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Final bugs for membrane models
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Additional bugs found when testing the code.
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zjuradoq committed Jan 16, 2025
1 parent 5ee4b3a commit e3e1395
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Showing 3 changed files with 581 additions and 70 deletions.
1 change: 0 additions & 1 deletion biocrnpyler/__init__.py
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Expand Up @@ -28,7 +28,6 @@
from .mechanisms_integrase import *
from .mechanisms_transport import *
from .mechanisms_signaling import *
from .multi_mixture_graph import *

# Core classes
from .mixture import *
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2 changes: 2 additions & 0 deletions biocrnpyler/mechanisms_transport.py
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Expand Up @@ -238,6 +238,8 @@ def update_reactions(self, membrane_carrier, substrate, product, component = Non
unbinding_rxn2 = Reaction.from_massaction(inputs=[complex2],
outputs=[product, membrane_carrier],
k_forward=ku2)

return [binding_rxn1,unbinding_rxn1, transport_rxn, unbinding_rxn2]

class Primary_Active_Transport_MM(Mechanism):
"""A mechanism to model the transport of a substrate through a membrane carrier.
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648 changes: 579 additions & 69 deletions examples/Specialized Tutorials/7. Transport_Models.ipynb

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