more documentation

docs/_quarto.yml

@@ -15,7 +15,8 @@ website:
         text: Installation
       - file: tutorials/
         text: Tutorials
-      - file: documentation.qmd
+      - file: attributes.qmd
+        text: Documentation
       - file: examples/
         text: Examples
       - file: cite/
@@ -35,10 +36,9 @@ website:
       align: left
       # pinned: true
       contents: 
-        - text: Docs
-          href: documentation.qmd
         - installation.qmd
         - attributes.qmd
+        - data_table.qmd
         - text: Nodes
           href: nodes/index.qmd
           contents: nodes/*

docs/attributes.qmd

@@ -1,29 +1,34 @@
 # Attributes
 
-Below are the attributes which are potentially created when a structure is imported
+Below are the attributes which are potentially created when a structure is imported.
+Explanations of type and domain conversions can be found in the Blender documentation [here](https://docs.blender.org/manual/en/latest/modeling/geometry_nodes/attributes_reference.html)
 
-more detailed explanations of type conversions can be found in the Blender documentation [here](https://docs.blender.org/manual/en/latest/modeling/geometry_nodes/attributes_reference.html)
+## World Scale
 
-- explain about world scale (1 angstrom == 1 cm in Blender, will be changed for 5.0 to be 1 nm = 1 m)
-- write-ups about different entities, ways to interact with them
+In Molecular Nodes, the world scale determines how real-world measurements are translated into the 3D environment of Blender which uses metres.
+Currently, 1 angstrom (Å) is equivalent to 1 centimeter (cm).
+Scaling structural coodinates by `0.01` correctly converts them and `0.01` is referred to as the world scale.
 
-When an attribute is going to be read from the geometry, it is colored red like so: `Index::Input`, `chain_id`, etc.
+This scale will change in Blender 5.0 to be `0.1` so 1 nm will equal 1 m.
+
+When an attribute is going to be read from the geometry, it is colored red like so: `Index::Input`, `chain_id`, while when a specific data type is refernce it will be colored accoring to the data type like so: `Int::Int`, `Float::Float`, `Vector::Vector`, etc.
 
 ## Data Types
 
 ### Attribute Types
+
 Attributes are always associated with `Geometry::Geometry`.
 They will be stored on one of the [domains](#domains) of the geometry.
 The type of the attribute is determined by the type of the data it contains.
 The following types are supported by Geometry Nodes.
 
 | Type | Description |
-|-------------------|-----------------------------------------------------|
+|-----------------------|-------------------------------------------------|
 | `Int::Int` | 32-bit integers |
 | `Float::Float` | 32-bit floating point numbers |
 | `Bool::Bool` | A simple `True::Bool` or `False::Bool` value |
 | `Vector::Vector` | 3D vectors |
-| `Matrix::Matrix` | 4x4 matrices, also references as `Transform::Matrix` inside of Geometry Nodes|
+| `Matrix::Matrix` | 4x4 matrices, also references as `Transform::Matrix` inside of Geometry Nodes |
 | `Color::Color` | RGBA colors, stored as 0..1 values |
 | `Rotation::Rotation` | A rotation that internally is represented as a quaternion, but can implicitly be converted to an `Euler::Vector` vector. |
 
@@ -32,7 +37,7 @@ The following types are supported by Geometry Nodes.
 Additional data types which are not supported as Attributes but can be used in the node tree are:
 
 | Type | Description |
-|-------------------|-----------------------------------------------------|
+|-----------------------|-------------------------------------------------|
 | `String::String` | String support in Geometry Nodes is limited at the moment and you cannot store strings as attributes |
 | `Object::Object` | Access to objects in the 3D scene and their associated data |
 | `Collection::Collection` | Access a collection of objects from the scene. Objects are returned as instances |
@@ -45,25 +50,61 @@ For `chain_id`, `entity_id` and other dynamic attributes, the unique values are
 
 For other attributes such as `res_name`, they are looked up from the dictionary and assigned an integer value.
 
