stcrpy 1.0.0__py3-none-any.whl → 1.0.5__py3-none-any.whl

stcrpy-1.0.0.dist-info/METADATA

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-Metadata-Version: 2.4
-Name: stcrpy
-Version: 1.0.0
-Summary: Set of methods to parse, annotate, and calculate features of TCR structures
-Maintainer: Nele Quast
-Maintainer-email: quast@stats.ox.ac.uk
-Description-Content-Type: text/markdown
-License-File: LICENCE
-License-File: stcrpy/tcr_geometry/TCRCoM_LICENCE
-Requires-Dist: biopython
-Requires-Dist: numpy==1.26.4
-Requires-Dist: lxml
-Requires-Dist: openbabel-wheel==3.1.1.21
-Requires-Dist: rdkit
-Requires-Dist: anarci-mhc
-Requires-Dist: pandas
-Requires-Dist: matplotlib
-Requires-Dist: scipy
-Requires-Dist: requests
-Requires-Dist: scikit-learn
-Dynamic: description
-Dynamic: description-content-type
-Dynamic: license-file
-Dynamic: maintainer
-Dynamic: maintainer-email
-Dynamic: requires-dist
-Dynamic: summary
-
-
-
-<img src="./stcrpy_logo.png" alt="drawing" width="300"/>
-
-
-# STCRpy 
-[![stcrpy installation](https://github.com/npqst/STCRpy/actions/workflows/conda-workflow.yml/badge.svg)](https://github.com/npqst/STCRpy/actions/workflows/conda-workflow.yml)
-[![stcrpy unittests](https://github.com/npqst/STCRpy/actions/workflows/unittest-workflow.yml/badge.svg)](https://github.com/npqst/STCRpy/actions/workflows/unittest-workflow.yml)
-[![stcrpy_docs](https://readthedocs.org/projects/stcrpy/badge/?version=latest)](https://stcrpy.readthedocs.io/en/latest/)
-
-
-Structural TCR python (STCRpy) is a software suite for analysing and processing T-cell receptor structures. 
-
-Please feel free to reach out with any comments or feedback.
-
-Under review, please cite: 
-
-**Quast, N. , Deane, C., & Raybould, M. (2025). STCRpy: a software suite for TCR:pMHC structure parsing, interaction profiling, and machine learning dataset preparation. BioRxiv. https://doi.org/10.1101/2025.04.25.650667**
-
-<img src="./stcrpy_main_fig.png" alt="drawing" width="1500"/>
-
-
-
-# Installation
-
-## TL;DR installation
-```
-pip install stcrpy
-pip install plip
-conda install -c conda-forge pymol-open-source  numpy -y
-ANARCI --build_models           # this step will take a few minutes
-```
-
-## Step by step installation
-We recommend installing STCRpy in a [conda](https://www.anaconda.com/docs/getting-started/miniconda/install#macos-linux-installation) (or [mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html)) environment using python 3.9 to 3.12: 
-```
-conda create -n stcrpy_env python==3.12 -y
-conda activate stcrpy_env
-```
-
-The core functionality of STCRpy can be installed as follows:
-```
-pip install stcrpy
-```
-
-After installing stcrpy, the anarci HMM models must be built to enable annotation.
-```
-ANARCI --build_models           # this step will take a few minutes
-```
-
-To enable interaction profiling, install PLIP (Adasme et. al., 2021):
-```
-pip install plip
-```
-
-To enable pymol visualisations, install pymol open source locally within the environment. Unfortunately, pymol currently needs to be installed even if you already have a pymol version. Be sure to install pymol within a managed conda (or mamba) environment to prevent interference with any existing versions. 
-```
-conda install -c conda-forge pymol-open-source  numpy -y
-```
-
-To generate pytorch and pytorch-geometric compatible datasets: 
-```
-pip install pytorch --index-url https://download.pytorch.org/whl/cpu
-pip install torch_geometric
-```
-Note that this installs the CPU version of pytorch, for GPU / CUDA versions install according to the [pytorch installation docs](https://pytorch.org/get-started/locally/).
-
-The EGNN example also uses `einops`. To install: 
-```
-pip install einops
-```
-
-# Documentation
-STCRpy [documentation](https://stcrpy.readthedocs.io/en/latest/) is hosted on ReadtheDocs.
-
-# Examples
-STCRpy generates and operates on TCR structure objects. The majority of the API can be accessed through functions of the format: `tcr.some_stcrpy_function()`. TCR objects are associated with their MHC and antigen if these are presented in the structure. 
-
-A notebook with examples can be found under [examples/STCRpy_examples.ipynb](./examples/STCRpy_examples.ipynb)
-
-First import STCRpy:
-```
-import stcrpy
-```
-
-### To fetch a TCR structure from STCRDab or the PDB: 
-```
-tcr = stcrpy.fetch_TCR("8gvb")
-```
-This will return a TCR strcuture or object, or, if there are multiple copies of TCR crystal structures in the PDB file, will return a list containing TCR structure objects. It may be useful to unpack the list into distinct objects, or use python generators to operate on the lists. 
-
-### To load a TCR structure from a PDB or MMCIF file:
-```
-tcr = stcrpy.load_TCR("filename.{pdb, cif}")
-```
-
-### To load multiple TCR structures from a list of files at once:
-```
-multiple_tcrs = stcrpy.load_TCRs([file_1, file_2, file_3])
-```
-
-### To save a TCR object to PDB or MMCIF files: 
-```
-tcr.save(filename.{pdb, cif})           # save the TCR and it's associated MHC and antigen
-tcr.save(filename.{pdb, cif}, TCR_only=True)           # save the TCR only
-```
-
-### To calculate the TCR to pMHC geometry:
-```
-tcr.calculate_geometry()            # change the 'mode' keyword argument to change the geometry calculation method. See paper / documentation for details.
-```
-
-### To score the TCR to pMHC geometry:
-```
-tcr.score_docking_geometry()
-```
-
-### To profile interactions: 
-```
-tcr.profile_peptide_interactions()          # interaction profiling parameters can be adjusted, see documentation for details
-```
-
-### To visualise interactions:
-```
-tcr.visualise_interactions()
-```
-
-### To run full analysis on a set of TCR structures: 
-```
-from stcrpy.tcr_methods.tcr_batch_operations import analyse_tcrs
-germlines_and_alleles_df, geometries_df, interactions_df = analyse_tcrs(list_or_dict_of_files)
-```
-
-### To generate graph datasets:
-```
-dataset = TCRGraphDataset(
-            root=PATH_TO_DATASET,
-            data_paths=PATH_TO_TCR_FILES
-        )
-```
-
-
-
-
-