A simple framework for representing biomolecular structure.
Project description
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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.