polychrom.starting_conformations module

polychrom.starting_conformations.create_random_walk(step_size, N)

Creates a freely joined chain of length N with step step_size

polychrom.starting_conformations.create_spiral(r1, r2, N)

Creates a “propagating spiral”, often used as an easy mitotic-like starting conformation.

Run it with r1=10, r2 = 13, N=5000, and see what it does.

polychrom.starting_conformations.grow_cubic(N, boxSize, method='standard')

This function grows a ring or linear polymer on a cubic lattice in the cubic box of size boxSize.

If method==”standard, grows a ring starting with a 4-monomer ring in the middle

if method ==”extended”, it grows a ring starting with a long ring going from z=0, center of XY face, to z=boxSize center of XY face, and back.

If method=”linear”, then it grows a linearly organized chain from 0 to size. The chain may stick out of the box by one, (N%2 != boxSize%2), or be flush with the box otherwise

Parameters:

• N (chain length. Must be even for rings.) –
• boxSize (size of a box where polymer is generated.) –
• method ("standard", "linear" or "extended") –