mimicpy 0.2.1

Companion library to the MiMiC framework for input preparation.

MiMiCPy

MiMiCPy is the companion library to the MiMiC framework for streamline preparation of input files. It includes a suite of command line tools and plugins for PyMOL/VMD. Visit the MiMiC homepage for more details and documentation.

Installation

To install, run the following command:

pip install mimicpy

The PrepQM plugins for PyMOL and/or VMD can be optionally installed by running:

mimicpy_plugin_installer -pymoldir /path/to/plugin/ -vmddir /path/to/plugin/

The path to the plugin is usually either the path to the PyMOL/VMD installation, or the user home directory.

Portability Issues

MiMiCPy requires Python >= 3.5, pandas >= 0.24.0 and numpy >= 1.12.0. The plugins have been tested with PyMOL version 2.3.4 and VMD version 1.9.4a38, although other versions are expected to work. If any incompatibilities are found, please post an issue here.

Demo

A demo of atom selection for the QM region, and generation of the MiMiC-based CPMD input file using MiMiCPy is shown below.

user@system:~$ mimicpy prepqm -top acetone.top -coords acetone.gro


 	                ***** MiMiCPy *****

 	 For more information type mimicpy [subcommand] --help

=====> Running prepqm <=====


**Reading topology**

Cannot find path to Gromacs installation.
Read atoms from acetone.itp.
No atoms found in acetone.top.

Some atom types had no atom numbers information.
They were guessed as follows:

+---------------------+
| Atom Type | Element |
+---------------------+
|     c     |    C    |
+---------------------+
|     c3    |    C    |
+---------------------+
|     o     |    O    |
+---------------------+
|     hc    |    H    |
+---------------------+

**Reading coordinates**  |Done

Please enter selection below. For more information type 'help'
> add resname is ACT
> q
Using default values for maxstep and timestep
Wrote Gromacs index file to index.ndx
Wrote new CPMD input script to cpmd.inp

=====> Done <=====