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Rosetta
2020.50
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#include <CartGrid.hh>
Public Types | |
typedef numeric::xyzVector< int > | GridPt |
This needs to be an int, as it can hold negative values. More... | |
Public Member Functions | |
CartGrid () | |
CartGrid (CartGrid< T > const &other) | |
CartGrid & | operator= (CartGrid< T > const &other) |
~CartGrid () override=default | |
void | setBase (core::Real x, core::Real y, core::Real z) |
void | setDimensions (core::Size nX, core::Size nY, core::Size nZ, core::Real lX, core::Real lY, core::Real lZ) |
void | set_name (std::string const &name) |
std::string | get_name () const |
core::Size | longestSide () const |
bool | equalDimensions (CartGrid< T > const &rhs) const |
bool | equalBase (CartGrid< T > const &rhs) const |
bool | is_in_grid (core::Real x, core::Real y, core::Real z) const |
bool | setupZones () |
void | translate (core::Real x, core::Real y, core::Real z) |
void | setValue (core::Size ix, core::Size iy, core::Size iz, T value) |
void | setValue (core::Real fx, core::Real fy, core::Real fz, T value) |
T | getValue (core::Size ix, core::Size iy, core::Size iz) const |
T | getValue (core::Real fx, core::Real fy, core::Real fz) const |
void | zero () |
void | setFullOccupied (T value) |
void | clone (CartGrid< T > ©) const |
void | reset_boundaries () |
void | read (std::string const &filename) |
void | write (std::string const &filename) const |
bool | isFullyOccupied () const |
bool | isEmpty () const |
utility::json_spirit::Value | serialize () const |
void | deserialize (utility::json_spirit::mObject grid_data) |
void | sum (utility::vector0< utility::pointer::shared_ptr< CartGrid< T > > > const &list_grids) |
void | expand (int expansion) |
core::Vector | getBase () const |
core::Vector | getTop () const |
void | getNumberOfPoints (core::Size &x, core::Size &y, core::Size &z) const |
core::Vector | getNumberOfPoints () const |
GridPt | gridpt (Vector const &coords) const |
Vector | coords (GridPt const &gridpt) const |
T | getValue (GridPt const &gridpt) const |
T | getValue (Vector const &coords) const |
T | getMinValue () const |
T | getMaxValue () const |
void | setValue (GridPt const &gridpt, T value) |
void | setValue (Vector const &coords, T value) |
void | write_to_BRIX (std::string const &filename) const |
void | write_to_BRIX (std::ostream &out) const |
Private Member Functions | |
void | setTop () |
bool | valid_index (core::Size index) const |
void | setValue (int ix, int iy, int iz, T value) |
void | setValue (core::Size index, T value) |
T | getValue (int ix, int iy, int iz) const |
T | getValue (core::Size index) const |
core::Size | get_index (core::Size ix, core::Size iy, core::Size iz) const |
core::Size | get_index (core::Real fx, core::Real fy, core::Real fz) const |
Private Attributes | |
core::Size | nX_ |
core::Size | nY_ |
core::Size | nZ_ |
core::Real | lX_ |
core::Real | lY_ |
core::Real | lZ_ |
core::Real | bX_ |
core::Real | bY_ |
core::Real | bZ_ |
core::Real | tX_ |
core::Real | tY_ |
core::Real | tZ_ |
std::string | name_ |
core::Size | npoints_ |
bool | fullyOccupied_ |
utility::vector0< T > | zones_ |
typedef numeric::xyzVector< int > core::grid::CartGrid< T >::GridPt |
This needs to be an int, as it can hold negative values.
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Referenced by core::grid::CartGrid< core::Real >::reset_boundaries().
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Referenced by protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(), protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(), protocols::qsar::scoring_grid::SingleGrid::get_point_value_list_within_range(), protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(), protocols::ligand_docking::grid_to_kin(), protocols::qsar::scoring_grid::PCSSingleGrid::refresh(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), protocols::qsar::scoring_grid::SingleGrid::set_ring(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), and protocols::ligand_docking::set_sphere().
