name |
-str, optional | +str | Name of the data collection. Default is “data”. | 'data' |
name |
-str, optional | +str | Name of the collection for the frames. Default is ““. | '' |
parent |
-bpy.types.Collection, optional | +bpy.types.Collection | A blender collection which will become the parent collection. Default is the MolecularNodes collection if None. | None |
| bpy.types.Collection | -The ‘MolecularNodes’ collection inside the Blender scene. If it doesn’t | -|
| exist, it will be created. | -+ | The ‘MolecularNodes’ collection inside the Blender scene. If it doesn’t exist, it will be created. |
``
-| Name | -Description | -
|---|---|
| SACCHARIDE_NAMES | -- |
| SACCHARIDE_REPRESENTATION | -- |
| atom_charge | -- |
| atom_names | -- |
| elements | -- |
| lipophobicity | -- |
| residues | -- |
file |
str | Path to the MRC file. | -required | +required |
name |
-str, optional | +str | If not None, renames the object with the new name. | None |
invert |
-bool, optional | +bool | Whether to invert the data from the grid, defaulting to False. Some file types such as EM tomograms have inverted values, where a high value == low density. | False |
world_scale |
-float, optional | +float | Scale of the object in the world. Defaults to 0.01. | 0.01 |
file |
str | The path to the MRC file. | -required | +required |
invert |
-bool, optional | +bool | Whether to invert the data from the grid, defaulting to False. Some file types such as EM tomograms have inverted values, where a high value == low density. | False |
file |
str | The path to the input MRC file. | -required | +required |
invert |
-bool, optional | +bool | Whether to invert the data from the grid, defaulting to False. Some file types such as EM tomograms have inverted values, where a high value == low density. | False |
world_scale |
-float, optional | +float | The scaling factor to apply to the voxel size of the input file. Defaults to 0.01. | 0.01 |
overwrite |
-bool, optional | +bool | If True, the .vdb file will be overwritten if it already exists. Defaults to False. | False |
panel(layout_function, scene)
path_to_vdb(file)
filefile``
-| Name | -Description | -
|---|---|
| molecule_esmfold | -- |
| open_structure_esm_fold | -- |
| panel | -- |
molecule_esmfold(amino_acid_sequence, MN_name='Name', center_molecule=False, del_solvent=True, include_bonds=True, starting_style=0, setup_nodes=True)
open_structure_esm_fold(amino_acid_sequence, include_bonds=True)
panel(layout_function)
Through biotite built-in method derivated from P-SEA algorithm (Labesse 1997) Returns an array with secondary structure for each atoms where: - 0 = ’’ = non-protein or not assigned by biotite annotate_sse - 1 = a = alpha helix - 2 = b = beta sheet - 3 = c = coil
Inspired from https://www.biotite-python.org/examples/gallery/structure/transketolase_sse.html
-create_molecule(MN_array, MN_name, center_molecule=False, file=None, calculate_ss=False, del_solvent=False, include_bonds=False, starting_style=0, collection=None)
get_chain_entity_id(file)
get_secondary_structure(MN_array, file)
This function uses the biotite.structure package to extract the secondary structure information from the MMTF file. The resulting secondary structures are 1: Alpha Helix, 2: Beta-sheet, 3: loop.
molecule_local(file_path, MN_name='Name', include_bonds=True, center_molecule=False, del_solvent=True, default_style=0, setup_nodes=True)
molecule_rcsb(pdb_code, center_molecule=False, del_solvent=True, include_bonds=True, starting_style=0, setup_nodes=True, cache_dir=None)
open_structure_local_pdb(file_path, include_bonds=True)
open_structure_local_pdbx(file_path, include_bonds=True)
open_structure_rcsb(pdb_code, cache_dir=None, include_bonds=True)
pdb_get_b_factors(file)
Get a list, which contains a numpy array for each model containing the b-factors.
-set_atom_entity_id(mol, file)
``
Importing molecular dynamics trajectories and associated files.
+| Name | +Description | +
|---|---|
| MN_UL_TrajectorySelectionListUI | +UI List | +
| TrajectorySelectionItem | +Group of properties for custom selections for MDAnalysis import. | +
| TrajectorySelection_OT_NewItem | +Add a new custom selection to the list. | +
MN_UL_TrajectorySelectionListUI()
UI List
+TrajectorySelectionItem()
Group of properties for custom selections for MDAnalysis import.
+TrajectorySelection_OT_NewItem()
Add a new custom selection to the list.
+| load_trajectory | Loads a molecular dynamics trajectory from the specified files. | -
| panel | -- |
FileNotFoundError If the topology or trajectory file is not found. IOError If there is an error reading the files.
