Related papers: Pythonic Black-box Electronic Structure Tool (PyBE…

To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…

Integrated information theory provides a mathematical framework to fully characterize the cause-effect structure of a physical system. Here, we introduce PyPhi, a Python software package that implements this framework for causal analysis…

Many tools exist for extracting structural and physiochemical descriptors from linear peptides to predict their properties, but similar tools for hydrocarbon-stapled peptides are lacking.Here, we present StaPep, a Python-based toolkit…

Tunneling ionization is at the core of strong-field and attosecond science. In this paper, we present PyStructureFactor - a general Python code towards the calculation of the structure factor in the tunneling ionization rate of common…

We introduce a Python open-source library for $\mathcal{X}$-armed bandit and online blackbox optimization named PyXAB. PyXAB contains the implementations for more than 10 $\mathcal{X}$-armed bandit algorithms, such as HOO, StoSOO, HCT, and…

Understanding the applicability and limitations of electronic-structure methods needs careful and efficient comparison with accurate reference data. Knowledge of the quality and errors of electronic-structure calculations is crucial to…

PyECLOUD is a newly developed code for the simulation of the electron cloud (EC) build-up in particle accelerators. Almost entirely written in Python, it is mostly based on the physical models already used in the ECLOUD code but, thanks to…

The CompactObject package is an open-source software framework developed to constrain the neutron star equation of state (EOS) through Bayesian statistical inference. It integrates astrophysical observational constraints from X-ray timing,…

Protein structure is central to biological function, and enabling multimodal protein models requires joint reasoning over sequence, structure, and function. A key barrier is the lack of principled protein structure tokenizers (PSTs):…

The Controlled Molecule Imaging group (CMI) at the Center for Free Electron Laser Science (CFEL) has developed the CMIstark software to calculate, view, and analyze the energy levels of adiabatic Stark energy curves of linear, symmetric top…

Quantum simulation of chemistry and materials is predicted to be an important application for both near-term and fault-tolerant quantum devices. However, at present, developing and studying algorithms for these problems can be difficult due…

Background and Objective: Data from electro-anatomical mapping (EAM) systems are playing an increasingly important role in computational modeling studies for the patient-specific calibration of digital twin models. However, data exported…

The Active Matter Evaluation Package (AMEP) is a Python library for analyzing simulation data of particle-based and continuum simulations. It provides a powerful and simple interface for handling large data sets and for calculating and…

We present pySecDec, a new version of the program SecDec, which performs the factorisation of dimensionally regulated poles in parametric integrals, and the subsequent numerical evaluation of the finite coefficients. The algebraic part of…

Malicious Python packages make software supply chains vulnerable by exploiting trust in open-source repositories like Python Package Index (PyPI). Lack of real-time behavioral monitoring makes metadata inspection and static code analysis…

As hybrid quantum-classical models gain traction in machine learning, there is a growing need for tools that assess their effectiveness beyond raw accuracy. We present QMetric, a Python package offering a suite of interpretable metrics to…

This paper describes the algorithms, features and implementation of PyDEC, a Python library for computations related to the discretization of exterior calculus. PyDEC facilitates inquiry into both physical problems on manifolds as well as…

Bibliometric and Scientometric analyses offer invaluable perspectives on the complex research terrain and collaborative dynamics spanning diverse academic disciplines. This paper presents pyBibX, a python library devised to conduct…

Electronic structure calculations of molecular systems are among the most promising applications for fault-tolerant quantum computing (FTQC) in quantum chemistry and drug design. However, while recent algorithmic advancements such as…

Over the past decade, the Python-based Simulations of Chemistry Framework (PySCF) has developed into a widely used open-source platform for electronic structure theory and quantum chemical method development. This article reviews the major…