-
Notifications
You must be signed in to change notification settings - Fork 86
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
update style and add some nodes docs
- Loading branch information
1 parent
c4dd714
commit ad78f4e
Showing
18 changed files
with
136 additions
and
184 deletions.
There are no files selected for viewing
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,76 +1,27 @@ | ||
| --- | ||
| title: "Node Documentation" | ||
| title: "Nodes" | ||
| editor: visual | ||
| number-sections: true | ||
| number-depth: 3 | ||
| --- | ||
|
|
||
| # Nodes | ||
| ## Syling | ||
|
|
||
| ## Properties | ||
| ### Atoms | ||
|
|
||
| ### Atomic Properties | ||
|  | ||
|
|
||
| The `MN_prop_setup` node associates all of the different atomic properties with their corresponding atoms in the structure. | ||
| #### Inputs: | ||
|
|
||
| #### Required Inputs | ||
| - Atoms | ||
|
|
||
| - | ||
| - Edges and Vertices containing atomic information to apply the style to. | ||
| - Selection | ||
| - A `` | ||
| - Eevee / Cycles | ||
| - Scale Radii | ||
| - Eevee: Subdivisions | ||
| - Eevee: Shade Smooth | ||
| - Material | ||
|
|
||
| - **Atoms:** mesh vertices or point-cloud that are the `XYZ` locations of the atoms. | ||
|
|
||
| - **Properties Collections:** The collection that contains the `NAME_properties_1` models that were imported alongside the structure. | ||
|
|
||
| #### Optional Inputs: | ||
|
|
||
| A boolean switch for each of the atomic properties. | ||
| By default the properties are enabled, but they can be disable if required to provide a slight performance improvement if not required. | ||
|
|
||
| #### Outputs | ||
|
|
||
| - **Atoms (**mesh vertices or point-cloud)**:** that are the `XYZ` locations of the atoms, that also have *named attributes* for each of the atomic properties that were selected for set up. | ||
|
|
||
| - **atomic_number** (integer field): integer number corresponding to the atomic number of the atom. | ||
| Defaults to 0 if *atomic_number* cannot be determined. | ||
|
|
||
| - **chain_number** (integer field): integer number corresponding to the chain that the atom belongs to. | ||
| Chains will be sorted into alphabetical order, then given a corresponding integer number starting from 1. | ||
| Defaults to 0 if *chain_number* cannot be determined. | ||
|
|
||
| - **atom_name_number** (integer field): integer number corresponding to the name of the atom within the structure ("CA" for the alpha carbon). | ||
| Defaults to 0 if *atom_name_number* cannot be determined. | ||
|
|
||
| - **AA_sequence_number** (integer field): integer number corresponding to the sequence number of the amino acid in the structure that the atom belongs to. | ||
| For LYS32 the *AA_sequence_number* will be 32. | ||
| Defaults to 0 if *AA_sequence_number* cannot be determined. | ||
|
|
||
| - **AA_name** (integer field): integer number corresponding to the different residue names. | ||
| Amino acids are numbered 1-20 based on alphabetical order. | ||
| See the `MN_sel_AA_name` node for the corresponding order. | ||
|
|
||
| - **atom_index** (integer field): integer number corresponding to the order of the atom within the structure file. | ||
|
|
||
| - **B_factor** (float field): a float number corresponding to the value that was present in the B factor column, also known as the *temperature factor*. | ||
|
|
||
| - **is_backbone** (boolean field): a boolean value (TRUE or FALSE, 1 or 0) as to whether or not the atom is part of the backbone of the protein. | ||
|
|
||
| - **is_alpha_carbon** (boolean field): a boolean value (TRUE or FALSE, 1 or 0) as to whether or not the atom is an *alpha carbon* of the amino acid. | ||
|
|
||
| {fig-align="center"} | ||
|
|
||
| ## Styling Nodes | ||
|
|
||
| ### Style Ribbon | ||
|
|
||
| This node uses the `is_alpha_carbon` property and the `chain_number` properties to generate a ribbon-representation of the structure as a mesh. | ||
| Options are available for the radius, smoothness and the resolution of the ribbon. | ||
|
|
||
| #### Required Inputs | ||
|
|
||
| - **Atoms** (mesh vertices or point cloud): atoms that contain at least the *is_alpha_carbon* named attribute and the *chain_number* attribute to ensure the ribbons are separated by chain. | ||
|
|
||
| #### Outputs | ||
|
|
||
| - **Ribbon** (mesh): a mesh that is the ribbon representation of the structure. | ||
|
|
||
| - **Curve** (spline / curve): a curve that goes through all of the alpha carbons in the structure, that is used to build the final ribbon mesh. | ||
|
|
||
| {fig-align="center"} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,66 @@ | ||
