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Rosetta
3.8
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#include <VdwGrid.hh>
Public Member Functions | |
VdwGrid () | |
virtual | ~VdwGrid () |
virtual void | refresh (core::pose::Pose const &pose, core::Vector const ¢er, core::Size const &) |
populate the grid with values based on a passed pose More... | |
virtual void | refresh (core::pose::Pose const &pose, core::Vector const ¢er) |
populate the grid with values based on a passed pose More... | |
virtual void | refresh (core::pose::Pose const &pose, core::Vector const ¢er, utility::vector1< core::Size >) |
populate the grid with values based on a passed pose More... | |
void | parse_my_tag (utility::tag::TagCOP tag) |
setup a grid based on RosettaScripts input More... | |
virtual core::Real | score (core::conformation::UltraLightResidue const &residue, core::Real const max_score, qsarMapOP qsar_map) |
return the current score of an UltraLightResidue using the current grid More... | |
virtual core::Real | atom_score (core::conformation::UltraLightResidue const &residue, core::Size atomno, qsarMapOP qsar_map) |
return the current score of an atom using the current grid More... | |
virtual core::Real | score (core::conformation::Residue const &residue, core::Real const max_score, qsarMapOP qsar_map) |
return the current score of a residue using the current grid More... | |
virtual core::Real | atom_score (core::conformation::Residue const &residue, core::Size atomno, qsarMapOP qsar_map) |
return the current score of an atom using the current grid More... | |
virtual utility::json_spirit::Value | serialize () |
serialize the Interpolator to a json_spirit object More... | |
virtual void | deserialize (utility::json_spirit::mObject data) |
deserialize a json_spirit object to a Interpolator More... | |
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SingleGrid (std::string type) | |
virtual | ~SingleGrid () |
virtual void | initialize (core::Vector const ¢er, core::Real width, core::Real resolution) |
initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms). More... | |
virtual void | set_chain (char chain) |
set the chain around which to calculate the grid More... | |
char | get_chain () |
get the chain around which the grid is calculated More... | |
core::grid::CartGrid < core::Real > const & | get_grid () |
return a constant reference to the grid More... | |
void | set_type (std::string type) |
set the grid type More... | |
virtual std::string | get_type () |
return the grids type More... | |
void | set_center (core::Vector center) |
set the center of the grid More... | |
core::Vector | get_center () |
get the center of the grid More... | |
core::Real | get_min_value () const |
get the max score value in the grid More... | |
core::Real | get_max_value () const |
get the minimum score value in the grid More... | |
core::Real | get_point (core::Real x, core::Real y, core::Real z) |
get the value of a single point in the grid based on pdb coordinates More... | |
core::Real | get_point (core::Vector coords) |
get the value of a single point in the grid based on pdb coordinates More... | |
numeric::xyzVector< core::Size > | get_dimensions () |
get dimensions of the grid More... | |
core::Vector | get_pdb_coords (int x, int y, int z) |
get the pdb coordinates based on grid point coordinates More... | |
core::Vector | get_pdb_coords (core::grid::CartGrid< core::Real >::GridPt gridpt) |
get the pdb coordinates based on grid point coordinates More... | |
void | grid_to_kin (utility::io::ozstream &out, core::Real min_val, core::Real max_val, core::Size stride) |
virtual bool | is_in_grid (core::conformation::UltraLightResidue const &residue) |
check to see if residue is in grid More... | |
virtual bool | is_in_grid (core::conformation::Residue const &residue) |
check to see if residue is in grid More... | |
std::list< std::pair < core::Vector, core::Real > > | get_point_value_list_within_range (core::Real lower_bound, core::Real upper_bound, core::Size stride) |
virtual void | dump_BRIX (std::string const &prefix) |
output a BRIX formatted grid. This really does not work well but is being left for legacy purposes More... | |
void | set_sphere (core::Vector const &coords, core::Real radius, core::Real value) |
void | set_ring (core::Vector const &coords, core::Real inner_radius, core::Real outer_radius, core::Real value) |
void | diffuse_ring (core::Vector const &coords, core::Real radius, core::Real width, core::Real magnitude) |
void | set_point (core::Vector const &coords, core::Real value) |
void | set_distance_sphere_for_atom (core::Real const &atom_shell, core::Vector const &coords, core::Real cutoff) |
void | set_score_sphere_for_atom (numeric::interpolation::spline::InterpolatorOP lj_spline, core::Vector const &coords, core::Real cutoff) |
void | fill_with_value (core::Real) |
the entire grid with some value More... | |
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GridBase () | |
virtual | ~GridBase () |
Static Public Member Functions | |
static std::string | grid_name () |
static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
Private Attributes | |
numeric::interpolation::spline::InterpolatorOP | lj_spline_ |
core::Real | cutoff_ |
protocols::qsar::scoring_grid::VdwGrid::VdwGrid | ( | ) |
References lj_spline_.
