Martin Elstner MartinEls

Do Deep Learning Methods Really Perform Better in Molecular Conformation Generation?

Authors: Gengmo Zhou, Zhifeng Gao, Zhewei Wei, Hang Zheng, Guolin Ke

We revisit the benchmark after simple traditional algorithms beat deep learning methods in conformation generation.

Data

Installing Jupyter notebook to AWS

This is an early draft of this guide, which currently does not include any screenshots. I may be making a lot of assumptions about what you do or do not know in this guide and so I welcome any constructive criticism to help make it more useful. Please feel free to fork this guide and annotate it where it does not work, I would welcome any pull requests to improve this documentation.

Setup amazon linux server (free tier)

From Amazon's EC2 page, go to Launch Instance
Choose an Amazon Linux 64-bit server and continue
Select t2.micro (this is the free tier)
Continue to the Add Storage page and adjust this up to 30GB if you're so inclined (default is 8GB, which is plenty)
Tag your instance with a name like "notebook"

	import numpy as np
	import pandas as pd
	from matplotlib.figure import Figure

	data_url = "https://cdn.jsdelivr.net/gh/holoviz/panel@master/examples/assets/occupancy.csv"
	data = pd.read_csv(data_url, parse_dates=["date"]).set_index("date")

	primary_color = "#0072B5"
	secondary_color = "#94EA84"

	import ast
	import requests

	url = 'http://localhost:5006/rest/post_data'

	def post(value):
	data = {'data': value}
	response = requests.post(url, data = data)
	if response.status_code==200:
	print(ast.literal_eval(response.text))

	import pandas as pd
	import hvplot.pandas
	import panel as pn

	pn.extension(sizing_mode="stretch_width")

	PALETTE = [
	"#ff6f69",
	"#ffcc5c",
	"#88d8b0",

	# From https://stackoverflow.com/a/68876046/1319998, which is itself inspired by https://stackoverflow.com/a/68814418/1319998

	from contextlib import contextmanager
	from collections import namedtuple
	from ctypes import cdll, byref, string_at, c_char_p, c_int, c_double, c_int64, c_void_p
	from ctypes.util import find_library
	from sys import platform


	def query(db_file, sql, params=()):

	# WARNING : This gist in the current form is a collection of command examples. Please exercise caution where mentioned.

	# Docker
	sudo apt-get update
	sudo apt-get remove docker docker-engine docker.io
	sudo apt install docker.io
	sudo systemctl start docker
	sudo systemctl enable docker
	docker --version