{"categories":[{"label":"Scientific/Engineering","url":"https://skillfed.io/packages/category/scientific-engineering/6"}],"enrichment":{"capability":"Provides Python bindings to the TM-align algorithm for comparing protein structures by computing optimal alignment, rotation, translation, and similarity scores.","skillfed_tags":["structural-biology","bioinformatics","protein-alignment"],"use_cases":["Compare two protein structures to compute their TM-score and optimal superposition for structural similarity assessment.","Validate a hypothesized protein alignment by supplying a custom alignment string and checking the resulting TM-score.","Parse PDB files with BioPython and extract coordinates and sequences for downstream structural comparison workflows.","Batch-compare a query protein structure against a library of known folds to identify homologous structures.","Integrate structural alignment into a protein design or validation pipeline that requires quantitative similarity metrics."],"what_it_does":"tmtools wraps the TM-align algorithm\u2014a widely-used structural biology tool for aligning protein coordinates\u2014into a Python interface. It takes two sets of 3D atomic coordinates and amino acid sequences, computes the optimal structural alignment, and returns the rotation matrix, translation vector, and TM-score (a normalized similarity metric). The package ships with pre-built wheels for modern Python versions and common platforms, minimizing compilation friction.\n\nThe core use case is comparing protein structures to assess similarity or find conserved folds. It supports both automatic alignment discovery and user-supplied alignment strings with gaps, making it useful for hypothesis testing or domain-guided comparisons. Optional integration with BioPython allows direct parsing of PDB files. The package is in alpha status and has not seen a release in several months, though the underlying TM-align algorithm is mature and well-cited in structural biology.","worth_installing":"Yes, if you need to compute protein structural alignments and TM-scores in Python. The pre-built wheels make installation straightforward, numpy is a common dependency, and the underlying algorithm is well-established. However, the GPLv3 license requires your project to be open-source; the aging maintenance status (no release in 278 days) suggests limited active development, so evaluate whether you need ongoing support or bug fixes. No known security vulnerabilities."},"id":"tmtools","links":{"html":"https://skillfed.io/packages/tmtools","md":"https://skillfed.io/packages/tmtools.md","pypi":"https://pypi.org/project/tmtools/"},"maintenance":{"status":"aging"},"meta":{"latest_release":"2025-11-09","license_spdx":null,"license_treatment":"copyleft","name":"tmtools","python_support":"unspecified","summary":"Python bindings around the TM-align code for structural alignment of proteins"},"popularity":{"monthly_downloads":151910,"position":10917,"tier":"top_15000"},"security":{"n_vulnerabilities":0},"version":"0.3.0"}