HenriqueCSJ · HenriqueCSJ · Jan 9, 2026 · Jan 9, 2026 · Jan 9, 2026 · Jan 9, 2026
diff --git a/.zenodo.json b/.zenodo.json
@@ -1,7 +1,7 @@
 {
   "title": "Q-Shape - Quantitative Shape Analyzer",
-  "version": "v1.4.0",
-  "description": "Q-Shape: Advanced coordination geometry analysis using Continuous Shape Measures (CShM). A web-based tool for analyzing molecular coordination geometries with 92 reference geometries (CN 2-12, 20, 24, 48, 60), real-time 3D visualization, and comprehensive quality metrics.",
+  "version": "v1.5.0",
+  "description": "Q-Shape: Advanced coordination geometry analysis using Continuous Shape Measures (CShM). A web-based tool for analyzing molecular coordination geometries with 92 reference geometries (CN 2-12, 20, 24, 48, 60), real-time 3D visualization, and comprehensive quality metrics. Supports XYZ and CIF file formats with multi-structure analysis.",
   "creators": [
     {
       "name": "Castro Silva Junior, Henrique",
@@ -20,7 +20,10 @@
     "computational chemistry",
     "web application",
     "Three.js",
-    "React"
+    "React",
+    "CIF",
+    "XYZ",
+    "crystallography"
   ],
   "license": {
     "id": "MIT"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,14 +5,41 @@ All notable changes to Q-Shape will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [1.5.0] - 2025-01-28
+## [1.5.0] - 2026-01-09
 
 ### 🎯 Overview
 
-**Piano Stool Complex Support** - This release adds comprehensive support for half-sandwich (piano stool) complexes, a major class of organometallic compounds that were previously not properly analyzed by the software.
+**Multi-File Support & CIF Format** - This release adds support for multiple file formats, multi-geometry XYZ files, and simultaneous analysis of multiple structures. Additionally, comprehensive support for half-sandwich (piano stool) complexes has been added.
 
 ### ✨ New Features
 
+#### Multi-Format File Support
+- **CIF File Support** - Parse Crystallographic Information Files using the `crystcif-parse` library
+  - Automatic fractional-to-Cartesian coordinate conversion
+  - Multi-block CIF files supported (each data block becomes a separate structure)
+  - Cell parameters and space group metadata preserved
+  - File validation with informative error messages
+
+- **Multi-Geometry XYZ Files** - Read XYZ files containing multiple concatenated structures
+  - Automatic frame detection and counting
+  - Structure names extracted from comment lines
+  - Perfect for analyzing conformational isomers or trajectory snapshots
+
+- **Multiple File Upload** - Upload several XYZ/CIF files simultaneously
+  - All structures loaded and accessible via navigator
+  - Mix different file formats in a single session
+
+#### Structure Navigator UI
+- **Dropdown Selector** - Easy switching between loaded structures
+- **Navigation Buttons** - First/Prev/Next/Last for quick browsing (shown for >5 structures)
+- **Structure Counter Badge** - Shows loaded structure count and file formats
+- **Per-Structure Analysis** - Each structure analyzed independently with proper naming
+
+#### Enhanced Reports
+- **Structure Names in PDF** - Reports now include structure name and source file
+- **Structure Column in CSV** - CSV exports include structure identification
+- **Multi-Structure Awareness** - Reports indicate which structure from which file
+
 #### Piano Stool (Half-Sandwich) Complex Recognition
 - **Problem:** Piano stool complexes like [CpMn(CO)₃] were analyzed as CN=8 (all atoms separately), giving poor CShM values (>15.0)
 - **Solution:** Automatic pattern detection and geometry-aware analysis
@@ -57,10 +84,24 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### 🔧 Technical Details
 
