def find_base_pairs(self, log=sys.stdout, use_segid=False, segids=None):
if not use_segid:
base_pairs = ""
stacking_pairs = ""
if self.pdb_hierarchy.contains_nucleic_acid():
stacking_pairs = nucleic_acids.get_phil_stacking_pairs(
pdb_hierarchy=self.pdb_hierarchy,
prefix="secondary_structure.nucleic_acid",
params=self.params.secondary_structure.nucleic_acid,
log=log)
if self.grm is not None:
base_pairs = nucleic_acids.get_phil_base_pairs(
pdb_hierarchy=self.pdb_hierarchy,
nonbonded_proxies=self.grm.pair_proxies(
sites_cart=self.pdb_hierarchy.atoms().extract_xyz()).\
nonbonded_proxies,
prefix="secondary_structure.nucleic_acid",
params=self.params.secondary_structure.nucleic_acid,
log=log,
verbose = self.verbose)
return "\n".join([base_pairs, stacking_pairs])
else:
assert len(segids) > 1
annotations = []
for segid in segids:
base_pairs = ""
stacking_pairs = ""
isel = self.selection_cache.selection("segid '%s'" %
segid).iselection()
selected_pdb_h = self.pdb_hierarchy.select(isel)
if selected_pdb_h.contains_nucleic_acid():
stacking_pairs = nucleic_acids.get_phil_stacking_pairs(
pdb_hierarchy=selected_pdb_h,
prefix="secondary_structure.nucleic_acid",
log=log,
add_segid=segid)
if self.grm is not None:
selected_grm = self.grm.select(iselection=isel)
base_pairs = nucleic_acids.get_phil_base_pairs(
pdb_hierarchy=selected_pdb_h,
nonbonded_proxies=selected_grm.pair_proxies(
sites_cart=selected_pdb_h.atoms().extract_xyz()).\
nonbonded_proxies,
prefix="secondary_structure.nucleic_acid",
log=log,
add_segid=segid,
verbose = self.verbose)
if (base_pairs is not None):
annotations.append(base_pairs)
if (stacking_pairs is not None):
annotations.append(stacking_pairs)
return "\n".join(annotations)
def find_base_pairs (self, log=sys.stdout, use_segid=False, segids=None):
if not use_segid:
base_pairs = ""
stacking_pairs = ""
if self.pdb_hierarchy.contains_nucleic_acid():
stacking_pairs = nucleic_acids.get_phil_stacking_pairs(
pdb_hierarchy=self.pdb_hierarchy,
prefix="secondary_structure.nucleic_acid",
params=self.params.secondary_structure.nucleic_acid,
log=log)
if self.grm is not None:
base_pairs = nucleic_acids.get_phil_base_pairs(
pdb_hierarchy=self.pdb_hierarchy,
nonbonded_proxies=self.grm.pair_proxies().nonbonded_proxies,
prefix="secondary_structure.nucleic_acid",
params=self.params.secondary_structure.nucleic_acid,
log=log,
verbose = self.verbose)
return "\n".join([base_pairs, stacking_pairs])
else:
assert len(segids) > 1
annotations = []
for segid in segids:
base_pairs = ""
stacking_pairs = ""
isel = self.selection_cache.selection("segid '%s'" % segid).iselection()
selected_pdb_h = self.pdb_hierarchy.select(isel)
if selected_pdb_h.contains_nucleic_acid():
stacking_pairs = nucleic_acids.get_phil_stacking_pairs(
pdb_hierarchy=selected_pdb_h,
prefix="secondary_structure.nucleic_acid",
log=log,
add_segid=segid)
if self.grm is not None:
selected_grm = self.grm.select(iselection=isel)
base_pairs = nucleic_acids.get_phil_base_pairs(
pdb_hierarchy=selected_pdb_h,
nonbonded_proxies=selected_grm.pair_proxies(
sites_cart=selected_pdb_h.atoms().extract_xyz()).\
nonbonded_proxies,
prefix="secondary_structure.nucleic_acid",
log=log,
add_segid=segid,
verbose = self.verbose)
if (base_pairs is not None) :
annotations.append(base_pairs)
if (stacking_pairs is not None) :
annotations.append(stacking_pairs)
return "\n".join(annotations)