semvec/pypi-packages huggingface dataset:
desmondtools 1.4.0
Tools for Desmond molecular dynamics
Requires Python: >=3.11
Keywords: Schrodinger, Desmond, Multisim, Molecular-Dynamics, Maestro

# Tools for Desmond Molecular Dynamics

## Introduction

DesmondTools have a set of command-line scripts and a python library written to make 
setting up the molecular dynamics simulations easier for Desmond.

## Install

```bash
$ pip install desmondtools
```

## Documentation

See https://sunghunbae.github.io/desmondtools/


## Use of `desmondtools` library

```python
from desmondtools import Multisim

# read template .msj and .cfg
md_msj = Multisim(template="desmond-md.msj")
md_cfg = Multisim(template="desmond-md.cfg")

with open(msj_file,"w") as msj:
    # modify desmond msj template
    md_msj.dot.simulate[-1].cfg_file = cfg_file_basename
    
    # Setting up restraints using the restraints keyword:
    # https://www.schrodinger.com/kb/332119
    if args.posres_force > 0.0:
        # print the restraints in the multisim log file
        md_msj.dot.simulate[-1].print_restraint = 'true'

        # add the new terms defined in "restraints.new" to existing restraints.
        # The default is restraints.existing = ignore which will 
        # delete existing terms before adding any new ones.
        # md_msj.dot.simulate[-1].restraints.existing = 'retain'

        md_msj.dot.simulate[-1].restraints.new = [
            {
                'name'              : 'posre_harm',
                'atoms'             : [ f'"{args.posres}"' ],
                'force_constants'   : [ args.posres_force, ] * 3,
            }
            ]
        # force constants in the x, y, and z direction

    md_msj.write(msj)

with open(cfg_file,"w") as cfg:
    # modify desmond cfg template
    md_cfg.dot.randomize_velocity.seed = random.randint(1000, 9999)
    md_cfg.dot.time = total_simulation_time
    md_cfg.dot.temperature = t_schedule
    md_cfg.dot.trajectory.interval = args.interval
    md_cfg.write(cfg)
```
discord-ext-modal-paginator 1.3.0
An extension for discord.py that allows you to paginate a Modal using buttons.
Requires Python: >=3.8
Keywords: discord.py, dpy, discord, extension, discord.ext, modal, forum

Welcome to discord-ext-modal-paginator's documentation!
========================================================
An extension for discord.py that allows you to paginate a Modal using buttons.

*As seen in the discord.py server's Showcase* `channel <https://canary.discord.com/channels/336642139381301249/1147536267811225600>`_.

Installation
-------------
.. code-block:: sh

    python -m pip install -U discord-ext-modal-paginator

**PyPI**: https://pypi.org/project/discord-ext-modal-paginator/

**GitHub**: https://github.com/Soheab/modal-paginator

Example
-------
See `examples/verify_command.py <https://github.com/Soheab/modal-paginator/blob/main/examples/verify_command.py>`_ for a complete example.
And read the source code for more information, it has docstrings and comments.

Documentation
-------------
The documentation is available at https://discord-ext-modal-paginator.readthedocs.io/

Contributing
------------
Feel free to open an issue or a pull request if you have any problems or improvements. 
I would appreciate it if you could tell me on Discord first though, see my info below.

Contact
-----------
You can contact me on Discord, my username is ``Soheab_`` (#6240) and ID `150665783268212746`. \
I'm fairly active on the `discord.py server <https://discord.gg/dpy>`_. Feel free to ping me there.

My own server is at https://discord.gg/yCzcfju.

License
-------
This project is licensed under the ``MLP-2.0`` license. See the `LICENSE <https://github.com/Soheab/modal-paginator/blob/main/LICENSE>`_  file for more information.