def test_interface_01(self):
PepperComplex.PREFIX = 'enum'
complexes, reactions = read_pil("""
# Domain Specifications
length a = 8
length b = 8
length c = 8
length d2 = 8
length d3 = 8
length t = 4
# Resting-set Complexes
e0 = d2( d3( + ) a* + a*( b*( c ) ) ) t*
e12 = d2 d3( + ) a*
e13 = t( d2( d3 + a*( b*( c ) ) ) )
e21 = d2 d3
e22 = t( d2( d3( + ) a*( + a* b*( c ) ) ) )
e27 = t( d2( d3( + ) a* + a*( b*( c ) ) ) )
gate = d2( d3( + ) a*( + a* b*( c ) ) ) t*
t23 = t d2 d3
# Transient Complexes
e5 = t( d2 d3 + d2( d3( + ) a*( + a* b*( c ) ) ) )
e7 = t( d2 d3 + d2( d3( + ) a* + a*( b*( c ) ) ) )
e18 = t( d2( d3 + d2 d3( + ) a*( + a* b*( c ) ) ) )
# Detailed Reactions
reaction [bind21 = 1.2e+06 /M/s ] e0 + t23 -> e7
reaction [branch-3way = 0.122307 /s ] e0 -> gate
reaction [branch-3way = 41.6667 /s ] e5 -> e7
reaction [branch-3way = 41.6667 /s ] e5 -> e18
reaction [open = 306.345 /s ] e5 -> t23 + gate
reaction [open = 306.345 /s ] e7 -> e0 + t23
reaction [branch-3way = 0.122307 /s ] e7 -> e5
reaction [branch-3way = 41.6667 /s ] e7 -> e12 + e13
reaction [branch-3way = 0.122307 /s ] e18 -> e5
reaction [branch-3way = 41.6667 /s ] e18 -> e12 + e13
reaction [branch-3way = 0.122307 /s ] e18 -> e22 + e21
reaction [branch-3way = 41.6667 /s ] e22 -> e27
reaction [branch-3way = 0.122307 /s ] e27 -> e22
reaction [branch-3way = 41.6667 /s ] gate -> e0
reaction [bind21 = 1.2e+06 /M/s ] t23 + gate -> e5
""")
enum = Enumerator(complexes.values(), reactions)
enum.release_cutoff = 7
enum.enumerate()
self.assertEqual(sorted(enum.reactions), sorted(reactions))
def test_zhang_cooperative_binding(self):
complexes, reactions = read_pil("""
# Figure 1 of David Yu Zhang, "Cooperative hybridization of oligonucleotides", JACS, 2012
# File generated by peppercorn-v0.5.0
# Domain Specifications
length d1 = 8
length d2 = 18
length d3 = 18
length d4 = 8
# Resting-set Complexes
C1 = d2( d3( + d4* ) ) d1*
L1 = d1( d2 + d2( d3( + d4* ) ) )
L2 = d1( d2( + d2 d3( + d4* ) ) )
Out = d2 d3
R1 = d2( d3( + d3 d4( + ) ) ) d1*
R2 = d2( d3 + d3( d4( + ) ) ) d1*
T1 = d1 d2
T2 = d3 d4
Waste = d1( d2( + d3( d4( + ) ) ) )
# Transient Complexes
L1R1 = d1( d2 + d2( d3( + d3 d4( + ) ) ) )
L1R2 = d1( d2 + d2( d3 + d3( d4( + ) ) ) )
L2R1 = d1( d2( + d2 d3( + d3 d4( + ) ) ) )
# Detailed Reactions
reaction [bind21 = 2.4e+06 /M/s ] C1 + T2 -> R1
reaction [bind21 = 2.4e+06 /M/s ] L1 + T2 -> L1R1
reaction [branch-3way = 18.5185 /s ] L1 -> L2
reaction [branch-3way = 18.5185 /s ] L1R1 -> L1R2
reaction [branch-3way = 18.5185 /s ] L1R1 -> L2R1
reaction [branch-3way = 18.5185 /s ] L1R2 -> L1R1
reaction [branch-3way = 18.5185 /s ] L1R2 -> Waste + Out
reaction [bind21 = 2.4e+06 /M/s ] L2 + T2 -> L2R1
reaction [branch-3way = 18.5185 /s ] L2 -> L1
reaction [branch-3way = 18.5185 /s ] L2R1 -> L1R1
reaction [branch-3way = 18.5185 /s ] L2R1 -> Waste + Out
reaction [branch-3way = 18.5185 /s ] R1 -> R2
reaction [branch-3way = 18.5185 /s ] R2 -> R1
reaction [bind21 = 2.4e+06 /M/s ] T1 + C1 -> L1
reaction [bind21 = 2.4e+06 /M/s ] T1 + R1 -> L1R1
