src.read.strand_motifs_trajectory module

strand_motifs_trajectory(filepaths: list, alphabet: list, motiflength: int = 4, times_unit: Quantity = None, skiprows: int = 2) → MotifTrajectory

reads from the complexes.txt of the RNAReactor simulation output and returns corresponding concentration vectors in motif space.

PARAMETERS:

filepathsstring or list of strings

Output file of the RNAReactor simulation

skiprowint, optional

Skip the first skiprow lines, including comments when reading the file; default : 2

RETURN:

strand_motifs_trajectory : MotifTrajectory

steps_and_times_and_complexes_from_complexes_txt(filepath: str, skiprows: int = 2) → array | list

Parameters:

filepath : str, skiprows : int = 2,

skip the first <skiprows> lines of the complex.txt file

Returns:

steps : nd-array with dtype int total_physical_time : nd-array with dtype np.float64 complexes : list

with every element of list is the list of complexes at that time the list of complexes at given time is again a list of the format complexes[time_index][complex_index]=[number_of_complex : int, structure_of_complex : str]

steps_and_times_and_sequence_trajectory_from_complexes_txt(filepath: str, skiprows: int = 2) → array | list

Parameters:

filepath : str, skiprows : int = 2,

skip the first <skiprows> lines of the complex.txt file

Returns:

steps : nd-array with dtype int total_physical_time : nd-array with dtype np.float64 complexes : list

with every element of list is the list of complexes at that time the list of complexes at given time is again a list of the format complexes[time_index][complex_index]=[number_of_complex : int, structure_of_complex : str]