pysoftk
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Python program for modelling and simulating polymers.
Coverage Report
File Stmts Miss Cover Missing /home/runner/.local/lib/python3.9/site-packages/pysoftk/folder_manager folder_creator.py 51 4 92% 38, 135, 157–158 /home/runner/.local/lib/python3.9/site-packages/pysoftk/format_printers format_mol.py 65 19 71% 59–60, 87–92, 116–121, 145–149, 156–157 /home/runner/.local/lib/python3.9/site-packages/pysoftk/htp_tools calculator_htp.py 52 13 75% 144–169, 244–250 /home/runner/.local/lib/python3.9/site-packages/pysoftk/linear_polymer super_monomer.py 51 7 86% 148–156 /home/runner/.local/lib/python3.9/site-packages/pysoftk/tools utils_rdkit.py 60 9 85% 44, 90, 146–148, 172–180 /home/runner/.local/lib/python3.9/site-packages/pysoftk/topologies branched.py 40 1 98% 120 diblock.py 55 1 98% 186 ranpol.py 75 10 87% 97, 106, 126, 182, 188, 195–199, 213, 223 /home/runner/.local/lib/python3.9/site-packages/pysoftk/torsional torsional.py 88 10 89% 49–50, 226–237 TOTAL 780 74 91%
Tests | Skipped | Failures | Errors | Time |
---|---|---|---|---|
72 | 0 :zzz: | 0 :x: | 0 :fire: | 17m 13s :stopwatch: |
PySoftK is a set of Python tools and programs for modelling and simulating polymers with different topologies. The program is still under active development and contributions are welcome. A complete introduction into the program can be found in this link Documentation.
Pip installation
To quickly install PySoftk, we encourage to do it inside a virtual environment, which can be achieved in the following way:
- Create a directory named as you want and access it (in this case called work_pol):
[~] mkdir work_pol
[~] cd work_pol
- Create a virtual environment named pol (this name can be changed, of course) and activate the environment:
[~] python -m venv pol
[~] source pol/bin/activate
- Get PySoftK from the GitHub repository:
git clone https://github.com/alejandrosantanabonilla/pysoftk.git
- Install PySoftK in this folder using the virtual environment
[~] cd pysoftk
[~] pip install .
NOTE: To use the calculators option, the code xtb needs to be installed and linked to the executable using the command:
export PATH="$PATH:$HOME/PATH_TO_FOLDER/xtb-X.X.X/bin"
export XTBHOME="PATH_TO_XTB_FOLDER/xtb-X.X.X"
ulimit -s unlimited
Conda installation
These are instructions to
- It is recommended to create a new virtual environment in which the PySoftK dependencies can be installed, for example
conda create --name pysoftk_env
conda activate pysoftk_env
- Make a directory to download PySoftK and change to this directory
(pysoftk_env) mkdir pysoftk_dir
(pysoftk_env) cd pysoftk_dir
- Download PySoftK from Github
(pysoftk_env) git clone https://github.com/alejandrosantanabonilla/pysoftk.git
- Install xtb using conda
conda install -c conda-forge xtb
- Install MDAnalysis using conda
conda install -c conda-forge mdanalysis
- Install PySoftK and its dependencies as required
(pysoftk_env) cd pysoftk
(pysoftk_env) pip install .
- You may need to add the PySoftK installation directory to your .bashrc or .zshrc file
PATH=$PATH:/<path to>/pysoftk_dir
That's it, you're ready to use PySoftK (remember to activate pysoftk_env!)
Replacing PATH_TO_FOLDER by the actual path where xtb is stored in your computer.
Testing your installation:
- To test PySoftK, navigate to the folders test_pysoftk and test_pol inside the test folder. Then, run the following command:
pytest -v
Contributors:
- Chris Lorenz (Polymer topologies and documentation)
- Rob Zioelek (Analysis tools and pysoftwhere developer utils)
- Raquel Lopez-Rios de Castro (Analysis tools main contributor, documentation)
- Alejandro Santana-Bonilla (Polymer topologies, utilities and mantaining)