reaction [bind21 = 2.4e+06 /M/s ] T1 + R2 -> L1R2
""")
enum = Enumerator(complexes.values(), reactions)
enum.k_fast = 0.01
enum.release_cutoff = 10
#enum.enumerate() # or enum.dry_run()
enum.dry_run()
enumRG = PepperCondensation(enum)
enumRG.condense()
"""
macrostate rC1 = [C1]
macrostate rL2 = [L2, L1]
macrostate rOut = [Out]
macrostate rR1 = [R1, R2]
macrostate rT1 = [T1]
macrostate rT2 = [T2]
macrostate rWaste = [Waste]
reaction [condensed = 2.4e+06 /M/s ] rT1 + rC1 -> rL2
reaction [condensed = 2.4e+06 /M/s ] rL2 + rT2 -> rWaste + rOut
reaction [condensed = 2.4e+06 /M/s ] rC1 + rT2 -> rR1
reaction [condensed = 2.4e+06 /M/s ] rT1 + rR1 -> rWaste + rOut
reaction [condensed = 0.00316623 /s ] rL2 -> rT1 + rC1
reaction [condensed = 0.00316623 /s ] rR1 -> rC1 + rT2
"""
L1 = complexes['L1']
L2 = complexes['L2']
rL2 = PepperMacrostate([L2, L1], memorycheck=False)
Out = complexes['Out']
rOut = PepperMacrostate([Out], memorycheck=False)
Waste = complexes['Waste']
rWaste = PepperMacrostate([Waste], memorycheck=False)
T2 = complexes['T2']
rT2 = PepperMacrostate([T2], memorycheck=False)
# calculated by hand...
cr1 = PepperReaction([rL2, rT2], [rWaste, rOut],
'condensed',
rate=2.4e6,
memorycheck=False)
found = False
for r in enumRG.condensed_reactions:
if r == cr1:
found = True
self.assertAlmostEqual(r.rate, cr1.rate)
self.assertTrue(found)
def test_fate_example(self):
PepperComplex.PREFIX = 'enum'
complexes, reactions = read_pil("""
# File generated by peppercorn-v0.5.0
# Domain Specifications
length a = 8
length b = 8
length c = 8
length d2 = 8
length d3 = 8
length t = 4
# Resting-set Complexes
e0 = d2( d3( + ) a* + a*( b*( c ) ) ) t*
e12 = d2 d3( + ) a*
e13 = t( d2( d3 + a*( b*( c ) ) ) )
e21 = d2 d3
e22 = t( d2( d3( + ) a*( + a* b*( c ) ) ) )
e27 = t( d2( d3( + ) a* + a*( b*( c ) ) ) )
gate = d2( d3( + ) a*( + a* b*( c ) ) ) t*
t23 = t d2 d3
# Transient Complexes
e5 = t( d2 d3 + d2( d3( + ) a*( + a* b*( c ) ) ) )
e7 = t( d2 d3 + d2( d3( + ) a* + a*( b*( c ) ) ) )
e18 = t( d2( d3 + d2 d3( + ) a*( + a* b*( c ) ) ) )
# Detailed Reactions
reaction [bind21 = 1.2e+06 /M/s ] e0 + t23 -> e7
reaction [branch-3way = 0.122307 /s ] e0 -> gate
reaction [branch-3way = 41.6667 /s ] e5 -> e7
reaction [branch-3way = 41.6667 /s ] e5 -> e18
reaction [open = 306.345 /s ] e5 -> t23 + gate
reaction [open = 306.345 /s ] e7 -> e0 + t23
reaction [branch-3way = 0.122307 /s ] e7 -> e5
reaction [branch-3way = 41.6667 /s ] e7 -> e12 + e13
reaction [branch-3way = 0.122307 /s ] e18 -> e5
reaction [branch-3way = 41.6667 /s ] e18 -> e12 + e13
reaction [branch-3way = 0.122307 /s ] e18 -> e22 + e21
reaction [branch-3way = 41.6667 /s ] e22 -> e27
reaction [branch-3way = 0.122307 /s ] e27 -> e22
reaction [branch-3way = 41.6667 /s ] gate -> e0
reaction [bind21 = 1.2e+06 /M/s ] t23 + gate -> e5
""")
gate = complexes['gate']
t23 = complexes['t23']
enum = Enumerator(complexes.values())
enum.release_cutoff = 6
enum.enumerate() # or enum.dry_run()
self.assertEqual(sorted(enum.reactions), sorted(reactions))
"""
# Resting sets
state re0 = [e0, gate]
