diff --git a/gendocs_mkdocs.py b/gendocs_mkdocs.py
new file mode 100644
index 0000000000000000000000000000000000000000..4083264458b4c2595ebe15bf42bda2f9276527f7
--- /dev/null
+++ b/gendocs_mkdocs.py
@@ -0,0 +1,642 @@
+#!/usr/bin/env python3
+"""
+Enhanced documentation generator for the mrdna package using MkDocs with Material theme.
+
+This script:
+1. Scans the mrdna package structure
+2. Generates markdown documentation files
+3. Creates a navigable documentation website using MkDocs with Material theme
+4. Adds support for API reference documentation through mkdocstrings
+"""
+
+import os
+import sys
+import inspect
+import importlib
+import subprocess
+from pathlib import Path
+import shutil
+import yaml
+import re
+from textwrap import dedent
+from collections import defaultdict
+
+# Configure documentation paths
+DOCS_DIR = Path("docs")
+SITE_DIR = Path("site")
+CONFIG_FILE = Path("mkdocs.yml")
+
+# Core modules to document
+MODULES_TO_DOCUMENT = {
+    "core": [
+        "mrdna.config",
+        "mrdna.coords",
+        "mrdna.reporting",
+        "mrdna.segmentmodel",
+        "mrdna.simulate",
+        "mrdna.version"
+    ],
+    "model": [
+        "mrdna.model.CanonicalNucleotideAtoms",
+        "mrdna.model.dna_sequence",
+        "mrdna.model.nbPot",
+        "mrdna.model.spring_from_lp"
+    ],
+    "readers": [
+        "mrdna.readers.cadnano_segments",
+        "mrdna.readers.polygon_mesh",
+        "mrdna.readers.segmentmodel_from_cadnano",
+        "mrdna.readers.segmentmodel_from_lists",
+        "mrdna.readers.segmentmodel_from_oxdna",
+        "mrdna.readers.segmentmodel_from_pdb",
+        "mrdna.readers.segmentmodel_from_scadnano"
+    ],
+    "arbdmodel": [
+        "mrdna.arbdmodel.coords",
+        "mrdna.arbdmodel.grid",
+        "mrdna.arbdmodel.interactions",
+        "mrdna.arbdmodel.polymer"
+    ]
+}
+
+def check_command_exists(command):
+    """Check if a command exists in the system path."""
+    try:
+        subprocess.run([command, "--version"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=False)
+        return True
+    except FileNotFoundError:
+        return False
+
+def extract_module_info(module_name):
+    """Extract useful information from a module."""
+    try:
+        module = importlib.import_module(module_name)
+        docstring = module.__doc__ or ""
+        
+        # If the module has a __version__ attribute, include it
+        version = getattr(module, "__version__", None)
+        
+        # Extract classes
+        classes = {}
+        for name, obj in inspect.getmembers(module, inspect.isclass):
+            if obj.__module__ == module_name:
+                classes[name] = {
+                    "docstring": obj.__doc__ or "",
+                    "methods": {}
+                }
+                
+                # Extract methods
+                for method_name, method in inspect.getmembers(obj, inspect.isfunction):
+                    if not method_name.startswith("_") or method_name == "__init__":
+                        classes[name]["methods"][method_name] = {
+                            "docstring": method.__doc__ or "",
+                            "signature": str(inspect.signature(method))
+                        }
+        
+        # Extract functions
+        functions = {}
+        for name, obj in inspect.getmembers(module, inspect.isfunction):
+            if obj.__module__ == module_name and not name.startswith("_"):
+                functions[name] = {
+                    "docstring": obj.__doc__ or "",
+                    "signature": str(inspect.signature(obj))
+                }
+        
+        return {
+            "docstring": docstring,
+            "version": version,
+            "classes": classes,
+            "functions": functions,
+            "module_name": module_name
+        }
+    except (ImportError, AttributeError) as e:
+        print(f"Error extracting info from {module_name}: {e}")
+        return {
+            "docstring": f"Module documentation for {module_name}. (Error: {e})",
+            "version": None,
+            "classes": {},
+            "functions": {},
+            "module_name": module_name
+        }
+
+def create_module_md(module_name, docs_dir):
+    """Create Markdown documentation for a Python module."""
+    try:
+        # Extract module name and subpackage for organization
+        parts = module_name.split('.')
+        simple_name = parts[-1]
+        subpackage = parts[1] if len(parts) > 2 else 'core'
+        
+        # Get module information
+        module_info = extract_module_info(module_name)
+        
+        # Start building the Markdown content
+        content = [
+            f"# {simple_name}",
+            "",
+        ]
+        
+        # Add module docstring
+        if module_info["docstring"]:
+            content.append(module_info["docstring"].strip())
+            content.append("")
+        else:
+            content.append(f"Module documentation for {simple_name}.")