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Referenced by protocols::qsar::scoring_grid::SingleGrid::deserialize().
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Referenced by core::grid::CartGrid< core::Real >::sum().
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Referenced by core::grid::CartGrid< core::Real >::sum().
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Referenced by protocols::qsar::scoring_grid::SingleGrid::show().
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Referenced by protocols::qsar::scoring_grid::SingleGrid::get_max_value().
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Referenced by protocols::qsar::scoring_grid::SingleGrid::get_min_value().
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Referenced by protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(), protocols::qsar::scoring_grid::SingleGrid::get_dimensions(), protocols::qsar::scoring_grid::SingleGrid::get_point_value_list_within_range(), protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(), protocols::ligand_docking::grid_to_kin(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), protocols::qsar::scoring_grid::SingleGrid::set_ring(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), and protocols::ligand_docking::set_sphere().
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Referenced by protocols::qsar::scoring_grid::SingleGrid::show().
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Referenced by protocols::qsar::scoring_grid::SingleGrid::atom_score(), protocols::qsar::scoring_grid::PCSSingleGrid::atom_score(), protocols::qsar::scoring_grid::SingleGrid::get_point(), protocols::qsar::scoring_grid::SingleGrid::get_point_value_list_within_range(), core::grid::CartGrid< core::Real >::getValue(), protocols::ligand_docking::grid_score(), protocols::ligand_docking::grid_score_atr_rep(), protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(), protocols::ligand_docking::grid_to_kin(), core::grid::CartGrid< core::Real >::reset_boundaries(), protocols::qsar::scoring_grid::SingleGrid::score(), protocols::qsar::scoring_grid::PCSSingleGrid::score(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), core::grid::CartGrid< core::Real >::sum(), core::grid::CartGrid< core::Real >::write(), and core::grid::CartGrid< core::Real >::write_to_BRIX().
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Referenced by protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), protocols::qsar::scoring_grid::SingleGrid::set_ring(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), protocols::ligand_docking::set_sphere(), and core::grid::CartGrid< core::Real >::write_to_BRIX().
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Referenced by protocols::qsar::scoring_grid::HbaGrid::atom_score(), protocols::qsar::scoring_grid::VdwGrid::atom_score(), protocols::qsar::scoring_grid::HbdGrid::atom_score(), protocols::qsar::scoring_grid::ChargeGrid::atom_score(), protocols::qsar::scoring_grid::SingleGrid::atom_score(), core::grid::CartGrid< core::Real >::get_index(), protocols::qsar::scoring_grid::SingleGrid::get_point(), protocols::ligand_docking::grid_score(), protocols::ligand_docking::grid_score_atr_rep(), protocols::qsar::scoring_grid::SingleGrid::is_in_grid(), protocols::qsar::scoring_grid::HbaGrid::score(), protocols::qsar::scoring_grid::VdwGrid::score(), protocols::qsar::scoring_grid::HbdGrid::score(), protocols::qsar::scoring_grid::ChargeGrid::score(), and protocols::qsar::scoring_grid::SingleGrid::score().
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Referenced by protocols::qsar::scoring_grid::SingleGrid::serialize().
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Referenced by protocols::qsar::scoring_grid::SingleGrid::fill_with_value().
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Referenced by protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(), core::grid::CartGrid< core::Real >::read(), core::grid::CartGrid< core::Real >::reset_boundaries(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), protocols::qsar::scoring_grid::SingleGrid::set_point(), protocols::qsar::scoring_grid::SingleGrid::set_ring(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), protocols::ligand_docking::set_sphere(), core::grid::CartGrid< core::Real >::setValue(), and core::grid::CartGrid< core::Real >::sum().
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This format was choosen because it's space-efficient for small integer values (such as are typically stored in grids) and PyMOL can read it. Typical extension is .brix or .omap
Referenced by protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(), and core::grid::CartGrid< core::Real >::write_to_BRIX().
