Dimorphite-DL

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Dimorphite-DL is an open-source software for enumerating ionization states of molecules created by Durrant Lab at University of Pittsburgh.

Original Publication : https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0336-9

Installation

1. Download software here : https://durrantlab.pitt.edu/dimorphite-dl/

2. You will need a python virtual environment with rdkit

- Anaconda/Miniconda environment (must use bash)

Install 
https://www.anaconda.com/products/distribution install instruction
Source and install rdkit
$ conda create -c conda-forge -n my-rdkit-env rdkit
$ conda activate my-rdkit-env

- python venv

Set up
$ python3.6 -m venv ddl-env
Source and install rdkit-pypi (rdkit-pypi is a older and light-weight version of RDKit that contains the essential libraries. If you want to use full RDKit please use Anaconda/Miniconda)
$ source ddl-env/bin/activate
or 
$ source ddl-env/bin/activate.csh (if you use C-Shell)
$ pip install rdkit-pypi

To check if RDKit is installed in the environment

$ python m 'import rdkit'
You should see no error

For BKS Cluster users

Dimorphite-DL can be found on Cluster 2 here

/mnt/nfs/home/khtang/soft/dimorphite_dl-1.2.4

You can also use existing ZINC environments

ZINC15

$ source /nfs/soft/www/apps/zinc15/envs/edge/env.csh

ZINC20 (on bash)

$ source /mnt/nfs/home/devtest/anaconda3/bin/activate /nfs/soft/www/apps/zinc21/envs/development

Run it

1. Source the environment

2. Run it

For guide
python /mnt/nfs/home/khtang/soft/dimorphite_dl-1.2.4/dimorphite_dl.py --help

Examples:
python dimorphite_dl.py --smiles_file sample_molecules.smi --max_variants 3 --silent

python dimorphite_dl.py --smiles_file sample_molecules.smi --max_variants 3 --output_file result.txt