def score_toeholds(toeholds):
ltoes = []
for toe in toeholds:
l = toe[0].lower()
ltoes.append(l)
aa = stickydesign.endclasses.endarray(array=ltoes, endtype="S")
aa = [aa, aa]
toe = aa[0]
energyarray = stickydesign.energy_array_uniform(
toe, stickydesign.EnergeticsBasic(temperature=37))
maxs = []
for arr in energyarray:
maxim = max(arr)
maxs.append(maxim)
e_var = statistics.variance(maxs)
e_rng = max(maxs) - min(maxs)
return (e_var, e_rng)
def calculate_unrestricted_toehold_characteristics(self):
import stickydesign as sd
ends = sd.easyends('TD',
self.length,
alphabet='h',
adjs=['c', 'g'],
energetics=self)
n_ends = len(ends)
e_array = sd.energy_array_uniform(ends, self)
e_array = e_array[n_ends:, :n_ends]
for i in range(n_ends):
e_array[i, i] = 0
e_spr = e_array.max() / self.targetdG
e_vec_ext = self.th_external_dG(ends)
e_vec_int = self.th_internal_dG(ends)
e_vec_all = np.concatenate((e_vec_int, e_vec_ext))
e_avg = e_vec_all.mean()
e_dev = np.max(np.abs(e_vec_all - self.targetdG))
return e_avg, e_spr, e_dev, n_ends
def from_yaml_endadj(ts, perfect=False, rotate=False):
import stickydesign as sd
import stickydesign.energetics as en
import numpy as np
# Combine ends and tile-specified adjacents
newtiles = []
newends = []
endslist = set()
doubleends = []
doubles = []
vdoubleends = []
vdoubles = []
newtiles.append({
'name': 'origami',
'edges': ['origami', 'origami', 'origami', 'origami'],
'stoic': 0,
'color': 'white'
})
atiles = [None] * 16
for tilename in ts['seed']['use_adapters']:
tile = [x for x in ts['seed']['adapters'] if x['name'] == tilename][0]
newtile = {}
newtile['edges'] = ['origami'
] + [re.sub('/', '_c', x)
for x in tile['ends']] + ['origami']
newtile['name'] = tile['name']
newtile['stoic'] = 0
newtile['color'] = 'white'
atiles[tile['loc'] - 1] = newtile
for tile in atiles:
if tile:
newtiles.append(newtile)
else:
newtiles.append({
'name': 'emptyadapt',
'edges': ['origami', 0, 0, 'origami'],
'stoic': 0,
'color': 'white'
})
if rotate:
rotatedtiles = []
for tile in ts['tiles']:
if tile['type'] == 'tile_daoe_3up' or tile[
'type'] == 'tile_daoe_5up':
newtile = copy.copy(tile)
newtile['name'] += '_lrf'
newtile['ends'] = [tile['ends'][x] for x in (1, 0, 3, 2)]
rotatedtiles.append(newtile)
newtile = copy.copy(tile)
newtile['name'] += '_udf'
newtile['type'] = 'tile_daoe_' + {
'5up': '3up',
'3up': '5up'
}[tile['type'][-3:]]
newtile['ends'] = [tile['ends'][x] for x in (3, 2, 1, 0)]
rotatedtiles.append(newtile)
newtile = copy.copy(tile)
newtile['name'] += '_bf'
newtile['type'] = 'tile_daoe_' + {
'5up': '3up',
'3up': '5up'
}[tile['type'][-3:]]
newtile['ends'] = [tile['ends'][x] for x in (2, 3, 0, 1)]
rotatedtiles.append(newtile)
elif tile['type'] == 'tile_daoe_doublehoriz_35up':
newtile = copy.copy(tile)
newtile['name'] += '_lrf'
newtile['type'] = 'tile_daoe_doublevert_53up'
newtile['ends'] = [tile['ends'][x] for x in (2, 1, 0, 5, 4, 3)]
rotatedtiles.append(newtile)
newtile = copy.copy(tile)
newtile['name'] += '_udf'
