Dimorphite-DL - Revision history

Khtang: /* Run it */

2022-08-04T22:01:59Z

Run it

← Older revision		Revision as of 22:01, 4 August 2022
Line 44:		Line 44:
	python /mnt/nfs/home/khtang/soft/dimorphite_dl-1.2.4/dimorphite_dl.py --help		python /mnt/nfs/home/khtang/soft/dimorphite_dl-1.2.4/dimorphite_dl.py --help

	~~Example run~~:		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 --silent

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

Khtang: /* For BKS Cluster users */

2022-08-04T21:57:56Z

For BKS Cluster users

← Older revision		Revision as of 21:57, 4 August 2022
Line 30:		Line 30:
	Dimorphite-DL can be found on Cluster 2 here		Dimorphite-DL can be found on Cluster 2 here
	/mnt/nfs/home/khtang/soft/dimorphite_dl-1.2.4		/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

	'''ZINC15'''		'''ZINC15'''
	$ source /nfs/soft/www/apps/zinc15/envs/edge/env.csh		$ source /nfs/soft/www/apps/zinc15/envs/edge/env.csh

Khtang: /* Installation */

2022-08-04T21:57:26Z

Installation

← Older revision		Revision as of 21:57, 4 August 2022
Line 6:		Line 6:
	1. Download software here : https://durrantlab.pitt.edu/dimorphite-dl/		1. Download software here : https://durrantlab.pitt.edu/dimorphite-dl/

	~~Dimorphite-DL can be found on Cluster 2 here~~
	~~/mnt/nfs/home/khtang/soft/dimorphite_dl-1.2.4~~
	2. You will need a python virtual environment with rdkit		2. You will need a python virtual environment with rdkit

Line 24:		Line 22:
	$ 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

	~~'''Note'''~~

	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

Khtang: /* Installation */

2022-08-04T21:56:02Z

Installation

← Older revision		Revision as of 21:56, 4 August 2022
Line 31:		Line 31:
	You should see no error		You should see no error
	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

Khtang: /* Run it */

2022-08-04T21:55:23Z

Run it

← Older revision		Revision as of 21:55, 4 August 2022
Line 38:		Line 38:
	== Run it ==		== Run it ==
	1. Source the environment		1. Source the environment

	2. Run it		2. Run it
	For guide		For guide

Khtang: Created page with "'''Dimorphite-DL is an open-source software for enumerating ionization states of molecules created by [https://durrantlab.pitt.edu/ Durrant Lab] at University of Pittsburgh.''..."

2022-08-04T21:54:42Z

Created page with "'''Dimorphite-DL is an open-source software for enumerating ionization states of molecules created by [https://durrantlab.pitt.edu/ Durrant Lab] at University of Pittsburgh.''..."

New page

'''Dimorphite-DL is an open-source software for enumerating ionization states of molecules created by [https://durrantlab.pitt.edu/ 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/

Dimorphite-DL can be found on Cluster 2 here
/mnt/nfs/home/khtang/soft/dimorphite_dl-1.2.4
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

'''Note'''

To check if RDKit is installed in the environment
$ python m 'import rdkit'
You should see no error
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