Contexts
contexts.ContextManager(yaml_paths=None, **kwargs)
¶
Contexts for WISP.
| PARAMETER | DESCRIPTION |
|---|---|
yaml_paths
|
Path(s) to YAML file(s) to load into the context.
TYPE:
|
contact_map_distance_limit = 4.5
instance-attribute
¶
If you use WISP's default contact-map generator, node pairs with average inter-node distances greater than this value will not be considered in calculating the covariance matrix. Use a value of 999999.999 to deactivate.
contact_map_path = None
instance-attribute
¶
A text file containing a user-specified contact map. If given, each element of the functionalized matrix will be multiplied by the corresponding value specified in the file. If not given, WISP's default contact map, based on the distances between average node locations, will be automatically applied. For convenience, WISP automatically saves a human-readable copy of the contact-map matrix to the file contact_map_matrix.txt in the output directory every time it is run.
frame_chunks = 96
instance-attribute
¶
When WISP is run with multiple processors, the frames from the PDB are loaded in chunks before being distributed to the many processors. This parameter specifies the number of frames to load before distribution.
functionalized_matrix_path = None
instance-attribute
¶
A text file containing a user-specified functionalized correlation matrix. If not given, WISP's default functionalized correlation matrix, as described in the WISP publication, will be automatically calculated. For convenience, WISP automatically saves a human-readable copy of the matrix used to the file functionalized_correlation_matrix.txt in the output directory every time it is run.
longest_path_b = 0.0
instance-attribute
¶
The color of the longest path is given by an RGB color code. This parameter specifies the B value, ranging from 0.0 to 1.0.
longest_path_g = 0.0
instance-attribute
¶
The color of the longest path is given by an RGB color code. This parameter specifies the G value, ranging from 0.0 to 1.0.
longest_path_opacity = 1.0
instance-attribute
¶
The opacity of the longest path, ranging from 0.0 (transparent) to 1.0 (fully opaque).
longest_path_r = 0.0
instance-attribute
¶
The color of the longest path is given by an RGB color code. This parameter specifies the R value, ranging from 0.0 to 1.0.
longest_path_radius = 0.01
instance-attribute
¶
This parameter specifies the radius of the longest path visualized, in Angstroms.
n_cores = 1
instance-attribute
¶
On unix-like machines, WISP can use multiple processors to significantly increase speed. This parameter specifies the number of processors to use.
n_paths = 1
instance-attribute
¶
The desired number of paths.
n_paths_max = 100000
instance-attribute
¶
Terminate calculation if the number of estimated paths is greater than this.
node_definition = 'RESIDUE_COM'
instance-attribute
¶
WISP calculates the covariance matrix by defining nodes associated with each protein residue. If node_definition is set to 'CA', the alpha carbon will be used. If set to 'RESIDUE_COM,', 'SIDECHAIN_COM,', or 'BACKBONE_COM,' the whole-residue, side-chain, or backbone center of mass will be used, respectively.
node_sphere_b = 0.0
instance-attribute
¶
The color of the node spheres is given by an RGB color code. This parameter specifies the B value, ranging from 0.0 to 1.0.
node_sphere_g = 0.0
instance-attribute
¶
The color of the node spheres is given by an RGB color code. This parameter specifies the G value, ranging from 0.0 to 1.0.
node_sphere_opacity = 1.0
instance-attribute
¶
The opacity of the node spheres, ranging from 0.0 (transparent) to 1.0 (fully opaque).
node_sphere_r = 0.0
instance-attribute
¶
The color of the node spheres is given by an RGB color code. This parameter specifies the R value, ranging from 0.0 to 1.0.
node_sphere_radius = 1.0
instance-attribute
¶
When visualizing in VMD, a number of cylinders and spheres are drawn. This parameter specifies the resolution to use.
output_dir = f'wisp_output__{time.strftime('%b_%d_%Y__%I_%M_%p')}'
instance-attribute
¶
A new directory where the WISP output should be written. If this parameter is not specified, a default output directory is created whose name includes the current date for future reference.
pdb_single_frame_path = None
instance-attribute
¶
By default, WISP uses the trajectory-average structure for positioning the nodes, visualizing the paths and protein, etc. However, if desired, a separate PDB structure with the same residue order and number can be specified for this purpose using the pdb_single_frame_path parameter.
seconds_to_wait_before_parallelizing_path_finding = 5.0
instance-attribute
¶
WISP identifies paths from the source to the sink by recursively visiting node neighbors. The program begins the recursion algorithm on a single processor before distributing the search efforts to multiple processors. This parameter specifies how long WISP should search for source-sink paths using a single processor before distributing the search effort over multiple processors. By waiting longer before distribution, the search efforts are ultimately distributed more evenly over the multiple processors, potentially increasing speed in the long run. On the other hand, specifiying a lower value for this parameter means the program will spend more time running on multiple processors, also potentially increasing speed. A balance must be struck.
shortest_path_b = 0.0
instance-attribute
¶
The color of the shortest path is given by an RGB color code. This parameter specifies the B value, ranging from 0.0 to 1.0.
shortest_path_g = 0.0
instance-attribute
¶
The color of the shortest path is given by an RGB color code. This parameter specifies the G value, ranging from 0.0 to 1.0.
shortest_path_opacity = 1.0
instance-attribute
¶
The opacity of the shortest path, ranging from 0.0 (transparent) to 1.0 (fully opaque).
shortest_path_r = 0.0
instance-attribute
¶
The color of the shortest path is given by an RGB color code. This parameter specifies the R value, ranging from 0.0 to 1.0.
shortest_path_radius = 0.1
instance-attribute
¶
WISP outputs a VMD state file to facilitate visualization. The shortest path is represented by a strand with the largest radius. Longer paths have progressively smaller radii. This parameter specifies the radius of the shortest path, in Angstroms.
sink_residues = []
instance-attribute
¶
This parameter specifies the sink residues for path generation. The format is the same as for the source_residues parameter.
source_residues = []
instance-attribute
¶
This parameter specifies the source residues for path generation. A list of residues should be constructed of the form 'CHAIN_RESNAME_RESID', separated by spaces. For example: 'X_SER_1 X_LEU_4'.
spline_smoothness = 0.01
instance-attribute
¶
The paths are represented by splines connecting the nodes. This parameter indicates the smoothness of the splines. Smaller values produce smoother splines, but take longer to render.
vmd_resolution = 6
instance-attribute
¶
When visualizing in VMD, a number of cylinders and spheres are drawn. This parameter specifies the resolution to use.
wisp_saved_matrix_path = None
instance-attribute
¶
If the covariance matrix (appropriately modified by a contact map) has been previously saved to a file, set this parameter to 'TRUE' to load the matrix instead of generating it from scratch. WISP automatically saves a copy of this matrix to the file 'functionalized_matrix_with_contact_map_applied.pickle' in the output directory every time it is run.
write_formatted_paths = False
instance-attribute
¶
Write a text file containing a simply formatted list of paths.
__enter__()
¶
Enter the context and return the current context as a dictionary.
__exit__(exc_type, exc_value, exc_tb)
¶
Exit the context.
| PARAMETER | DESCRIPTION |
|---|---|
exc_type
|
Type of the exception.
|
exc_value
|
Value of the exception.
|
exc_tb
|
Traceback information.
|
from_yaml(yaml_path)
¶
Load context information from a YAML file. This will only update data contained in the YAML file.
| PARAMETER | DESCRIPTION |
|---|---|
yaml_path
|
Path to YAML file to load.
TYPE:
|
get()
¶
Retrieve the context.
| RETURNS | DESCRIPTION |
|---|---|
dict[str, Any]
|
A dictionary representing the current context. |
update(attr_dict)
¶
Update attributes with values from the provided dictionary.
| PARAMETER | DESCRIPTION |
|---|---|
attr_dict
|
Dictionary containing attribute names and their
TYPE:
|