Rosetta
2019.07
|
#include <xyzStripeHash.hh>
Classes | |
struct | const_iterator |
struct | iter_base |
struct | ushort2 |
Public Types | |
typedef unsigned short | ushort |
typedef numeric::xyzVector< float > | Vec |
Public Types inherited from utility::pointer::ReferenceCount | |
typedef platform::Size | Size |
typedef platform::Size | size_type |
Public Member Functions | |
xyzStripeHash (float grid_size=0.0, utility::vector1< Ball > const &balls=utility::vector1< Ball >()) | |
void | init (utility::vector1< Ball > const &balls) |
virtual | ~xyzStripeHash () |
const_iterator | begin () const |
const_iterator | end () const |
bool | sanity_check () const |
std::string | debug_pdb (Xform const &x=numeric::Xform::identity()) const |
int | nbcount (Vec const &v_in) const |
int | nbcount_raw (Vec const &v) const |
bool | clash (Vec const &v_in) const |
bool | clash_not_resid (Vec const &v_in, int const &resid, int const &resid2=0) const |
bool | clash_raw (Vec const &v) const |
float | clash_amount (Vec const &v_in) const |
int | clash_check_ball (Ball const &b) const |
bool | clash_check_residue_pairs (utility::vector1< Ball > const &test_balls, std::map< Size, Size > &residue_pairs) const |
void | fill_pairs (xyzVector_float const &v, int const &ir, utility::vector1< std::pair< int, int > > &pairs, float maxd2=0.0) const |
template<typename Visitor > | |
void | visit (Vec const &v_in, Visitor &visitor) const |
template<typename Visitor > | |
void | visit_lax (Vec const &v_in, float const vr, Visitor &visitor) const |
Ball const * | grid_atoms () const |
Size | size () const |
int | natom () const |
int | xdim () const |
int | ydim () const |
int | zdim () const |
float | grid_size () const |
float | grid_size2 () const |
xyzVector_float const & | translation () const |
xyzVector< Real > | translation_real () const |
ushort2 const * | grid_stripe () const |
Ball const & | ball (Size const &ib) const |
xyzVector_float | xyz (Size const &ib) const |
Size | resi (Size const &ib) const |
Public Member Functions inherited from utility::pointer::ReferenceCount | |
ReferenceCount () | |
Default constructor. More... | |
virtual | ~ReferenceCount () |
Private Member Functions | |
short | short_min (short const a, short const b) |
short | short_max (short const a, short const b) |
short | ushort_min (unsigned short const a, unsigned short const b) |
short | ushort_max (unsigned short const a, unsigned short const b) |
Private Attributes | |
float | grid_size_ |
float | grid_size2_ |
int | nballs_ |
Ball const * | grid_balls_ |
ushort2 const * | grid_stripe_ |
int | xdim_ |
int | ydim_ |
int | zdim_ |
float | xmx_ |
float | ymx_ |
float | zmx_ |
numeric::xyzVector< float > | translation_ |
typedef unsigned short numeric::geometry::hashing::xyzStripeHash::ushort |
numeric::geometry::hashing::xyzStripeHash::xyzStripeHash | ( | float | grid_size = 0.0 , |
utility::vector1< Ball > const & | balls = utility::vector1<Ball>() |
||
) |
References init().
|
inlinevirtual |
References grid_balls_, and grid_stripe_.
References grid_balls_, and nballs_.
Referenced by clash_check_residue_pairs().
|
inline |
References grid_balls_.
References test.Workshop3test::a2, grid_balls_, grid_size2_, grid_size_, grid_stripe_, numeric::max(), numeric::min(), translation_, test.T850_SubClassing::v, numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.
References test.Workshop3test::a2, numeric::geometry::hashing::Ball::atomno(), utility::io::oc::cout, grid_balls_, grid_size2_, grid_size_, grid_stripe_, numeric::max(), numeric::min(), numeric::geometry::hashing::Ball::resi(), translation_, test.T850_SubClassing::v, numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.
References test.Workshop3test::a2, grid_balls_, grid_size_, grid_stripe_, numeric::max(), numeric::min(), numeric::geometry::hashing::Ball::radius(), translation_, numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::xyz(), numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.
Referenced by clash_check_residue_pairs().
bool numeric::geometry::hashing::xyzStripeHash::clash_check_residue_pairs | ( | utility::vector1< Ball > const & | test_balls, |
std::map< Size, Size > & | residue_pairs | ||
) | const |
References ball(), clash_check_ball(), and numeric::geometry::hashing::Ball::resi().
bool numeric::geometry::hashing::xyzStripeHash::clash_not_resid | ( | Vec const & | v_in, |
int const & | resid, | ||
int const & | resid2 = 0 |
||
) | const |
References test.Workshop3test::a2, grid_balls_, grid_size2_, grid_size_, grid_stripe_, numeric::max(), numeric::min(), numeric::geometry::hashing::Ball::resid_, translation_, test.T850_SubClassing::v, numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.
