Addition of membrane comp/transport mech #265
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Added compartment attribute to Component under set_species.
Made lines shorter
Addition of 2 components and 2 mechanism for Membrane Proteins
Addition of direction to material type such that it appears in the name. Rewriting some membrane channel attributes and fix of some if statements.
Small indent edit
Updates for transport mechanism and membrane components. Includes example notebook.
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Code looks well written, there were some parts I was confused about in terms of how things work and what the model is supposed to do. I think being more careful about choosing variable names and adding some comments will help resolve most of these issues. A few other small changes are listed to make the code slightly more customizable / reusable.
| class IntegralMembraneProtein(Component): | ||
| """A class to represent transmembrane proteins or integral membrane proteins. | ||
| This membrane class is to classify a membrane channel that will intergrate into the membrane. | ||
| Uses a mechanism called "catalysis". |
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I'm confused why membrane proteins are Enzymes by default. Is there an example you have in mind?
| if direction is None: | ||
| self.product = self.set_species(product, material_type= 'Passive') | ||
| else: | ||
| self.product = self.set_species(product, material_type= direction) |
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'passive' and direction do not seem like materials a molecule is built out of. Maybe I am missing something about what you are doing here though.
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Maybe this should be an attribute?
| else: | ||
| self.product = self.set_species(product, material_type= direction) | ||
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| if size is None: |
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What is size being used for?
| self.substrate = None | ||
| else: | ||
| product=substrate | ||
| self.substrate = self.set_species(substrate, compartment='Internal',attributes=attributes) |
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I usually think of catalysis as substrate --> product. Why are you setting substrate = product?
| self.substrate = None | ||
| else: | ||
| product=substrate | ||
| self.substrate = self.set_species(substrate, compartment='Internal',attributes=attributes) |
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Can internal_compartment and external_compartment be variables set in the constructor 'internal' and 'external' are great defaults, but it would be nice to be able to change the compartment names.
| else: | ||
| complex4 = complex4 | ||
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| return [membrane_pump, Sub, Prod, complex1, complex2, complex3, complex4] |
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Energy and Waste are not returned.
| else: | ||
| complex2 = complex2 | ||
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| nATP=membrane_pump.ATP |
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Could this be a parameter in a file instead of a variable attached to the membrane_pump? This way, I could use this Mechanism with a different Component.
For example, you might type:
n_E = component.get_parameter(n_E, part_id, self)
| k_reverse=ku2) | ||
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| # Sub:MT:E --> Prod:MT:W | ||
| binding_rxn3 = Reaction.from_massaction(inputs=[complex3], |
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This is not a binding reaction, so maybe we shouldn't call the parameter "kb"?
| class MembraneChannel(Component): | ||
| """A class to represent Membrane Channels. | ||
| Assumes the membrane channel transport substrates in a specific direction across the membrane | ||
| Uses a mechanism called "catalysis" |
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I think it would be better for the mechanism type to be called "transport" - otherwise, if we cannot use your transport Mechanisms at the same time a different catalysis mechanism is used (say for metabolism).
| class MembranePump(Component): | ||
| """A class to represent Membrane Channels. | ||
| Assumes the membrane channel transport substrates in a specific direction across the membrane | ||
| Uses a mechanism called "catalysis" |
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See above comment on mechanism type.
| if direction is None: | ||
| self.product = self.set_species(product, material_type= 'Passive') | ||
| else: | ||
| self.product = self.set_species(product, material_type= direction) |
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Maybe this should be an attribute?
| return self.membrane_protein | ||
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| def update_species(self): | ||
| mech_cat = self.get_mechanism('catalysis') |
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This should be a different type of mechanism e.g. 'membrane_insertion'
| """ | ||
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| # PROTEIN | ||
| self.membrane_protein = self.set_species(membrane_protein, material_type='protein', attributes=attributes) |
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#Set Internal and Membrane Compartments
self.internal_compartment = ...
self.membrane_compartment = ...
self.membrane_protein_free = self.set_species(membrane_protein, material_type = 'protein', compartment = internal_compartment, attributes = attributes)
self.membrane_protein_integrated = self.set_species(membrane_protein, material_type = 'protein', attributes = attributes, compartment = membrane_compartment)
| Assumes the membrane channel transport substrates in a specific direction across the membrane | ||
| Uses a mechanism called "catalysis" | ||
| """ | ||
| def __init__(self, integral_membrane_protein: Union[Species, str, Component], |
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In all the inits, can you add compartment keywords e.g. internal_compartment = "Internal"
Added membrane components and transport mechanism. A notebook is included for example of transport.