#include <MolecularSurfaceCalculator.hh>

Inheritance diagram for core::scoring::sc::MolecularSurfaceCalculator:

Public Types
typedef float	ScValue

typedef numeric::xyzVector< float >	Vec3

Public Member Functions
	MolecularSurfaceCalculator ()
	MolecularSurfaceCalculator constructor, initializes default settings. More...

virtual	~MolecularSurfaceCalculator ()

virtual int	Init ()
	Initializes calculation and GPU (if used) Init() is also called implicitly by the static CalcSc() function. More...

virtual 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)

RESULTS const &	GetResults ()

Public Attributes
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< Atom >	atoms

std::vector< DOT >	dots [2]

std::vector< PROBE >	probes

Vec3	prevp

int	prevburied

Protected Member Functions
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)

virtual int	AssignAttentionNumbers (std::vector< Atom > &atom)

Protected Attributes
struct {
ScValue radmax

RESULTS results

std::vector< Atom > atoms

std::vector< DOT > dots [2]

std::vector< PROBE > probes

Vec3 prevp

int prevburied

}	run_

Static Protected Attributes
static std::vector< ATOM_RADIUS >	radii_

Private Member Functions
int	CalcDotsForAllAtoms (std::vector< Atom > &atoms)

int	CalcDotsForAtoms (std::vector< Atom > &atoms)

int	FindNeighbordsAndBuriedAtoms (Atom &atom)

int	FindNeighborsForAtom (Atom &atom1)

int	GenerateToroidalSurface (Atom &atom1, Atom &atom2, Vec3 const uij, Vec3 const tij, ScValue rij, int between)

int	GenerateConvexSurface (Atom const &atom1)

int	GenerateConcaveSurface ()

int	SecondLoop (Atom &pAtom1)

int	ThirdLoop (Atom &pAtom1, Atom &pAtom, Vec3 const &uij, Vec3 const &tij, ScValue const rij)

int	CheckAtomCollision2 (Vec3 const &pijk, Atom const &atom1, Atom const &atom2, std::vector< Atom * > const &atoms)

int	CheckPointCollision (Vec3 const &pcen, std::vector< Atom * > const &atoms)

int	CheckProbeCollision (Vec3 const &point, std::vector< const PROBE * > const nears, ScValue const r2)

ScValue	DistancePointToLine (Vec3 const &cen, Vec3 const &axis, Vec3 const &pnt)

ScValue	SubArc (Vec3 const &cen, ScValue const rad, Vec3 const &axis, ScValue const density, Vec3 const &x, Vec3 const &v, std::vector< Vec3 > &points)

ScValue	SubDiv (Vec3 const &cen, ScValue const rad, Vec3 const &x, Vec3 const &y, ScValue angle, ScValue density, std::vector< Vec3 > &points)

ScValue	SubCir (Vec3 const &cen, ScValue const rad, Vec3 const &north, ScValue const density, std::vector< Vec3 > &points)

Member Typedef Documentation

typedef float core::scoring::sc::MolecularSurfaceCalculator::ScValue

typedef numeric::xyzVector< float > core::scoring::sc::MolecularSurfaceCalculator::Vec3

Constructor & Destructor Documentation

core::scoring::sc::MolecularSurfaceCalculator::MolecularSurfaceCalculator ( )

MolecularSurfaceCalculator constructor, initializes default settings.

References Reset(), and settings.

core::scoring::sc::MolecularSurfaceCalculator::~MolecularSurfaceCalculator ( )

virtual

References Reset().

Member Function Documentation

int core::scoring::sc::MolecularSurfaceCalculator::AddAtom	(	int	molecule,
		Atom &	atom
	)

Add an atom to a molecule for computation.

Add an core::scoring::sc::Atom to the molecule. Normally this is called by AddResidue(). Explicit addition of atoms via this function is rarely needed. This function also looks-up the atom radius and density. Returns true on success.

References core::scoring::sc::Atom::access, core::scoring::sc::Atom::atom, core::scoring::sc::Atom::density, core::scoring::sc::Atom::molecule, core::scoring::sc::Atom::natom, core::scoring::sc::Atom::radius, core::scoring::sc::Atom::residue, and core::scoring::TR().