-**Modified Files:**
+**New Files:**
+- `src/utils/cifParser.js` - Complete CIF file parser with validation and metadata extraction
+- `src/utils/fileParser.test.js` - Extended with 14 new tests for multi-frame XYZ functions
+
+**Modified Files (Multi-File/CIF Support):**
+- `src/utils/fileParser.js` - Added `parseXYZAuto()`, `parseMultiXYZ()`, `isMultiFrameXYZ()`, `countXYZFrames()`, `validateMultiXYZ()`
+- `src/hooks/useFileUpload.js` - Rewritten for multi-file/multi-format support with structure state management
+- `src/components/FileUploadSection.jsx` - Added structure selector UI with navigation buttons
+- `src/services/reportGenerator.js` - Added structure name and format to PDF/CSV reports
+- `src/App.js` - Updated to use new structure selection props
+
+**Modified Files (Piano Stool Support):**
 - `src/constants/algorithmConstants.js` - Added `PIANO_STOOL_GEOMETRIES` constant
 - `src/services/coordination/patterns/geometryBuilder.js` - Implemented intelligent geometry filtering
 
+**New Dependencies:**
+- `crystcif-parse` (^0.2.9) - CIF file parsing library with fractional-to-Cartesian conversion
+
 **Key Algorithm Changes:**
 1. Piano stool patterns detected with 85% confidence
 2. Centroid-based coordination number calculation

diff --git a/CITATION.cff b/CITATION.cff
@@ -10,8 +10,8 @@ authors:
 repository-code: "https://github.com/HenriqueCSJ/q-shape"
 url: "https://henriquecsj.github.io/q-shape"
 license: MIT
-version: "v1.4.0"
-date-released: "2025-11-25"
+version: "v1.5.0"
+date-released: "2026-01-09"
 keywords:
   - "coordination chemistry"
   - "continuous shape measures"
@@ -26,7 +26,7 @@ identifiers:
 preferred-citation:
   type: software
   title: "Q-Shape - Quantitative Shape Analyzer"
-  version: "v1.4.0"
+  version: "v1.5.0"
   year: 2025
   authors:
     - given-names: Henrique

diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 
 ![Q-Shape Logo](https://img.shields.io/badge/Q--Shape-Molecular%20Geometry%20Analysis-blue?style=for-the-badge&logo=react&logoColor=white)
 
-[![Version](https://img.shields.io/badge/version-1.4.0-blue.svg?style=flat-square)](https://github.com/HenriqueCSJ/q-shape/releases/tag/v1.4.0)
+[![Version](https://img.shields.io/badge/version-1.5.0-blue.svg?style=flat-square)](https://github.com/HenriqueCSJ/q-shape/releases/tag/v1.5.0)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17717110.svg)](https://doi.org/10.5281/zenodo.17717110)
 [![MIT License](https://img.shields.io/badge/License-MIT-green.svg?style=flat-square)](https://choosealicense.com/licenses/mit/)
 [![Website](https://img.shields.io/website?down_color=red&down_message=offline&style=flat-square&up_color=green&up_message=online&url=https%3A%2F%2Fhenriquecsj.github.io%2Fq-shape)](https://henriquecsj.github.io/q-shape)
@@ -46,6 +46,14 @@
 ✅ **Comprehensive Metrics** - Bond statistics, angular distortion, quality scoring
 ✅ **PDF Reports** - Professional output suitable for publication
 
+### File Format Support (v1.5.0)
+
+✅ **XYZ Files** - Standard molecular geometry format
+✅ **Multi-Geometry XYZ** - Multiple structures in a single file (trajectory-like format)
+✅ **CIF Files** - Crystallographic Information Files with automatic coordinate conversion
+✅ **Multi-File Upload** - Analyze multiple files simultaneously
+✅ **Structure Navigator** - Easy switching between loaded structures
+
 ### Analysis Modes
 
 **Standard Mode** (~5-10 seconds)
@@ -70,12 +78,13 @@ Visit **[https://henriquecsj.github.io/q-shape](https://henriquecsj.github.io/q-
 
