def init_db():
db.create_all()
if not Structure.query.get(2004):
asset_safety = Structure(
id=2004,
name='Asset Safety',
system_id=None,
corporation_id=None,
)
db.session.add(asset_safety)
db.session.commit()
def parse_ct(self, ct_filepath, transcript_id, experiment_config):
structure = None
n_structs = 0
with open(ct_filepath) as ct_file:
for line in ct_file:
# if it's an energy line, we're looking at a brand new structure
# the .ct format is a bit annoying because it's not tab delimited.
# instead it's delimited by variable numbers of spaces.
# calling split() with no parameter makes it split on any length
# of whitespace - i.e. so that each element is 1 word
# from_pos = bits[0]
bits = line.strip().split()
if len(bits) != 6: # brand new structure
# save existing structure to DB
if structure != None:
db_session.add(structure)
# Parse the energy out using regex
search = re.search('ENERGY = (-[0-9\.]+)', line)
if search == None:
# No energy data - for some reason this happens for some structures.
# If this happens, just ignore the entire ct file by returning
return
energy = search.group(1)
# Create the new structure object, we'll commit it later...
structure = Structure(
structure_prediction_run_id=experiment_config["structure_prediction_run_id"],
transcript_id=transcript_id,
energy=energy
)
# insert the experiment into the DB. can now access ID
db_session.commit()
n_structs += 1
else:
to_pos = bits[4]
structure.add_value(to_pos)
db_session.add(structure)
db_session.commit() # insert remaining data into DB
print ("["+str(n_structs)+"] structures added")
def setUp(self):
self.stiffness = 10.0
self.original_length = 0.9
self.spacing = 1.0
self.mass = 1.0
#set up the structure
self.structure = Structure("001")
for i in range(10):
self.structure.addNode(
MassedNode2d("%s" % str(i + 1), (self.spacing * i), 0.0,
self.mass))
for i in range(9):
self.structure.addElement(
Spring2d("%s" % str(i + 1), self.structure.n[i],
self.structure.n[i + 1], self.stiffness,
self.original_length))
self.structure.n[0].cx = True
self.structure.n[0].cy = True
self.structure.n[9].cx = True
self.structure.n[9].cy = True
def setUp(self):
self.structure=Structure('001')