References test.Workshop3test::a2, grid_balls_, grid_size2_, grid_size_, grid_stripe_, numeric::max(), numeric::min(), numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.
std::string numeric::geometry::hashing::xyzStripeHash::debug_pdb | ( | Xform const & | x = numeric::Xform::identity() | ) | const |
References basic::options::OptionKeys::score::fiber_diffraction::b, ObjexxFCL::format::F(), pyrosetta.tests.distributed.test_dask::format, grid_balls_, test.T110_Numeric::I, nballs_, erraser_single_res_analysis::out, translation_, test.T850_SubClassing::v, numeric::xyzVector< typename >::x(), numeric::geometry::hashing::Ball::xyz(), numeric::xyzVector< typename >::y(), and numeric::xyzVector< typename >::z().
|
inline |
References grid_balls_, and nballs_.
void numeric::geometry::hashing::xyzStripeHash::fill_pairs | ( | xyzVector_float const & | v, |
int const & | ir, | ||
utility::vector1< std::pair< int, int > > & | pairs, | ||
float | maxd2 = 0.0 |
||
) | const |
References test.Workshop3test::a2, grid_balls_, grid_size2_, grid_size_, grid_stripe_, numeric::max(), numeric::min(), numeric::geometry::hashing::Ball::resid_, translation_, test.T850_SubClassing::v, numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.
|
inline |
References grid_balls_.
|
inline |
References grid_size_.
|
inline |
References grid_size2_.
|
inline |
References grid_stripe_.
void numeric::geometry::hashing::xyzStripeHash::init | ( | utility::vector1< Ball > const & | balls | ) |
References basic::options::OptionKeys::score::fiber_diffraction::b, demo.D060_Folding::f, grid_balls_, grid_size2_, grid_size_, grid_stripe_, numeric::max(), numeric::min(), nballs_, basic::options::OptionKeys::cluster::radius, translation_, utility_exit_with_message, numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.
Referenced by xyzStripeHash().
References test.Workshop3test::a2, clean_pdb_keep_ligand::count, grid_balls_, grid_size2_, grid_size_, grid_stripe_, numeric::max(), numeric::min(), translation_, test.T850_SubClassing::v, numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.
References test.Workshop3test::a2, clean_pdb_keep_ligand::count, grid_balls_, grid_size2_, grid_size_, grid_stripe_, numeric::max(), numeric::min(), numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.
References grid_balls_, nballs_, and numeric::geometry::hashing::Ball::resi().
bool numeric::geometry::hashing::xyzStripeHash::sanity_check | ( | ) | const |
References pyrosetta.tests.distributed.test_dask::format, grid_balls_, grid_size_, grid_stripe_, utility_exit_with_message, numeric::geometry::hashing::xyzStripeHash::ushort2::x, xdim_, numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, ydim_, numeric::crick_equations::z(), and zdim_.
|
inlineprivate |
|
inlineprivate |
|
inline |
References translation_.
|
inlineprivate |
|
inlineprivate |
|
inline |
References grid_balls_, grid_size2_, grid_size_, grid_stripe_, numeric::max(), numeric::min(), translation_, test.T850_SubClassing::v, numeric::crick_equations::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.
|
inline |
References grid_balls_, grid_size_, grid_stripe_, numeric::max(), numeric::min(), numeric::geometry::hashing::Ball::radius(), translation_, test.T850_SubClassing::v, numeric::crick_equations::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.
|
inline |
References grid_balls_, nballs_, translation_, and numeric::geometry::hashing::Ball::xyz().
|
private |
Referenced by ball(), begin(), clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), debug_pdb(), end(), fill_pairs(), grid_atoms(), init(), nbcount(), nbcount_raw(), resi(), sanity_check(), visit(), visit_lax(), xyz(), and ~xyzStripeHash().
|
private |
Referenced by clash(), clash_amount(), clash_not_resid(), clash_raw(), fill_pairs(), grid_size2(), init(), nbcount(), nbcount_raw(), and visit().
|
private |
Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), grid_size(), init(), nbcount(), nbcount_raw(), sanity_check(), visit(), and visit_lax().
|
private |
Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), grid_stripe(), init(), nbcount(), nbcount_raw(), sanity_check(), visit(), visit_lax(), and ~xyzStripeHash().
|
private |
|
private |
Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), debug_pdb(), fill_pairs(), init(), nbcount(), translation(), translation_real(), visit(), visit_lax(), and xyz().
|
private |
Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), init(), nbcount(), nbcount_raw(), sanity_check(), visit(), visit_lax(), and xdim().
|
private |
Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), init(), nbcount(), nbcount_raw(), visit(), and visit_lax().
|
private |
Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), init(), nbcount(), nbcount_raw(), sanity_check(), visit(), visit_lax(), and ydim().
|
private |
Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), init(), nbcount(), nbcount_raw(), visit(), and visit_lax().
|
private |
Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), init(), nbcount(), nbcount_raw(), sanity_check(), visit(), visit_lax(), and zdim().
|
private |
Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), init(), nbcount(), nbcount_raw(), visit(), and visit_lax().