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Despite the inherently fuzzy nature of reconstructions in historical linguistics, most scholars do not represent their uncertainty when proposing proto-forms. With the increasing success of recently proposed approaches to automating certain…
Chemical representation learning has gained increasing interest due to the limited availability of supervised data in fields such as drug and materials design. This interest particularly extends to chemical language representation learning,…
Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in…
Recently proposed modifications of the standard particle-in-cell (PIC) method resolve long-standing limitations such as exact preservation of physically conserved quantities and unbiased ensemble down-sampling. Such advances pave the way…
Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating…
Mayavi is an open-source, general-purpose, 3D scientific visualization package. It seeks to provide easy and interactive tools for data visualization that fit with the scientific user's workflow. For this purpose, Mayavi provides several…
We present PyAtoms, an interactive open-source software that rapidly simulates atomic-scale scanning tunneling microscopy (STM) and other scanning probe microscopy (SPM) images of two-dimensional (2D) layered materials, moir\'{e} systems,…
Creating and maintaining computer readable geometries for use in Monte Carlo Radiation Transport (MCRT) simulations is an error-prone and time-consuming task. Simulating a system often requires geometry from different sources and modelling…
This paper introduces PROOFTOOL, the graphical user interface for the General Architecture for Proof Theory (GAPT) framework. Its features are described with a focus not only on the visualization but also on the analysis and transformation…
Artificial intelligence (AI) and machine learning (ML) are expanding in popularity for broad applications to challenging tasks in chemistry and materials science. Examples include the prediction of properties, the discovery of new reaction…
We report the development of a user-friendly nano-visualization software program which can acquaint high-school students with nanotechnology. The visual introduction to atoms and molecules, which are the building blocks of this technology,…
This article describes a volumetric approach for procedural shape modeling and a new Procedural Shape Modeling Language (PSML) that facilitates the specification of these models. PSML provides programmers the ability to describe shapes in…
Molecular evolution is the process of simulating the natural evolution of molecules in chemical space to explore potential molecular structures and properties. The relationships between similar molecules are often described through…
The Protein Secondary Structure Visualizer ProS2Vi is a novel Python-based visualization tool designed to enhance the analysis and accessibility of protein secondary structures calculated and identified by the Dictionary of Secondary…
Drawing and visualisation of molecular structures are some of the most common tasks carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools…
We present a means of formulating and solving the well known structure-and-motion problem in computer vision with probabilistic graphical models. We model the unknown camera poses and 3D feature coordinates as well as the observed 2D…
This paper introduces GIMP-ML v1.1, a set of Python plugins for the widely popular GNU Image Manipulation Program (GIMP). It enables the use of recent advances in computer vision to the conventional image editing pipeline. Applications from…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural…
Recently, Multimodal Large Language Models (MLLMs) that enable Large Language Models (LLMs) to interpret images through visual instruction tuning have achieved significant success. However, existing visual instruction tuning methods only…