Our Work

Make CIF field lookup case insensitive, so mmCIF files writing _atom_site.cartn_x resolve fields like Cartn_x instead of leaving coordinates at 0,0,0 (#1941) Headless rendering: Allow consumers to pro…

Make CIF field lookup case insensitive, so mmCIF files writing _atom_site.cartn_x resolve fields like Cartn_x instead of leaving coordinates at 0,0,0 (#1941) Headless rendering: Allow consumers to provide gl version 6 through 8 Fix browser-only layout/canvas access when rendering without a DOM Fix version handling in commonjs Tests for HeadlessPluginContext Merge representation render-objects to reduce draw-calls Optimize Renderable culling with a frame token guard Improve dynamic trackball controls and show param Fix altloc in PDB files receive different atom names (#156) Add volume-tools/segmentor: interactive segmentation of a volume into bodies (polygon labelling from several views, remainder assignment, dust removal, handedness flip, per-body extend + cosine soft edge, MRC mask export) Breaking: move the volume-mask extension to volume-tools/mask, alongside the new segmentor; ViewMask, its projection and the in-place volume operations are now shared at volume-tools/. Update imports from extensions/volume-mask to extensions/volume-tools/mask Merge the volume-mask example into a volume-tools example, with a landing page and one page per tool Fix CCP4Writer.writeMrc for volumes with a non-canonical axis order Fix CCP4Writer.writeMrc writing ISPG = 0, which marks the data as an image stack rather than a volume Add squaredDistanceTransform3D (exact Euclidean distance transform) to mol-math/geometry Optimize GridLookup3D building for sparse grids Optimize calcInstanceGrid by reducing amount of data copied Viewer app: keep track of instances in static Viewer.instances Fix missing reset time for Canvas3dInteractionHelper Remove unused floodfill param from the gaussian density volume representation Fix CPU surface/volume visuals rebuilding on every update if GPU path is unavailable Fix floodfill not applied on the gaussian surface wireframe Fix traceOnly update being ignored by the molecular surface wireframe visuals Fix SSAO artifacts near viewport edges by clamping off-screen samples instead of discarding them Fix illumination trace reading color/normal/depth outside viewport bounds Added support for molecular atom_style in lammps data files Added element symbol detection in lammps data file Fix inconsistent atomic weight for some elements in ElementAtomWeights Fix extra Hydrogens not in chemcomp dict. are disconnected (#1888) Use IUPAC names for Nh/Mc/Ts/Og elements Add mergeBySymmetry option to root structure transform (merge units with same symmetry operator) Add support for multi-chain units in sequence UI Add script to generate spacegroup data from CCP4 syminfo.lib Refactor spacegroup construction Use syminfo.lib spacegroup data as source Generate operators from Hall symbols Introduce change-of-basis settings Move base functionality from SpacegroupCell to Cell Improve Cell handling Fix volume calculation for non-orthogonal cells Use as base for Unitcell shape Add order property (for AU volume estimation) Add per-format cache for FormatProperty Use for ModelSymmetry and ComponentBond ModelSymmetry improvements Fix property not being dynamic Defer Symmetry calculation in ModelSymmetry.fromData Support non-default CRYSIN setting in MOL2 format (#338) Fix ssao-blur background test: the RG-packed depth never equals 1.0 Fix picking/hover-highlight of the nucleic cartoon polymer-trace on partial structures Fix stale marker data in VolumeVisual when a geometry update changes the group count Add Spherical Harmonics to mol-math Add blob-surface structure representation Bin atoms to grid or cluster Fast option fits ellipsoids to bins Artistic option fits spherical harmonics to bins Mesh and wireframe visuals, per-unit & per-structure Illumination Remove firstStepSize tracing parameter, derive automatically Fix illumination auto thickness mode never correctly being applied Fix illumination ray marching stepping over occluders Evaluate illumination auto thickness at the surface being tested Fix NaN in illumination shadows when a light color channel sums to zero Fix illumination indirect light ignoring exposure and the shading clamp Remove illumination glow parameter Fix sphere/cylinder impostors writing their near surface in the back-depth pass Fix mesh back faces & cylinder far hits being discarded as interior in the back-depth pass Fix illumination shadows not weighing occlusion by per-light irradiance Add .parseRaw to DataFormatProvider for out of state tree parsing Carbohydrate symbols All carbohydrate symbols are rendered with 2 groups (primary and secondary) and can be potentially colored in two colors CarbohydrateSymbolColorTheme decides which shape will be colored by one or two colors Changed side length ratio of FlatBox shape from 2:2:1 to 2:1:1 Camera improvements Support multiple camera transition shapes Add transitionTrajectory and transitionEasing parameters to PluginState.Snapshot (MOLJ) and Plugin State > Save Options Add trajectory and easing parameters to FocusLoci behavior Add cameraResetTrajectory and cameraResetEasing parameters to Canvas3DParams Fix camera reset handling for (temporary) empty scenes (#1903) MolViewSpec Added transition node with params duration_ms, trajectory, easing Snapshot metadata: linger_duration_ms renamed to duration_ms, deprecated transition_duration_ms MVS-related custom model properties (and custom structure properties) are hidden in UI (fixes override of default custom properties) Added shape node for rendering meshes from vtp, ply and obj resources Added support for MolQL selectors (e.g., select a residue + 5 ang surroundings) Add support for split colors (e.g. 'red/white', applies to carbohydrate symbols and nucleic cartoon) Add CarbohydrateSymbol color palette Remove new Function usage for CSP / SOC2 compliance; server path templates use a whitelist of ${id...} string methods Fix CCP4/MRC volumes with unset cell angles failing to load Fix CCP4/MRC volume sigma being taken from the header when the header rms is negative Add Particles as first class objects ParticleList and ParticleTrajectory Formats: ariatomi-em, cryoet-ndjson, dynamo-tbl, relion-star, simularium, cellpack & petworld mmcif Properties: position, orientation, radius, entity, compartment, custom attributes, fibers Particles can be decorated with structure, volume, and shape visuals Fix bumpiness artifacts on impostor seams and clip boundaries Change bumpFrequency defaults of ball-and-stick (5) and backbone (4)

