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
v2.1.0
- Adds
load_mmcif_filefunction - Adds more typing information
- Tidies up
__repr__strings
v2.0.0
- Breaking change: removes
find_aa_infofunction 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_idto enable non-continuous sequences to be selected.
v1.5.0
- Adds rotamer classification with the
classify_angle_as_rotamerin theanalyse_proteinmodule. - Fixes a bug with parsing structure files
v1.4.0
- Adds
get_ss_regionstoampal.dssp. This function can be used to extract all regions of a protein in a particular secondary structure. - Fixes bug with DSSP
ss_regiontagging. 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
mkdsspcommand available on your path, you can use theampal.tag_dssp_datafunction to add secondary structure information to the tags dictionary of the residues in your structure. - Adds the
ampal.alignmodule. Contains a simple class for aligning twoPolypeptidesusing MMC. The simplest interface is thealign_backbonesfunction.- This is currently super inefficient and will be reimplemented.
v1.1.0
- Adds the centroid property to residues.
3 maintainers
Metadata
3 maintainers
Release files for ampal 2.1.1
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
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| ampal-2.1.1.tar.gz | 2.6 MB | With provenance | Details for ampal-2.1.1.tar.gz |
Built distributions (wheels)
Total release size: 42.6 MB
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