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Rosetta
2021.16
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Rosetta
2021.16
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#include <ShapeComplementarityCalculator.hh>
Public Member Functions | |
| ShapeComplementarityCalculator () | |
| ShapeComplementarityCalculator constructor, initializes default settings. More... | |
| ~ShapeComplementarityCalculator () override | |
| int | Calc () override |
| Run the SC calculation for previously defined molecules (via AddResidue or add_atom calls) More... | |
| int | Calc (core::pose::Pose const &pose, core::Size jump_id) override |
| Run the SC calculation on a Pose, partitionied by jump_id. More... | |
 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... | |
| 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 () |
Static Public Member Functions | |
| static core::Real | CalcSc (core::pose::Pose const &pose, core::Size jump_id=1, int quick=0) |
| Run the SC calculation on Pose and return just the sc statistic or -1 on error. More... | |
Protected Member Functions | |
| 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 | |
| ScValue | TrimPeripheralBand (std::vector< DOT > const &sdots, std::vector< const DOT * > &trimmed_dots) |
| int | TrimPeripheralBandCheckDot (DOT const &dot, std::vector< DOT > const &sdots) |
| int | CalcNeighborDistance (int const molecule, std::vector< const DOT * > const &my_dots, std::vector< const DOT * > const &their_dots) |
| 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 |
| 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_ |
| core::scoring::sc::ShapeComplementarityCalculator::ShapeComplementarityCalculator | ( | ) |
ShapeComplementarityCalculator constructor, initializes default settings.
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overridedefault |
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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 Calc().
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overridevirtual |
Run the SC calculation for previously defined molecules (via AddResidue or add_atom calls)
This function should be called the residues / atoms making up the two molecular surfaces have been explicitly defined. Returns true on success.
Reimplemented from core::scoring::sc::MolecularSurfaceCalculator.
References AssignAttentionNumbers(), CalcNeighborDistance(), core::scoring::sc::ShapeComplementarityCalculatorException::error, core::scoring::sc::MolecularSurfaceCalculator::GenerateMolecularSurfaces(), core::scoring::sc::MolecularSurfaceCalculator::run_, core::scoring::sc::MolecularSurfaceCalculator::settings, core::id::to_string(), core::scoring::TR(), and TrimPeripheralBand().
Referenced by core::scoring::sc::ElectrostaticComplementarityCalculator::Calc(), CalcSc(), protocols::simple_filters::ShapeComplementarityFilter::compute(), and protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc().
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overridevirtual |
Run the SC calculation on a Pose, partitionied by jump_id.
This non-static function requires an instance of the ShapeComplementarityCalculator class. The jump_id is used to partition the pose into two molecular surfaces. To control what residues make up either surface, use the AddResidue() or even add_atom() function instead. Returns true on success. Results are retrieved with GetResults().
Example: core::scoring::sc::ShapeComplementarityCalculator calc; core::Real sc; if(calc.Calc( pose )) sc = calc.GetResults().sc;
Reimplemented from core::scoring::sc::MolecularSurfaceCalculator.
References core::scoring::sc::MolecularSurfaceCalculator::Calc(), core::pose::Pose::num_jump(), and core::scoring::TR().
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private |
References core::pack::dunbrack::c, CalcNeighborDistanceFindClosestNeighbor(), core::scoring::sc::_DOT::coor, MAX, MIN, core::scoring::sc::_DOT::outnml, core::scoring::sc::MolecularSurfaceCalculator::run_, core::scoring::sc::MolecularSurfaceCalculator::settings, protocols::analysis::total, and core::scoring::TR().
Referenced by Calc().
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private |
References core::scoring::sc::_DOT::buried, and core::scoring::sc::_DOT::coor.
Referenced by CalcNeighborDistance().
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static |
Run the SC calculation on Pose and return just the sc statistic or -1 on error.
This is a static function and can be called without instantiating ShapeComplementarityCalculator. The jump_id is used to partition the pose into two molecular surfaces; the first jump (1) is used is no jump_id is explicity specified. Those desiring more control as to what residues make up either surface should use the AddResidue() or even add_atom() function instead. Setting quick to true will perform a much faster calculation (~5-10 times faster) at the expense of accuracy (about 0.05 units).
Example: core::Real sc = core::scoring::sc::ShapeComplementarityCalculator( pose );
References Calc(), core::scoring::sc::MolecularSurfaceCalculator::density, core::scoring::sc::MolecularSurfaceCalculator::GetResults(), core::scoring::sc::_RESULTS::sc, and core::scoring::sc::MolecularSurfaceCalculator::settings.
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private |
References core::scoring::sc::_DOT::area, core::scoring::sc::_DOT::buried, core::scoring::sc::MolecularSurfaceCalculator::settings, and TrimPeripheralBandCheckDot().
Referenced by Calc().
1.8.7