Adaptive high-order numerical simulations of hyperbolic PDEs in Julia

1.54.6 (2026-09-28) ENH: Add France's RGF93 EPSG code in vectors FIX: Handle correctly the case geopandas >= 1 is installed but pyogrio is missing (cf. ArcGis Pro) CI: Manage InvalidVersion except…

1.54.6 (2026-09-28) ENH: Add France's RGF93 EPSG code in vectors FIX: Handle correctly the case geopandas >= 1 is installed but pyogrio is missing (cf. ArcGis Pro) CI: Manage InvalidVersion exception from packaging.version DEPS: Drop Python 3.10 support

Computational chemistry toolkit providing formula handling, species management, stoichiometric matrix construction, thermodynamic equilibrium via Gibbs free energy minimization, extended Debye-Hückel …

Computational chemistry toolkit providing formula handling, species management, stoichiometric matrix construction, thermodynamic equilibrium via Gibbs free energy minimization, extended Debye-Hückel and Davies activity models, ideal and Redlich-Kister solid solution phases, interoperability with ThermoFun and Cemdata databases, and a kinetics module for mineral dissolution/precipitation coupled to ODE-based integration (Parrott-Killoh model, semi-adiabatic calorimetry). Initially focused on cement chemistry but applicable more broadly.

Automated molecular-dynamics system builder for amorphous network polymers. Generates atomistic models of cross-linked polymer networks, together with the Gromacs topology and parameter files needed t…

Automated molecular-dynamics system builder for amorphous network polymers. Generates atomistic models of cross-linked polymer networks, together with the Gromacs topology and parameter files needed to simulate them, from only the monomer structures, a description of the polymerization chemistry, and a handful of system-size and composition options. Atom typing and parameter generation use the General Amber Force Field.

Material suplementario del artículo «Evaluación de la interacción verbal en psicoterapia: Desarrollo, bases conceptuales y alcance metodológico del Sistema ACOVEO&raq…

Material suplementario del artículo «Evaluación de la interacción verbal en psicoterapia: Desarrollo, bases conceptuales y alcance metodológico del Sistema ACOVEO», enviado a la revista Psicothema. Este documento contiene la guía completa de categorización del Sistema ACOVEO.

