def _SetupFiles(model,reference):
# create temporary directory
tmp_dir_name=tempfile.mkdtemp()
dia = 'PDB'
for chain in model.chains:
if chain.name==" ":
raise RuntimeError("One of the chains in the model has no name. Cannot "
"calculate CAD score")
if len(chain.name) > 1:
dia = 'CHARMM'
break;
for res in chain.residues:
if len(res.name) > 3:
dia = 'CHARMM'
break;
io.SavePDB(model, os.path.join(tmp_dir_name, 'model.pdb'), dialect=dia)
dia = 'PDB'
for chain in reference.chains:
if chain.name==" ":
raise RuntimeError("One of the chains in the reference has no name. "
"Cannot calculate CAD score")
if len(chain.name) > 1:
dia = 'CHARMM'
break;
for res in chain.residues:
if len(res.name) > 3:
dia = 'CHARMM'
break;
io.SavePDB(reference, os.path.join(tmp_dir_name, 'reference.pdb'),dialect=dia)
return tmp_dir_name
def AssignDSSP(ent, pdb_path="", extract_burial_status=False, tmp_dir=None,
dssp_bin=None):
"""
Assign secondary structure states to peptide residues in the structure. This
function uses the DSSP command line program.
If you already have a DSSP output file and would like to assign the secondary
structure states to an entity, use :func:`LoadDSSP`.
:param ent: The entity for which the secondary structure should be calculated
:type ent: :class:`~ost.mol.EntityHandle` or :class:`~ost.mol.EntityView`
:param extract_burial_status: If true, also extract burial status and store
as float-property
``relative_solvent_accessibility`` at residue
level
:param tmp_dir: If set, overrides the default tmp directory of the
operating system
:param dssp_bin: The path to the DSSP executable
:raises: :class:`~ost.settings.FileNotFound` if the dssp executable is not
in the path.
:raises: :class:`RuntimeError` when dssp is executed with errors
"""
entity_saved = False
# use of mktemp is a safty problem (use mkstemp and provide file handle to
# subsequent process
pdb_path=tempfile.mktemp(suffix=".pdb",prefix="temp_entity",
dir=tmp_dir)
io.SavePDB(ent, pdb_path)
entity_saved = True
#TODO: exception handling (currently errors occuring here
# are handled in the parser LoadDSSP)
temp_dssp_path=_ExecuteDSSP(pdb_path, dssp_bin)
if not os.path.exists(temp_dssp_path):
raise RuntimeError('DSSP output file does not exist.')
# assign DSSP to entity
try:
LoadDSSP(temp_dssp_path, ent, extract_burial_status,
entity_saved)
except Exception as e:
# clean up
print("Exception in DSSP:", e)
_Cleanup(pdb_path, temp_dssp_path, entity_saved)
raise RuntimeError(e)
# clean up
#print pdb_path, temp_dssp_path
_Cleanup(pdb_path, temp_dssp_path, entity_saved)
return ent
def _SetupFiles(models):
# create temporary directory
tmp_dir_name=tempfile.mkdtemp()
dia = 'PDB'
for index, model in enumerate(models):
for chain in model.chains:
if len(chain.name) > 1:
dia = 'CHARMM'
break;
for res in chain.residues:
if len(res.name) > 3:
dia = 'CHARMM'
break;
io.SavePDB(model, os.path.join(tmp_dir_name, 'model%02d.pdb' % (index+1)), dialect=dia)
return tmp_dir_name
def _SetupFiles(entity, selection, scratch_dir, max_number_of_atoms):
"""
Setup files for naccess calculation in temporary directory
:param entity: OST entity to calculate surface
:param selection: Calculate surface for subset of entity
:param scratch_dir: Scratch directory. A subfolder for temporary files
is created in there. If not specified, a default
directory is used (see :func:`tempfile.mkdtemp`).
:param max_number_of_atoms: Max Number of atoms in the entity (i.e. is limited
in the default NACCESS version to 50 000)
:returns: Tuple containing temporary directory, input filename for naccess and
directory of the input file
:exception: RuntimeError if selection is not valid or too many atoms
"""
# create temporary directory
tmp_dir_name = ""
if scratch_dir != None:
tmp_dir_name = tempfile.mkdtemp(dir=scratch_dir)
else:
tmp_dir_name = tempfile.mkdtemp()
# select as specified by user
if selection != "":
entity_view = entity.Select(selection)
else:
entity_view = entity
if len(entity_view.atoms) > max_number_of_atoms:
raise RuntimeError("Too much atoms for NACCESS (> %s)" %
max_number_of_atoms)
if not entity_view.IsValid():
raise RuntimeError("Could not create view for selection (%s)" %
(selection))
# write entity to tmp file
tmp_file_name = "entity.pdb"
tmp_file_base = os.path.join(tmp_dir_name, "entity")
io.SavePDB(entity_view, os.path.join(tmp_dir_name, tmp_file_name))
return (tmp_dir_name, tmp_file_name, tmp_file_base)