 ### Basic Workflow
 
-1. **Upload** your XYZ file (drag-and-drop or file picker)
-2. **Select** metal center (auto-detected or manual selection)
-3. **Adjust** coordination sphere radius if needed
-4. **Run** analysis (standard or intensive mode)
-5. **Visualize** results in 3D and review shape measures
-6. **Export** PDF report for your records
+1. **Upload** your structure file(s) - XYZ or CIF format (drag-and-drop or file picker)
+2. **Select** structure if multiple were loaded (use dropdown or navigation buttons)
+3. **Select** metal center (auto-detected or manual selection)
+4. **Adjust** coordination sphere radius if needed
+5. **Run** analysis (standard or intensive mode)
+6. **Visualize** results in 3D and review shape measures
+7. **Export** PDF report or CSV data for your records
 
 ---
 
@@ -203,16 +212,18 @@ Q-Shape has been validated against SHAPE 2.1 (Fortran reference implementation):
 
 ## Input Format
 
-Q-Shape accepts standard XYZ molecular structure files:
+Q-Shape accepts multiple molecular structure formats:
+
+### XYZ Format (Single Structure)
 
 ```xyz
 <number of atoms>
-<comment line (optional)>
+<comment line (structure name extracted from here)>
 <element> <x-coordinate> <y-coordinate> <z-coordinate>
 ...
 ```
 
-### Example: Octahedral Iron Complex
+**Example: Octahedral Iron Complex**
 
 ```xyz
 7
@@ -226,6 +237,58 @@ O    0.000   0.000   2.100
 O    0.000   0.000  -2.100
 ```
 
+### Multi-Geometry XYZ Format (v1.5.0)
+
+Multiple structures concatenated in a single file:
+
+```xyz
+7
+Structure_A - First geometry
+Fe   0.000   0.000   0.000
+O    2.100   0.000   0.000
+...
+7
+Structure_B - Second geometry
+Fe   0.000   0.000   0.000
+O    2.050   0.000   0.000
+...
+```
+
+Each structure is automatically detected and can be analyzed separately using the structure navigator.
+
+### CIF Format (v1.5.0)
+
+Q-Shape supports Crystallographic Information Files (CIF):
+
+```cif
+data_example_structure
+_cell_length_a   10.0
+_cell_length_b   10.0
+_cell_length_c   10.0
+_cell_angle_alpha   90.0
+_cell_angle_beta    90.0
+_cell_angle_gamma   90.0
+
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+Fe1  Fe  0.5  0.5  0.5
+O1   O   0.71 0.5  0.5
+...
+```
+
+**CIF Features:**
+- Automatic fractional-to-Cartesian coordinate conversion
+- Multi-block CIF files supported (each data block becomes a structure)
+- Space group and cell parameter metadata preserved
+
+### Multiple File Upload (v1.5.0)
+
+Upload multiple XYZ and/or CIF files at once. All structures are loaded and accessible via the structure navigator dropdown.
+
 **Expected Result**: CShM(Octahedron) ≈ 0.00-0.10 (perfect geometry)
 
 ---
@@ -339,7 +402,7 @@ If you use Q-Shape in your research, please cite:
 
 **APA:**
 ```
-Castro Silva Junior, H. (2025). Q-Shape - Quantitative Shape Analyzer (v1.4.0).
+Castro Silva Junior, H. (2025). Q-Shape - Quantitative Shape Analyzer (v1.5.0).
 Zenodo. https://doi.org/10.5281/zenodo.17717110
 ```
 
@@ -348,7 +411,7 @@ Zenodo. https://doi.org/10.5281/zenodo.17717110
 @software{qshape2025,
   author = {Castro Silva Junior, Henrique},
   title = {Q-Shape - Quantitative Shape Analyzer},
-  version = {1.4.0},
+  version = {1.5.0},
   year = {2025},
   doi = {10.5281/zenodo.17717110},
   url = {https://doi.org/10.5281/zenodo.17717110},