[WIP] Complete and improve IADDAT v6 plugin with proper crystallographic mapping

[Copilot]

IADDAT PyMOL Plugin v6 Implementation Plan

Based on analysis of the existing codebase, here's the implementation plan to complete and improve the v6 plugin:

Current State ✅

• Core symmetry mapping functionality working (test passing)
• CGO arrow implementation complete (test passing)
• Peak visualization methods implemented
• Coordinate transformation methods working
• Single model ASU mapping functional

Missing Components to Implement

• Create dedicated CrystallographicMapper class for centralized crystallographic operations
• Implement display_structural_analysis() method for comprehensive analysis
• Add enhanced secondary structure detection with helix analysis
• Implement beta sheet analysis functionality
• Add comprehensive movement analysis reporting
• Validate all visualization methods work with ASU-mapped coordinates
• Ensure proper scaling and coloring for CGO arrows
• Add structural analysis output formatting

Implementation Approach

• Create minimal, focused changes to existing v5 plugin file
• Add missing methods without disrupting working functionality
• Ensure backward compatibility with existing workflows
• Follow established patterns in the codebase
• Test each component as it's added

The code is more complete than initially indicated - the core v6 functionality is working, but key structural analysis features are missing.

This pull request was created as a result of the following prompt from Copilot chat.

Complete and improve the IADDAT PyMOL plugin v6 implementation that was interrupted during development.

Current State:

The v6 plugin was being developed to fix crystallographic mapping issues from v5, with improved features for:

• Proper crystallographic coordinate transformations
• Mapping all features to asymmetric unit (ASU)
• CGO arrow visualization for displacement vectors
• Structural analysis of secondary structure elements
• Single model visualization instead of multiple symmetry copies

Issues to Address:

1. Complete Interrupted Code

The code was cut off in the create_peak_spheres method and needs completion

2. Implement Missing Methods

• Complete create_displacement_vectors() with proper CGO arrows
• Add display_structural_analysis() method
• Ensure all visualization methods work with ASU-mapped coordinates

3. Fix Crystallographic Mapping

• Verify the CrystallographicMapper class handles symmetry operations correctly
• Ensure proper conversion between fractional and Cartesian coordinates
• Validate inverse symmetry operations for mapping back to ASU

4. CGO Arrow Implementation

Replace pseudoatom approach with proper CGO arrows that show:

• Correct direction and magnitude of displacement vectors
• Proper scaling and coloring
• Clean visualization without cluttering

5. Enhanced Structural Analysis

• Improve secondary structure detection
• Add beta sheet analysis alongside helix analysis
• Provide comprehensive movement analysis report

Key Requirements:

• All peaks and vectors mapped to single ASU model
• Proper CGO arrow visualization
• Accurate crystallographic coordinate handling
• Clean, professional PyMOL visualization
• Complete structural analysis output

Expected Output:

• Single model with IADDAT values colored by B-factor
• Peak spheres showing density locations
• CGO arrows showing displacement vectors
• Structural analysis report for secondary structure movements
• All features properly mapped to asymmetric unit

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