scoring_grid

Bindings for protocols::qsar::scoring_grid namespace

class pyrosetta.rosetta.protocols.qsar.scoring_grid.AllAtomNormalization

Bases: ScoreNormalization

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AllAtomNormalization, : pyrosetta.rosetta.protocols.qsar.scoring_grid.AllAtomNormalization) → pyrosetta.rosetta.protocols.qsar.scoring_grid.AllAtomNormalization

C++: protocols::qsar::scoring_grid::AllAtomNormalization::operator=(const class protocols::qsar::scoring_grid::AllAtomNormalization &) –> class protocols::qsar::scoring_grid::AllAtomNormalization &

get_name(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AllAtomNormalization) → str

C++: protocols::qsar::scoring_grid::AllAtomNormalization::get_name() const –> std::string

class pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid

Bases: SingleGrid

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid, : pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid

C++: protocols::qsar::scoring_grid::AtrGrid::operator=(const class protocols::qsar::scoring_grid::AtrGrid &) –> class protocols::qsar::scoring_grid::AtrGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::AtrGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json_spirit object to a SingleGrid

C++: protocols::qsar::scoring_grid::AtrGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

diffuse_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, width: float, magnitude: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, prefix: str) → None

C++: protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(const std::string &) const –> void

fill_with_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, : float) → None

the entire grid with some value

C++: protocols::qsar::scoring_grid::SingleGrid::fill_with_value(double) –> void

get_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

get the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_center() const –> class numeric::xyzVector<double>

get_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

get the chain around which the grid is calculated

C++: protocols::qsar::scoring_grid::SingleGrid::get_chain() –> char

get_dimensions(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t

get dimensions of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_dimensions() –> class numeric::xyzVector<unsigned long>

get_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.core.grid.CartGrid_double_t

return a constant reference to the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_grid() const –> const class core::grid::CartGrid<double> &

get_max_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the minimum score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_max_value() const –> double

get_min_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the max score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_min_value() const –> double

get_pdb_coords(*args, **kwargs)

Overloaded function.

1. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: int, y: int, z: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(int, int, int) –> class numeric::xyzVector<double>

2. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, gridpt: pyrosetta.rosetta.numeric.xyzVector_int_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(class numeric::xyzVector<int>) –> class numeric::xyzVector<double>

get_point(*args, **kwargs)

Overloaded function.

1. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: float, y: float, z: float) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(double, double, double) const –> double

2. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(class numeric::xyzVector<double>) const –> double

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

return the grids type

C++: protocols::qsar::scoring_grid::SingleGrid::get_type() const –> std::string

static grid_name() → str

C++: protocols::qsar::scoring_grid::AtrGrid::grid_name() –> std::string

grid_to_kin(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.utility.io.ozstream, min_val: float, max_val: float, stride: int) → None

C++: protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(class utility::io::ozstream &, double, double, unsigned long) –> void

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid) → str

C++: protocols::qsar::scoring_grid::AtrGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::SingleGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

C++: protocols::qsar::scoring_grid::AtrGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::AtrGrid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_id_to_exclude: int) -> None

C++: protocols::qsar::scoring_grid::AtrGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::qsar::scoring_grid::AtrGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_ids_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::qsar::scoring_grid::AtrGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of a residue using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize the SingleGrid to a json_spirit object

C++: protocols::qsar::scoring_grid::AtrGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

set the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_center(class numeric::xyzVector<double>) –> void

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, chain: str) → None

set the chain around which to calculate the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_chain(char) –> void

set_distance_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, atom_shell: float, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(const double &, const class numeric::xyzVector<double> &, double) –> void

set_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_point(const class numeric::xyzVector<double> &, double) –> void

set_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, inner_radius: float, outer_radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

set_score_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, lj_spline: pyrosetta.rosetta.numeric.interpolation.spline.Interpolator, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(class std::shared_ptr<const class numeric::interpolation::spline::Interpolator>, const class numeric::xyzVector<double> &, double) –> void

set_sphere(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_sphere(const class numeric::xyzVector<double> &, double, double) –> void

set_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, type: str) → None

set the grid type

C++: protocols::qsar::scoring_grid::SingleGrid::set_type(std::string) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::SingleGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGridCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGridCreator

