ampal 1.0.1

A simple framework for representing biomolecular structure.

AMPAL

A simple, intuitive and Pythonic framework for representing biomolecular structure.

Installation

You can install AMPAL from pip:

pip install ampal

Or from source by downloading/cloning this repository, navigating to the folder and typing:

pip install .

AMPAL uses Cython, so if you're installing from source make sure you have it installed.

Super Quick Start

Load a PDB file into AMPAL:

my_structure = ampal.load_pdb('3qy1.pdb')
print(my_structure)
# OUT: <Assembly (3qy1) containing 2 Polypeptides, 449 Ligands>

Select regions of the structure in an intuitive manner:

my_atom = my_structure['A']['56']['CA']
print(my_structure['A']['56']['CA'])
# OUT: <Carbon Atom (CA). Coordinates: (6.102, -4.287, -29.607)>

Then climb all the way back up the hierachy:

print(my_atom.parent)
# OUT: <Residue containing 9 Atoms. Residue code: GLU>
print(my_atom.parent.parent)
# OUT: <Polypeptide containing 215 Residues. Sequence: DIDTLISNNALW...>
print(my_atom.parent.parent.parent)
# OUT: <Assembly (3qy1) containing 2 Polypeptides, 449 Ligands>

This is just a quick introduction, AMPAL contain tonnes of tools for making complex selections and performing analysis. Take a look at the docs to find out more.