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Referenced by core::grid::CartGrid< core::Real >::clone(), core::grid::CartGrid< core::Real >::coords(), core::grid::CartGrid< core::Real >::equalBase(), core::grid::CartGrid< core::Real >::expand(), core::grid::CartGrid< core::Real >::get_index(), core::grid::CartGrid< core::Real >::getBase(), core::grid::CartGrid< core::Real >::gridpt(), core::grid::CartGrid< core::Real >::reset_boundaries(), core::grid::CartGrid< core::Real >::serialize(), core::grid::CartGrid< core::Real >::setBase(), core::grid::CartGrid< core::Real >::setTop(), core::grid::CartGrid< core::Real >::translate(), and core::grid::CartGrid< core::Real >::write().
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Referenced by core::grid::CartGrid< core::Real >::clone(), core::grid::CartGrid< core::Real >::coords(), core::grid::CartGrid< core::Real >::equalBase(), core::grid::CartGrid< core::Real >::expand(), core::grid::CartGrid< core::Real >::get_index(), core::grid::CartGrid< core::Real >::getBase(), core::grid::CartGrid< core::Real >::gridpt(), core::grid::CartGrid< core::Real >::reset_boundaries(), core::grid::CartGrid< core::Real >::serialize(), core::grid::CartGrid< core::Real >::setBase(), core::grid::CartGrid< core::Real >::setTop(), core::grid::CartGrid< core::Real >::translate(), and core::grid::CartGrid< core::Real >::write().
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Referenced by core::grid::CartGrid< core::Real >::clone(), core::grid::CartGrid< core::Real >::coords(), core::grid::CartGrid< core::Real >::equalBase(), core::grid::CartGrid< core::Real >::expand(), core::grid::CartGrid< core::Real >::get_index(), core::grid::CartGrid< core::Real >::getBase(), core::grid::CartGrid< core::Real >::gridpt(), core::grid::CartGrid< core::Real >::reset_boundaries(), core::grid::CartGrid< core::Real >::serialize(), core::grid::CartGrid< core::Real >::setBase(), core::grid::CartGrid< core::Real >::setTop(), core::grid::CartGrid< core::Real >::translate(), and core::grid::CartGrid< core::Real >::write().
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Referenced by core::grid::CartGrid< core::Real >::clone(), core::grid::CartGrid< core::Real >::coords(), core::grid::CartGrid< core::Real >::equalDimensions(), core::grid::CartGrid< core::Real >::expand(), core::grid::CartGrid< core::Real >::get_index(), core::grid::CartGrid< core::Real >::gridpt(), core::grid::CartGrid< core::Real >::reset_boundaries(), core::grid::CartGrid< core::Real >::serialize(), core::grid::CartGrid< core::Real >::setDimensions(), core::grid::CartGrid< core::Real >::setTop(), core::grid::CartGrid< core::Real >::write(), and core::grid::CartGrid< core::Real >::write_to_BRIX().
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Referenced by core::grid::CartGrid< core::Real >::clone(), core::grid::CartGrid< core::Real >::coords(), core::grid::CartGrid< core::Real >::equalDimensions(), core::grid::CartGrid< core::Real >::expand(), core::grid::CartGrid< core::Real >::get_index(), core::grid::CartGrid< core::Real >::gridpt(), core::grid::CartGrid< core::Real >::reset_boundaries(), core::grid::CartGrid< core::Real >::serialize(), core::grid::CartGrid< core::Real >::setDimensions(), core::grid::CartGrid< core::Real >::setTop(), core::grid::CartGrid< core::Real >::write(), and core::grid::CartGrid< core::Real >::write_to_BRIX().
