molbiomeduab / rcbs.py

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.

RCBS.py

Description

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.

Installation

Using pip

pip install RCBS.py

From source code

1. Clone the repository in you local machine

   git clone https://github.com/dynamicsUAB/RCBS.py.git

2. Move to the folder

   cd RCBS.py

3. Install the package using pip or pip3

   pip install .

Usage

md_analyser

md_analyser is made of two principal scripts: measurements.py and calculators.py.

measurements.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.

calculators.py

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.

Future additions

• Create a script for automatically add new calculators to measurements.py.
• Add more calculators.
• Create the qmmm module.

rcbs.py's Issues

Add RMSF

Add RMSF as a measurement.

Change given example to MDAnalysis standard example suite

Script for adding a measurement from a calculator

When a calculator is created (in calculators.py), a question-based script would be useful for faster/easier implementation in measurements.py.

When more than one measure with the same name is calculated, the old and the new are appended in the same m.results list.

Add an option to overwrite the old content and make it the default, keeping the option to not overwrite.

Add the possibility to select only backbone bonds of residue (or any other selection)

Empty measurement class checker

Add an initial checker that checks if no measurement has been added so it prevents running the measures without measuring nothing.

Per-residue, per-frame pKa

Not possible to make a list of integers with sel_type=res_num

Residue-Residue interactions for variants comparison

Step for run_measure

m.run_measure(step=n) analyses only each n steps

Add an option to remove a measurement in a Measurement object

H bond analyser

Residue selection without backbone