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Python bindings around the TM-align code for structural alignment of proteins

Project description

TM-Tools

Python bindings for the TM-align algorithm and code developed by Zhang et al for protein structure comparison.

Installation

From the console, simply run

    pip install git+https://github.com/jvkersch/tmtools.git#egg=tmtools

The package supports Python 3.6 and up. You will need a fairly recent version of pip, as well as a C++ compiler that supports C++ 14.

This package supports Linux, macOS, and Windows.

Usage

The function tmtools.tm_align takes two NumPy arrays with coordinates for the residues (with shape (N, 3)) and two sequences of peptide codes, performs the alignment, and returns the optimal rotation matrix and translation, along with the TM score:

>>> import numpy as np
>>> from tmtools import tm_align
>>>
>>> coords1 = np.array(
...     [[1.2, 3.4, 1.5],
...      [4.0, 2.8, 3.7],
...      [1.2, 4.2, 4.3],
...      [0.0, 1.0, 2.0]])
>>> coords2 = np.array(
...     [[2.3, 7.4, 1.5],
...      [4.0, 2.9, -1.7],
...      [1.2, 4.2, 4.3]])
>>>
>>> seq1 = "AYLP"
>>> seq2 = "ARN"
>>>
>>> res = tm_align(coords1, coords2, seq1, seq2)
>>> res.t
array([ 2.94676159,  5.55265245, -1.75151383])
>>> res.u
array([[ 0.40393231,  0.04161396, -0.91384187],
       [-0.59535733,  0.77040999, -0.22807475],
       [ 0.69454181,  0.63618922,  0.33596866]])
>>> res.tm_norm_chain1
0.3105833326322145
>>> res.tm_norm_chain2
0.414111110176286

If you already have some PDB files, you can use the functions from tmalign.io to retrieve the coordinate and sequence data:

>>> from tmtools.io import get_structure, get_residue_data
>>> from tmtools.testing import get_pdb_path
>>> s = get_structure(get_pdb_path("2gtl"))
>>> s
<Structure id=2gtl>
>>> chain = next(s.get_chains())
>>> coords, seq = get_residue_data(chain)
>>> seq
'DCCSYEDRREIRHIWDDVWSSSFTDRRVAIVRAVFDDLFKHYPTSKALFERVKIDEPESGEFKSHLVRVANGLKLLINLLDDTLVLQSHLGHLADQHIQRKGVTKEYFRGIGEAFARVLPQVLSCFNVDAWNRCFHRLVARIAKDLP'
>>> coords.shape
(147, 3)

These functions are light-weight wrappers around BioPython.

Credits

This package arose out of a personal desire to better understand both the TM-score algorithm and the pybind11 library to interface with C++ code. At this point in time it contains no original research code.

If you use the package for research, you should cite the original TM-score papers:

  • Y. Zhang, J. Skolnick, Scoring function for automated assessment of protein structure template quality, Proteins, 57: 702-710 (2004).
  • J. Xu, Y. Zhang, How significant is a protein structure similarity with TM-score=0.5? Bioinformatics, 26, 889-895 (2010).

License

The original TM-align software (version 20210224, released under the MIT license) is bundled with this repository (src/extern/TMalign.cpp). Some small tweaks had to be made to compile the code on macOS and to embed it as a library. This modifications are also released under the MIT license.

The rest of the codebase is released under the GPL v3 license.

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