Referenced by AddResidue().

void core::scoring::sc::MolecularSurfaceCalculator::AddDot	(	int const	molecule,
		int const	type,
		Vec3 const	coor,
		ScValue const	area,
		Vec3 const	pcen,
		Atom const &	atom
	)

protected

References core::scoring::sc::_DOT::buried, core::scoring::sc::Atom::buried, core::scoring::sc::_DOT::outnml, run_, and settings.

Referenced by GenerateConcaveSurface(), GenerateConvexSurface(), and GenerateToroidalSurface().

core::Size core::scoring::sc::MolecularSurfaceCalculator::AddResidue	(	int	molecule,
		core::conformation::Residue const &	residue
	)

Add a rosetta residue to a specific molecule.

Call this function when explicitly defining which residues belong to which the molecular surface. If partitioning by jump_id is sufficient for your application, you may use the Calc() or CalcSc() functions instead. Returns number of atoms added for the specified residue.

Example: core::scoring::sc::MolecularSurfaceCalculator calc; core::Real sc; calc.Init(); calc.Reset(); // Only needed when re-using the calculator for(core::Size i = 1; i <= pose.n_residue(); i++) calc.AddResidue((i < 100), pose.residue(i)); if(calc.Calc()) sc = calc.GetResults().sc;

References AddAtom(), AssignAtomRadius(), core::scoring::sc::Atom::atom, core::conformation::Residue::atom_name(), Init(), core::chemical::ResidueType::is_metal(), core::conformation::Residue::is_virtual(), core::conformation::Residue::name3(), core::conformation::Residue::nheavyatoms(), core::scoring::sc::Atom::nresidue, core::scoring::sc::Atom::radius, core::scoring::sc::Atom::residue, core::conformation::Residue::seqpos(), core::scoring::TR(), core::conformation::Residue::type(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

Referenced by Calc(), protocols::simple_filters::ShapeComplementarityFilter::compute(), and protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc().

int core::scoring::sc::MolecularSurfaceCalculator::AssignAtomRadius ( Atom & atom )

protected

References core::scoring::sc::Atom::atom, radii_, core::scoring::sc::Atom::radius, core::scoring::sc::Atom::residue, core::scoring::TR(), and WildcardMatch().

Referenced by AddResidue().

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

protectedvirtual

Reimplemented in core::scoring::sc::ShapeComplementarityCalculator.

References core::scoring::sc::ATTEN_BURIED_FLAGGED, and run_.

Referenced by Calc().

int core::scoring::sc::MolecularSurfaceCalculator::Calc	(	core::pose::Pose const &	pose,
		core::Size	jump_id = `0`
	)

virtual

Generate molecular surfaces for the given pose. //.

Generate molecular surfaces for the given pose.

This function initializes the calculator, adds all residues in the given pose, and generates molecular surfaces.

The pose is partitioned into separate molecules across the given jump. If the given jump is 0, the entire pose is loaded as molecule 1. To control what residues make up either surface, use the AddResidue() or even AddAtom() function instead. Returns true on success. Results are retrieved with GetResults().

Example: core::scoring::sc::MolecularSurfaceCalculator calc; if(calc.Calc( pose )) ... = calc.GetResults();

Reimplemented in core::scoring::sc::ShapeComplementarityCalculator.

References AddResidue(), Calc(), core::pose::Pose::fold_tree(), Init(), core::chemical::ResidueType::is_metal(), core::pose::Pose::n_residue(), core::chemical::ResidueType::name(), core::pose::Pose::num_jump(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::scoring::TR(), and core::conformation::Residue::type().

int core::scoring::sc::MolecularSurfaceCalculator::Calc ( )

virtual

Generate molecular surfaces for loaded atoms. //.

Generate molecular surfaces for loaded atoms.

This function generates molecular surfaces for atoms added via AddAtom and AddResidue.

Init() must be called before this function. Returns true on success.

Reimplemented in core::scoring::sc::ShapeComplementarityCalculator.

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

Referenced by core::scoring::sc::ShapeComplementarityCalculator::Calc(), and Calc().

int core::scoring::sc::MolecularSurfaceCalculator::CalcDotsForAllAtoms ( std::vector< Atom > & atoms )

private

References core::scoring::sc::Atom::access, core::scoring::sc::Atom::atten, core::scoring::sc::ATTEN_6, core::scoring::sc::ATTEN_BLOCKER, core::scoring::sc::Atom::buried, FindNeighbordsAndBuriedAtoms(), GenerateConcaveSurface(), GenerateConvexSurface(), run_, and settings.

