tcrgeometry 0.1.0

TCR geometry calculation and visualization tools

Extra dependencies

For TCR numbering, ANARCI must be installed via bioconda:

conda install -c bioconda anarci

For visualization, PyMOL must be installed via bioconda:

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

Set up environment

The file environment.yml specifies the dependencies required to run the TRangle package. You can create a conda environment using this file:

conda env create -f environment.yml

In the main project directory run

pip install -e .

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.

python trangle/calc_geometry.py --input_pdb path/to/your/input.pdb

This will output a CSV file with the measured angles and distances. It will also output a PDB of the extracted variable domain, was well as a visualiseation of the measured angles and distance saved as an image and a .pse file which can be opened in PyMOL.

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.

python trangle/calc_geometry_MD.py --input_pdb path/to/your/input.pdb --input_md path/to/your/input.traj

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.

python trangle/change_geometry.py --input_pdb path/to/your/input.pdb --BA 113.22 --BC1 98.75 --BC2 9.35 --AC1 71.58 --AC2 154.62 --dc 23.98

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. It will also generate a visualization of the modified structure for inspection.

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.

python trangle/get_anchor_coords.py path/to/your/input.pdb

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%)