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.
Release Notes
v1.4.0
- Adds
get_ss_regions
toampal.dssp
. This function can be used to extract all regions of a protein in a particular secondary structure. - Fixes bug with DSSP
ss_region
tagging. End residues used to be missed.
v1.3.0
- Adds an interface for NACCESS. Functions for using NACCESS to calculate solvent accessibility.
v1.2.0
- Adds an interface for DSSP. If you have DSSP on your computer and have the
mkdssp
command available on your path, you can use theampal.tag_dssp_data
function to add secondary structure information to the tags dictionary of the residues in your structure. - Adds the
ampal.align
module. Contains a simple class for aligning twoPolypeptides
using MMC. The simplest interface is thealign_backbones
function.- This is currently super inefficient and will be reimplemented.
v1.1.0
- Adds the centroid property to residues.
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