C++: protocols::qsar::scoring_grid::AtrGridCreator::operator=(const class protocols::qsar::scoring_grid::AtrGridCreator &) –> class protocols::qsar::scoring_grid::AtrGridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::AtrGridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::AtrGridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGridCreator) → str

C++: protocols::qsar::scoring_grid::AtrGridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::AtrGridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom

Bases: pybind11_object

a very light representation of an atom that is just a charge and a cartesian space position

property charge

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

C++: protocols::qsar::scoring_grid::ChargeAtom::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

property neighbor_count

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

C++: protocols::qsar::scoring_grid::ChargeAtom::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

property xyz

class pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid

Bases: SingleGrid

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid, : pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid

C++: protocols::qsar::scoring_grid::ChargeGrid::operator=(const class protocols::qsar::scoring_grid::ChargeGrid &) –> class protocols::qsar::scoring_grid::ChargeGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::ChargeGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::ChargeGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::ChargeGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json_spirit object to a SingleGrid

C++: protocols::qsar::scoring_grid::ChargeGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

diffuse_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, width: float, magnitude: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, prefix: str) → None

C++: protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(const std::string &) const –> void

fill_with_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, : float) → None

the entire grid with some value

C++: protocols::qsar::scoring_grid::SingleGrid::fill_with_value(double) –> void

get_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

get the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_center() const –> class numeric::xyzVector<double>

get_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

get the chain around which the grid is calculated

C++: protocols::qsar::scoring_grid::SingleGrid::get_chain() –> char

get_dimensions(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t

get dimensions of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_dimensions() –> class numeric::xyzVector<unsigned long>

get_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.core.grid.CartGrid_double_t

return a constant reference to the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_grid() const –> const class core::grid::CartGrid<double> &

get_max_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the minimum score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_max_value() const –> double

get_min_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the max score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_min_value() const –> double

get_pdb_coords(*args, **kwargs)

Overloaded function.

1. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: int, y: int, z: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(int, int, int) –> class numeric::xyzVector<double>

2. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, gridpt: pyrosetta.rosetta.numeric.xyzVector_int_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(class numeric::xyzVector<int>) –> class numeric::xyzVector<double>

get_point(*args, **kwargs)

Overloaded function.

1. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: float, y: float, z: float) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(double, double, double) const –> double

2. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(class numeric::xyzVector<double>) const –> double

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

return the grids type

C++: protocols::qsar::scoring_grid::SingleGrid::get_type() const –> std::string

static grid_name() → str

C++: protocols::qsar::scoring_grid::ChargeGrid::grid_name() –> std::string

grid_to_kin(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.utility.io.ozstream, min_val: float, max_val: float, stride: int) → None

C++: protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(class utility::io::ozstream &, double, double, unsigned long) –> void

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid) → str

C++: protocols::qsar::scoring_grid::ChargeGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::SingleGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

C++: protocols::qsar::scoring_grid::ChargeGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::ChargeGrid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_id_to_exclude: int) -> None

C++: protocols::qsar::scoring_grid::ChargeGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::qsar::scoring_grid::ChargeGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_ids_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::qsar::scoring_grid::ChargeGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::ChargeGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

C++: protocols::qsar::scoring_grid::ChargeGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize the SingleGrid to a json_spirit object

C++: protocols::qsar::scoring_grid::ChargeGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

set the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_center(class numeric::xyzVector<double>) –> void

