kinetic_folding_rate.py 文件源码

def get_folding_rate_for_seq(seq, secstruct, temp, refT=37.0):
    """Scale the predicted kinetic folding rate of a protein to temperature T, based on the relationship ln(k_f)?1/T

    Args:
        seq (str, Seq, SeqRecord): Amino acid sequence
        secstruct (str): Structural class: ``all-alpha``, ``all-beta``, ``mixed``, or ``unknown``
        temp (float): Temperature in degrees C
        refT (float): Reference temperature, default to 37 C

    Returns:
        float: Kinetic folding rate k_f at temperature T.

    """

    # Not much data available on this slope value, however its effect on growth rate in a model is very small
    slope = 22000

    # Get folding rate for the reference temperature
    ref_rate = get_foldrate(seq, secstruct)
    preFactor = float(ref_rate) + slope / (float(refT) + 273.15)

    # Calculate folding rate at desired temperature
    rate = math.exp(preFactor - slope / (float(temp) + 273.15))

    return rate