dg-thesis-code

MATLAB code associated with my PhD thesis on distance geometry and protein structure reconstruction.

This repository is kept as a historical research codebase. It contains prototype implementations and numerical routines developed during the thesis work. Parts of this material were later superseded by more recent C implementations, especially in bpbm-3d-iddgp.

Maintenance Status

This repository is preserved mainly as thesis-associated historical code and is not maintained with the same level of care as the newer C implementations.

If you need clarification about the code, data layout, or expected behavior, please contact me by email:

wdarocha [at] ime.unicamp.br

The functionality in this repository is being migrated progressively to better structured C code.

• The iBP implementation from this MATLAB repository is already available in the C repository bpbm-3d-iddgp.
• In the newer C repository, the corresponding implementation was renamed to iTBP.
• The iTBP function in this MATLAB thesis repository is not the same as the iTBP implementation currently available in the C repository.
• The MATLAB iTBP functionality has not yet been fully reimplemented in C, but this migration is in progress.

Scope

The repository currently includes:

• MATLAB implementations of iBP and iTBP
• helper routines for interval manipulation, torsion-angle computations, and vertex ordering
• a thesis-era experiment script for comparing iTBP and iBP

Repository Layout

• src/algorithms: main algorithm implementations and branching routines
• src/analysis: quality metrics and result-reporting helpers
• src/geometry: geometric and torsion-angle routines
• src/instances: instance conversion and vertex-ordering helpers
• src/intervals: interval manipulation utilities
• src/probability: Gaussian intersection and combination helpers
• scripts: thesis-era experiment scripts
• data: thesis-era experiment inputs
• scriptITBPVsIBP.m: convenience wrapper for the main experiment script

Usage Notes

This repository is provided primarily for archival and reference purposes.

• The repository includes thesis-era input data under data/.
• I no longer maintain an environment to validate the full MATLAB workflow end to end.
• The code is preserved to document the computational material used in the thesis.

Running the Main Script

Add the repository source tree to the MATLAB path:

run('startup.m');

Then run the main experiment script:

run('scripts/scriptITBPVsIBP.m');

Alternatively, you may use the wrapper in the repository root:

run('scriptITBPVsIBP.m');

In this setup:

• scriptITBPVsIBP.m in the repository root is only a lightweight entry-point wrapper.
• scripts/scriptITBPVsIBP.m contains the thesis-era experiment logic.

The script expects thesis-era input files under:

data/<IDCODE>/eps_1_tau_40/

Thesis Reference

This repository is associated with the following PhD thesis:

da Rocha, Wagner Alan Aparecido. Ordenacao em vertices de grafos de proteinas.
2022. Tese (Doutorado em Matematica Aplicada) - Universidade Estadual de Campinas,
Instituto de Matematica, Estatistica e Computacao Cientifica, Campinas, SP, 2022.

Alternate title:

A new vertex order for protein graphs

Related Repositories

• Current C implementation of BP-based methods: https://github.com/wdarocha/bpbm-3d-iddgp
• Benchmark and experiment data: https://github.com/wdarocha/benchmarks

Citation

If you reference this repository, cite it as thesis-associated computational material. Citation metadata is provided in CITATION.cff.