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Molecular Surface Computation
[Molecular Structure]


Classes

class  GraphEdge< Vertex, Edge, Face >
 Generic GraphEdge Class. More...
class  GraphFace< Vertex, Edge, Face >
 Generic GraphFace Class. More...
class  GraphTriangle< Vertex, Edge, Face >
 Generic GraphTriangle Class. More...
class  GraphVertex< Vertex, Edge, Face >
 Generic GraphVertex Class. More...
class  ReducedSurface
 Generic ReducedSurface Class. More...
class  RSComputer
 Generic RSComputer Class. More...
class  RSEdge
 Generic RSEdge Class. More...
class  RSFace
 Generic RSFace Class. More...
class  RSVertex
 Generic RSVertex Class. More...
class  SASEdge
 Generic SASEdge Class. More...
class  SASFace
 Generic SASFace Class. More...
class  SASVertex
 Generic SASVertex Class. More...
class  SESEdge
 Generic SESEdge Class. More...
class  SESFace
 Generic SESFace Class. More...
class  SESVertex
 Generic SESVertex Class. More...
class  SolventAccessibleSurface
 Generic SolventAccessibleSurface Class. More...
class  SolventExcludedSurface
 Generic SolventExcludedSurface Class. More...
class  SESComputer
 Generic SESComputer Class. More...
class  SESSingularityCleaner
 Generic SESComputer Class. More...
class  SurfaceProcessor
 SurfaceProcessor. More...
class  Triangle
 Generic TriangleEdge Class. More...
class  TriangleEdge
 Generic TriangleEdge Class. More...
class  TrianglePoint
 Generic TriangleEdge Class. More...
class  TriangulatedSAS
 Generic TriangulatedSAS Class. More...
class  SASTriangulator
 Generic SASTriangulator Class. More...
class  TriangulatedSES
 Generic TriangulatedSES Class. More...
class  SESTriangulator
 Generic SESTriangulator Class. More...
class  TriangulatedSurface
 Generic TriangulatedSurface Class. More...
class  TriangulatedSphere
 Generic TriangulatedSphere Class. More...

Fast Numerical Calculation of Solvent Accessible Surface Area.

These functions use the algorithm by Eisenhaber, Lijnzaad, Argos, Sander, and Scharf ("The Double Cubic Lattice Method: Efficient Approaches to numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies", J.

Comput. Chem. (1995), 15 , 273-284).

BALL_EXPORT float calculateSASArea (const AtomContainer &fragment, float probe_radius=1.5, Size number_of_dots=400)
 Calculate the solvent accessible surface area numerically.
BALL_EXPORT float calculateSASVolume (const AtomContainer &fragment, float probe_radius=1.5, Size number_of_dots=400)
 Calculate the solvent accessible volume numerically.
BALL_EXPORT float calculateSASAtomAreas (const AtomContainer &fragment, HashMap< const Atom *, float > &atom_areas, float probe_radius=1.5, Size number_of_dots=400)
 Calculate the Solvent Accessible Surface area for each atom.
BALL_EXPORT float calculateSASPoints (const AtomContainer &fragment, Surface &surface_points, float probe_radius=1.5, Size number_of_dots=400)
 Calculate a point set on the Solvent Accessible Surface.
BALL_EXPORT float calculateSASAtomPoints (const AtomContainer &fragment, std::vector< std::pair< Vector3, Surface > > &atom_surfaces, float probe_radius=1.5, Size number_of_dots=400)
 Calculate a point set on the Solvent Accessible Surface for each atom.

Storers

BALL_EXPORT std::ostream & operator<< (std::ostream &s, const TriangulatedSurface &surface)
 Output- Operator.

Functions

BALL_EXPORT float calculateSESAtomAreas (const AtomContainer &fragment, HashMap< const Atom *, float > &atom_areas, float probe_radius=1.5)
 Calculate the solvent excluded surface area analytically.
BALL_EXPORT float calculateSESArea (const AtomContainer &fragment, float probe_radius=1.5)
 Calculate the solvent excluded surface area analytically.
BALL_EXPORT float calculateSESVolume (const AtomContainer &fragment, float probe_radius=1.5)
 Calculate the solvent excluded volume analytically.

Function Documentation

BALL_EXPORT float calculateSASArea (  const AtomContainer &  fragment,
float  probe_radius = 1.5,
Size  number_of_dots = 400
) 
 

Calculate the solvent accessible surface area numerically.

