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from biotite.structure.io.pdb import get_structure, PDBFile

#################################################
# residue id, atom name : value in [0..1] domain
# input data
values = {
    (1, 'CA'): 0.5,
    (2, 'C'): 0.8,
}

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conda env export --no-builds | grep -v "prefix" > environment.yml

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'1': 5mC>T
'2': AID/APOBEC
'13': AID/APOBEC
'3': HR DDR defect
'4': Tobacco
'10a': Polymerase epsilon
'10b': Polymerase epsilon
'14': Polymerase epsilon + MMR
'15': MMR
'7b': UV light

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# from https://www.mdanderson.org/documents/Labs/Wood-Laboratory/human-dna-repair-genes.html

BER:
    - UNG
    - SMUG1
    - MBD4
    - TDG
    - OGG1
    - MUTYH
    - MYH

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# FROM https://habr.com/ru/post/494546/

#Траектория частицы
Track = True

#длина траектории
Track_time = 5

#Гравитационная постоянная
G = 5

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import argparse


class Test():
    def __init__(self):

        """INITIALIZE PARSER"""
        parser = argparse.ArgumentParser()
        parser.add_argument('--name', type=str, required=False, default='World')
        parser.add_argument(

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#!/usr/bin/python
#
# Created by Albert Au Yeung (2010)
#
# An implementation of matrix factorization
#
try:
    import numpy
except:
    print "This implementation requires the numpy module."

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import multiprocessing
import json
import requests
import urllib
from requests.packages.urllib3.exceptions import InsecureRequestWarning
requests.packages.urllib3.disable_warnings(InsecureRequestWarning)


def mp_ensembl_worker(raw_mutations_chunk):
    """ Helper function for ENSEMBL API call """

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%matplotlib inline
import seaborn as sns
sns.set(style="ticks")

df = sns.load_dataset("iris")
sns.pairplot(df, x_vars=["sepal_length", "sepal_width"], y_vars=["petal_length", "petal_width"], markers=".", kind="reg")

# round(df.corr()**2, 2)
sns.heatmap(df.corr(), cmap=sns.color_palette("RdBu_r", 7), annot=True, fmt=".2f", center=0, vmin=-1.0, vmax=1.0)

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import requests
import json

# MUTAGENE_URL = "https://www.ncbi.nlm.nih.gov/research/mutagene"
# MUTAGENE_URL = "https://dev.ncbi.nlm.nih.gov/research/mutagene"
MUTAGENE_URL = "https://mwebdev2/research/mutagene"
# MUTAGENE_URL = "http://localhost:5000"


def get_motifs(fname, assembly=37):