newtile['type'] = 'tile_daoe_doublevert_53up'
newtile['ends'] = [tile['ends'][x] for x in (5, 4, 3, 2, 1, 0)]
rotatedtiles.append(newtile)
newtile = copy.copy(tile)
newtile['name'] += '_bf'
newtile['ends'] = [tile['ends'][x] for x in (3, 4, 5, 0, 1, 2)]
rotatedtiles.append(newtile)
elif tile['type'] == 'tile_daoe_doublevert_35up':
newtile = copy.copy(tile)
newtile['name'] += '_lrf'
newtile['type'] = 'tile_daoe_doublehoriz_53up'
newtile['ends'] = [tile['ends'][x] for x in (2, 1, 0, 5, 4, 3)]
rotatedtiles.append(newtile)
newtile = copy.copy(tile)
newtile['name'] += '_udf'
newtile['type'] = 'tile_daoe_doublehoriz_53up'
newtile['ends'] = [tile['ends'][x] for x in (5, 4, 3, 2, 1, 0)]
rotatedtiles.append(newtile)
newtile = copy.copy(tile)
newtile['name'] += '_bf'
newtile['ends'] = [tile['ends'][x] for x in (3, 4, 5, 0, 1, 2)]
rotatedtiles.append(newtile)
ts['tiles'] += rotatedtiles
for tile in ts['tiles']:
if tile['type'] == 'tile_daoe_3up' or tile['type'] == 'tile_daoe_5up':
newtile = {}
newtile['edges'] = [re.sub('/', '_c', x) for x in tile['ends']]
if 'name' in tile: newtile['name'] = tile['name']
if 'conc' in tile: newtile['stoic'] = tile['conc']
if 'color' in tile: newtile['color'] = tile['color']
newtiles.append(newtile)
if tile['type'] == 'tile_daoe_doublehoriz_35up' or tile[
'type'] == 'tile_daoe_doublehoriz_53up':
newtile1 = {}
newtile2 = {}
newtile1['edges'] = [ re.sub('/','_c',x) for x in tile['ends'][0:1] ] \
+ [ tile['name']+'_db' ] \
+ [ re.sub('/','_c',x) for x in tile['ends'][4:] ]
newtile2['edges'] = [ re.sub('/','_c',x) for x in tile['ends'][1:4] ] \
+ [ tile['name']+'_db' ]
newtile1['name'] = tile['name'] + '_left'
newtile2['name'] = tile['name'] + '_right'
doubleends.append(tile['name'] + '_db')
doubles.append((newtile1['name'], newtile2['name']))
if 'conc' in tile:
newtile1['stoic'] = tile['conc']
newtile2['stoic'] = tile['conc']
if 'color' in tile:
newtile1['color'] = tile['color']
newtile2['color'] = tile['color']
newtiles.append(newtile1)
newtiles.append(newtile2)
if tile['type'] == 'tile_daoe_doublevert_35up' or tile[
'type'] == 'tile_daoe_doublevert_53up':
newtile1 = {}
newtile2 = {}
newtile1['edges'] = [ re.sub('/','_c',x) for x in tile['ends'][0:2] ] \
+ [ tile['name']+'_db' ] \
+ [ re.sub('/','_c',x) for x in tile['ends'][5:] ]
newtile2['edges'] = [tile['name'] + '_db'] + [
re.sub('/', '_c', x) for x in tile['ends'][2:5]
]
newtile1['name'] = tile['name'] + '_top'
newtile2['name'] = tile['name'] + '_bottom'
vdoubleends.append(tile['name'] + '_db')
vdoubles.append((newtile1['name'], newtile2['name']))
if 'conc' in tile:
newtile1['stoic'] = tile['conc']
newtile2['stoic'] = tile['conc']
if 'color' in tile:
newtile1['color'] = tile['color']
newtile2['color'] = tile['color']
newtiles.append(newtile1)
newtiles.append(newtile2)
newends.append({'name': 'origami', 'strength': 100})
for end in doubleends:
newends.append({'name': end, 'strength': 10})
for end in vdoubleends:
newends.append({'name': end, 'strength': 10})
gluelist = []
if not perfect:
glueends = {'DT': [], 'TD': []}
for end in ts['ends']:
newends.append({'name': end['name'], 'strength': 0})
newends.append({'name': end['name'] + '_c', 'strength': 0})
if (end['type'] == 'TD') or (end['type'] == 'DT'):
glueends[end['type']].append((end['name'], end['fseq']))
ef = en.energetics_santalucia(mismatchtype='max')
for t in ['DT', 'TD']:
names, fseqs = zip(*glueends[t])
allnames = names + tuple(x + '_c' for x in names)
ea = sd.endarray(fseqs, t)
ar = sd.energy_array_uniform(ea, ef)
for i1, n1 in enumerate(names):
for i2, n2 in enumerate(allnames):
gluelist.append([n1, n2, float(ar[i1, i2])])
else:
if 'ends' not in ts.keys():
ts['ends'] = []
endsinlist = set(e['name'] for e in ts['ends'])
endsintiles = set()
for tile in ts['tiles']:
endsintiles.update(
re.sub('/', '', e) for e in tile['ends'] if e != 'hp')
for end in ts['ends'] + list({'name': e} for e in endsintiles):
newends.append({'name': end['name'], 'strength': 0})
newends.append({'name': end['name'] + '_c', 'strength': 0})
gluelist.append([end['name'], end['name'] + '_c', 1.0])
newends.append({'name': 'hp', 'strength': 0})
xga = {}
xga['doubletiles'] = [list(x) for x in doubles]
xga['vdoubletiles'] = [list(x) for x in vdoubles]
xga.update(ts['xgrow_options'])
xga.update(ts['xgrow_options'])
sts = {
'tiles': newtiles,
'bonds': newends,
'xgrowargs': xga,
'glues': gluelist
}
return sts
# ta tb tr tc tq td tg
aa = stickydesign.endclasses.endarray(array=b, endtype="S")
aa = [aa, aa]
#aa=stickydesign.easyends('S',6,number=7, maxspurious=0.4,interaction=0, tries=2,energetics=stickydesign.EnergeticsBasic(temperature=37), adjs=['c','g'],alphabet='h')
print(aa)
i = 1
toe = aa[0]
print('ta tb tr tc tq td tg')
energyarray = stickydesign.energy_array_uniform(
toe, stickydesign.EnergeticsBasic(temperature=37))
maxs = []
for arr in energyarray:
maxim = max(arr)
maxs.append(maxim)
print('Maxs:', maxs)
print("Variance of %s set is % s" % (i, statistics.variance(maxs)))
print("Mean of %s set is % s" % (i, statistics.mean(maxs)))
print("Max Energy toehold %s - Min Energy Toehold %s is %s" %
(max(maxs), min(maxs), max(maxs) - min(maxs)))
fig = stickydesign.plots.heatmap(toe,
stickydesign.EnergeticsBasic(temperature=37))
pyplot.show(fig)
i = i + 1
if args.number:
n_ths = args.number
else:
n_ths = 3
############## end Interpret arguments
# Give the energetics instance the target energy
ef = energetics.energyfuncs()
ef.targetdG = thold_e
# new_toeholds returns 1 when second toehold assignment fails. Use a while
# loop to run the toehold generation until successful.
ends_all = None
while type(ends_all) is not sd.endarray:
ends_all = new_toeholds(ef, n_ths, thold_l, thold_e, e_dev, m_spurious)
if type(ends_all) == int:
if ends_all == 1:
print(
'Not enough appropriate first toeholds found. Trying again.'
)
if ends_all == 2:
print('First-second toehold pairing failed. Trying again.')
if ends_all == 3:
print("dunno")
# Plot energy array
e_array = sd.energy_array_uniform(ends_all, ef)
print('Done!')