Referenced by GenerateMolecularSurfaces().

int core::scoring::sc::MolecularSurfaceCalculator::CalcDotsForAtoms ( std::vector< Atom > & atoms )

private

int core::scoring::sc::MolecularSurfaceCalculator::CheckAtomCollision2	(	Vec3 const &	pijk,
		Atom const &	atom1,
		Atom const &	atom2,
		std::vector< Atom * > const &	atoms
	)

private

References core::scoring::sc::Atom::radius, and settings.

Referenced by ThirdLoop().

int core::scoring::sc::MolecularSurfaceCalculator::CheckPointCollision	(	Vec3 const &	pcen,
		std::vector< Atom * > const &	atoms
	)

private

References settings.

Referenced by GenerateConvexSurface().

int core::scoring::sc::MolecularSurfaceCalculator::CheckProbeCollision	(	Vec3 const &	point,
		std::vector< const PROBE * > const	nears,
		ScValue const	r2
	)

private

References protocols::hybridization::r2.

Referenced by GenerateConcaveSurface().

MolecularSurfaceCalculator::ScValue core::scoring::sc::MolecularSurfaceCalculator::DistancePointToLine	(	Vec3 const &	cen,
		Vec3 const &	axis,
		Vec3 const &	pnt
	)

private

Referenced by GenerateToroidalSurface().

int core::scoring::sc::MolecularSurfaceCalculator::FindNeighbordsAndBuriedAtoms ( Atom & atom )

private

References FindNeighborsForAtom(), core::scoring::sc::Atom::neighbors, and SecondLoop().

Referenced by CalcDotsForAllAtoms().

int core::scoring::sc::MolecularSurfaceCalculator::FindNeighborsForAtom ( Atom & atom1 )

private

References core::scoring::sc::Atom::access, core::scoring::sc::Atom::atom, core::scoring::sc::Atom::atten, core::scoring::sc::ATTEN_6, core::scoring::sc::ATTEN_BURIED_FLAGGED, core::scoring::sc::Atom::buried, core::scoring::sc::Atom::molecule, core::scoring::sc::Atom::natom, core::scoring::sc::Atom::neighbors, core::scoring::sc::Atom::radius, core::scoring::sc::Atom::residue, run_, and settings.

Referenced by FindNeighbordsAndBuriedAtoms().

int core::scoring::sc::MolecularSurfaceCalculator::GenerateConcaveSurface ( )

private

References AddDot(), core::scoring::sc::ATTEN_6, CheckProbeCollision(), density, run_, settings, SubArc(), and SubCir().

Referenced by CalcDotsForAllAtoms().

int core::scoring::sc::MolecularSurfaceCalculator::GenerateConvexSurface ( Atom const & atom1 )

private

References ABS, AddDot(), CheckPointCollision(), core::scoring::sc::Atom::density, core::scoring::sc::Atom::molecule, core::scoring::sc::Atom::natom, core::scoring::sc::Atom::neighbors, core::scoring::sc::Atom::radius, run_, settings, SubArc(), and SubCir().

Referenced by CalcDotsForAllAtoms().

void core::scoring::sc::MolecularSurfaceCalculator::GenerateMolecularSurfaces ( )

protected

Generate untrimmed surfaces for the defined molecules.

This function should be called within a try/catch block for ShapeComplementarityCalculatorException. Raises exception on error.

References CalcDotsForAllAtoms(), run_, settings, and core::scoring::TR().

Referenced by core::scoring::sc::ShapeComplementarityCalculator::Calc(), and Calc().

int core::scoring::sc::MolecularSurfaceCalculator::GenerateToroidalSurface	(	Atom &	atom1,
		Atom &	atom2,
		Vec3 const	uij,
		Vec3 const	tij,
		ScValue	rij,
		int	between
	)

private

References core::scoring::sc::Atom::access, AddDot(), core::scoring::sc::Atom::atten, core::scoring::sc::ATTEN_2, core::scoring::sc::ATTEN_6, core::scoring::sc::Atom::buried, core::scoring::sc::Atom::density, density, DistancePointToLine(), core::scoring::sc::Atom::molecule, core::scoring::sc::Atom::neighbors, core::scoring::sc::Atom::radius, run_, settings, SubArc(), and SubCir().

