def __init__(self, *args, **kargs):
"""
Initialization:
Keyword Arguments:
sequence [type=str] -- Flat sequence to use for this complex.
structure [type=str] -- Flat structure to use for this complex.
name [type=str] -- Name of the complex. If None (the default),
it is automatically generated with the
form 'automatic' + a unique integer.
boltzmann_sample [type=bool] -- Whether we should boltzmann sample this
complex.
You must include both of the required keyword arguments to create a Complex with the new style init, or pass it the old style arguments used in `old_init`.
"""
if len(args) == 4 or len(args) == 5:
self.old_init(*args, **kargs)
return
elif 'sequence' in kargs and 'structure' in kargs:
self.strand_list = [
Strand(sequence=i) for i in kargs['sequence'].split("+")
]
self._fixed_structure = str(kargs['structure'])
elif 'strands' in kargs and 'structure' in kargs:
self.strand_list = kargs['strands']
self._init_parse_structure(str(kargs['structure']))
self.id = Complex.unique_id
self.name = kargs.get('name') or "automatic" + str(Complex.unique_id)
# note: Boltzmann sampling is somewhat confusing if you pass a
# structure that is anything other than all "."'s. So maybe we
# should check for that.
self.boltzmann_sample = kargs.get('boltzmann_sample', False)
self._last_boltzmann_structure = False
self._boltzmann_sizehint = 1
self._boltzmann_queue = []
# Adjust here for default Boltzmann Parameters. 'None' in this case means to not pass that parameter and let the sample binary use its default. Substrate defaults to DNA.
self._dangles = None
self._substrate_type = None
self._temperature = None
# Taken to be 1, unless it is EXPLICITLY stated otherwise!
self.boltzmann_supersample = 1
Complex.unique_id += 1
def __init__(self):
self.led_on = False
self.connected = False
self.pattern = None
self.color_spectrum = None
self.error = False
self.errormsg = None
self.aws_access_key_id = None
self.aws_secret_access_key = None
self.aws_default_region = None
self.aws_kinesis_stream_name = None
self.device_state = {}
if config.device_type == 'strand':
self.strand = Strand()
elif config.device_type == 'cam':
self.cam = Cam()
elif config.device_type == 'flame':
self.flame = Flame()
def __add__(self, other):
if isinstance(other, Domain):
return Strand(domains=[self, other])
else:
return NotImplemented
def __init__(self, seq: str = None):
self.seq: str = seq
strand: Strand = None
if seq is not None:
strand = Strand(seq, self)
self.strand5p: Strand = strand