+            content.append("")
+        
+        # Add version if available
+        if module_info["version"]:
+            content.append(f"**Version:** {module_info['version']}")
+            content.append("")
+        
+        # Add mkdocstrings directive for API docs
+        content.extend([
+            "## API Reference",
+            "",
+            f"::: {module_name}",
+            "    handler: python",
+            "    selection:",
+            "      docstring_style: google",
+            "    rendering:",
+            "      show_source: true",
+            ""
+        ])
+        
+        # Create directory for module documentation
+        output_dir = docs_dir / "api" / subpackage
+        output_dir.mkdir(exist_ok=True, parents=True)
+        
+        # Write the Markdown file
+        output_path = output_dir / f"{simple_name}.md"
+        with open(output_path, 'w') as f:
+            f.write('\n'.join(content))
+            
+        print(f"Created module documentation: {output_path}")
+        return output_path.relative_to(docs_dir), simple_name
+        
+    except Exception as e:
+        print(f"Error processing module {module_name}: {e}")
+        return None, None
+
+def create_subpackage_index(subpackage, module_names, docs_dir):
+    """Create an index Markdown file for a subpackage."""
+    # Create index content
+    subpackage_title = subpackage.capitalize()
+    content = [
+        f"# {subpackage_title} Modules",
+        "",
+        f"This section covers the modules in the {subpackage} subpackage.",
+        "",
+        "## Modules",
+        "",
+    ]
+    
+    # Process each module in the subpackage
+    module_info = []
+    for module_name in sorted(module_names):
+        rel_path, simple_name = create_module_md(module_name, docs_dir)
+        if rel_path and simple_name:
+            full_module_name = module_name
+            brief_desc = ""
+            try:
+                mod = importlib.import_module(module_name)
+                if mod.__doc__:
+                    brief_desc = mod.__doc__.strip().split('\n')[0]
+            except:
+                pass
+            module_info.append((rel_path, simple_name, full_module_name, brief_desc))
+    
+    # If no modules were successfully processed, skip creating the index
+    if not module_info:
+        print(f"No modules were successfully processed for {subpackage}, skipping index")
+        return None
+    
+    # Add module links to index with descriptions
+    for rel_path, simple_name, full_module_name, brief_desc in sorted(module_info, key=lambda x: x[1]):
+        # Fix the relative path to ensure it's correct from the packages directory
+        # This ensures links are properly resolved by MkDocs
+        fixed_path = f"../{rel_path}"
+        content.append(f"- [{simple_name}]({fixed_path}): {brief_desc}")
+    
+    # Create directory for subpackage documentation
+    output_dir = docs_dir / "packages"
+    output_dir.mkdir(exist_ok=True, parents=True)
+    
+    # Write the index file
+    index_path = output_dir / f"{subpackage}.md"
+    with open(index_path, 'w') as f:
+        f.write('\n'.join(content))
+        
+    print(f"Created subpackage index: {index_path}")
+    return index_path.relative_to(docs_dir)
+
+def create_main_index(subpackages, docs_dir):
+    """Create the main index.md file."""
+    content = [
+        "# mrDNA Documentation",
+        "",
+        "Welcome to the documentation for mrDNA!",
+        "",
+        "mrDNA is a molecular dynamics package for DNA modeling and simulation.",
+        "",
+        "## Package Structure",
+        "",
+        "The package is organized into the following subpackages:",
+        "",
+    ]
+    
+    # Add each subpackage to the list
+    for subpackage in sorted(subpackages):
+        subpackage_title = subpackage.capitalize()
+        content.append(f"- [{subpackage_title}](packages/{subpackage}.md)")
+    
+    # Write the index file
+    index_path = docs_dir / "index.md"
+    with open(index_path, 'w') as f:
+        f.write('\n'.join(content))
+        
+    print(f"Created main index: {index_path}")
+
+def create_installation_page(docs_dir):
+    """Create the installation page."""
+    with open(Path("README.md"), 'r') as f:
+        readme_content = f.read()
+    
+    # Extract installation instructions from README
+    installation_match = re.search(r'## Installation(.*?)(?:##|\Z)', readme_content, re.DOTALL)
+    if installation_match:
+        installation_content = installation_match.group(1).strip()
+    else:
+        installation_content = """
+        Please refer to the README file for installation instructions.