| --- | ||
| title: "Nodes" | ||
| editor: visual | ||
| number-sections: true | ||
| number-depth: 2 | ||
| toc-depth: 3 | ||
| --- | ||
|
|
||
| ## Styling | ||
|
|
||
| ### Atoms | ||
|
|
||
| Style to apply the traditional space-filling atomic representation of atoms. Spheres are scaled based on the `vdw_radii` attribute. By default the `Point Cloud` rendering system is used, which is only visible inside of Cycles. | ||
|
|
||
|  | ||
|
|
||
| #### Inputs: | ||
|
|
||
| | Name | Data Type | Default | Description | | ||
| |------------|------------|------------|--------------------------------------| | ||
| | Atoms | Geometry | | Vertices + edges describing atomic data to apply the style to. | | ||
| | Selection | Boolean \<*Field*\> | `True` | Boolean field, defining whether or not to apply the style. | | ||
| | Eevee / Cycles | Boolean \<*Field*\> | `False` | Boolean field, defining whether or not to instance geoemtry for Eevee or use Point Cloud rendering for Cycles. | | ||
| | Scale Radii | Float \<*Field*\> | `0.8` | Scale the resulting spheres to a proportion of the atoms Van der Waal radii. | | ||
| | Eevee: Subdivisions | Integer \<*Field\>* | `2` | Number of subdivisions for the instanced geometry, when using Eevee atoms. | | ||
| | Eevee: Shade Smooth | Boolean \<*Field*\> | `True` | Boolean field, whether to shade the Eevee atoms smooth. | | ||
| | Material | Material | `MN_atomic_material` | Material to apply to the resulting geometry. | | ||
|
|
||
| ### Cartoon | ||
|
|
||
| Style to apply the traditional cartoon representation of protein structures. This style highlights alpha-helices and beta-sheets with arrows and cylinders. | ||
|
|
||
|  | ||
|
|
||
| | Name | Data Type | Default | Description | | ||
| |------------|------------|------------|--------------------------------------| | ||
| | Atoms | Geometry | | Vertices + edges describing atomic data to apply the style to. | | ||
| | Selection | Boolean \<*Field*\> | `True` | Boolean field, defining whether or not to apply the style. | | ||
| | Quality | Integer \<*Field\>* | `2` | Integer field controlling the number of subdivisions and thus 'quality' of the cartoon. | | ||
| | Smooth / Sharp | Boolean \<*Field*\> | `False` | Boolean field, whether or not to create smooth or sharp styler cartoon geometry. | | ||
| | Arrows | Boolean \<*Field*\> | `True` | Boolean field, whether or not to create arrows for beta-sheet cartoons. | | ||
| | Cylinders | Boolean \<*Field*\> | `False` | Boolean field, whether or not to create cylinders for alpha-helix. | | ||
| | Thickness | Float \<*Field*\> | `0.4` | Float field controlling the thickness of the cartoons. | | ||
| | Width | Float \<*Field*\> | `1.8` | Float field controlling the width of alpha-helices and beta-sheets, along the 'flat' part of the cartoon mesh. | | ||
| | Loop Radius | Float \<*Field*\> | `0.18` | Float field controlling the radius of the loop geometry between secondary structure cartoons. | | ||
| | BS Smooth | Float \<*Field*\> | `1.00` | Factor from `0` to `1`, controlling the amount to smooth the beta-sheet geometry that is created. | | ||
| | Shade Smooth | Boolean \<*Field*\> | `True` | Boolean field, whether to shade the resulting cartoon mesh smooth. | | ||
| | Material | Material | `MN_atomic_material` | Material to apply to the resulting geometry. | | ||
|
|
||
| ### Ribbon | ||
|
|
||
| Style that creates a continuous solid ribbon or licorice tube through the alpha-carbons of the structure. | ||
|
|
||
|  | ||
|
|
||
| | Name | Data Type | Default | Description | | ||
| |------------|------------|------------|--------------------------------------| | ||
| | Atoms | Geometry | | Vertices + edges describing atomic data to apply the style to. | | ||
| | Selection | Boolean \<*Field*\> | `True` | Boolean field, defining whether or not to apply the style. | | ||
| | Quality | Integer \<*Field\>* | `2` | Integer field controlling the number of subdivisions and thus 'quality' of the cartoon. | | ||
| | Radius | Float \<*Field*\> | `0.18` | Float field controlling the radius of the loop geometry between secondary structure cartoons. | | ||
| | BS Smooth | Float \<*Field*\> | `1.00` | Factor from `0` to `1`, controlling the amount to smooth the beta-sheet geometry that is created. | | ||
| | Shade Smoothing | Boolean \<*Field*\> | `True` | Boolean field, whether to shade the resulting cartoon mesh smooth. | | ||
| | Material | Material | `MN_atomic_material` | Material to apply to the resulting geometry. | | ||
|
|
||
| ## Selection |
Binary file not shown.
Binary file not shown.
Binary file not shown.
Oops, something went wrong.