ZhouGengmo

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

[arXiv]

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

MarcSkovMadsen

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"

MarcSkovMadsen

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))

MarcSkovMadsen

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

pn.extension(sizing_mode="stretch_width")

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

michalc

# 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=()):

nathzi1505

# 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

djsegal

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"