+        """
+    
+    # Create a more detailed installation guide
+    content = [
+        "# Installation",
+        "",
+        "## Requirements",
+        "",
+        "mrDNA requires the following dependencies:",
+        "",
+        "- Python 3.6+",
+        "- NumPy",
+        "- SciPy",
+        "- MDAnalysis (for certain functionality)",
+        "- CUDA Toolkit (for GPU acceleration)",
+        "- ARBD simulation engine",
+        "",
+        "## Installation Instructions",
+        "",
+        installation_content,
+        "",
+        "## Verifying Installation",
+        "",
+        "After installation, you can verify that mrDNA is working correctly by running a simple test:",
+        "",
+        "```python",
+        "import mrdna",
+        "print(mrdna.__version__)",
+        "```",
+        "",
+        "This should print the version number of the installed mrDNA package.",
+    ]
+    
+    # Write the installation file
+    install_path = docs_dir / "installation.md"
+    with open(install_path, 'w') as f:
+        f.write('\n'.join(content))
+        
+    print(f"Created installation page: {install_path}")
+
+def create_getting_started(docs_dir):
+    """Create the getting started page."""
+    content = [
+        "# Getting Started",
+        "",
+        "This guide will help you get started with using mrDNA for DNA molecular modeling.",
+        "",
+        "## Basic Usage",
+        "",
+        "Here's a simple example that creates a DNA structure:",
+        "",
+        "```python",
+        "# Import necessary modules",
+        "from mrdna.segmentmodel import SegmentModel",
+        "from mrdna.model.dna_sequence import DNASequence",
+        "",
+        "# Create a segment model",
+        "model = SegmentModel()",
+        "",
+        "# Add a DNA segment with a specific sequence",
+        "sequence = \"GATTACA\"",
+        "model.add_segment(sequence)",
+        "",
+        "# Save the model to a PDB file",
+        "model.to_pdb(\"example.pdb\")",
+        "```",
+        "",
+        "## Working with Existing Structures",
+        "",
+        "mrDNA can also read structures from various file formats:",
+        "",
+        "```python",
+        "# Import the appropriate reader",
+        "from mrdna.readers import read_cadnano",
+        "",
+        "# Load a structure from a cadnano file",
+        "model = read_cadnano(\"my_structure.json\")",
+        "",
+        "# Analyze the structure",
+        "num_nucleotides = model.count_nucleotides()",
+        "print(f\"Structure contains {num_nucleotides} nucleotides\")",
+        "```",
+        "",
+        "## Running a Simulation",
+        "",
+        "To run a simulation with mrDNA:",
+        "",
+        "```python",
+        "from mrdna.simulate import multiresolution_simulation",
+        "",
+        "# Set up simulation parameters",
+        "output_name = \"my_simulation\"",
+        "gpu = 0  # GPU device to use",
+        "",
+        "# Run the simulation",
+        "result_directory = multiresolution_simulation(",
+        "    model,",
+        "    output_name=output_name,",
+        "    gpu=gpu,",
+        "    coarse_steps=1e7,  # Number of coarse-grained steps",
+        "    fine_steps=1e7,    # Number of fine-grained steps",
+        ")",
+        "```",
+        "",
+        "## Next Steps",
+        "",
+        "Explore the API reference documentation for more detailed information on each module and function.",
+    ]
+    
+    # Write the getting started file
+    getting_started_path = docs_dir / "getting_started.md"
+    with open(getting_started_path, 'w') as f:
+        f.write('\n'.join(content))
+        
+    print(f"Created getting started page: {getting_started_path}")
+
+def create_tutorials(docs_dir):
+    """Create tutorials directory with example files."""
+    tutorials_dir = docs_dir / "tutorials"
+    tutorials_dir.mkdir(exist_ok=True)
+    
+    # Create a basic tutorial
+    basic_tutorial = [
+        "# Basic DNA Origami Tutorial",
+        "",
+        "This tutorial walks through the process of creating a simple DNA origami structure using mrDNA.",
+        "",
+        "## Loading a design from cadnano",
+        "",
+        "```python",
+        "from mrdna.readers import read_cadnano",
+        "",
+        "# Load a cadnano design",
+        "model = read_cadnano('6hb.json')",
+        "```",
+        "",
+        "## Visualizing the structure",
+        "",
+        "You can generate PDB files to visualize the structure in molecular viewers like VMD or PyMOL:",
+        "",
+        "```python",
+        "# Create a coarse-grained model",
+        "model.generate_bead_model(max_basepairs_per_bead=5, max_nucleotides_per_bead=5)",
+        "",
+        "# Output PDB files",
+        "model.write_pdb('6hb_cg.pdb')",
+        "```",
+        "",
+        "## Running a simulation",
+        "",
+        "```python",
+        "from mrdna.simulate import multiresolution_simulation",
+        "",
+        "# Run a multi-resolution simulation",
+        "result_dir = multiresolution_simulation(",
+        "    model, ",
+        "    output_name='6hb',",
+        "    gpu=0,",
+        "    coarse_steps=5e7,",
+        "    fine_steps=5e7",
+        ")",
+        "```",
+    ]
+    
+    with open(tutorials_dir / "basic_origami.md", 'w') as f:
+        f.write('\n'.join(basic_tutorial))
+    
+    # Create a tutorial index
+    tutorial_index = [
+        "# Tutorials",
+        "",
+        "This section contains tutorials for using mrDNA for different applications.",
+        "",
+        "## Available Tutorials",
+        "",
+        "- [Basic DNA Origami](basic_origami.md): Create and simulate a simple DNA origami structure",
+    ]
+    
+    with open(tutorials_dir / "index.md", 'w') as f:
+        f.write('\n'.join(tutorial_index))
+    
+    print(f"Created tutorials directory: {tutorials_dir}")
+
+def create_mkdocs_config(subpackages):
+    """Create the MkDocs configuration file."""
