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

is_actionable()

Check if the secondary structure query has any actionable filters.

Returns:

Type	Description
bool	True if any of the filters are set, False otherwise.

SecondaryStructureFilterResult dataclass

Result of filtering on secondary structure.

Parameters:

Name	Type	Description	Default
stats	SecondaryStructureStats	The secondary structure statistics.	required
passed	bool	Whether the structure passed the filtering criteria.	False

SecondaryStructureStats dataclass

Statistics about the secondary structure of a protein.

Parameters:

Name	Type	Description	Default
nr_residues	PositiveInt	Total number of residues in the structure.	required
nr_helix_residues	PositiveInt	Number of residues in helices.	required
nr_sheet_residues	PositiveInt	Number of residues in sheets.	required
helix_ratio	Ratio	Ratio of residues in helices.	required
sheet_ratio	Ratio	Ratio of residues in sheets.	required

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.