Xponge.analysis.sasa
SPONGE 1.4 的 Xponge API 文档。¶ Xponge.analysis.sasa
This module implements the SASA calculation
¶ subpackages
¶ submodules
¶ functions
¶ classes
¶ SASA
This class implements the SASA calculation
| parameters | explanation |
|---|---|
| u | the instance of the MDAnalysis universe |
| r_probe | radius of the probe |
| n_points | resolution of the surface of each atom |
| radii_dict | dict of atomic radii to update the default RADII dict |
| r_atoms | if specify, the atomic radii will directly use the value here instead of looking up in radii_dict. |
¶ main
This function does the real calculation.
| parameters | explanation |
|---|---|
| need_area | whether keep the area. If True, the surface will stored in self.surface_area |
| need_surface | whether need the surface. If True, the surface will stored in self.surface |
¶ write_surface_xyz
This function writes the surface information to a file
| parameters | explanation |
|---|---|
| filename | the name of the output file |
| headlines | whether the headlines and fake elements are written to the file |
¶ get_sasa_result
This function gets the sasa result
| parameters | explanation |
|---|---|
| select | the sasa sum of the selected atoms |