ampal 2.0.0

A framework for representing biomolecular structure.

AMPAL

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

Installation

AMPAL is currently tested with version of Python above 3.7, although it should still work with earlier versions. 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

v2.0.0

• Breaking change: removes find_aa_info function and tests, which enables us to remove the requests dependency. This kind of functionality is better handled by the user, as there is a security concern regarding making HTTP requests without the user explicitly opting in.
• Updates project to use modern structure, enabling easier installation on all platforms.
• Automated builds and uploads to PyPI on new version updates.

v1.5.3

• Fixes bug with get_slice_from_res_id to enable non-continuous sequences to be selected.

v1.5.0

• Adds rotamer classification with the classify_angle_as_rotamer in the analyse_protein module.
• Fixes a bug with parsing structure files

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.