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, chain: str) → None

set the chain around which to calculate the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_chain(char) –> void

set_distance_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, atom_shell: float, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(const double &, const class numeric::xyzVector<double> &, double) –> void

set_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_point(const class numeric::xyzVector<double> &, double) –> void

set_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, inner_radius: float, outer_radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

set_score_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, lj_spline: pyrosetta.rosetta.numeric.interpolation.spline.Interpolator, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(class std::shared_ptr<const class numeric::interpolation::spline::Interpolator>, const class numeric::xyzVector<double> &, double) –> void

set_sphere(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_sphere(const class numeric::xyzVector<double> &, double, double) –> void

set_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, type: str) → None

set the grid type

C++: protocols::qsar::scoring_grid::SingleGrid::set_type(std::string) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::SingleGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGridCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGridCreator

C++: protocols::qsar::scoring_grid::ChargeGridCreator::operator=(const class protocols::qsar::scoring_grid::ChargeGridCreator &) –> class protocols::qsar::scoring_grid::ChargeGridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::ChargeGridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::ChargeGridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGridCreator) → str

C++: protocols::qsar::scoring_grid::ChargeGridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::ChargeGridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.ChiAngleNormalization

Bases: ScoreNormalization

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChiAngleNormalization, : pyrosetta.rosetta.protocols.qsar.scoring_grid.ChiAngleNormalization) → pyrosetta.rosetta.protocols.qsar.scoring_grid.ChiAngleNormalization

C++: protocols::qsar::scoring_grid::ChiAngleNormalization::operator=(const class protocols::qsar::scoring_grid::ChiAngleNormalization &) –> class protocols::qsar::scoring_grid::ChiAngleNormalization &

get_name(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ChiAngleNormalization) → str

C++: protocols::qsar::scoring_grid::ChiAngleNormalization::get_name() const –> std::string

class pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid

Bases: SingleGrid

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid, : pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid

C++: protocols::qsar::scoring_grid::ClassicGrid::operator=(const class protocols::qsar::scoring_grid::ClassicGrid &) –> class protocols::qsar::scoring_grid::ClassicGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::ClassicGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json_spirit object to a SingleGrid

C++: protocols::qsar::scoring_grid::ClassicGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

diffuse_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, width: float, magnitude: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, prefix: str) → None

C++: protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(const std::string &) const –> void

fill_with_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, : float) → None

the entire grid with some value

C++: protocols::qsar::scoring_grid::SingleGrid::fill_with_value(double) –> void

get_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

get the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_center() const –> class numeric::xyzVector<double>

get_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

get the chain around which the grid is calculated

C++: protocols::qsar::scoring_grid::SingleGrid::get_chain() –> char

get_dimensions(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t

get dimensions of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_dimensions() –> class numeric::xyzVector<unsigned long>

get_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.core.grid.CartGrid_double_t

return a constant reference to the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_grid() const –> const class core::grid::CartGrid<double> &

get_max_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the minimum score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_max_value() const –> double

get_min_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the max score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_min_value() const –> double

get_pdb_coords(*args, **kwargs)

Overloaded function.

1. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: int, y: int, z: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(int, int, int) –> class numeric::xyzVector<double>

2. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, gridpt: pyrosetta.rosetta.numeric.xyzVector_int_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(class numeric::xyzVector<int>) –> class numeric::xyzVector<double>

get_point(*args, **kwargs)

Overloaded function.

1. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: float, y: float, z: float) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(double, double, double) const –> double

2. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(class numeric::xyzVector<double>) const –> double

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

return the grids type

C++: protocols::qsar::scoring_grid::SingleGrid::get_type() const –> std::string

static grid_name() → str

C++: protocols::qsar::scoring_grid::ClassicGrid::grid_name() –> std::string

grid_to_kin(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.utility.io.ozstream, min_val: float, max_val: float, stride: int) → None

C++: protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(class utility::io::ozstream &, double, double, unsigned long) –> void

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid) → str

C++: protocols::qsar::scoring_grid::ClassicGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::SingleGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

C++: protocols::qsar::scoring_grid::ClassicGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::ClassicGrid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_id_to_exclude: int) -> None