Referenced by SecondLoop().

std::vector<Atom> const& core::scoring::sc::MolecularSurfaceCalculator::GetAtoms ( )

inline

References run_.

std::vector<DOT> const& core::scoring::sc::MolecularSurfaceCalculator::GetDots ( int const moleculeid )

inline

References run_.

RESULTS const& core::scoring::sc::MolecularSurfaceCalculator::GetResults ( )

inline

References run_.

Referenced by protocols::simple_filters::ShapeComplementarityFilter::apply(), core::scoring::sc::ShapeComplementarityCalculator::CalcSc(), protocols::simple_filters::ShapeComplementarityFilter::compute(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc(), and protocols::simple_filters::ShapeComplementarityFilter::report_sm().

int core::scoring::sc::MolecularSurfaceCalculator::Init ( )

virtual

Initializes calculation and GPU (if used) Init() is also called implicitly by the static CalcSc() function.

References radii_, and ReadScRadii().

Referenced by AddResidue(), protocols::docking::membrane::MPFindInterfaceMover::apply(), Calc(), protocols::simple_filters::ShapeComplementarityFilter::compute(), and protocols::pockets::PocketGrid::get_connolly_surfacePoints().

int core::scoring::sc::MolecularSurfaceCalculator::ReadScRadii ( )

protected

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.

References core::scoring::sc::_ATOM_RADIUS::atom, radii_, core::scoring::sc::_ATOM_RADIUS::radius, core::scoring::sc::_ATOM_RADIUS::residue, and core::scoring::TR().

Referenced by Init().

void core::scoring::sc::MolecularSurfaceCalculator::Reset ( )

virtual

Reset calculator for another calculation. Must be used when the MolecularSurfaceCalculator instance is re-used.

Atom, probe and surface dot vectors are reset here. We don't clear them after the calculation is finished in case the caller would like to use those data elsewhere.

References core::pose::motif::a(), and run_.

Referenced by protocols::simple_filters::ShapeComplementarityFilter::apply(), protocols::simple_filters::ShapeComplementarityFilter::compute(), MolecularSurfaceCalculator(), protocols::simple_filters::ShapeComplementarityFilter::report_sm(), and ~MolecularSurfaceCalculator().

int core::scoring::sc::MolecularSurfaceCalculator::SecondLoop ( Atom & pAtom1 )

private

References ABS, core::scoring::sc::Atom::access, core::scoring::sc::Atom::atten, core::scoring::sc::ATTEN_BLOCKER, GenerateToroidalSurface(), core::scoring::sc::Atom::neighbors, core::scoring::sc::Atom::radius, settings, and ThirdLoop().

Referenced by FindNeighbordsAndBuriedAtoms().

MolecularSurfaceCalculator::ScValue core::scoring::sc::MolecularSurfaceCalculator::SubArc	(	Vec3 const &	cen,
		ScValue const	rad,
		Vec3 const &	axis,
		ScValue const	density,
		Vec3 const &	x,
		Vec3 const &	v,
		std::vector< Vec3 > &	points
	)

private

References PI, and SubDiv().

Referenced by GenerateConcaveSurface(), GenerateConvexSurface(), and GenerateToroidalSurface().

MolecularSurfaceCalculator::ScValue core::scoring::sc::MolecularSurfaceCalculator::SubCir	(	Vec3 const &	cen,
		ScValue const	rad,
		Vec3 const &	north,
		ScValue const	density,
		std::vector< Vec3 > &	points
	)

private

References ABS, PI, and SubDiv().

Referenced by GenerateConcaveSurface(), GenerateConvexSurface(), and GenerateToroidalSurface().

MolecularSurfaceCalculator::ScValue core::scoring::sc::MolecularSurfaceCalculator::SubDiv	(	Vec3 const &	cen,
		ScValue const	rad,
		Vec3 const &	x,
		Vec3 const &	y,
		ScValue	angle,
		ScValue	density,
		std::vector< Vec3 > &	points
	)