pyxmolpp2 0.0.1

Utils for processing MD

master	dev

Goal

We want our scripts to

• run fast

• be easy to read

• be easy to write correct

• be hard to write incorrect

So we need a library which

• is reliable

• full of features

Well-written C++ code gives us speed. An IDE augmented with static type system should prevent many occasional pythonic mistakes before script is run. Moderate functional style programming contributes to readability. At least it’s how it was meant to be)

Feature list

To be written

Usage examples

Translate all atoms by (1,2,3):

from pyxmolpp2.pdb import PdbFile
from pyxmolpp2.geometry import XYZ

def translate_by(dr):
    def translate(a):
        a.r = a.r+dr
    return translate

frame = PdbFile("test.pdb").get_frame()

frame.asAtoms.for_each(translate_by(XYZ(1,2,3)))

# write as pdb
frame.to_pdb("out.pdb")

Install

from PyPi package

PyPi package contains all C++ dependencies, total size is about ~4 mb. Install command:

python -m pip install pyxmolpp2

from git repository

Caution!

Total size of repository with sub-repositories exceeds 100mb

To install from master branch run command

python -m pip install git+https://github.com/sizmailov/pyxmolpp2.git

API Reference

To be written

Project structure

1. C++ library xmol, the core

2. Python library pyxmolpp2, wraps xmol by pybind11

3. User scripts, are written for daily duties

Credits

Written by Sergei Izmailov in BioNMR lab at SPbSU