C++: protocols::qsar::scoring_grid::ClassicGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::qsar::scoring_grid::ClassicGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_ids_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::qsar::scoring_grid::ClassicGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of a residue using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize the SingleGrid to a json_spirit object

C++: protocols::qsar::scoring_grid::ClassicGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

set the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_center(class numeric::xyzVector<double>) –> void

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, chain: str) → None

set the chain around which to calculate the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_chain(char) –> void

set_distance_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, atom_shell: float, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(const double &, const class numeric::xyzVector<double> &, double) –> void

set_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_point(const class numeric::xyzVector<double> &, double) –> void

set_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, inner_radius: float, outer_radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

set_score_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, lj_spline: pyrosetta.rosetta.numeric.interpolation.spline.Interpolator, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(class std::shared_ptr<const class numeric::interpolation::spline::Interpolator>, const class numeric::xyzVector<double> &, double) –> void

set_sphere(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_sphere(const class numeric::xyzVector<double> &, double, double) –> void

set_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, type: str) → None

set the grid type

C++: protocols::qsar::scoring_grid::SingleGrid::set_type(std::string) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::SingleGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGridCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGridCreator

C++: protocols::qsar::scoring_grid::ClassicGridCreator::operator=(const class protocols::qsar::scoring_grid::ClassicGridCreator &) –> class protocols::qsar::scoring_grid::ClassicGridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::ClassicGridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::ClassicGridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGridCreator) → str

C++: protocols::qsar::scoring_grid::ClassicGridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::ClassicGridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase

Bases: GridBase

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase) → pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase

C++: protocols::qsar::scoring_grid::ConstantScoreBase::operator=(const class protocols::qsar::scoring_grid::ConstantScoreBase &) –> class protocols::qsar::scoring_grid::ConstantScoreBase &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.core.conformation.UltraLightResidue, : int, : pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::ConstantScoreBase::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.core.conformation.Residue, : int, : pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::ConstantScoreBase::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::ConstantScoreBase::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json spirit Value into a GridBase object

C++: protocols::qsar::scoring_grid::ConstantScoreBase::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : str) → None

output a BRIX formatted grid. This really does not work well but is being left for legacy purposes

C++: protocols::qsar::scoring_grid::ConstantScoreBase::dump_BRIX(const std::string &) const –> void

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase) → str

get the type of the grid

C++: protocols::qsar::scoring_grid::ConstantScoreBase::get_type() const –> std::string

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase) → str

Return a string representing the settings which don’t change based on reinitialization

C++: protocols::qsar::scoring_grid::GridBase::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.numeric.xyzVector_double_t, : float, : float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::ConstantScoreBase::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

determine if all residue atoms are in a grid

C++: protocols::qsar::scoring_grid::ConstantScoreBase::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.core.conformation.Residue) -> bool

determine if all residue atoms are in a grid

C++: protocols::qsar::scoring_grid::ConstantScoreBase::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, tag: pyrosetta.rosetta.utility.tag.Tag) → None

a grid based on RosettaScripts input

C++: protocols::qsar::scoring_grid::ConstantScoreBase::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.numeric.xyzVector_double_t, : int) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::ConstantScoreBase::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::ConstantScoreBase::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::ConstantScoreBase::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::ConstantScoreBase::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of a residue using the current grid

C++: protocols::qsar::scoring_grid::ConstantScoreBase::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

Serialize the GridBase object into a json_spirit Value

C++: protocols::qsar::scoring_grid::ConstantScoreBase::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : str) → None

set the chain the grid applies to

C++: protocols::qsar::scoring_grid::ConstantScoreBase::set_chain(char) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::ConstantScoreBase::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, : pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::GridBase::operator=(const class protocols::qsar::scoring_grid::GridBase &) –> class protocols::qsar::scoring_grid::GridBase &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::GridBase::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::GridBase::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

Note that due to the heavy use of modification to reset positions you need to be sure to do deep copying on anything that can be changed with refresh/initialize.

