Sails::SolventAccessibility
class Sails::SolventAccessibility
Class for calculating solvent accessibility of glycosites in a structure.
This class provides methods to calculate the solvent accessibility of glycosites in a given structure. The solvent accessibility is calculated using a grid-based approach where if a given residue is within n Angstroms of the surface of the solvent mask, it is solvent accessible
Summary
Members | Descriptions |
|---|---|
| Constructor for SolventAccessibility class. |
| Average and flatten the solvent accessibility map. |
| Calculates the solvent accessibility for each glycosite in the structure. |
| |
| Pointer to a gemmi::Structure for use when calculating solvent mask and bounding box. |
| Solvent mask calculated during constructor. |
| Calculates the bounding box of the structure. |
| Create a solvent accessibility map. |
| Calculates the solvent mask for the structure. |
Members
public inline explicitSolventAccessibility(gemmi::Structure * structure)
Constructor for SolventAccessibility class.
Parameters
structureA pointer to a gemmi::Structure object.
This constructor initializes a SolventAccessibility object with the given gemmi::Structure object. It sets up the solvent mask from the structure and calculates the solvent mask.
public SolventAccessibilityMapaverage_solvent_accessibilty_map(const SolventAccessibilityMap & map)
Average and flatten the solvent accessibility map.
Parameters
mapThe original solvent accessibility map.
Returns
The flattened solvent accessibility map, where the average solvent accessibility for each residue site is calculated.
public std::map<Glycosite, double >calculate_solvent_accessibility()
Calculates the solvent accessibility for each glycosite in the structure.
Returns
A map containing the solvent accessibility value for each glycosite.
typedefSolventAccessibilityMap
private gemmi::Structure *m_structure
Pointer to a gemmi::Structure for use when calculating solvent mask and bounding box.
private gemmi::Gridm_solvent_mask
Solvent mask calculated during constructor.
private gemmi::Box< gemmi::Position >calculate_box()
Calculates the bounding box of the structure.
This method calculates the bounding box of the structure by iterating over all models, chains, residues, and atoms in the structure and extending the box to include each atom position. The calculated box is then expanded by adding a margin of 8 Angstroms to each side.
Returns
The calculated bounding box of the structure.
private SolventAccessibilityMapcreate_solvent_accessibility_map()
Create a solvent accessibility map.
This method creates a solvent accessibility map for the given structure. The solvent accessibility map is a mapping of the glycosite (model index, chain index, residue index, atom index) to its corresponding solvent accessibility value.
The solvent accessibility value is initially set to 0 for each glycosite.
Returns
The created solvent accessibilty map.
private voidcalculate_solvent_mask()
Calculates the solvent mask for the structure.
It applies a mask on the grid based on the atomic radii set and the model index of the structure.