Merge remote-tracking branch 'refs/remotes/origin/master'

docs_ref/mkdocs_rtd/docs/installation.md

+# Installation
+
+## Requirements
+
+mrDNA requires the following dependencies:
+
+- Python 3.6+
+- NumPy
+- SciPy
+- MDAnalysis (for certain functionality)
+
+## Installing from Source
+
+Clone the repository and install with pip:
+
+```bash
+git clone https://gitlab.com/your-username/mrdna.git
+cd mrdna
+pip install -e .
+```
+
+This will install the package in development mode, allowing you to modify the code and immediately see the effects.
\ No newline at end of file

docs_ref/mkdocs_rtd/docs/requirements.txt

+
+mkdocs==1.6.1
+mkdocs-material==9.1.21
+mkdocstrings==0.23.0
+mkdocstrings-python==1.7.5
+pymdown-extensions==10.3.1
+pyyaml==6.0.1

docs_ref/mkdocs_rtd/docs/subpackages/arbdmodel.md

+# Arbdmodel Modules
+
+This section covers the modules in the arbdmodel subpackage.
+
+## Modules
+
+- [arbdmodel](../api/core/arbdmodel.md)
+- [coords](../api/arbdmodel/coords.md)
+- [grid](../api/arbdmodel/grid.md)
+- [ibi](../api/arbdmodel/ibi.md)
+- [interactions](../api/arbdmodel/interactions.md)
+- [polymer](../api/arbdmodel/polymer.md)
+- [shape_cg](../api/arbdmodel/shape_cg.md)
\ No newline at end of file

docs_ref/mkdocs_rtd/docs/subpackages/core.md

+# Core Modules
+
+This section covers the modules in the core subpackage.
+
+## Modules
+
+- [config](../api/core/config.md)
+- [coords](../api/core/coords.md)
+- [reporting](../api/core/reporting.md)
+- [segmentmodel](../api/core/segmentmodel.md)
+- [simulate](../api/core/simulate.md)
+- [version](../api/core/version.md)
\ No newline at end of file

docs_ref/mkdocs_rtd/docs/subpackages/model.md

+# Model Modules
+
+This section covers the modules in the model subpackage.
+
+## Modules
+
+- [CanonicalNucleotideAtoms](../api/model/CanonicalNucleotideAtoms.md)
+- [dna_sequence](../api/model/dna_sequence.md)
+- [nbPot](../api/model/nbPot.md)
+- [nonbonded](../api/model/nonbonded.md)
+- [spring_from_lp](../api/model/spring_from_lp.md)
\ No newline at end of file

docs_ref/mkdocs_rtd/docs/subpackages/readers.md

+# Readers Modules
+
+This section covers the modules in the readers subpackage.
+
+## Modules
+
+- [cadnano_segments](../api/readers/cadnano_segments.md)
+- [polygon_mesh](../api/readers/polygon_mesh.md)
+- [segmentmodel_from_cadnano](../api/readers/segmentmodel_from_cadnano.md)
+- [segmentmodel_from_lists](../api/readers/segmentmodel_from_lists.md)
+- [segmentmodel_from_oxdna](../api/readers/segmentmodel_from_oxdna.md)
+- [segmentmodel_from_pdb](../api/readers/segmentmodel_from_pdb.md)
+- [segmentmodel_from_scadnano](../api/readers/segmentmodel_from_scadnano.md)
\ No newline at end of file

docs_ref/mkdocs_rtd/docs/tutorials.md

+# Tutorials
+
+This section contains step-by-step tutorials for common mrDNA tasks.
+
+## Tutorial 1: Creating a Simple DNA Structure
+
+This tutorial shows how to create a simple DNA structure from scratch.
+
+```python
+# Import necessary modules
+from mrdna.segmentmodel import SegmentModel, DoubleStrandedSegment
+import numpy as np
+
+# Create a segment model
+model = SegmentModel()
+
+# Create a linear double-stranded DNA segment
+dsDNA = DoubleStrandedSegment(
+    name="segment1",
+    num_bp=21,  # 21 base pairs
+    start_position=np.array([0, 0, 0]),
+    end_position=np.array([0, 0, 70]),  # ~3.4Å per base pair
+    sequence="ATGCATGCATGCATGCATGCA"
+)
+
+# Add the segment to the model
+model.add_segment(dsDNA)
+
+# Generate an atomic model
+model.generate_atomic_model()
+
+# Write out the model as PDB
+model.write_pdb("simple_dsdna.pdb")
+```
+
+## Tutorial 2: Loading and Manipulating a cadnano Design
+
+This tutorial demonstrates how to load a cadnano design and make modifications.
+
+```python
+# Import necessary modules
+from mrdna.readers import read_cadnano
+
+# Load a cadnano design
+model = read_cadnano("my_design.json")
+
+# Print some information about the model
+print(f"The model contains {len(model.segments)} segments")
+print(f"Total number of nucleotides: {model.count_nucleotides()}")
+
+# Modify the sequence of the first segment
+model.segments[0].sequence = "ATGCATGCATGC"
+
+# Run a simulation to relax the structure
+from mrdna.simulate import multiresolution_simulation
+output_dir = multiresolution_simulation(model, "relaxed_design")
+```
\ No newline at end of file

docs_ref/mkdocs_rtd/index.md

+# ARBD Model
+
+::: {.toctree maxdepth="4"}
+arbdmodel
+:::

docs_ref/mkdocs_rtd/mkdocs.yml

+site_name: mrDNA Documentation
+site_description: Documentation for the mrDNA DNA molecular modeling package
+repo_url: https://gitlab.com/your-username/mrdna
+
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+  palette:
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+    accent: indigo
+  features:
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+    - navigation.expand
+    - navigation.indexes
+    - content.code.copy
+    - search.highlight
+    - search.share
+  icon:
+    repo: fontawesome/brands/gitlab
+
+markdown_extensions:
+  - pymdownx.highlight
+  - pymdownx.superfences
+  - pymdownx.tabbed
+  - pymdownx.arithmatex:
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+  - admonition
+  - footnotes
+  - attr_list
+  - pymdownx.details
+  - pymdownx.emoji
+  - toc:
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+
+plugins:
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+  - mkdocstrings:
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+      handlers:
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+          import:
+            - https://docs.python.org/3/objects.inv
+          options:
+            show_source: true
+            show_submodules: true
+            docstring_style: google
+
+nav:
+  - Home: index.md
+  - Installation: installation.md
+  - Getting Started: getting_started.md
+  - Tutorials: tutorials.md
+  - Examples: examples.md
+  - FAQ: faq.md
+  - API Reference:
+    - Arbdmodel: subpackages/arbdmodel.md
+    - Core: subpackages/core.md
+    - Model: subpackages/model.md
+    - Readers: subpackages/readers.md
+  - Contributors: contributors.md

docs_ref/sphinx_docs/build/.buildinfo

+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: a62b352a4cc8eac657341a274cc39e75
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