state re12 = [e12]
state re13 = [e13]
state re21 = [e21]
state re22 = [e22, e27]
state rt23 = [t23]
reaction [condensed = 287342 /M/s ] re0 + rt23 -> re13 + re12
reaction [condensed = 2.45499 /M/s ] re0 + rt23 -> re21 + re22
"""
enumRG = PepperCondensation(enum)
enumRG.condense()
self.assertEqual(len(list(enumRG.resting_macrostates)), 6)
self.assertEqual(len(list(enumRG.condensed_reactions)), 2)
def test_zhang_cooperative_binding(self):
complexes, reactions = read_pil("""
# Figure 1 of David Yu Zhang, "Cooperative hybridization of oligonucleotides", JACS, 2012
# File generated by peppercorn-v0.5.0
# Domain Specifications
length d1 = 8
length d2 = 18
length d3 = 18
length d4 = 8
# Resting-set Complexes
C1 = d2( d3( + d4* ) ) d1*
L1 = d1( d2 + d2( d3( + d4* ) ) )
L2 = d1( d2( + d2 d3( + d4* ) ) )
Out = d2 d3
R1 = d2( d3( + d3 d4( + ) ) ) d1*
R2 = d2( d3 + d3( d4( + ) ) ) d1*
T1 = d1 d2
T2 = d3 d4
Waste = d1( d2( + d3( d4( + ) ) ) )
# Transient Complexes
L1R1 = d1( d2 + d2( d3( + d3 d4( + ) ) ) )
L1R2 = d1( d2 + d2( d3 + d3( d4( + ) ) ) )
L2R1 = d1( d2( + d2 d3( + d3 d4( + ) ) ) )
# Detailed Reactions
reaction [bind21 = 2.4e+06 /M/s ] C1 + T2 -> R1
reaction [bind21 = 2.4e+06 /M/s ] L1 + T2 -> L1R1
reaction [branch-3way = 18.5185 /s ] L1 -> L2
reaction [branch-3way = 18.5185 /s ] L1R1 -> L1R2
reaction [branch-3way = 18.5185 /s ] L1R1 -> L2R1
reaction [branch-3way = 18.5185 /s ] L1R2 -> L1R1
reaction [branch-3way = 18.5185 /s ] L1R2 -> Waste + Out
reaction [bind21 = 2.4e+06 /M/s ] L2 + T2 -> L2R1
reaction [branch-3way = 18.5185 /s ] L2 -> L1
reaction [branch-3way = 18.5185 /s ] L2R1 -> L1R1
reaction [branch-3way = 18.5185 /s ] L2R1 -> Waste + Out
reaction [branch-3way = 18.5185 /s ] R1 -> R2
reaction [branch-3way = 18.5185 /s ] R2 -> R1
reaction [bind21 = 2.4e+06 /M/s ] T1 + C1 -> L1
reaction [bind21 = 2.4e+06 /M/s ] T1 + R1 -> L1R1
reaction [bind21 = 2.4e+06 /M/s ] T1 + R2 -> L1R2
""")
enum = Enumerator(complexes.values(), reactions)
enum.k_fast = 0.01
enum.release_cutoff = 10
enum.enumerate() # or enum.dry_run()
enumRG = PepperCondensation(enum)
enumRG.condense()
"""
macrostate rC1 = [C1]
macrostate rL2 = [L2, L1]
macrostate rOut = [Out]
macrostate rR1 = [R1, R2]
macrostate rT1 = [T1]
macrostate rT2 = [T2]
macrostate rWaste = [Waste]
reaction [condensed = 2.4e+06 /M/s ] rT1 + rC1 -> rL2
reaction [condensed = 2.4e+06 /M/s ] rL2 + rT2 -> rWaste + rOut
reaction [condensed = 2.4e+06 /M/s ] rC1 + rT2 -> rR1
reaction [condensed = 2.4e+06 /M/s ] rT1 + rR1 -> rWaste + rOut
reaction [condensed = 0.00316623 /s ] rL2 -> rT1 + rC1
reaction [condensed = 0.00316623 /s ] rR1 -> rC1 + rT2
"""
try:
L1 = complexes['L1']
L2 = complexes['L2']
L = PepperMacrostate([L1, L2])
except SingletonError as err:
L = err.existing
O = PepperMacrostate([complexes['Out']])
W = PepperMacrostate([complexes['Waste']])
T = PepperMacrostate([complexes['T2']])
# calculated by hand...
cr1 = PepperReaction([L, T], [W, O], 'condensed')
assert cr1 in enumRG.condensed_reactions
assert cr1.rate_constant == (2.4e6, '/M/s')
