Dimorphite-DL: Difference between revisions
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1. Download software here : https://durrantlab.pitt.edu/dimorphite-dl/ | 1. Download software here : https://durrantlab.pitt.edu/dimorphite-dl/ | ||
2. You will need a python virtual environment with rdkit | 2. You will need a python virtual environment with rdkit | ||
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$ source ddl-env/bin/activate.csh (if you use C-Shell) | $ source ddl-env/bin/activate.csh (if you use C-Shell) | ||
$ pip install rdkit-pypi | $ pip install rdkit-pypi | ||
To check if RDKit is installed in the environment | To check if RDKit is installed in the environment | ||
$ python m 'import rdkit' | $ python m 'import rdkit' | ||
You should see no error | 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 with RDKit already installed on Cluster 2 | You can also use existing ZINC environments with RDKit already installed on Cluster 2 | ||
'''ZINC15''' | '''ZINC15''' | ||
$ source /nfs/soft/www/apps/zinc15/envs/edge/env.csh | $ source /nfs/soft/www/apps/zinc15/envs/edge/env.csh |
Revision as of 21:57, 4 August 2022
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 with RDKit already installed on Cluster 2 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 Example run: python dimorphite_dl.py --smiles_file sample_molecules.smi --max_variants 3 --silent