Sails::Dot
struct Sails::Dot
The Dot class is used to generate dotfiles for glycosites in a given structure.
This class generates dotfiles for glycosites in a given structure, which can then be used to create an SNFG. The dotfiles can be obtained for all glycosites or for a specific glycosite.
The class also provides methods to add a header and footer to the dotfile, as well as a method to identify the format of a glycosite.
Summary
Members | Descriptions |
|---|---|
| Constructor for Dot object. |
| Retrieves all dot files for all N-glycosylation glycosites in the structure. |
| Generates a DOT file representation of the given glycosite. |
| Internal structure - used to find linkages |
| Internal residue database - used to find linkages |
| Internal topology - used to find linkages |
| Get the format string for the given glycosite. |
| Return the header string for the Glycan graph. |
| Generates a footer for the dot file. |
Members
public explicitDot(gemmi::Structure & structure)
Constructor for Dot object.
Parameters
structureThe structure object to use for generating Dot files, which are used to create SNFGs.
Returns
None.
public std::map<Glycosite, std::string >get_all_dotfiles()
Retrieves all dot files for all N-glycosylation glycosites in the structure.
This method returns a map where the Glycosite is the key and the associated dot file is the value. The dot file contains information about the glycosite and its surrounding residues in a specific structure.
Returns
A map where the Glycosite is the key and the associated dot file is the value.
public std::stringget_dotfile(Sails::Glycosite& glycosite)
Generates a DOT file representation of the given glycosite.
This method takes a Glycosite object and returns a string that represents a DOT file containing the topology information of the glycosite.
Parameters
glycositeThe glycosite for which the DOT file will be generated.
Returns
A string representing the DOT file of the glycosite.
private gemmi::Structurem_structure
Internal structure - used to find linkages
private ResidueDatabasem_database
Internal residue database - used to find linkages
privateTopologym_topology
Internal topology - used to find linkages
private std::stringget_format(constGlycosite& site)
Get the format string for the given glycosite.
This method retrieves the format string for the given glycosite. The format string contains information about the fill color, shape, and label of the glycosite.
Parameters
siteThe glycosite for which the format is requested.
Returns
The format string for the given glycosite.
private static std::stringheader()
Return the header string for the Glycan graph.
This method returns the header string for the Glycan graph in DOT format. The header string includes properties such as rank direction, padding, node separation, and rankset.
Returns
The header string for the Glycan graph.
private static std::stringfooter()
Generates a footer for the dot file.
This method returns a string that represents the footer of a dot file.
Returns
The footer string.