C++: protocols::qsar::scoring_grid::GridBase::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json spirit Value into a GridBase object

C++: protocols::qsar::scoring_grid::GridBase::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, prefix: str) → None

output a BRIX formatted grid. This really does not work well but is being left for legacy purposes

C++: protocols::qsar::scoring_grid::GridBase::dump_BRIX(const std::string &) const –> void

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase) → str

get the type of the grid

C++: protocols::qsar::scoring_grid::GridBase::get_type() const –> std::string

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase) → str

Return a string representing the settings which don’t change based on reinitialization

C++: protocols::qsar::scoring_grid::GridBase::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::GridBase::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

determine if all residue atoms are in a grid

C++: protocols::qsar::scoring_grid::GridBase::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

determine if all residue atoms are in a grid

C++: protocols::qsar::scoring_grid::GridBase::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, tag: pyrosetta.rosetta.utility.tag.Tag) → None

a grid based on RosettaScripts input

C++: protocols::qsar::scoring_grid::GridBase::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_id_to_exclude: int) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::GridBase::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_ids_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::GridBase::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::GridBase::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current scoer of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::GridBase::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of a residue using the current grid

C++: protocols::qsar::scoring_grid::GridBase::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

Serialize the GridBase object into a json_spirit Value

C++: protocols::qsar::scoring_grid::GridBase::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, chain: str) → None

set the chain the grid applies to

C++: protocols::qsar::scoring_grid::GridBase::set_chain(char) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::GridBase::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator

Bases: pybind11_object

Abstract class fora mover factory. The creator class is responsible for creating a particular mover class

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator

C++: protocols::qsar::scoring_grid::GridCreator::operator=(const class protocols::qsar::scoring_grid::GridCreator &) –> class protocols::qsar::scoring_grid::GridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::GridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::GridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator) → str

C++: protocols::qsar::scoring_grid::GridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::GridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.GridFactory

Bases: SingletonBase_protocols_qsar_scoring_grid_GridFactory_t

factory_register(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridFactory, creator: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator) → None

C++: protocols::qsar::scoring_grid::GridFactory::factory_register(class std::shared_ptr<class protocols::qsar::scoring_grid::GridCreator>) –> void

static get_instance() → protocols::qsar::scoring_grid::GridFactory

C++: utility::SingletonBase<protocols::qsar::scoring_grid::GridFactory>::get_instance() –> class protocols::qsar::scoring_grid::GridFactory *

new_grid(*args, **kwargs)

Overloaded function.

1. new_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridFactory, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

create Grid given grid tag

C++: protocols::qsar::scoring_grid::GridFactory::new_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. new_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridFactory, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

create Grid given a serialized grid object

C++: protocols::qsar::scoring_grid::GridFactory::new_grid(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridFactory, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::GridFactory::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

static scoring_grid_xml_schema_group_name() → str

C++: protocols::qsar::scoring_grid::GridFactory::scoring_grid_xml_schema_group_name() –> std::string

class pyrosetta.rosetta.protocols.qsar.scoring_grid.GridManager

Bases: SingletonBase_protocols_qsar_scoring_grid_GridManager_t

get_grids(*args, **kwargs)

Overloaded function.

1. get_grids(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridManager, prototype: protocols::qsar::scoring_grid::GridSet, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, chain: str) -> protocols::qsar::scoring_grid::GridSet

2. get_grids(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridManager, prototype: protocols::qsar::scoring_grid::GridSet, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, chain: str, exclude: bool) -> protocols::qsar::scoring_grid::GridSet

3. get_grids(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridManager, prototype: protocols::qsar::scoring_grid::GridSet, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, chain: str, exclude: bool, fuzz_factor: float) -> protocols::qsar::scoring_grid::GridSet

Get a set of grids for the given pose, centered on the given center, including/excluding the given chains.

