Python RNA.md方法代码示例

# 需要导入模块: import RNA [as 别名]
# 或者: from RNA import md [as 别名]
def temperature_reactivity( sequence, structure, temperature1, temperature2 ):
    """Evaluate temperature-dependent difference in energy, entropy, enthalpy."""
    temperature_model1 = RNA.md()
    temperature_model2 = RNA.md()
    temperature_model1.temperature = temperature1
    temperature_model2.temperature = temperature2
    fc1 = RNA.fold_compound(sequence, temperature_model1)
    fc2 = RNA.fold_compound(sequence, temperature_model2)
    energy_of_struct1 = fc1.eval_structure(structure)
    energy_of_struct2 = fc2.eval_structure(structure)
    # normalize delta_energy, add 0.001 to prevent division by 0
    delta_energy = abs((energy_of_struct2 - energy_of_struct1) / (energy_of_struct2 + 0.001))

    return (delta_energy, energy_of_struct1, energy_of_struct2)

# 需要导入模块: import RNA [as 别名]
# 或者: from RNA import md [as 别名]

#.........这里部分代码省略.........
    # Compare --minh, --min-rate, --t8 and --tX :
    if args.verbose:
        dG_min = -_RT * math.log(1 / args.t_fast / args.k0)
        print('# --t-fast: {} s => {} kcal/mol barrier height and {} /s rate at k0 = {}'.format(
            args.t_fast, dG_min, 1/args.t_fast, args.k0))
        if args.t_slow is not None:
            dG_max = -_RT * math.log(1 / args.t_slow / args.k0)
            print('# --t-slow {} s => {} kcal/mol barrier height and {} /s rate at k0 = {}'.format(
                args.t_slow, dG_max, 1/args.t_slow, args.k0))

    if args.t_fast * 10 > args.t_ext:
        raise Exception("""Conflicting Settings: rate for equilibration must be
                much faster than for nucleotide extension.""")

    if args.t_slow is not None and args.t_end * 100 > args.t_slow:
        raise Exception("""Conflicting Settings: 1/--min-rate should be much
                longer than the simulation time --t_end.""")

    try:
        check_version(args.treekin, ril._MIN_TREEKIN_VERSION)
    except ExecError:
        pass

    def versiontuple(rv):
        return tuple(map(int, (rv.split("."))))
    if versiontuple(RNA.__version__) < versiontuple(ril._MIN_VIENNARNA_VERSION):
        raise VersionError('ViennaRNA', RNA.__version__, ril._MIN_VIENNARNA_VERSION)

    ############################
    # Start with DrTransformer #
    ############################

    # Set model details.
    vrna_md = RNA.md()
    vrna_md.noLP = 1
    vrna_md.temperature = args.temperature

    if args.pyplot:
        all_courses = []

    # Write logging output
    if args.stdout == 'log' or lfh:
        fdata  = "# File generated using DrTransformer v{}\n".format(ril.__version__)
        fdata += "#\n"
        fdata += "# >{}\n# {} \n".format(name, fullseq)
        fdata += "#\n"
        fdata += "# Co-transcriptional folding paramters:\n"
        fdata += "# --t-ext: {} sec\n".format(args.t_ext)
        fdata += "# --t-end: {} sec\n".format(args.t_end)
        fdata += "# --temperature: {} C\n".format(args.temperature)
        fdata += "# --start: {}\n".format(args.start)
        fdata += "# --stop: {}\n".format(args.stop)
        fdata += "#\n"
        fdata += "# Algorithm paramters:\n"
        fdata += "# --min-occupancy: {}\n".format(args.min_occupancy)
        fdata += "# --t-fast: {} sec\n".format(args.t_fast)
        fdata += "# --t-slow: {} sec\n".format(args.t_slow)
        fdata += "# --findpath-search-width: {}\n".format(args.findpath_search_width)
        fdata += "# --structure-search-mode: {}\n".format(args.structure_search_mode)
        fdata += "# --min-breathing: {} nuc\n".format(args.min_breathing)
        fdata += "# --detailed-pruning: {}\n".format(args.detailed_pruning)
        fdata += "# --k0: {}\n".format(args.k0)
        fdata += "#\n"
        fdata += "#\n"
        fdata += "# Results:\n"
        fdata += "# Tanscription Step | Energy-sorted structure index | Structure | Energy | Occupancy | Structure ID (-> Plotting ID)\n"

# 需要导入模块: import RNA [as 别名]
# 或者: from RNA import md [as 别名]
"""Calculate the mfes and the partition function of the sequences for both temperatures."""

import sys
import RNA
import matplotlib
import Bio
import re # for regular expressions
import matplotlib.pyplot as plt
from math import exp
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
from matplotlib.backends.backend_pdf import PdfPages

MODEL_LOW_TEMPERATURE = RNA.md()
MODEL_HIGH_TEMPERATURE = RNA.md()

MODEL_LOW_TEMPERATURE.temperature = 30
MODEL_HIGH_TEMPERATURE.temperature = 37
RRS = 'AAGGAG'
SPACER = 6
START = 'AUG'
BOLTZMANN_K = 1.9872041e-3

def str2filename ( string ):
    """ turn string into suitable filename """
    rawstring = repr(string)
    newstring = re.sub(r'[\W]', '-',rawstring)
    newstring = newstring.strip('-')
    # cut at 31 characters, remove remaining '-' or '_' at the end