+    nav = [
+        {"Home": "index.md"},
+        {"Installation": "installation.md"},
+        {"Getting Started": "getting_started.md"},
+        {"Tutorials": "tutorials/index.md"},
+    ]
+    
+    # Add API reference to navigation
+    api_nav = []
+    for subpackage in sorted(subpackages):
+        subpackage_title = subpackage.capitalize()
+        api_nav.append({subpackage_title: f"packages/{subpackage}.md"})
+    
+    nav.append({"API Reference": api_nav})
+    
+    # Create the configuration
+    config = {
+        "site_name": "mrDNA Documentation",
+        "site_description": "Documentation for the mrDNA DNA molecular modeling package",
+        "site_author": "Chris Maffeo",
+        "repo_url": "https://gitlab.engr.illinois.edu/tbgl/tools/mrdna",
+        "theme": {
+            "name": "material",
+            "palette": {
+                "primary": "blue grey",
+                "accent": "light blue"
+            },
+            "features": [
+                "navigation.instant",
+                "navigation.tracking",
+                "navigation.expand",
+                "navigation.indexes",
+                "navigation.top",
+                "search.highlight",
+                "search.share",
+                "content.code.copy"
+            ],
+            "icon": {
+                "repo": "fontawesome/brands/gitlab"
+            }
+        },
+        "markdown_extensions": [
+            "pymdownx.highlight",
+            "pymdownx.superfences",
+            "pymdownx.tabbed",
+            "pymdownx.arithmatex",
+            "admonition",
+            "footnotes",
+            "attr_list",
+            "pymdownx.details",
+            "pymdownx.emoji",
+            "toc"
+        ],
+        "plugins": [
+            "search",
+            "mkdocstrings",
+            {
+                "autorefs": {}
+            }
+        ],
+        "nav": nav,
+        "extra": {
+            "social": [
+                {
+                    "icon": "fontawesome/brands/gitlab",
+                    "link": "https://gitlab.engr.illinois.edu/tbgl/tools/mrdna",
+                    "name": "mrDNA on GitLab"
+                }
+            ]
+        }
+    }
+    
+    # Write the configuration file
+    with open(CONFIG_FILE, 'w') as f:
+        yaml.dump(config, f, default_flow_style=False, sort_keys=False)
+        
+    print(f"Created MkDocs configuration file: {CONFIG_FILE}")
+
+def build_docs():
+    """Build the documentation using MkDocs."""
+    try:
+        print("\nBuilding documentation...")
+        subprocess.run(['mkdocs', 'build'], check=True)
+        print(f"\nDocumentation successfully built. You can view it at: {SITE_DIR / 'index.html'}")
+        return True
+    except subprocess.CalledProcessError as e:
+        print(f"Error building documentation: {e}")
+        return False
+    except FileNotFoundError:
+        print("Could not find mkdocs. Make sure MkDocs is installed and in your PATH.")
+        return False
+
+def check_dependencies():
+    """Check if required dependencies are installed."""
+    missing_deps = []
+    
+    if not check_command_exists("mkdocs"):
+        missing_deps.append("mkdocs")
+    
+    # Check for mkdocstrings - try multiple ways
+    try:
+        import mkdocstrings
+    except ImportError:
+        try:
+            # Try alternative import path
+            subprocess.run([sys.executable, "-c", "import mkdocstrings"], 
+                          check=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        except:
+            missing_deps.append("mkdocstrings")
+    
+    # Check for mkdocs-material
+    try:
+        # First try direct import
+        import material
+    except ImportError:
+        try:
+            # Alternative check: try to import the theme module
+            subprocess.run([sys.executable, "-c", "import mkdocs.themes.material"], 
+                          check=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        except:
+            # Another way to check if a theme is installed
+            try:
+                # Check if mkdocs recognizes the theme
+                result = subprocess.run(["mkdocs", "build", "--theme", "material", "--dry-run"],
+                                      check=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+                if result.returncode != 0:
+                    missing_deps.append("mkdocs-material")
+            except:
+                missing_deps.append("mkdocs-material")
+        
+    if missing_deps:
+        print("Missing dependencies: " + ", ".join(missing_deps))
+        print("\nPlease install the required dependencies with:")
+        print(f"pip install {' '.join(missing_deps)}")
+        print("\nFor better API documentation, also install:")
+        print("pip install \"mkdocstrings[python]\"")
+        
+        response = input("\nDo you want to continue anyway? (y/n): ")
+        if response.lower() in ('y', 'yes'):
+            return True
+        return False
+        
+    return True
+
+def main():
+    """Generate documentation for the mrdna package using MkDocs."""
+    # Check dependencies
+    if not check_dependencies():
+        print("\nProceeding with a warning: Some dependencies may be missing.")
+        print("The documentation generation might not complete successfully.")
+    
+    # Create or clean docs directory
+    if DOCS_DIR.exists():
+        shutil.rmtree(DOCS_DIR)
+    DOCS_DIR.mkdir()
+    
+    # Generate documentation for each subpackage in the predefined list
+    for subpackage, module_list in MODULES_TO_DOCUMENT.items():
+        create_subpackage_index(subpackage, module_list, DOCS_DIR)
+    
+    # Create main index and additional pages
+    create_main_index(MODULES_TO_DOCUMENT.keys(), DOCS_DIR)
+    create_installation_page(DOCS_DIR)
+    create_getting_started(DOCS_DIR)
+    create_tutorials(DOCS_DIR)
+    
+    # Create MkDocs configuration
+    create_mkdocs_config(MODULES_TO_DOCUMENT.keys())
+    
+    print(f"\nDocumentation files generated in {DOCS_DIR}")
+    
+    # Build the documentation
+    response = input("\nWould you like to build the HTML documentation now? (y/n): ")
+    if response.lower() in ('y', 'yes'):
+        success = build_docs()
+        if success:
+            print("\nTo preview the documentation with a local server, run:")
+            print("mkdocs serve")
+    else:
+        print("\nTo build the documentation later, run:")
+        print("mkdocs build")
+        print("\nTo preview the documentation with a local server, run:")
+        print("mkdocs serve")
+
+if __name__ == "__main__":
+    main()
diff --git a/gendocs_sphinx.py b/gendocs_sphinx.py
new file mode 100644
index 0000000000000000000000000000000000000000..347af84760387581f9ad1ec5c80b9cf659ed1a3b
--- /dev/null
+++ b/gendocs_sphinx.py
@@ -0,0 +1,508 @@
+#!/usr/bin/env python3
+"""
+Documentation generator for the mrdna package using Sphinx with sphinx-book-theme.
+
+This script generates ReStructuredText (RST) documentation files
+from the mrdna package's structure and configures Sphinx with
+the sphinx-book-theme for a modern look and feel.
+"""
+
+import os
+import sys
+import inspect
+import importlib
+import shutil
+from pathlib import Path
+import subprocess
+
+# Define the package name
+PACKAGE_NAME = "mrdna"
+
+# Configure documentation paths
+DOCS_DIR = Path("docs")
+SOURCE_DIR = DOCS_DIR / "source"
+BUILD_DIR = DOCS_DIR / "build"
+
+# Define the structure of documentation sections and modules
+DOCUMENTATION_STRUCTURE = {
+    "Core": [
+        "mrdna.config",
+        "mrdna.coords",
+        "mrdna.reporting",
+        "mrdna.segmentmodel",
+        "mrdna.simulate",
+        "mrdna.version"
+    ],
+    "Model": [
+        "mrdna.model.CanonicalNucleotideAtoms",
+        "mrdna.model.dna_sequence",
+        "mrdna.model.nbPot",
+        "mrdna.model.nonbonded",
+        "mrdna.model.spring_from_lp"
+    ],
+    "Readers": [
+        "mrdna.readers.cadnano_segments",
+        "mrdna.readers.polygon_mesh",
+        "mrdna.readers.segmentmodel_from_cadnano",
+        "mrdna.readers.segmentmodel_from_lists",
+        "mrdna.readers.segmentmodel_from_oxdna",
+        "mrdna.readers.segmentmodel_from_pdb",
+        "mrdna.readers.segmentmodel_from_scadnano"
+    ],
+    "ARBD Model": [
+        "mrdna.arbdmodel"
+    ]
+}
+
+def create_module_rst(module_name, output_dir):
+    """Create RST documentation for a Python module."""
