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 💤	0 ❌	0 🔥	17m 13s ⏱️

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:

1. Create a directory named as you want and access it (in this case called work_pol):

  [~] mkdir work_pol
  [~] cd work_pol

2. 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

3. Get PySoftK from the GitHub repository:

  git clone https://github.com/alejandrosantanabonilla/pysoftk.git

4. 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

1. 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

2. Make a directory to download PySoftK and change to this directory

   (pysoftk_env) mkdir pysoftk_dir
   (pysoftk_env) cd pysoftk_dir

3. Download PySoftK from Github

   (pysoftk_env) git clone https://github.com/alejandrosantanabonilla/pysoftk.git

4. Install xtb using conda

   conda install -c conda-forge xtb

5. Install MDAnalysis using conda

   conda install -c conda-forge mdanalysis

6. Install PySoftK and its dependencies as required

   (pysoftk_env) cd pysoftk
   (pysoftk_env) pip install .

7. 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:

5. 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)