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Referenced by core::grid::CartGrid< core::Real >::clone(), core::grid::CartGrid< core::Real >::coords(), core::grid::CartGrid< core::Real >::equalDimensions(), core::grid::CartGrid< core::Real >::expand(), core::grid::CartGrid< core::Real >::get_index(), core::grid::CartGrid< core::Real >::gridpt(), core::grid::CartGrid< core::Real >::reset_boundaries(), core::grid::CartGrid< core::Real >::serialize(), core::grid::CartGrid< core::Real >::setDimensions(), core::grid::CartGrid< core::Real >::setTop(), core::grid::CartGrid< core::Real >::write(), and core::grid::CartGrid< core::Real >::write_to_BRIX().
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Referenced by core::grid::CartGrid< core::Real >::clone(), core::grid::CartGrid< core::Real >::deserialize(), core::grid::CartGrid< core::Real >::get_index(), core::grid::CartGrid< core::Real >::isEmpty(), core::grid::CartGrid< core::Real >::serialize(), core::grid::CartGrid< core::Real >::setFullOccupied(), core::grid::CartGrid< core::Real >::setupZones(), core::grid::CartGrid< core::Real >::valid_index(), and core::grid::CartGrid< core::Real >::zero().
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Referenced by core::grid::CartGrid< core::Real >::clone(), core::grid::CartGrid< core::Real >::equalDimensions(), core::grid::CartGrid< core::Real >::expand(), core::grid::CartGrid< core::Real >::get_index(), core::grid::CartGrid< core::Real >::getNumberOfPoints(), core::grid::CartGrid< core::Real >::longestSide(), core::grid::CartGrid< core::Real >::reset_boundaries(), core::grid::CartGrid< core::Real >::serialize(), core::grid::CartGrid< core::Real >::setDimensions(), core::grid::CartGrid< core::Real >::setTop(), core::grid::CartGrid< core::Real >::setupZones(), core::grid::CartGrid< core::Real >::write(), and core::grid::CartGrid< core::Real >::write_to_BRIX().
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Referenced by core::grid::CartGrid< core::Real >::clone(), core::grid::CartGrid< core::Real >::equalDimensions(), core::grid::CartGrid< core::Real >::expand(), core::grid::CartGrid< core::Real >::get_index(), core::grid::CartGrid< core::Real >::getNumberOfPoints(), core::grid::CartGrid< core::Real >::longestSide(), core::grid::CartGrid< core::Real >::reset_boundaries(), core::grid::CartGrid< core::Real >::serialize(), core::grid::CartGrid< core::Real >::setDimensions(), core::grid::CartGrid< core::Real >::setTop(), core::grid::CartGrid< core::Real >::setupZones(), core::grid::CartGrid< core::Real >::write(), and core::grid::CartGrid< core::Real >::write_to_BRIX().
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Referenced by core::grid::CartGrid< core::Real >::clone(), core::grid::CartGrid< core::Real >::equalDimensions(), core::grid::CartGrid< core::Real >::expand(), core::grid::CartGrid< core::Real >::get_index(), core::grid::CartGrid< core::Real >::getNumberOfPoints(), core::grid::CartGrid< core::Real >::longestSide(), core::grid::CartGrid< core::Real >::reset_boundaries(), core::grid::CartGrid< core::Real >::serialize(), core::grid::CartGrid< core::Real >::setDimensions(), core::grid::CartGrid< core::Real >::setTop(), core::grid::CartGrid< core::Real >::setupZones(), core::grid::CartGrid< core::Real >::write(), and core::grid::CartGrid< core::Real >::write_to_BRIX().
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Referenced by core::grid::CartGrid< core::Real >::clone(), core::grid::CartGrid< core::Real >::deserialize(), core::grid::CartGrid< core::Real >::getMaxValue(), core::grid::CartGrid< core::Real >::getMinValue(), core::grid::CartGrid< core::Real >::getValue(), core::grid::CartGrid< core::Real >::isEmpty(), core::grid::CartGrid< core::Real >::serialize(), core::grid::CartGrid< core::Real >::setFullOccupied(), core::grid::CartGrid< core::Real >::setupZones(), core::grid::CartGrid< core::Real >::setValue(), and core::grid::CartGrid< core::Real >::zero().