This method returns the total Solvent Accessible Surface (SAS) of a BALL kernel object. Atoms with a radius of 0 are ignored.

Parameters:
fragment the kernel object containing the atoms
probe_radius the probe radius used for the SAS
number_of_dots the number of dots used per atom
Returns:
the total SAS area in $ A^2$

BALL_EXPORT float calculateSASAtomAreas (  const AtomContainer &  fragment,
HashMap< const Atom *, float > &  atom_areas,
float  probe_radius = 1.5,
Size  number_of_dots = 400
) 
 

Calculate the Solvent Accessible Surface area for each atom.

This method returns the surface fraction of each atom at the Solvent Accessible Surface (SAS). Atoms with a radius of 0 are ignored. All areas are in $ A^2$.

Parameters:
atom_areas a hash map containing the areas of the atoms (returned)
fragment the kernel object containing the atoms
probe_radius the probe radius used for the SAS
number_of_dots the number of dots used per atom
Returns:
the total SAS area in $ A^2$

BALL_EXPORT float calculateSASAtomPoints (  const AtomContainer &  fragment,
std::vector< std::pair< Vector3, Surface > > &  atom_surfaces,
float  probe_radius = 1.5,
Size  number_of_dots = 400
) 
 

Calculate a point set on the Solvent Accessible Surface for each atom.

This method returns the point sets on the SAS used to calculate the surface area for each atom.

See also:
calculateSASAtomAreas
Parameters:
fragment the kernel object containing the atoms
atom_surfaces a hashmap of atoms and Surface objects containing the point sets for each atom (returned)
probe_radius the probe radius used for the SAS
number_of_dots the number of dots used per atom
Returns:
the total SAS area in $ A^2$

BALL_EXPORT float calculateSASPoints (  const AtomContainer &  fragment,
Surface &  surface_points,
float  probe_radius = 1.5,
Size  number_of_dots = 400
) 
 

Calculate a point set on the Solvent Accessible Surface.

This method returns the points on the Solvent Accessible Surface (SAS) used to calculate the surface area. The Surface object holds just the vertices, it does not contain any triangles. The normals for each point normals to the SAS in that point, their length equals the fraction of the surface area represented by this point in $ A^2$:

\[ |\vec{n_i}| = \frac{\mathrm{SAS\quad\ of \quad atom} \quad i}{\mathrm{number\quad of\quad points\quad on\quad the\quad SAS\quad of\quad atom} \quad i} \]

Atoms with a radius of 0 are ignored.

Parameters:
surface_points a surface object containing the point coordinates and their normals (returned)
fragment the kernel object containing the atoms
probe_radius the probe radius used for the SAS
number_of_dots the number of dots used per atom
Returns:
the total SAS area in $ A^2$

BALL_EXPORT float calculateSASVolume (  const AtomContainer &  fragment,
float  probe_radius = 1.5,
Size  number_of_dots = 400
) 
 

Calculate the solvent accessible volume numerically.

This method returns the total volume enclosd by the Solvent Accessible Surface (SAS) of a BALL kernel object. Atoms with a radius of 0 are ignored.

Parameters:
fragment the kernel object containing the atoms
probe_radius the probe radius used for the SAS
number_of_dots the number of dots used per atom
Returns:
the volume in $ A^3$

BALL_EXPORT float calculateSESArea (  const AtomContainer &  fragment,
float  probe_radius = 1.5
) 
 

Calculate the solvent excluded surface area analytically.

This method uses the algorithm by Michael L. Connolly. ?????

Parameters:
fragment the kernel object containing the atoms
probe_radius the probe radius used for the SAS
Returns:
the SES area in $\AA^2$

BALL_EXPORT float calculateSESAtomAreas (  const AtomContainer &  fragment,
HashMap< const Atom *, float > &  atom_areas,
float  probe_radius = 1.5
) 
 

Calculate the solvent excluded surface area analytically.

This method uses the algorithm by Michael L. Connolly. ?????

Parameters:
fragment the kernel object containing the atoms
probe_radius the probe radius used for the SAS
atom_areas 
Returns:
the SES area in $\AA^2$

BALL_EXPORT float calculateSESVolume (  const AtomContainer &  fragment,
float  probe_radius = 1.5
) 
 

Calculate the solvent excluded volume analytically.

This method uses the algorithm by Michael L. Connolly. ?????

Parameters:
fragment the kernel object containing the atoms
probe_radius the probe radius used for the SAS
Returns:
the volume in $\AA^3$