tcrgeometry 0.1.8

TCR geometry calculation and visualization tools

Installation

This package can be installed via

pip install tcrgeometry

Extra dependencies

For TCR numbering, ANARCII must be installed via pip: (using the newest version)

pip install anarcii

Sometimes the legacy version ANARCI works better, so it must also be installed via conda:

conda install bioconda::anarci

For visualization, PyMOL must be installed via bioconda:

conda install conda-forge::pymol-open-source

Measure angles of existing TCR structures

To measure angles in existing TCR structures, you can use the new_calc.py script provided in the TRangle package. This script allows you to calculate angles and distances in a TCR structure file.

tcr-calc --input_pdb file.pdb --out_path ./out

Add the --vis flag to generate a visualization of the modified structure. It will save a visualisation of the measured angles and distance saved as an image and a .pse file which can be opened in PyMOL.

or with the API:

import tcrgeometry
calc_results = tcrgeometry.calc_tcr_geometry(pdb_file, out_path="./out")

Set the vis=True flag to generate a visualization of the modified structure.

This will output a CSV file with the measured angles and distances.

Measure angles of existing TCR trajectories

To measure angles in existing TCR trajectories, you can use the new_calc_MD.py script provided in the TRangle package. This script allows you to calculate angles and distances in a TCR trajectory file.

tcr-calc-md --input_pdb file.pdb --input_md trajectory.traj --out_path ./out

or with the API:

import tcrgeometry
md_results = tcrgeometry.calc_tcr_geometry_MD(pdb_file, md_path, out_path="./out")

Change geometry of a TCR structure

To change the geometry of a TCR structure, you can use the change_geometry.py script provided in the TRangle package. This script allows you to modify angles and distances in a TCR structure based on a configuration file.

tcr-change --input file.pdb --out_path ./out --BA 113 --BC1 98.7 --BC2 9.3 --AC1 71.5 --AC2 154 --dc 24

Add the --vis flag to generate a visualization of the modified structure.

or with the API:

import tcrgeometry
changed_pdb=tcrgeometry.change_tcr_geometry(pdb_file, out_path="./out", BA=113, BC1=98.7, BC2=9.3, AC1=71.5, AC2=154, dc=24)

Set the vis=True flag to generate a visualization of the modified structure.

This script will read the configuration file, apply the specified changes to the angles and distances, and output a new PDB file with the modified geometry.

Extract loop anchor residue coordinates

To extract the coordinates of loop anchor residues from a TCR structure, you can use the extract_loop_anchor.py script provided in the TRangle package. This script allows you to specify the loop anchor residues and extract their coordinates from a TCR structure file.

tcr-extract-anchor path/to/your/input.pdb

or with the API:

import tcrgeometry
anchor_coords = tcrgeometry.get_anchor_coords(pdb_file)

This will output a CSV file containing the coordinates of the specified loop anchor residues, which can be used for input to the CDR loop diffusion model.

Dataset: From STCRDB get non-redundant abTCR set of IMGT-numbered structures (resolution cutoff 3.0, sequence identity cutoff 70%)