core::scoring::sc::ContactMolecularSurfaceCalculator Class Reference

#include <ContactMolecularSurfaceCalculator.hh>

Inheritance diagram for core::scoring::sc::ContactMolecularSurfaceCalculator:

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, bool apolar_only=false)
	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 @defailed 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
core::Real   near_squared_size
bool   use_rosetta_radii
}	settings
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
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_RADIUS >	radii_

Constructor & Destructor Documentation

ContactMolecularSurfaceCalculator()

core::scoring::sc::ContactMolecularSurfaceCalculator::ContactMolecularSurfaceCalculator

(

)

ContactMolecularSurfaceCalculator constructor, initializes default settings.

~ContactMolecularSurfaceCalculator()

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

overridedefault

Member Function Documentation

AssignAttentionNumbers()

int core::scoring::sc::ContactMolecularSurfaceCalculator::AssignAttentionNumbers ( std::vector< Atom > &  atom )

overrideprotectedvirtual

Reimplemented from core::scoring::sc::MolecularSurfaceCalculator.

References core::scoring::sc::ATTEN_BLOCKER, core::scoring::sc::ATTEN_BURIED_FLAGGED, core::scoring::sc::MolecularSurfaceCalculator::run_, and core::scoring::sc::MolecularSurfaceCalculator::settings.

Referenced by CalcContactArea().

CalcContactArea()

MolecularSurfaceCalculator::ScValue core::scoring::sc::ContactMolecularSurfaceCalculator::CalcContactArea

(

)

References AssignAttentionNumbers(), CalcContactMolecularSurface(), core::scoring::sc::ShapeComplementarityCalculatorException::error, core::scoring::sc::MolecularSurfaceCalculator::GenerateMolecularSurfaces(), core::scoring::sc::MolecularSurfaceCalculator::run_, and core::scoring::TR().

Referenced by protocols::simple_filters::ContactMolecularSurfaceFilter::compute().

CalcContactMolecularSurface()

ContactMolecularSurfaceCalculator::ScValue core::scoring::sc::ContactMolecularSurfaceCalculator::CalcContactMolecularSurface ( std::vector< DOT > const &  my_dots, std::vector< DOT > const &  their_dots  )

protected

References core::scoring::sc::_DOT::area, core::scoring::sc::_DOT::buried, CalcNeighborDistanceFindClosestNeighbor(), core::scoring::sc::_DOT::coor, core::scoring::sc::get_n_neighbors(), and core::scoring::sc::MolecularSurfaceCalculator::settings.

Referenced by CalcContactArea().

CalcNeighborDistanceFindClosestNeighbor()

DOT const * core::scoring::sc::ContactMolecularSurfaceCalculator::CalcNeighborDistanceFindClosestNeighbor ( DOT const &  dot1, std::vector< const DOT * > const &  their_dots  )

private

References core::scoring::sc::_DOT::buried, and core::scoring::sc::_DOT::coor.

Referenced by CalcContactMolecularSurface().

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

• src/core/scoring/sc/ContactMolecularSurfaceCalculator.hh
• src/core/scoring/sc/ContactMolecularSurfaceCalculator.cc