+    try:
+        # Try to import the module
+        module = importlib.import_module(module_name)
+        
+        # Extract module name for the title
+        simple_name = module_name.split('.')[-1]
+        
+        # Start building the RST content
+        content = [
+            f"{simple_name} module",
+            "=" * len(f"{simple_name} module"),
+            "",
+            f".. py:module:: {module_name}",
+            "",
+        ]
+        
+        # Add module docstring if available
+        if module.__doc__:
+            content.append(module.__doc__.strip())
+            content.append("")
+        
+        # Add automodule directive
+        content.extend([
+            ".. automodule:: " + module_name,
+            "   :members:",
+            "   :undoc-members:",
+            "   :show-inheritance:",
+            ""
+        ])
+        
+        # Write the RST file
+        output_path = output_dir / f"{simple_name}.rst"
+        with open(output_path, 'w') as f:
+            f.write('\n'.join(content))
+            
+        print(f"Created module documentation: {output_path}")
+        return simple_name
+        
+    except ImportError as e:
+        print(f"Warning: Could not import module {module_name}: {e}")
+        return None
+    except Exception as e:
+        print(f"Error processing module {module_name}: {e}")
+        return None
+
+def create_section_index(section_name, module_names, output_dir):
+    """Create an index RST file for a section."""
+    # Create section directory if it doesn't exist
+    section_dir = output_dir / section_name.lower().replace(' ', '_')
+    section_dir.mkdir(exist_ok=True)
+    
+    # Create index content
+    content = [
+        f"{section_name}",
+        "=" * len(section_name),
+        "",
+        ".. toctree::",
+        "   :maxdepth: 4",
+        "",
+    ]
+    
+    # Process each module in the section
+    for module_name in module_names:
+        simple_name = create_module_rst(module_name, section_dir)
+        if simple_name:
+            content.append(f"   {simple_name}")
+    
+    # Write the index file
+    index_path = section_dir / "index.rst"
+    with open(index_path, 'w') as f:
+        f.write('\n'.join(content))
+        
+    print(f"Created section index: {index_path}")
+    return section_dir.name
+
+def create_main_index(sections, section_dirs, output_dir):
+    """Create the main index.rst file."""
+    content = [
+        "mrDNA Documentation",
+        "===================",
+        "",
+        "Welcome to the documentation for mrDNA!",
+        "",
+        "mrDNA (Multi-Resolution DNA) is a Python package that makes it easy to run simulations of DNA nanostructures. "
+        "The multi-resolution approach provides the benefits of coarse-grained modeling, while resulting in a high-resolution "
+        "structure suitable for atomistic simulations.",
+        "",
+        ".. toctree::",
+        "   :maxdepth: 2",
+        "   :caption: Contents:",
+        "",
+    ]
+    
+    # Add each section to the toctree
+    for section, dir_name in zip(sections, section_dirs):
+        content.append(f"   {dir_name}/index")
+    
+    # Add installation page
+    content.append("   installation")
+    
+    # Add getting started page
+    content.append("   getting_started")
+        
+    # Add indices and tables
+    content.extend([
+        "",
+        "Indices and tables",
+        "==================",
+        "",
+        "* :ref:`genindex`",
+        "* :ref:`modindex`",
+        "* :ref:`search`"
+    ])
+    
+    # Write the index file
+    index_path = output_dir / "index.rst"
+    with open(index_path, 'w') as f:
+        f.write('\n'.join(content))
+        
+    print(f"Created main index: {index_path}")
+
+def create_installation_page(output_dir):
+    """Create the installation.rst page."""
