RCBS.py (Reactivity of Chemical and Biochemical Systems) is a Python package that contains several scripts, functions and classes that simplify the analysis of chemical and biochemical simulations. It is built on top of MDAnalysis package.
The package currently is divided in one main module, md_analyser. This module is mainly built in top of MDAnalysis' and is designed in order to symplify the analysis of MD simulations. In the future, capabilities for building QM/MM models from simulations will be added in a new module.
pip install RCBS.py- Clone the repository in you local machine
git clone https://github.com/dynamicsUAB/RCBS.py.git
- Move to the folder
cd RCBS.py - Install the package using pip or pip3
pip install .
md_analyser is made of two principal scripts: measurements.py and calculators.py.
This is the main file that has to be imported. In it a class called Measurement is created. This class has one only argument: a preloaded MDAnalysis' Universe. Once the object is created, measurements such as distances or angles can be created using the add_* functions from the class. They require previous creation of atom groups using the select_atoms function form Universe or the selections.selection function from RCBS.py. The syntax for the addition of a measurement is the following (shown using a distance as an example):
from RCBS.md_analyser import measurements
m = measurements.Measurement(u)
m.add_distance('name', sel1, sel2)More examples are available in the example Notebook from RCBS.py-examples.
Once all measurements are added, m.run_measure() has to be used in order to run the measurements. The code works in such a way that each frame is loaded, each of the measurements is calculated and the next frame is loaded. A progress bar is shown during the process.
Once the measures are ran, m.run_boolean() can be used to do simple statistical studies. Examples can be found in the example Notebook.
In this file all the calculators are stored (work is being done to move all the calculators from measurements.py). Calculators can do very different things --in fact, anything you can think and code-- from the given selections. Calculators have to be implemented so they do the measure over only one structure (or frame) and they return a single variable.
calculators.py is loaded from measurements.py. Each calculator has to be incorporated in measurements.py, both as a add_* function and in the run_measurement function.
- Create a script for automatically add new calculators to
measurements.py. - Add more calculators.
- Create the
qmmmmodule.