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Public Member Functions | Protected Member Functions | Private Member Functions | List of all members
core::scoring::sc::ContactMolecularSurfaceCalculator Class Reference

#include <ContactMolecularSurfaceCalculator.hh>

Inheritance diagram for core::scoring::sc::ContactMolecularSurfaceCalculator:
Inheritance graph
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Public Member Functions

 ContactMolecularSurfaceCalculator ()
 ContactMolecularSurfaceCalculator constructor, initializes default settings. More...
 
 ~ContactMolecularSurfaceCalculator () override
 
MolecularSurfaceCalculator::ScValue CalcContactArea ()
 
- Public Member Functions inherited from core::scoring::sc::MolecularSurfaceCalculator
 MolecularSurfaceCalculator ()
 MolecularSurfaceCalculator constructor, initializes default settings. More...
 
 ~MolecularSurfaceCalculator () override
 
virtual int Init ()
 Initializes calculation and GPU (if used) Init() is also called implicitly by the static CalcSc() function. More...
 
void Reset ()
 Reset calculator for another calculation. Must be used when the MolecularSurfaceCalculator instance is re-used. More...
 
int AddAtom (int molecule, Atom &atom)
 Add an atom to a molecule for computation. More...
 
core::Size AddResidue (int molecule, core::conformation::Residue const &residue)
 Add a rosetta residue to a specific molecule. More...
 
virtual int Calc (core::pose::Pose const &pose, core::Size jump_id=0)
 Generate molecular surfaces for the given pose. //. More...
 
virtual int Calc ()
 Generate molecular surfaces for loaded atoms. //. More...
 
std::vector< Atom > const & GetAtoms ()
 
std::vector< DOT > const & GetDots (int const moleculeid)
 
std::vector< const DOT * > const & GetTrimmedDots (int const moleculeid)
 
RESULTS const & GetResults ()
 

Protected Member Functions

ScValue CalcContactMolecularSurface (std::vector< DOT > const &, std::vector< DOT > const &)
 
int AssignAttentionNumbers (std::vector< Atom > &atom) override
 
- Protected Member Functions inherited from core::scoring::sc::MolecularSurfaceCalculator
void GenerateMolecularSurfaces ()
 Generate untrimmed surfaces for the defined molecules. More...
 
int AssignAtomRadius (Atom &atom)
 
int WildcardMatch (char const *query, char const *pattern, int const l)
 
int ReadScRadii ()
 Read atom radius definitions from file This function is implicitly called, but can be overloaded or called explicitly for custom handling of the atom radii library. Returns true on success. More...
 
void AddDot (int const molecule, int const type, Vec3 const &coor, ScValue const area, Vec3 const &pcen, Atom const &atom)
 

Private Member Functions

DOT const * CalcNeighborDistanceFindClosestNeighbor (DOT const &dot1, std::vector< const DOT * > const &their_dots)
 

Additional Inherited Members

- Public Types inherited from core::scoring::sc::MolecularSurfaceCalculator
typedef float ScValue
 
typedef numeric::xyzVector< float > Vec3
 
- Public Attributes inherited from core::scoring::sc::MolecularSurfaceCalculator
struct {
   core::Real   rp
 
   core::Real   density
 
   core::Real   band
 
   core::Real   sep
 
   core::Real   weight
 
   core::Real   binwidth_dist
 
   core::Real   binwidth_norm
 
settings
 
ScValue radmax
 
RESULTS results
 
std::vector< Atomatoms
 
std::vector< DOTdots [2]
 
std::vector< const DOT * > trimmed_dots [2]
 
std::vector< PROBEprobes
 
Vec3 prevp
 
int prevburied
 
- Protected Attributes inherited from core::scoring::sc::MolecularSurfaceCalculator
struct {
   ScValue   radmax
 
   RESULTS   results
 
   std::vector< Atom >   atoms
 
   std::vector< DOT >   dots [2]
 
   std::vector< const DOT * >   trimmed_dots [2]
 
   std::vector< PROBE >   probes
 
   Vec3   prevp
 
   int   prevburied
 
run_
 
- Static Protected Attributes inherited from core::scoring::sc::MolecularSurfaceCalculator
static std::vector< ATOM_RADIUSradii_
 

Constructor & Destructor Documentation

core::scoring::sc::ContactMolecularSurfaceCalculator::ContactMolecularSurfaceCalculator ( )

ContactMolecularSurfaceCalculator constructor, initializes default settings.

core::scoring::sc::ContactMolecularSurfaceCalculator::~ContactMolecularSurfaceCalculator ( )
overridedefault

Member Function Documentation

int core::scoring::sc::ContactMolecularSurfaceCalculator::AssignAttentionNumbers ( std::vector< Atom > &  atom)
overrideprotectedvirtual
MolecularSurfaceCalculator::ScValue core::scoring::sc::ContactMolecularSurfaceCalculator::CalcContactArea ( )
ContactMolecularSurfaceCalculator::ScValue core::scoring::sc::ContactMolecularSurfaceCalculator::CalcContactMolecularSurface ( std::vector< DOT > const &  my_dots,
std::vector< DOT > const &  their_dots 
)
protected
DOT const * core::scoring::sc::ContactMolecularSurfaceCalculator::CalcNeighborDistanceFindClosestNeighbor ( DOT const &  dot1,
std::vector< const DOT * > const &  their_dots 
)
private

The documentation for this class was generated from the following files: