ss
Module for dealing with secondary structure.
SecondaryStructureFilterQuery
dataclass
Query object to filter on secondary structure.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
abs_min_helix_residues
|
PositiveInt | None
|
Minimum number of residues in helices (absolute). |
None
|
abs_max_helix_residues
|
PositiveInt | None
|
Maximum number of residues in helices (absolute). |
None
|
abs_min_sheet_residues
|
PositiveInt | None
|
Minimum number of residues in sheets (absolute). |
None
|
abs_max_sheet_residues
|
PositiveInt | None
|
Maximum number of residues in sheets (absolute). |
None
|
ratio_min_helix_residues
|
Ratio | None
|
Minimum number of residues in helices (relative). |
None
|
ratio_max_helix_residues
|
Ratio | None
|
Maximum number of residues in helices (relative). |
None
|
ratio_min_sheet_residues
|
Ratio | None
|
Minimum number of residues in sheets (relative). |
None
|
ratio_max_sheet_residues
|
Ratio | None
|
Maximum number of residues in sheets (relative). |
None
|
filter_file_on_secondary_structure(file_path, query)
Filter a structure file based on secondary structure criteria.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
file_path
|
Path
|
The path to the structure file to analyze. |
required |
query
|
SecondaryStructureFilterQuery
|
The filtering criteria to apply. |
required |
Returns:
| Type | Description |
|---|---|
SecondaryStructureFilterResult
|
Filtering statistics and whether file passed. |
filter_files_on_secondary_structure(file_paths, query)
Filter multiple structure files based on secondary structure criteria.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
file_paths
|
Iterable[Path]
|
A list of paths to the structure files to analyze. |
required |
query
|
SecondaryStructureFilterQuery
|
The filtering criteria to apply. |
required |
Yields:
| Type | Description |
|---|---|
Generator[tuple[Path, SecondaryStructureFilterResult]]
|
For each file returns the filtering statistics and whether structure passed. |
filter_on_secondary_structure(structure, query)
Filter a structure based on secondary structure criteria.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
structure
|
Structure
|
The gemmi Structure object to analyze. |
required |
query
|
SecondaryStructureFilterQuery
|
The filtering criteria to apply. |
required |
Returns:
| Type | Description |
|---|---|
SecondaryStructureFilterResult
|
Filtering statistics and whether structure passed. |
nr_of_residues_in_helix(structure)
Count the number of residues in alpha helices.
Requires structure to have secondary structure information.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
structure
|
Structure
|
The gemmi Structure object to analyze. |
required |
Returns:
| Type | Description |
|---|---|
int
|
The number of residues in alpha helices. |
nr_of_residues_in_sheet(structure)
Count the number of residues in beta sheets.
Requires structure to have secondary structure information.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
structure
|
Structure
|
The gemmi Structure object to analyze. |
required |
Returns:
| Type | Description |
|---|---|
int
|
The number of residues in beta sheets. |
nr_of_residues_in_total(structure)
Count the total number of residues in the structure.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
structure
|
Structure
|
The gemmi Structure object to analyze. |
required |
Returns:
| Type | Description |
|---|---|
int
|
The total number of residues in the structure. |