Open-source alternatives to Pathsim

The official sources for the RDKit library

Colour Science for Python

Biopython is a bioinformatics library for Python providing tools to parse, manipulate, and analyze biological sequences, molecular structures, and phylogenetic trees. It serves as a biological sequence parser for genomic and proteomic data across multiple industry-standard file formats and acts as an interface for querying biological data and citations from NCBI Entrez repositories. The project distinguishes itself through specialized toolkits for protein structure analysis and phylogenetic tree construction. It includes a protein structure analyzer for processing PDB and mmCIF files to calcu

SciPy is a scientific computing library for Python that provides a comprehensive collection of mathematical algorithms and numerical tools for research and engineering. It functions as a high-performance numerical analysis framework, bridging high-level Python code with compiled C and Fortran routines to execute complex computations at hardware speeds. The library is built upon array-based data structures that utilize strided memory layouts to enable efficient data manipulation and slicing. By employing vectorized operation dispatch and linking to optimized hardware-specific linear algebra li

Shapely is a library for the manipulation and analysis of planar geometric objects, serving as a Python wrapper for the GEOS C++ engine. It provides a framework for calculating geometric properties, evaluating spatial relationships, and performing topological predicates within a Cartesian plane. The project distinguishes itself through a vectorized geometry processor capable of executing spatial operations across large arrays of shapes to increase throughput. It also includes a spatial indexing system based on R-trees to accelerate the retrieval of intersecting geometries and nearest neighbor

Statsmodels is a comprehensive Python library designed for statistical modeling, econometric research, and data analysis. It provides a robust framework for estimating and diagnosing a wide range of statistical models, enabling users to perform rigorous hypothesis testing, regression analysis, and complex data exploration within structured environments. The library distinguishes itself through its support for advanced statistical methodologies, including state space representation for dynamic systems and generalized linear frameworks that accommodate non-normal response variables. It offers s

SymPy is a Python computer algebra system and symbolic mathematics library. It performs algebraic manipulations, calculus, and equation solving using symbolic representations to achieve exact computations rather than numerical approximations. The library includes a LaTeX expression parser that converts mathematical strings into symbolic representations for computation and formula manipulation. It also incorporates a mathematical benchmarking suite to measure execution speed and detect performance regressions across different software versions. The system provides capabilities for automated m

Manim is a scriptable, code-driven framework designed for generating precise technical visualizations and mathematical animations. By using a high-level programming interface, it allows users to define geometric shapes, motion paths, and animation logic that are compiled into high-quality video assets. The system functions as a specialized engine for creating reproducible, data-driven representations of complex mathematical concepts and geometric transformations. The framework distinguishes itself through an interpolation-based engine that calculates intermediate states between keyframes to e

Mesa is a Python framework for agent-based modeling and complex systems simulation. It provides a toolkit for creating simulations where autonomous agents interact within a shared environment to observe emergent global behaviors. The project includes a browser-based interface for real-time visualization of simulation states and agent interactions. It also functions as a data analysis library for recording and processing metrics from model runs to quantify system behavior. The framework supports multiple environmental topologies, including grid-based spatial mapping and network-graph topologi

Parsers and algorithms for computational chemistry logfiles

NetworkX is a Python library designed for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. It provides a comprehensive framework for modeling relationships between entities as graphs, directed graphs, or multigraphs, allowing users to attach arbitrary metadata and properties to nodes and edges. The library distinguishes itself through a modular architecture that decouples graph analysis logic from data storage, utilizing nested dictionaries and adjacency lists to manage topology. It features a pluggable backend system that delegates computat

Numba is a just-in-time compiler that translates high-level Python functions into optimized machine code at runtime. By leveraging the LLVM compiler infrastructure, it provides a framework for accelerating numerical data processing and mathematical computations, enabling performance levels comparable to statically compiled languages. The project distinguishes itself through its ability to perform type-inference-based specialization, which generates machine instructions tailored to the specific data types used during execution. It employs a lazy compilation pipeline that defers translation unt

NumPy is a foundational library for scientific computing in Python, providing a comprehensive framework for managing and manipulating large-scale numerical information. It centers on high-performance multidimensional array objects that serve as the primary data structure for complex mathematical operations and data analysis workflows. The library distinguishes itself through specialized mechanisms for handling multidimensional data, including advanced indexing, slicing, and broadcasting techniques that allow for efficient operations across arrays of varying shapes. It utilizes strided metadat

Astropy is a core Python library for astronomy, providing a unified framework for astronomical data analysis, coordinate and time computations, and physical constants and unit handling. It is designed as a standard tool for the astronomy community, enabling consistent reading, processing, and visualization of FITS files and ASCII tables through a modular subpackage system that shares common interfaces and conventions. The library distinguishes itself through broad interoperability across astronomy software, establishing shared protocols for data exchange and collaboration. It includes a coord

Foragax is an Agent-Based Modelling (ABM) package based on JAX. It provides scalable and efficient ABM simulations by leveraging JAX's automatic vectorization and just-in-time compilation capabilities. The main features of Foragax include:

Differentiable Ray Tracing Toolbox for Radio Propagation Simulations

Master repository for the JGraphT project

SCICO is a Python package for solving the inverse problems that arise in scientific imaging applications. Its primary focus is providing methods for solving ill-posed inverse problems by using an appropriate prior model of the reconstruction space. SCICO includes a growing suite of operators,…

astronomix (formerly jf1uids) is a differentiable hydrodynamics and magnetohydrodynamics code written in JAX with a focus on astrophysical applications. astronomix is easy to use, well-suited for fast method development, scales to multiple GPUs and its differentiability opens the door for…

NetKet is an open-source project delivering cutting-edge methods for the study of many-body quantum systems with artificial neural networks and machine learning techniques. It is a Python library built on JAX.

See the full documentation.

A dependency-free statistics, linear algebra, and machine learning library for the V programming language, with a focus on product analytics and experimentation. Includes A/B testing, funnel analysis, cohort retention, causal inference, time series analysis, and growth metrics alongside…

A photovoltaic simulator with automatic differentation, built on JAX.

A list of recommended Python libraries, and resources, intended for scientific Python users.

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