SUMMARY: VTX is a molecular visualization software capable to handle most molecular structures and dynamics trajectories file formats. It features a real-time high-performance molecular graphics engine, based on modern OpenGL, optimized for the visualization of massive molecular systems and molecular dynamics trajectories. VTX includes multiple interactive camera and user interaction features, notably free-fly navigation and a fully modular graphical user interface designed for increased usability. It allows the production of high-resolution images for presentations and posters with custom background. VTX design is focused on performance and usability for research, teaching, and educative purposes. AVAILABILITY AND IMPLEMENTATION: VTX is open source and free for non-commercial use. Builds for Windows and Ubuntu Linux are available at http://vtx.drugdesign.fr. The source code is available at https://github.com/VTX-Molecular-Visualization.

We present a novel comprehensive construction algorithm of Apollonius diagrams designed for GPUs. Efficient and robust algorithms have been proposed for the computation of Voronoi diagrams or Power diagrams. In contrast, Apollonius cells are neither convex nor bounded by straight boundaries, making their computation complex, especially in more than two dimensions. Their parallel computation also represents a challenge because of the sequential nature of state-of-the-art algorithms. In this article, we tackle the computation of these diagrams from the geometry of their cells. Our strategy is based on a core cell topology update allowing the iterative insertion of new sites found through nearest neighbor queries. To benefit from the highly parallel environment of modern GPUs and fit their memory restriction, we define a lightweight data structure allowing the representation of the complex topology of Apollonius cells. Additionally, we provide several space exploration procedures for their efficient construction under both homogeneous and heterogeneous spatial distributions. Our method outperforms the fastest state-of-the-art CPU implementation while computing the complete geometry. As a possible use case, we show an application for molecular illustration.

The Solvent-Excluded Surface (SES) is an essential representation of molecules which is massively used in molecular modeling and drug discovery since it represents the interacting surface between molecules. Based on its properties, it supports the visualization of both large scale shapes and details of molecules. While several methods targeted its computation, the ability to process large molecular structures to address the introduction of big complex analysis while leveraging the massively parallel architecture of GPUs has remained a challenge. This is mostly caused by the need for consequent memory allocation or by the complexity of the parallelization of its processing. In this paper, we leverage the last theoretical advances made for the depiction of the SES to provide fast analytical computation with low impact on memory. We show that our method is able to compute the complete surface while handling large molecular complexes with competitive computation time costs compared to previous works.

In the pneumatic industry, quality control is an essential step in assessing tire compliance. Artificial neural networks are increasingly used to accomplish this task. Their training requires a large number of images of the controlled products. However, at the launch production of a new tire, the lack of images causes a performance loss for the network. To solve this problem, we propose to translate perfect tires computer-based images into ad hoc manufacturing context-realistic ones as pre-manufacturing step to improve robustness and ensure production quality. The challenging work is to extract features in real images and apply them to computer-based images while maintaining the original geometry. In the paper, we propose Prefab-GEN, a novel architecture based on Cycle-GAN. In the generator part, an Inception U-Net architecture is developed to enforce geometrical structure conversion and extract more detailed features. The qualitative and quantitative evaluation on tire dataset shows improvements compared with state-of-art.

MOTIVATION: Protein-protein docking aims at predicting the geometry of protein interactions to gain insights into the mechanisms underlying these processes and develop new strategies for drug discovery. Interactive and user-oriented manipulation tools can support this task complementary to automated software. RESULTS: This article presents an interactive multi-body protein-protein docking software, UDock2, designed for research but also usable for teaching and popularization of science purposes due to its high usability. In UDock2, the users tackle the conformational space of protein interfaces using an intuitive real-time docking procedure with on-the-fly scoring. UDock2 integrates traditional computer graphics methods to facilitate the visualization and to provide better insight into protein surfaces, interfaces, and properties. AVAILABILITY AND IMPLEMENTATION: UDock2 is open-source, cross-platform (Windows and Linux), and available at http://udock.fr. The code can be accessed at https://gitlab.com/Udock/Udock2.

Molecular diagnosis is an essential step of patient care. An increasing number of Copy Number Variations (CNVs) have been identified that are involved in inherited and somatic diseases. However, there are few existing tools to identify them among amplicon sequencing data generated by Next Generation Sequencing (NGS). We present here a new tool, CovCopCan, that allows the rapid and easy detection of CNVs in inherited diseases, as well as somatic data of patients with cancer, even with a low ratio of cancer cells to healthy cells. This tool could be very useful for molecular geneticists to rapidly identify CNVs in an interactive and user-friendly way.

