cheminfo_tutorial_20241028

cheminfomratics handson @ CBI2024年大会

Breaf introduction

This is the material for cheminformatics hands-on session at CBI2024

Participants requirements

• Basic skill of python programming
• Basic knowledge of cheminfomratics
• Unfortunately it's difficult to support Windows os. The code will be tested on Linux, Mac OS but not Windows(inculdes WSL).

Prerequreiment

• Install anaconda or mambaforge
• Install REINVENT ver4
• Install Autodock Vina
• Install Gypsum-DL
• Install Maize-contrib ver 0.5.5

Tips

• mamba is a reimplementation of the conda package manager in C++. And it works faster than conda but it maight be cause problem for building process.
• Following examples use conda but you can use mama at your own risk.
• miniconda
• mambaforge

INSTALL

FOR Ubuntu24.04

REINVENT4

$ git clone https://github.com/MolecularAI/REINVENT4.git
$ cd REINVENT4
$ conda create --name reinvent4 python=3.10
$ conda activate reinvent4
$ pip install torch==2.2.1 torchvision==0.17.1 torchaudio==2.2.1 --index-url https://download.pytorch.org/whl/rocm5.7
$ pip install --no-deps .

Autodock Vina

The example put vina on /opt/vina but you can put vina any place.

$ wget https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.5/vina_split_1.2.5_linux_x86_64
$ sudo mkdir -p /opt/vina/bin/
$ sudo mv vina_split_1.2.5_linux_x86_64 /opt/vina/bin
$ sudo ln -s /opt/vina/bin/vina_split_1.2.5_linux_x86_64 /opt/vina/bin/vina
$ export PATH=/opt/vina/bin/:$PATH

Gypsum-DL

if you don't have mpi, remove mpi4py from the following command.

$ sudo apt info openmpi-bin
$ conda create --name gypsum python=3.10
$ conda activate gypsum
$ conda install -c conda-forge rdkit numpy scipy mpi4py
$ git clone https://github.com/durrantlab/gypsum_dl.git

Maize-contrib

$ git clone https://github.com/MolecularAI/maize-contrib.git
$ cd maize-contrib
$ conda env create -f env-users.ymlhttps://github.com/DavidAnson/markdownlint/blob/v0.35.0/doc/md014.md
$ conda activate maize
$ pip install --no-deps ./
$ conda install -c conda-forge pymol-open-source

FOR MacOS 14.61(M3)

Set the directory to be used for the hands-on session.

$ cd ~
$ mkdir CBI
$ cd CBI

REINVENT4

$ git clone https://github.com/MolecularAI/REINVENT4.git
$ cd REINVENT4
$ conda create --name reinvent4 python=3.10
$ conda activate reinvent4
$ pip install torch
$ pip install --no-deps .

Autodock Vina

$ wget https://vina.scripps.edu/wp-content/uploads/sites/55/2020/12/autodock_vina_1_1_2_mac_64bit.tar.gz
$ tar xvfz autodock_vina_1_1_2_mac_64bit.tar.gz
$ sudo mkdir -p /opt/vina/bin/
$ sudo mv autodock_vina_1_1_2_mac_catalina_64bit/bin/vina /opt/vina/bin/.

Gypsum-DL

$ sudo apt info openmpi-bin
$ conda create --name gypsum python=3.10
$ conda activate gypsum
$ conda install -c conda-forge rdkit numpy scipy
$ git clone https://github.com/durrantlab/gypsum_dl.git

Maize-contrib & Maize

$ git clone https://github.com/MolecularAI/maize-contrib.git
$ cd maize-contrib
$ conda env create -f env-users.ymlhttps://github.com/DavidAnson/markdownlint/blob/v0.35.0/doc/md014.md
$ conda activate maize
$ pip install --no-deps .
$ git clone https://github.com/Mishima-syk/maize.git
$ cd maize
$ pip install --no-deps .
$ conda install -c conda-forge pymol-open-source jupyter
## data/maize.tomlを書き換えます。
$ export XDG_CONFIG_HOME="/Users/kzfm/CBI/cheminfo_tutorial_20241028/data" #pathはユーザーごとに異なります

Reference & Link

• Anaconda
• REINVENT ver4
• reinvent4 Github
• Autodock Vina
• Gypsum-DL
• Maize-contrib

Misc

• maize cofiguration file

  • By default Config will look for a configuration file named maize.toml in $XDG_CONFIG_HOME (usually at ~/.config/,) detail
  • The repo provides example maize.toml for SBDD WF. We will configure it in this handson training ;-)

  $ echo $XDG_CONFIG_HOME
  /home/iwatobipen/.config
  $ cat /home/iwatobipen/.config/maize.toml
  # maize global configuration file example
  # Where to save temporary files and all workflow directories
  scratch = "/tmp"

• Tested OS

  • [x] Ubuntu24.04
  • [ ] Ubuntu22.04
  • [ ] MacOS M1
  • [ ] MacOS M2
  • [x] MacOS14 M3
  • [ ] Windows

Author

• Kazufumi Ohkawa
• Koichiro Arai
• Natsumi Miyano
• Kazutoshi Takahashi
• Takayuki Serizawa