mythos.input.sequence_dependence

Functions for handling sequence-dependent inputs.

Functions

read_ss_weights(→ dict[str, jax.numpy.ndarray])

Read and oxDNA sequence-dependent weights file to a dictionary.

Module Contents

mythos.input.sequence_dependence.read_ss_weights(file: str) → dict[str, jax.numpy.ndarray][source]

Read and oxDNA sequence-dependent weights file to a dictionary.

This produces a dictionary of the parameters that are influenced by this file, which include stacking parameters:

  • ss_stack_weights (from STCK_X_Y entries)

  • eps_stack_kt_coeff (from STCK_FACT_EPS)

and hydrogen-bonding parameters:

  • ss_hb_weights (from HYDR_X_Y entries, requires on or both of HYDR_A_T or HYDR_T_A and HYDR_G_C or HYDR_C_G to be present)

File should be of the form KEY=VALUE, one per line, whitespace is ignore and float values may use ‘f’ suffix, but it is not required.