FHOPS v1.1.0a1 Alpha status FHOPS 1.1.0a1 is an alpha prerelease for the new TOPM-inspired tactical–operational planning layer. The existing schema 1.0.0 operational workflows remain backward-compatib…

FHOPS v1.1.0a1 Alpha status FHOPS 1.1.0a1 is an alpha prerelease for the new TOPM-inspired tactical–operational planning layer. The existing schema 1.0.0 operational workflows remain backward-compatible, but the new tactical contract, CLI surfaces, and MILP behavior should be treated as provisional until broader practitioner testing is complete. Use this alpha to evaluate the workflow and report defects or API friction. Do not treat the tactical outputs as calibrated operational advice without local validation. Scope This prerelease adds a separate tactical–operational planning layer while preserving existing operational scenario bundles and CLI workflows. Highlights Tactical–operational contract — a separate aggregate planning contract supports 1–5 year horizons, configurable periods, products, facilities, transport arcs, inventories, purchases, roads, silviculture, and fleet options. Aggregate MILP — Pyomo/HiGHS support for continuous, semi-continuous, and whole-block harvest modes with cost, discounted-profit, and NPV objective profiles. Scenario workflows — sparse overlays, scenario diffs, batch manifests, and normalized CSV/Parquet/Markdown reports. Operational handoff — tactical commitments can be compiled into existing operational scenario bundles for detailed shift/day scheduling. Validation evidence — includes the copyright-safe topm-mini fixture, a practitioner-scale synthetic case, a guided tactical notebook, and a full-scale 500-block × 5-year HiGHS benchmark (optimal in about 41 seconds on the recorded host). Docs/API — the tactical guide, canonical formulation, and API reference are published in the Sphinx documentation set. New CLI surfaces fhops validate tactical-operational scenario.yaml fhops plan tactical-operational scenario.yaml --out-json result.json fhops scenario overlay base.yaml overlay.yaml --out candidate.yaml fhops scenario diff base.yaml candidate.yaml fhops scenario batch batch.yaml --out-dir results/ fhops scenario benchmark --blocks 500 --years 5 --periods-per-year 4 --out-dir benchmark/ fhops synth tactical --out scale.yaml fhops synth tactical-practitioner --out practitioner.yaml fhops report tactical result.json --out-dir report/ fhops plan compile-tactical result.json operational/scenario.yaml --block-map B1=B01 --out-dir compiled/ Compatibility and alpha limitations Existing operational Scenario bundles remain schema 1.0.0 and are unchanged. Tactical–operational scenarios use the separate tactical_operational contract (schema_version 0.1.0). The tactical layer is validated on synthetic/redistributable fixtures; practitioner calibration data should be reviewed before operational use. Tactical API names, report schemas, and objective semantics may change before the stable 1.1.0 release. Decomposition is intentionally deferred: the recorded 500-block × 5-year benchmark is optimal within the documented smoke envelope, so no Benders/Dantzig–Wolfe complexity is added yet. The SoftwareX manuscript is maintained in the separate fhops-manuscript repository; this package prerelease does not edit manuscript content. Verification Full test suite: 390 passed, 211 skipped. Ruff, MyPy, full pre-commit, Sphinx warnings-as-errors, and formulation drift checks passed. GitHub Pages deployment from main completed after the docs CI fixes.

Code for paper "Evaluation of optimisation and Bayesian inference methods for reaction rates in atmospheric chemical mechanisms" https://doi.org/10.48550/arXiv.2609.14569

Data and code reproducing every table and figure in "Severe Safeguards and Fiscal Capacity: The Political Economy of Intergovernmental Retaliation", from raw INEGI, CONAPO and Banco de México sources …

Data and code reproducing every table and figure in "Severe Safeguards and Fiscal Capacity: The Political Economy of Intergovernmental Retaliation", from raw INEGI, CONAPO and Banco de México sources through to the reported estimates.