)
return cablam_results.as_secondary_structure()
else:
print >> self.log, " WARNING: Unknown search method for SS. No SS found."
return iotbx.pdb.secondary_structure.annotation.from_records()