+### Point Attributes
+
 | Attribute | Type | Description |
-|--------------|--------------|--------------------------------------------|
-| `sec_struct` | `Int::Int` | Secondary structure identifier |
-| `chain_id` | `Int::Int` | Identifier for the chain in the structure |
-| `entity_id` | `Int::Int` | Identifier for the entity in the structure |
-| `res_id` | `Int::Int` | Residue identifier |
-| `res_name` | `Int::Int` | Residue name identifier |
-| `atom_name` | `Int::Int` | Atom name identifier |
-| `atom_id` | `Int::Int` | Atom identifier |
-| `is_alpha_carbon` | `Bool::Bool` | Boolean indicating if the atom is an alpha carbon |
+|------------------|------------------|------------------------------------|
+| `Position` | `Vector::Vector` | Coordinates in 3D space of the points, read from the molecular data file. They are scaled by the world scale `0.01::Float` on import so that 1 Å == 1 cm. |
+| `b_factor` | `Float::Float` | The temperature factor for the atom on import. If importing an AlphaFold structure this corresponds to the `pLDDT::Float` value. |
+| `vdw_radii` | `Float::Float` | The radii of the atom, stored in world space (\~`0.015::Float`). Values sourced from [Wikipedia](https://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page)). |
+| `sec_struct` | `Int::Int` | Defines secondary structure for the residue the atom is part of. `0::Int` for not a protein. `1::Int` for helices, `2::Int` for sheets, `3::Int` for coils / unstructured. |
+| `mass` | `Float::Float` | Mass of the element |
+| `chain_id` | `Int::Int` | The integer representation of the chain ID, for it's position in the sorted list of chain IDs in the structure. |
+| `entity_id` | `Int::Int` | Multiple chains can be the same `entity`, if they are copies of the same protein that appear multiple times in the structure. Also sorted and assigned integers on import. |
+| `res_id` | `Int::Int` | The 20 canonical amino acids are `0::Int` to `19::Int` sorted alphabetically. DNA bases dAdCdGdT are `30::Int` - `33::Int`, RNA bases are ACGU from `40::Int` - `43::Int`. |
+| `res_name` | `Int::Int` | Residues are mapped to integer values based on the [lookup table](data_table.qmd#residue-names). |
+| `atomic_number` | `Int::Int` | Stores the atomic number of the atom for it's position on the periodic table, instead of the element's name. |
+| `atom_name` | `Int::Int` | Atom names are mapped to integer values based on the [lookup table](attributes.qmd#atom-names). |
+| `Color` | `Color::Color` | Color of the atom, assigned on import but often changed in node trees. |
+| `atom_id` | `Int::Int` | Unique ascending value for each atom in the file, starting at `1::Int` |
+| `is_alpha_carbon` | `Bool::Bool` | Computed on import or from the `atom_name` attribute. |
+| `is_side_chain` | `Bool::Bool` | Computed on import or from the `atom_name` attribute. |
+| `is_backbone` | `Bool::Bool` | Computed on import or from the `atom_name` attribute. |
+| `is_solvent` | `Bool::Bool` | Computed on import or from the `atom_name` attribute. |
+| `is_nucleic` | `Bool::Bool` | Computed on import or from the `atom_name` attribute. |
+| `is_peptide` | `Bool::Bool` | Computed on import or from the `atom_name` attribute. |
+| `is_hetero` | `Bool::Bool` | Computed on import or from the `atom_name` attribute. |
+| `is_carb` | `Bool::Bool` | Computed on import or from the `atom_name` attribute. |
+
+### Edge Attributes
+
+Bonds between atoms are represented as edges in the geometry, and only the bond type is stored on the edge domain.
+
+| Attribute   | Type       | Description                         |
+|-------------|------------|-------------------------------------|
+| `bond_type` | `Int::Int` | The type of bond between the atoms. |
+
+Bond types are currently the values used by [`biotite`](https://www.biotite-python.org/latest/apidoc/biotite.structure.BondType.html)
+
+| Bond Type         | Integer Value | Description                             |
+|------------------|:----------------:|------------------------------------|
+| `ANY`             |   `0::Int`    | Used if the actual type is unknown      |
+| `SINGLE`          |   `1::Int`    | Single bond                             |
+| `DOUBLE`          |   `2::Int`    | Double bond                             |
+| `TRIPLE`          |   `3::Int`    | Triple bond                             |
+| `QUADRUPLE`       |   `4::Int`    | A quadruple bond                        |
+| `AROMATIC_SINGLE` |   `5::Int`    | Aromatic bond with a single formal bond |
+| `AROMATIC_DOUBLE` |   `6::Int`    | Aromatic bond with a double formal bond |
+| `AROMATIC_TRIPLE` |   `7::Int`    | Aromatic bond with a triple formal bond |
 
 ## Domains {#domains}
 
 | Domain | Description |
-|-----------------|-------------------------------------------------------|
-| `Point::Geometry` | Attributes associated with individual points of the geometry |
-| `Edge::Geometry` | Attributes associated with edges connecting points |
-| `Face Corner::Geometry` | Attributes associated with corners of faces formed by edges |
-| `Face::Geometry` | Attributes associated with faces formed by edges |
-| `Point Cloud::Geometry` | Attributes associated with points in a point cloud |
-| `Curve: Points::Geometry` | Attributes associated with individual points of a curve |
-| `Curve: Spline::Geometry` | Attributes associated with splines of a curve |
+|---------------------|---------------------------------------------------|
+| `Point::Geometry` | Individual points of geometry. These can be the vertices in a mesh, the points in a point cloud, or the control points of a curve. |
+| `Edge::Geometry` | The edges of a mesh, defined as the indices between two points. |
+| `Face::Geometry` | A face of a mesh, defined as a collection of edges. |
+| `Corner::Geometry` | Corners of a face, where two edges meet. |
+| `Curve::Geometry` | A curve object, which contains multiple control points, but can itself store attributes. |
+| `Instance::Geometry` | Instances are references to other geometry. Instancing is useful for making lots of copies of some geometry for performance. |
+| `Layer::Geometry` | Layers are for Grease Pencil, and contain a collection of curves. |