Abstract Rendering materials such as metallic paints, scratched metals and rough plastics requires glint integrators that can capture all micro‐specular highlights falling into a pixel footprint, faithfully replicating surface appearance. Specular normal maps can be used to represent a wide range of arbitrary micro‐structures. The use of normal maps comes with important drawbacks though: the appearance is dark overall due to back‐facing normals and importance sampling is suboptimal, especially when the micro‐surface is very rough. We propose a new glint integrator relying on a multiple‐scattering patch‐based BRDF addressing these issues. To do so, our method uses a modified version of microfacet‐based normal mapping [SHHD17] designed for glint rendering, leveraging symmetric microfacets. To model multiple‐scattering, we re‐introduce the lost energy caused by a perfectly specular, single‐scattering formulation instead of using expensive random walks. This reflectance model is the basis of our patch‐based BRDF, enabling robust sampling and artifact‐free rendering with a natural appearance. Additional calculation costs amount to about 40% in the worst cases compared to previous methods [YHMR16, CCM18].

Weathering effects are ubiquitous phenomena in cities. Buildings age and deteriorate over time as they interact with the environment. Pollution accumulating on facades is a particularly visible consequence of this. Even though relevant work has been done to produce impressive images of virtual urban environments including weathering effects, so far, no technique using a global approach has been proposed to deal with weathering effects. Here, we propose a technique based on a fast physically-inspired approach, that focuses on modeling the changes in appearance due to pollution soiling on an urban scale. We consider pollution effects to depend on three main factors: wind, rain and sun exposure, and we take into account three intervening steps: deposition, reaction and washing. Using a low-cost pre-computation, we evaluate the pollution distribution throughout the city. Based on this and the use of screen-space operators, our method results in an efficient approach able to generate realistic images of urban scenes by combining the intervening factors at interactive rates. In addition, the pre-computation demands a reduced amount of memory to store the resulting pollution map and, as it is independent from scene complexity, it can suit large and complex models by adapting the map resolution.

SUMMARY: In order to help molecular geneticists to rapidly identify CNVs responsible for inherited diseases among amplicons sequencing data generated by NGS, we designed a user-friendly tool ' Cov'Cop '. Using the run's coverage file provided by the sequencer, Cov'Cop simultaneously analyzes all the patients of the run using a two-stage algorithm containing correction and normalization levels and provides an easily understandable output, showing with various colors, potentially deleted and duplicated amplicons. AVAILABILITY AND IMPLEMENTATION: https://git.unilim.fr/merilp02/CovCop. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Abstract In urban design, estimating solar exposure on complex city models is crucial but existing solutions typically focus on simplified building models and are too demanding in terms of memory and computational time. In this paper, we propose an interactive technique that estimates solar exposure on detailed urban scenes. Given a directional exposure map computed over a given time period, we estimate the sky visibility factor that serves to evaluate the final exposure at each visible point. This is done using a screen‐space method based on a two‐scale approach, which is geometry independent and has low storage costs. Our method performs at interactive rates and is designer‐oriented. The proposed technique is relevant in architecture and sustainable building design as it provides tools to estimate the energy performance of buildings as well as weathering effects in urban environments.

Abstract We propose a novel approach for authoring large scenes with automatic enhancement of objects to create geometric decoration details such as snow cover, icicles, fallen leaves, grass tufts or even trash. We introduce environmental objects that extend an input object geometry with a set of procedural effects that defines how the object reacts to the environment, and by a set of scalar fields that defines the influence of the object over of the environment. The user controls the scene by modifying environmental variables, such as temperature or humidity fields. The scene definition is hierarchical: objects can be grouped and their behaviours can be set at each level of the hierarchy. Our per object definition allows us to optimize and accelerate the effects computation, which also enables us to generate large scenes with many geometric details at a very high level of detail. In our implementation, a complex urban scene of 10 000 m2, represented with details of less than 1 cm, can be locally modified and entirely regenerated in a few seconds.

Interaction inside virtual reality applications begins usually with simple selection tasks that can be achieved with moderate degrees of performances. More complex operations like modeling or sculpting inside an immersive environment raises however increased needs for precise 3D selections and visual feedback. In a modeling context any 3D location must be targetable, even ones that are outside of initial reach or not graphically represented. Common interaction techniques in virtual reality do not fullfill these goals without switching between different tools. We present an extensive and precise selection technique called the 3D arrow, used for moving and sculpting inside an immersive terrain modeling application. Composed of a graphic mouse-like pointer constrained inside a workspace defined by the region of space at arm's reach, the 3D arrow allow the users to seamlessly reach and target any position of space within the same interaction paradigm and to rotate the view around the pointer. The graphic appearance of the pointer is carefully designed to help users estimate its global and local position in the terrain scenery.

