# ---
# jupyter:
#   jupytext:
#     text_representation:
#       extension: .py
#       format_name: light
#       format_version: '1.5'
#       jupytext_version: 1.14.4
#   kernelspec:
#     display_name: Python 3
#     language: python
#     name: python3
# ---

# # Title
# The title of the notebook should be coherent with file name. Namely, file name should be:    
# *author's initials_progressive number_title.ipynb*    
# For example:    
# *EF_01_Data Exploration.ipynb*
#
# ## Purpose
# State the purpose of the notebook.
#
# ## Methodology
# Quickly describe assumptions and processing steps.
#
# ## WIP - improvements
# Use this section only if the notebook is not final.
#
# Notable TODOs:
# - todo 1;
# - todo 2;
# - todo 3.
#
# ## Results
# Describe and comment the most important results.
#
# ## Suggested next steps
# State suggested next steps, based on results obtained in this notebook.

# # Setup
#
# ## Library import
# We import all the required Python libraries

# +
# Data manipulation
import pandas as pd
import numpy as np
import os
import glob
from biopandas.pdb import PandasPdb
from pymol import cmd

# Options for pandas
pd.options.display.max_columns = 50
pd.options.display.max_rows = 30

# Visualizations
import plotly
import plotly.graph_objs as go
import plotly.offline as ply
plotly.offline.init_notebook_mode(connected=True)

import matplotlib.pyplot as plt
import seaborn as sns

# Autoreload extension
if 'autoreload' not in get_ipython().extension_manager.loaded:
    # %load_ext autoreload
    
# %autoreload 2
# -

# ### Change directory
# If Jupyter lab sets the root directory in `notebooks`, change directory.

if "notebook" in os.getcwd():
    os.chdir("..")

# ## Local library import
# We import all the required local libraries libraries

# +
# Include local library paths
import sys
# sys.path.append("./src") # uncomment and fill to import local libraries

# Import local libraries
# import src.utilities as utils
# -

# # Parameter definition
# We set all relevant parameters for our notebook. By convention, parameters are uppercase, while all the 
# other variables follow Python's guidelines.

#
# # Data import
# We retrieve all the required data for the analysis.

# # Data processing
# Put here the core of the notebook. Feel free to further split this section into subsections.

# # References
# We report here relevant references:
# 1. author1, article1, journal1, year1, url1
# 2. author2, article2, journal2, year2, url2



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