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Compatibility with latest version of PySB #13

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Compatibility with latest version of PySB #13

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3433a1e
Swapped <> operator for | in order to recover compatibility with late…
acorbat Mar 27, 2020
957d910
Correct shared import in shen_modules
acorbat Oct 28, 2020
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4 changes: 2 additions & 2 deletions earm/albeck_modules.py
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Original file line number Diff line number Diff line change
Expand Up @@ -307,7 +307,7 @@ def Bax_tetramerizes(bax_active_state='A', rate_scaling_factor=1):
Bax(s1=2, s2=1, **active_unbound) %
Bax(s1=3, s2=2, **active_unbound) %
Bax(s1=4, s2=3, **active_unbound))
Rule('Bax_dimerization', active_bax_monomer + active_bax_monomer <> bax2,
Rule('Bax_dimerization', active_bax_monomer + active_bax_monomer | bax2,
Parameter('Bax_dimerization_kf', KF*rate_scaling_factor),
Parameter('Bax_dimerization_kr', KR))
# Notes on the parameter values used below:
Expand All @@ -321,7 +321,7 @@ def Bax_tetramerizes(bax_active_state='A', rate_scaling_factor=1):
# - BNG apparently applies a scaling factor of 2 to the reverse reaction
# rate, for reasons we do not entirely understand. The factor of 0.5 is
# applied here to make the rate match the original Albeck ODEs.
Rule('Bax_tetramerization', bax2 + bax2 <> bax4,
Rule('Bax_tetramerization', bax2 + bax2 | bax4,
Parameter('Bax_tetramerization_kf', 2*KF*rate_scaling_factor),
Parameter('Bax_tetramerization_kr', 0.5*KR))

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10 changes: 5 additions & 5 deletions earm/shared.py
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Expand Up @@ -194,7 +194,7 @@ def pore_rule_name(rule_expression):

# Create the pore formation rule
macros._macro_rule('spontaneous_pore',
free_subunit + free_subunit + free_subunit + free_subunit <>
free_subunit + free_subunit + free_subunit + free_subunit |
subunit(s1=1, s2=4) % subunit(s1=2, s2=1) % \
subunit(s1=3, s2=2) % subunit(s1=4, s2=3),
klist, ['kf', 'kr'], name_func=pore_rule_name)
Expand All @@ -221,7 +221,7 @@ def displace_reversibly(lig1, lig2, target, klist):
"""

return macros._macro_rule('displace',
lig1({'bf':None}) + lig2({'bf':1}) % target({'bf':1}) <>
lig1({'bf':None}) + lig2({'bf':1}) % target({'bf':1}) |
lig1({'bf':1}) % target({'bf':1}) + lig2({'bf':None}),
klist, ['fwd_kf', 'rev_kf'])

Expand All @@ -239,7 +239,7 @@ def catalyze_convert(sub1, sub2, product, klist, site='bf'):
macros._verify_sites(sub2, site)

components = macros._macro_rule('bind',
sub1({site: None}) + sub2({site: None}) <>
sub1({site: None}) + sub2({site: None}) |
sub1({site: 1}) % sub2({site: 1}),
klist[0:2], ['kf', 'kr'])
components |= macros._macro_rule('convert',
Expand All @@ -258,7 +258,7 @@ def one_step_conv(sub1, sub2, product, klist, site='bf'):
macros._verify_sites(sub2, site)

return macros._macro_rule('convert',
sub1({site: None}) + sub2({site: None}) <> product,
sub1({site: None}) + sub2({site: None}) | product,
klist, ['kf', 'kr'])

def pore_bind(subunit, sp_site1, sp_site2, sc_site, size, cargo, c_site,
Expand Down Expand Up @@ -342,7 +342,7 @@ def pore_bind_rule_name(rule_expression, size):
# Create the rules
name_func = functools.partial(pore_bind_rule_name, size=size)
components |= macros._macro_rule('pore_bind',
pore_free + cargo_free <> pc_complex,
pore_free + cargo_free | pc_complex,
klist[0:2], ['kf', 'kr'],
name_func=name_func)

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2 changes: 1 addition & 1 deletion earm/shen_modules.py
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Expand Up @@ -69,7 +69,7 @@
# We'll need everything from the pysb core and some macros:

from pysb import *
from shared import *
from earm.shared import *
from pysb.macros import catalyze_one_step_reversible, catalyze_one_step, \
synthesize_degrade_table, degrade, equilibrate
from pysb.util import alias_model_components
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2 changes: 1 addition & 1 deletion earm/tests/test_albeck_models.py
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Expand Up @@ -86,7 +86,7 @@ def add_caspase8(model):
model.add_component(kc)

rb = Rule('bind_C8A_BidU_to_C8ABidU',
C8(state='A', bf=None) + Bid(state='U', bf=None) <>
C8(state='A', bf=None) + Bid(state='U', bf=None) |
C8(state='A', bf=1) % Bid(state='U', bf=1),
kf, kr, _export=False)
rc = Rule('catalyze_C8ABidU_to_C8A_BidT',
Expand Down