Replace functions related to indirect correlation matrix #9
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The previous functions used to calculate the indirect correlation matrices have been replaced with a single function,
generate_indirect_connectivity. The previous implementation was slow for larger systems, and systems with higher IL concentration. The new implementation largely relies on numpy commands, and runs significantly faster as a result.The new implementation has been tested against the old, both yielding the same indirect matrix for several trajectories. In the old implementation, it was necessary to calculate the matrix at least twice, as it was necessary to check the validity. I believe the new implementation only requires one function call to yield a valid indirect matrix.
Tests have been updated to reflect changes for the functions.