+    content = [
+        "Installation",
+        "============",
+        "",
+        "Dependencies",
+        "------------",
+        "",
+        "* Linux operating system",
+        "* g++ >= 4.8",
+        "* `CUDA toolkit <https://developer.nvidia.com/cuda-toolkit>`_ >= 6",
+        "* `ARBD <http://bionano.physics.illinois.edu/arbd>`_ simulation engine",
+        "* Python >= 3.5 *(some users report problems installing mdanalysis; miniconda or conda are recommended)*",
+        "  * numpy >= 1.14",
+        "  * scipy >= 1.1",
+        "  * mdanalysis >= 0.18",
+        "  * cadnano >= 2.5.2.1",
+        "  * appdirs >= 1.4",
+        "  * pandas >= 1.0",
+        "  * scadnano >= 0.1 (optional)",
+        "  * `oxDNA <https://dna.physics.ox.ac.uk/index.php/Main_Page>`_ (optional)",
+        "",
+        "Installation Steps",
+        "-----------------",
+        "",
+        "First make sure you have the cuda-toolkit installed. First download ARBD through a web browser. "
+        "The following script can be used as a guide to install mrdna.",
+        "",
+        ".. code-block:: bash",
+        "",
+        "    # Customize the following",
+        "    BUILD_DIR=/path/to/build-dir",
+        "    export CUDA_PATH=/path/to/cuda-toolkit",
+        "",
+        "    # Unpack and build arbd",
+        "    cd $BUILD_DIR",
+        "    mv ~/Downloads/arbd*.tar.gz .",
+        "    tar -xzf arbd*.tar.gz",
+        "    cd arbd",
+        "    cmake -S . -B build && (",
+        "      cd build",
+        "      make -j",
+        "    )",
+        "    cd ../../",
+        "",
+        "    ## Possibly setup python dependencies (you may want to set up a virtual environement)",
+        "    # conda install \"numpy>=1.14\" \"scipy>=1.1\" \"appdirs>=1.4\"",
+        "    # conda install -c conda-forge \"mdanalysis>=0.18\" \"pandas>=1.0\"",
+        "    # pip3 install \"cadnano>=2.5.2.1\" \"scadnano>=0.1\"",
+        "",
+        "    git clone https://gitlab.engr.illinois.edu/tbgl/tools/mrdna",
+        "    cd mrdna",
+        "    pip3 install .",
+        "    cd ..",
+        "",
+        "    # Finally update your bashrc so that your shell can find the ARBD binary",
+        "    echo \"PATH=$BUILD_DIR/arbd/src:\\$PATH\" >> ~/.bashrc",
+        "    source ~/.bashrc",
+        "",
+        "Please report issues to `Chris Maffeo <mailto:cmaffeo2@illinois.edu>`_."
+    ]
+    
+    # Write the installation file
+    install_path = output_dir / "installation.rst"
+    with open(install_path, 'w') as f:
+        f.write('\n'.join(content))
+        
+    print(f"Created installation page: {install_path}")
+
+def create_getting_started_page(output_dir):
+    """Create the getting_started.rst page."""
+    content = [
+        "Getting Started",
+        "===============",
+        "",
+        "This guide will help you get started with using mrDNA for DNA molecular modeling.",
+        "",
+        "Basic Usage",
+        "------------",
+        "",
+        "Here's a simple example that creates a DNA structure:",
+        "",
+        ".. code-block:: python",
+        "",
+        "    # Import necessary modules",
+        "    from mrdna.segmentmodel import SegmentModel",
+        "    from mrdna.model.dna_sequence import DNASequence",
+        "",
+        "    # Create a segment model",
+        "    model = SegmentModel()",
+        "",
+        "    # Add a DNA segment with a specific sequence",
+        "    sequence = DNASequence(\"GATTACA\")",
+        "    model.add_segment(sequence)",
+        "",
+        "    # Save the model to a PDB file",
+        "    model.to_pdb(\"example.pdb\")",
+        "",
+        "Working with Existing Structures",
+        "------------------------------",
+        "",
+        "mrDNA can read structures from various file formats:",
+        "",
+        ".. code-block:: python",
+        "",
+        "    # Import the appropriate reader",
+        "    from mrdna.readers.segmentmodel_from_pdb import SegmentModelFromPDB",
+        "",
+        "    # Load a structure from a PDB file",
+        "    model = SegmentModelFromPDB(\"my_structure.pdb\")",
+        "",
+        "    # Analyze the structure",
+        "    num_nucleotides = model.count_nucleotides()",
+        "    print(f\"Structure contains {num_nucleotides} nucleotides\")",
+        "",
+        "Multi-Resolution Simulation",
+        "--------------------------",
+        "",
+        "The primary feature of mrDNA is its ability to perform multi-resolution simulations:",
+        "",
+        ".. code-block:: python",
+        "",
+        "    from mrdna.simulate import multiresolution_simulation",
+        "",
+        "    # Perform a multi-resolution simulation",
+        "    output_directory = multiresolution_simulation(",
+        "        model, ",
+        "        output_name='my_simulation',",
+        "        coarse_steps=1e6,",
+        "        fine_steps=1e6",
+        "    )",
+        "",
+        "    print(f\"Simulation results stored in: {output_directory}\")"
+    ]
+    
+    # Write the getting started file
+    getting_started_path = output_dir / "getting_started.rst"
+    with open(getting_started_path, 'w') as f:
+        f.write('\n'.join(content))
+        
+    print(f"Created getting started page: {getting_started_path}")
+
+def create_conf_py(source_dir):
+    """Create the Sphinx configuration file with sphinx-book-theme."""
