Create a path_graph argument and update to_compound to allow for visu… #2
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| def visualize(self, bead_color="#5d8aa8"): |
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We should add a bead size parameter here, since the radii and bond lengths of these paths are often at coarse-grained length scales, the default bead size of 0.3 can look pretty small. Maybe add a parameter and use a default of 0.7.
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| class Path: | ||
| def __init__(self, N=None, coordinates=None, bond_graph=None): | ||
| def __init__(self, N=None, coordinates=None, bond_graph=None, path_graph=None): |
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I'm kind of confused about the difference between bond_graph and path_graph here. With the current behavior, you pass in a networkx graph, and that is used to create the bond graph when converting the path to a compound with the set_bond_graph method in Compound.
So, a linear path graph is achieved by passing in:
bond_graph = nx.path_graph(N)
But..now as I'm typing this up, I realize that one of the issues with this is that you have to predefine N. This works for random walk paths, but not ones where you don't know N initially (Lamellar, Circular in certain cases). Does the "linear" graph solve this?
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