Claude/dev v1.5.0 lp im6#94
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Major Features: - Unified parseInput API supporting XYZ (single/multi-frame) and CIF formats - Auto-detection of file format from extension and content - Multi-frame XYZ trajectory parsing with per-frame structure IDs - Basic CIF parsing with fractional-to-Cartesian coordinate conversion - Batch mode UI with structure selector and summary table - "Analyze All Structures" batch processing with progress tracking - Manual override panel for metal center, radius, and target CN - Per-structure override storage with "apply to all" option Report & Export Enhancements: - Batch PDF report with summary table and per-structure detail sections - Wide summary CSV (one row per structure, best match only) - Long detailed CSV (one row per structure/geometry pair, all results) - All reports now include ALL geometries, not just best match UI/UX Improvements: - File upload now accepts .xyz and .cif files - Batch mode indicator shows when multiple structures detected - Structure ID displayed in results panel and coordination summary - Selected structure highlighted in batch summary table - Scene key-based 3D re-rendering for reliable visualization updates State Management: - Unified Structure data model (src/types/structureTypes.js) - useBatchAnalysis hook for batch state orchestration - State properly resets on new file upload - Structure overrides preserved during analysis Testing: - 23 new unit tests for parseInput API - TESTING.md manual E2E checklist - Regression checklist for known issues Technical Notes: - CIF parsing uses basic implementation (gemmi-wasm can be added later) - Fractional coordinates converted using standard crystallographic matrix - STRICT_MODE config available for parse error handling behavior
…override panel - Remove ManualOverridePanel component (controls integrated into AnalysisControls) - Add BatchSummaryTable component for batch results display with interactive selection - Make Report/CSV buttons context-aware (auto-switch between batch and single mode) - Add "Apply to All" buttons in AnalysisControls for batch mode - Position batch summary table below action buttons, closer to 3D viewer - Update CoordinationSummary to include "Analyze All Structures" button
- Remove duplicate Batch Analysis Summary from BatchModePanel (now only in BatchSummaryTable) - Fix CoordinationSummary crash when atoms[selectedMetal] is undefined - Fix 3D viewer misalignment by using sceneKey in useThreeScene dependency array - Enhance batch PDF report with full details for each structure: - Analysis Summary (metal, CN, radius, geometry, ligands) - Quality Metrics (overall score, angular distortion, bond uniformity, RMSD) - Bond Statistics (mean/stddev/range, angles) - All geometry comparisons table
- Remove rotation limits in OrbitControls for full 360° rotation freedom - Increase zoom range (minDistance: 3, maxDistance: 60) - Enable screen space panning for better interaction - Add smooth rotation/zoom/pan speed settings Color scheme improvements in BatchSummaryTable: - Selected rows now use cohesive blue palette throughout - All text in selected row uses consistent #1e40af blue - Quality badge in selected row uses blue background/text - Non-selected rows retain semantic colors (green/yellow/red) - Added hover effect for non-selected rows
…ch report 3D Viewer: - Switch from OrbitControls to TrackballControls for unrestricted 360° rotation - No more gimbal lock or rotation limits - Manual auto-rotation implementation for TrackballControls - Smooth damping with dynamicDampingFactor BatchSummaryTable color scheme: - Softer blue gradient for selected rows (#f0f7ff to #e8f2ff) - Lighter blue left border (#60a5fa) - Muted text color (#1e3a5f) for better readability - Softer badge backgrounds with reduced opacity Batch PDF Report: - Add Coordinating Atoms section for each structure - Shows element, distance, and coordinates for each ligand
- Added null checks in useThreeScene.js to prevent 'x' undefined crash - Fixed batch analysis to store coordAtoms for complete report generation - Enhanced batch PDF report with all sections from single report: - Q-Shape analysis overview info box per structure - Ligand Groups Analysis section - Full header with citation info - Complete footer with university info - Report now shows reference geometry counts per CN
- Updated package.json, CITATION.cff, .zenodo.json to v1.5.0 - Updated README.md with v1.5.0 badge and batch analysis features - Enhanced CHANGELOG.md with multi-structure batch analysis section - Updated all version references in source files (reportGenerator, workers) - Added batch analysis workflow documentation to README
- Created src/constants/appMetadata.js with APP_VERSION, BUILD_DATE, APP_FULL_NAME, CITATION object, and helper functions - Updated App.js to use centralized constants for header display - Updated reportGenerator.js to use constants in all PDF reports - Single source of truth for version info across entire codebase
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Summary
This release introduces Multi-Structure Batch Analysis - analyze multiple structures from a single XYZ/CIF file.
New Features
src/constants/appMetadata.jsBug Fixes
Cannot read properties of undefined (reading 'x')crashStats
24 files changed, +3,819/-187 lines
Test plan