Concurrence #28
Concurrence #28
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contact_map/concurrence.py
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| ---------- | ||
| values : list of list of bool | ||
| the whether a contact is present for each contact pair at each | ||
| point in time; outer list is length number of frames, inner list |
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this is the other way around outer list is length contact pair and inner list is frame
contact_map/concurrence.py
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| labels = [str(contact[0]) for contact in atom_contacts] | ||
| distances = md.compute_distances(trajectory, atom_pairs=atom_pairs) | ||
| vector_f = np.vectorize(lambda d: d < cutoff) | ||
| values = list(map(list, zip(*vector_f(distances)))) |
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please add a comment for this magic
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and this could be changed into: list(map(list, vector_f(distances).T)
as you do want to map the transpose of the array to a list and I suspect this is more performant as it used numpy instead of zip. But I didn't check my suspicion
contact_map/concurrence.py
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| distances = md.compute_distances(trajectory, | ||
| atom_pairs=atom_pairs) | ||
| min_dists = [min(dists) for dists in distances] | ||
| values.append(list(map(lambda d: d < cutoff, min_dists))) |
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list comprehension should be more readable
contact_map/concurrence.py
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| list : | ||
| list in the format of ``ContactCount.most_common()`` | ||
| """ | ||
| if isinstance(contact_input, contact_map.ContactFrequency): |
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shouldn't this be isinstance(contact_input, contact_map.ContactObject) ? As this statement would be False for a ContactMap or ContactDifference
contact_map/concurrence.py
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| """ | ||
| if isinstance(contact_input, ContactObject): | ||
| contact_input = contact_input.contacts[atom_or_res] | ||
| if isinstance(contact_input, contact_map.ContactCount): |
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can you put an extra blank line, this tripped me up and I read if, elif
When looking at the behavior of contacts, it is often not only important to see how often a contact occurs, but also what other contacts occur simultaneously. These simultaneous contacts (which we refer to as "concurrence") can be used to define stable states.