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A simple framework for representing biomolecular structure.

Project description

AMPAL

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

CircleCI Python Version MIT licensed

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 to ampal.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 the ampal.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 two Polypeptides using MMC. The simplest interface is the align_backbones function.
    • This is currently super inefficient and will be reimplemented.

v1.1.0

  • Adds the centroid property to residues.

Project details


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