Abstract This paper presents a physically based method for simulating the heat transfers between the different environmental elements to synthesize realistic winter sceneries. We simulate the snow fall over the ground, as well as the conductive, convective and radiative thermal transfers using a finite volume method according to the variations of air and dew point temperatures, the amount of snow, cloud cover and day‐night cycles. Our approach takes into account phase changes such as snow melting into water or water freezing into ice.

Abstract In this paper, we present a framework for representing complex terrains with such features as overhangs, arches and caves and including different materials such as sand and rocks. Our hybrid model combines a volumetric discrete data structure that stores the different materials and an implicit representation for sculpting and reconstructing the surface of the terrain. Complex scenes can be edited and sculpted interactively with high level tools. We also propose an original rock generation technique that enables us to automatically generate complex rocky sceneries with piles of rocks without any computationally demanding physically‐based simulation.

Abstract In this paper, we present a tiling method for generating piles of rocks without any computationally demanding physically‐based simulation. Previous techniques rely on a periodic tiling of rocks and generate unrealistic repetitive patterns. In contrast, our approach relies on a modified corner cube algorithm to generate a set of aperiodic tiles. We generalize the construction method so that the geometry of rocks should straddle corner cubes with a view to avoiding unrealistic gaps in the arrangement of rocks. Moreover, we propose an original technique to control the shape of rocks into contact by computing the Voronoï cells using a parameterized anisotropic distance. Our method has been successfully used to generate landscapes and stone huts and walls with thousands of rocks piled together.

Abstract This paper presents a method for the accurate rendering of path‐based surface details such as grooves, scratches and similar features. The method is based on a continuous representation of the features in texture space, and the rendering is performed by means of two approaches: one for isolated or non‐intersecting grooves and another for special situations like intersections or ends. The proposed solutions perform correct antialiasing and take into account visibility and inter‐reflections with little computational effort and memory requirements. Compared to anisotropic BRDFs and scratch models, we have no limitations on the distribution of grooves over the surface or their geometry, thus allowing more general patterns. Compared to displacement mapping techniques, we can efficiently simulate features of all sizes without requiring additional geometry or multiple representations.

Abstract Individually visible scratches, also called isolated scratches, are very common in real world surfaces. Although their microgeometry is not visible, they are individually perceptible by the human eye, lying into a representation scale between BRDF and texture. In order to simulate this kind of scratches in synthetic images we need to know their position over the surface (texture scale), so we can determine where to use the specific scratch BRDF instead of the ordinary surface BRDF. Computing the BRDF of a scratch is difficult because it depends on the scratch's invisible microgeometry. In this paper, we propose a new physically based model to derive this microgeometry by simulating the formation process of scratches. We allow specifying intuitively the parameters involved in the process such as the scratching tool, the penetration forces, and the material properties of the object. From these parameters, we derive the microgeometries of the scratches by taking into account the real behaviour of the process. This behaviour has been determined by analysing existing models in the field of materials engineering and some ``scratch tests'' that we performed on metals. Our method has the advantages of easily simulating scratches with a wide range of microgeometries and taking into account the variability of their microgeometry along the scratch path. Another contribution is related to the location of the scratches over the surface. Instead of using an image of the paths as in previous work, we present a new representation based on curves defining the paths. This offers an independence on the image resolution or the distance from the observer and accurately provides the scratch direction in order to compute scratch BRDFs. Categories and Subject Descriptors (according to ACM CCS): I.3.7 [Computer Graphics]: Color, shading, shadowing, and texture.

The behavior of light interacting with materials is a crucial factor in achieving a high degree of realism in image synthesis. Local illumination processes, describing the interactions between a point of the surface and a shading ray, are evaluated by bidirectional reflectance distribution functions (BRDFs). Current theoretical BRDFs use surface models restricted to roughness only, sometimes at different scales. We present a more complete surface micro-geometry description, suitable for some common surface defects, including porosity and micro-cracks; both of them are crucial surface features since they strongly influence light reflection properties. These new features are modeled by holes inserted in the surface profile, depending on two parameters: the proportion of surface covered by the defects and the mean geometric characteristic of these defects. In order to preserve the advantages and characteristics of existing BRDFs, a postprocessing method is adopted (we integrate our technique into existing models, instead of defining a completely new one). Beyond providing graphical results closely matching real behaviors, this method moreover opens the way to various important new considerations in computer graphics (for example, changes of appearance due to the degree of humidity).