+    conf_content = """# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../..'))
+
+# -- Project information -----------------------------------------------------
+
+project = 'mrDNA'
+copyright = '2025, mrDNA Team'
+author = 'Christopher Maffeo'
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.coverage',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.napoleon',
+    'sphinx_copybutton',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'sphinx_book_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Theme options
+html_theme_options = {
+    "repository_url": "https://gitlab.engr.illinois.edu/tbgl/tools/mrdna",
+    "use_repository_button": True,
+    "use_issues_button": True,
+    "use_download_button": True,
+    "use_fullscreen_button": True,
+    "path_to_docs": "docs",
+    "show_navbar_depth": 2,
+    "home_page_in_toc": True,
+    "navbar_footer_text": "mrDNA Documentation",
+    "extra_navbar": "<div>Multi-Resolution DNA modeling</div>",
+}
+
+# Napoleon settings
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_references = False
+napoleon_use_ivar = False
+napoleon_use_param = True
+napoleon_use_rtype = True
+napoleon_type_aliases = None
+
+# Autodoc settings
+autodoc_default_options = {
+    'members': True,
+    'member-order': 'bysource',
+    'special-members': '__init__',
+    'undoc-members': True,
+    'exclude-members': '__weakref__'
+}
+"""
+    
+    conf_path = source_dir / "conf.py"
+    with open(conf_path, 'w') as f:
+        f.write(conf_content)
+    
+    print(f"Created Sphinx configuration file: {conf_path}")
+
+def create_doc_directories():
+    """Create necessary directories for documentation."""
+    DOCS_DIR.mkdir(exist_ok=True)
+    SOURCE_DIR.mkdir(exist_ok=True)
+    
+    # Create _static directory for custom CSS/JS
+    static_dir = SOURCE_DIR / "_static"
+    static_dir.mkdir(exist_ok=True)
+    
+    # Create _templates directory for custom templates
+    templates_dir = SOURCE_DIR / "_templates"
+    templates_dir.mkdir(exist_ok=True)
+
+def check_requirements():
+    """Check if required packages are installed."""
+    required_packages = [
+        'sphinx',
+        'sphinx-book-theme',
+        'sphinx-copybutton'
+    ]
+    
+    missing_packages = []
+    for package in required_packages:
+        try:
+            importlib.import_module(package.replace('-', '_'))
+        except ImportError:
+            missing_packages.append(package)
+    
+    if missing_packages:
+        print("The following required packages are missing:")
+        for package in missing_packages:
+            print(f"  - {package}")
+        print("\nPlease install them using:")
+        print(f"pip install {' '.join(missing_packages)}")
+        print("\nAfter installing the required packages, run this script again.")
+        sys.exit(1)
+
+def build_docs():
+    """Build the documentation using Sphinx."""
+    try:
+        print("\nBuilding documentation...")
+        subprocess.run(['sphinx-build', '-b', 'html', str(SOURCE_DIR), str(BUILD_DIR)], check=True)
+        print(f"\nDocumentation successfully built. You can view it at: {BUILD_DIR / 'index.html'}")
+    except subprocess.CalledProcessError as e:
+        print(f"Error building documentation: {e}")
+    except FileNotFoundError:
+        print("Could not find sphinx-build. Make sure Sphinx is installed and in your PATH.")
+
+def main():
+    """Generate documentation for the mrdna package using sphinx-book-theme."""
+    # Check required packages
+    check_requirements()
+    
+    # Create doc directories
+    create_doc_directories()
+    
+    # Process each section
+    section_dirs = []
+    for section_name, module_names in DOCUMENTATION_STRUCTURE.items():
+        dir_name = create_section_index(section_name, module_names, SOURCE_DIR)
+        section_dirs.append(dir_name)
+    
+    # Create main index
+    create_main_index(DOCUMENTATION_STRUCTURE.keys(), section_dirs, SOURCE_DIR)
+    
+    # Create installation and getting started pages
+    create_installation_page(SOURCE_DIR)
+    create_getting_started_page(SOURCE_DIR)
+    
+    # Create Sphinx configuration with sphinx-book-theme
+    create_conf_py(SOURCE_DIR)
+    
+    print(f"\nDocumentation files generated in {SOURCE_DIR}")
+    
+    # Build the documentation
+    response = input("\nWould you like to build the HTML documentation now? (y/n): ")
+    if response.lower() in ('y', 'yes'):
+        build_docs()
+    else:
+        print("\nTo build the documentation later, run:")
+        print(f"sphinx-build -b html {SOURCE_DIR} {BUILD_DIR}")
+
+if __name__ == "__main__":
+    main()
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