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NanoShaper
0.3.1
NanoShaper is a tool able to triangulate and inspect an arbitray triangulated surface or several types of molecular surfaces such as the Gaussian, Skin and the SES
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NanoShaper
0.3.1
NanoShaper is a tool able to triangulate and inspect an arbitray triangulated surface or several types of molecular surfaces such as the Gaussian, Skin and the SES
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| Atom | An atom: an atom is a point in R^3 with radius, charge and dielectric value |
| BlobbySurface | This class builds the blobby surface, triangulate it and the use mesh surface routines for the rest of the work |
| ConnollyCell | |
| ConnollySurface | This class builds and converts to a DelPhi suitable representation the Connolly Surface. All the gathered info is analytically computed both the intersections and the projections. First the alpha shape of the set of atoms is computed, then from that the Connolly surface is computed |
| Del0Cell | |
| Del1Cell | |
| Del2Cell | |
| Del3Cell | |
| DelPhiShared | This class is the DelPhi Shared variables environment which emulates the DelPhi environment |
| EdgeCell | |
| ExternalSurface | This class is wrapper and loads an external surface using the files epsmapx.txt, epsmapy.txt, epsmapz.txt, status.txt and projections.txt that is the list of the boundary grid points indexes,values and normals |
| FacetCell | |
| MeshSurface | This class represents a converter from an arbitray triangulated mesh surface to a DelPhi compatible representation. Vertex normals are computed by averaging among surrounding plane normals |
| MixedCell | |
| Point | A point in R^3 |
| PointCell | |
| SkinSurface | This class builds and converts to a DelPhi suitable representation the Skin Surface. All the gathered info is analytically computed both the intersections and the projections. In order to get an accurate result for the projection routine, as root finding algorithm is used the method of the companion matrix |
| Surface | Surface class is the general interface that a surface class should have to be plugged inside DelPhi. Some functions implementations are mandatory such as load, save, build, etc... Note that the surface is not necessarly a molecular surface. Build function computes an internal representation of the surface; getSurf translates that representation in the DelPhi compatible representation. Note that in order to put a new surface in DelPhi a surface must provide epsmap, idebmap, computations of the surface area inside a grid cube, identification and projections of boundary grid points and their surface normals; these computations must be done in getSurf while the surface construction must be performed in build. |
