semvec/pypi-packages huggingface dataset:
pinda 0.2.0rc2
Pip-INstallable Dockerized Applications

# pinda

Pip-INstallable Dockerized Applications

*pinda* is designed to deliver dockerized versions of software packages that have a user interface that is as identical
as possible to what would be available if the package was installed in the conventional way.

*pinda* has been developed primarily to simplify the process of provisioning cloud compute resources, 
and at present it focusses on software tools useful for biomolecular simulation; but it may be used 
on other platforms and extended to other domains.

For example, to install Gromacs version 2019:
```
% pinda install gromacs 2019
```
Once the installation is complete, you will find the 'gmx' command in your path.

## Installation:

Easiest via pip:
```
% pip install pinda
% pinda update
```

## Usage:

To see a list of packages available via *pinda*:
```
% pinda list
  NAMD       2.12       NAMD parallel molecular dynamics code, version 2.12
  ambertools 18         AmberTools version 18
  chimeratools 1.0.0      Molecular images via Chimera
  fpocket    3.0        FPocket version 3.0
  g_mmpbsa   5.1        g_mmpbsa for Gromacs 5.1
* gromacs    2019       Gromacs version 2019
  gromacs    2019-cuda  Gromacs version 2019 with CUDA support
  gromacs    5.1.4      Gromacs version 5.1.4
  gromacs    5.1.4-cuda Gromacs version 5.1.4 with CUDA support
  obabel     2.4.1      Open Babel version 2.4.1
  procheck   3.5.4      PROCHECK protein structure quality assessment tools
* propka     3.1.0      PROPKA version 3.1
  pymolqc    1.8.5.1    Python scripting interface to PyMOL without a GUI
  reduce     3.3.160602 REDUCE version 3.3.160602
* vina       1.1.2      AutoDock Vina and selected AutoDock Tools
%
```
Packages that you have already installed are asterisked.

To install a package:
```
% pinda install ambertools 18
%
```

To uninstall a package:
```
% pinda uninstall obabel 2.4.1
%
```

For detailed information on a package:
```
% pinda info ambertools 18

AmberTools version 18

This pinda distribution provides the following commands:

    "sander"      : the Amber/Ambertools "sander" command
    "amber-shell" : drops you into a bash shell from which all other
                    AmberTools commands are accessible (e.g. tleap).

For full license and usage information, please visit http://ambermd.org

%
```
## Limitations:

You need to have [Docker](http://docker.com) installed on your machine. The containerised versions of the applications can
only 'see' files that are in the directory a command in invoked from, or a subdirectory of this, so for example:
```
% gmx mdrun -s bpti.tpr # This is fine
% gmx mdrun -s ../bpti.tpr # This won't work
```

## Author:

Charlie Laughton charles.laughton@nottingham.ac.uk

## License:

BSD 3-clause