-panel(layout_function, scene)
``
-| Name | -Description | -
|---|---|
| mn_data_file | -- |
| socket_types | -- |
| Append MN_atomic_material to the .blend file it it doesn’t already exist, | |||||
| add_custom_node_group | -- | ||||
| add_custom_node_group_to_node | -- | ||||
| add_node | -- | ||||
| append | -- | ||||
| chain_color | Given the input list of chain names, will create a node group which uses | Given a an input_list, will create a node which takes an Integer input, | |||
| create_assembly_node_tree | -- | ||||
| create_custom_surface | -- | ||||
| create_starting_node_tree | -- | ||||
| create_starting_nodes_density | -- | ||||
| create_starting_nodes_starfile | -- | ||||
| gn_new_group_empty | -- | ||||
| nodes_to_geometry | -- | ||||
| resid_multiple_selection | Returns a node group that takes an integer input and creates a boolean | ||||
| split_geometry_to_instances | Create a Node to Split Geometry by an Attribute into Instances |
name |
str | The name of the mesh object to be created. | -required | +required | |
collection |
bpy.types.Collection | The collection to which the mesh object will be added. | -required | +required | |
locations |
-array-like | +array - like | The list of vertex locations for the mesh, an nx3 np array of locations. Each element in the list represents a 3D point (x, y, z) for a vertex. | -required | +required |
bonds |
-list of tuples, optional | +list of tuples | The list of vertex index pairs representing bonds as edges for the mesh. Each tuple should contain two vertex indices (e.g., (index1, index2)). | [] |
obj |
bpy.types.Object | The Blender object from which the attribute will be retrieved. | -required | +required |
att_name |
-str, optional | +str | The name of the attribute to retrieve. Default is ‘position’. | 'position' |
|
Returns |
-- | - | required | + +
| Type | +Description | |
|---|---|---|
np |
-+ | |
| np.array | The attribute data as a NumPy array. | -required |
| Name | +Description | +
|---|---|
| InstallationError | +Exception raised when there is an error installing a package. | +
InstallationError(self, package_name, error_message)
Exception raised when there is an error installing a package.
+| Name | +Type | +Description | +
|---|---|---|
| package_name | +str | +The name of the package that failed to install. | +
| error_message | +str | +The error message returned by pip. | +
requirements |
-str, optional | +str | The path to the requirements file. If not provided, the function looks for a requirements.txt file in the same directory as the script. |
None |
self |
object | The object instance. | -required | +required |
context |
… | The context parameter (description missing). | -required | +required |
edit_text |
… | The edit_text parameter (description missing). | -required | +required |
pypi_mirror_provider |
-str, optional | +str | The PyPI mirror to use for package installation. Defaults to ‘Default’, which uses the official PyPI repository. | 'Default' |
package |
str | The name of the package to install. | -required | +required |
pypi_mirror_provider |
-str, optional | +str | The name/url of the PyPI mirror provider to use. Default is ‘Default’. | 'Default' |
| list | -A list of tuples containing the command list, return code, stdout, and stderr | -|
| for each pip command run. | -+ | A list of tuples containing the command list, return code, stdout, and stderr for each pip command run. |
package |
str | The name of the package to check. | -required | +required |
version |
-str, optional | +str | The version of the package to check. | None |
package |
str | The name of the package to check. | -required | +required |
pypi_mirror_providercmd_list |
-list, optional | +list | List of pip commands to be executed. Defaults to None. | None |
mirror_url |
-str, optional | +str | URL of a package repository mirror to be used for the command. Defaults to ’’. | '' |
timeout |
-int, optional | +int | Time in seconds to wait for the command to complete. Defaults to 600. | 600 |
| tuple | -A tuple containing the command list, command return code, command standard output, | -|
| and command standard error. | -+ | A tuple containing the command list, command return code, command standard output, and command standard error. |
logfile_name |
-str, optional | +str | The name of the log file. Defaults to ‘side-packages-install’. | 'side-packages-install' |
| logging.Logger | A Logger object that can be used to write log messages. |
| This function sets up a logging configuration with a specified log file name and logging level. | ++ |
The log file will be created in the ADDON_DIR/logs directory. If the directory |
++ |
| does not exist, it will be created. The function returns a Logger object that can be used to | ++ |
| write log messages. | ++ |
This function sets up a logging configuration with a specified log file name and logging level. The log file will be created in the ADDON_DIR/logs directory. If the directory does not exist, it will be created. The function returns a Logger object that can be used to write log messages.
``
-| Name | -Description | -
|---|---|
| load_star_file | -- |
| panel | -- |
load_star_file(file_path, obj_name='NewStarInstances', node_tree=True, world_scale=0.01)
panel(layout_function, scene)
``
-| Name | -Description | -
|---|---|
| MN_PT_panel_ui | -- |
| MN_add_node_menu | -- |
| MN_change_import_interface | -- |
| button_custom_color | -- |
| button_custom_selection | -- |
| default_style | -- |
| menu_item_interface | -- |
| panel_local | -- |
| panel_rcsb | -- |
MN_PT_panel_ui(layout_function, scene)
MN_change_import_interface(layout_function, label, interface_value, icon)
default_style(layout, label, panel_display)
panel_local(layout_function)
panel_rcsb(layout_function)