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return the current score of an atom using the current grid
Reimplemented from protocols::qsar::scoring_grid::SingleGrid.
References protocols::qsar::scoring_grid::SingleGrid::get_grid(), protocols::qsar::scoring_grid::SingleGrid::get_point(), core::grid::CartGrid< T >::is_in_grid(), lj_spline_, and core::conformation::UltraLightResidue::residue().
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return the current score of an atom using the current grid
Reimplemented from protocols::qsar::scoring_grid::SingleGrid.
References core::conformation::Residue::atom_type(), protocols::qsar::scoring_grid::SingleGrid::get_grid(), protocols::qsar::scoring_grid::SingleGrid::get_point(), core::grid::CartGrid< T >::is_in_grid(), core::chemical::AtomType::lj_radius(), lj_spline_, and core::conformation::Residue::xyz().
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deserialize a json_spirit object to a Interpolator
Reimplemented from protocols::qsar::scoring_grid::SingleGrid.
References cutoff_, protocols::qsar::scoring_grid::SingleGrid::deserialize(), and lj_spline_.
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Referenced by protocols::qsar::scoring_grid::VdwGridCreator::keyname(), and provide_xml_schema().
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setup a grid based on RosettaScripts input
Implements protocols::qsar::scoring_grid::SingleGrid.
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populate the grid with values based on a passed pose
Implements protocols::qsar::scoring_grid::SingleGrid.
Referenced by refresh().
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populate the grid with values based on a passed pose
Implements protocols::qsar::scoring_grid::SingleGrid.
References core::conformation::Residue::atom_type(), core::conformation::Residue::chain(), cutoff_, protocols::qsar::scoring_grid::SingleGrid::fill_with_value(), protocols::qsar::scoring_grid::SingleGrid::get_chain(), core::pose::get_chain_id_from_chain(), core::chemical::AtomType::lj_radius(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), core::pose::Pose::size(), protocols::kinmatch::xyz(), and core::pose::Pose::xyz().
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populate the grid with values based on a passed pose
Implements protocols::qsar::scoring_grid::SingleGrid.
References refresh().
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return the current score of an UltraLightResidue using the current grid
Reimplemented from protocols::qsar::scoring_grid::SingleGrid.
References protocols::qsar::scoring_grid::SingleGrid::get_grid(), protocols::qsar::scoring_grid::SingleGrid::get_point(), core::grid::CartGrid< T >::is_in_grid(), lj_spline_, core::conformation::UltraLightResidue::natoms(), and core::conformation::UltraLightResidue::residue().
Referenced by score().
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return the current score of a residue using the current grid
Reimplemented from protocols::qsar::scoring_grid::SingleGrid.
References core::conformation::Residue::atom_type(), protocols::qsar::scoring_grid::SingleGrid::get_grid(), protocols::qsar::scoring_grid::SingleGrid::get_point(), core::grid::CartGrid< T >::is_in_grid(), core::chemical::AtomType::lj_radius(), lj_spline_, core::conformation::Residue::natoms(), score(), and core::conformation::Residue::xyz().
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serialize the Interpolator to a json_spirit object
Reimplemented from protocols::qsar::scoring_grid::SingleGrid.
References cutoff_, lj_spline_, and protocols::qsar::scoring_grid::SingleGrid::serialize().
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Referenced by deserialize(), refresh(), and serialize().
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Referenced by atom_score(), deserialize(), score(), serialize(), and VdwGrid().