C++: protocols::qsar::scoring_grid::GridManager::get_grids(const class protocols::qsar::scoring_grid::GridSet &, const class core::pose::Pose &, const class numeric::xyzVector<double> &, const std::string &, bool, double) –> class std::shared_ptr<const class protocols::qsar::scoring_grid::GridSet>

4. get_grids(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridManager, prototype: protocols::qsar::scoring_grid::GridSet, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, chain: str) -> protocols::qsar::scoring_grid::GridSet

5. get_grids(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridManager, prototype: protocols::qsar::scoring_grid::GridSet, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, chain: str, exclude: bool) -> protocols::qsar::scoring_grid::GridSet

6. get_grids(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridManager, prototype: protocols::qsar::scoring_grid::GridSet, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, chain: str, exclude: bool, fuzz_factor: float) -> protocols::qsar::scoring_grid::GridSet

Get a set of grids for the given pose, centered on the given center, including/excluding the given chains.

C++: protocols::qsar::scoring_grid::GridManager::get_grids(const class protocols::qsar::scoring_grid::GridSet &, const class core::pose::Pose &, const class numeric::xyzVector<double> &, char, bool, double) –> class std::shared_ptr<const class protocols::qsar::scoring_grid::GridSet>

7. get_grids(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridManager, prototype: protocols::qsar::scoring_grid::GridSet, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, chains: pyrosetta.rosetta.utility.vector1_std_string) -> protocols::qsar::scoring_grid::GridSet

8. get_grids(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridManager, prototype: protocols::qsar::scoring_grid::GridSet, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, chains: pyrosetta.rosetta.utility.vector1_std_string, exclude: bool) -> protocols::qsar::scoring_grid::GridSet

9. get_grids(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridManager, prototype: protocols::qsar::scoring_grid::GridSet, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, chains: pyrosetta.rosetta.utility.vector1_std_string, exclude: bool, fuzz_factor: float) -> protocols::qsar::scoring_grid::GridSet

Get a set of grids for the given pose, centered on the given center, including/excluding the given chains,

using the given prototype as the prototype. fuzz_factor is the distance by which to consider the center “close enough” not to regenerate

C++: protocols::qsar::scoring_grid::GridManager::get_grids(const class protocols::qsar::scoring_grid::GridSet &, const class core::pose::Pose &, const class numeric::xyzVector<double> &, const class utility::vector1<std::string, class std::allocator<std::string > > &, bool, double) –> class std::shared_ptr<const class protocols::qsar::scoring_grid::GridSet>

static get_instance() → protocols::qsar::scoring_grid::GridManager

C++: utility::SingletonBase<protocols::qsar::scoring_grid::GridManager>::get_instance() –> class protocols::qsar::scoring_grid::GridManager *

class pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet

Bases: pybind11_object

A set of related grids

add_grid(*args, **kwargs)

Overloaded function.

1. add_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, name: str, grid: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase) -> None

2. add_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, name: str, grid: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase, weight: float) -> None

Add a grid to the GridSet under the given name.

C++: protocols::qsar::scoring_grid::GridSet::add_grid(const std::string &, class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>, double) –> void

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, : pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet

C++: protocols::qsar::scoring_grid::GridSet::operator=(const class protocols::qsar::scoring_grid::GridSet &) –> class protocols::qsar::scoring_grid::GridSet &

atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, pose: pyrosetta.rosetta.core.pose.Pose, residue: pyrosetta.rosetta.core.conformation.Residue, atomindex: int) → pyrosetta.rosetta.std.map_std_string_double

get a map of (unweighted, unnormalized) scoring terms and scores for each term given a residue and atom number

C++: protocols::qsar::scoring_grid::GridSet::atom_score(const class core::pose::Pose &, const class core::conformation::Residue &, unsigned long) const –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

average_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, residues: pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue) → float

return the average score of multiple residues on the grid

C++: protocols::qsar::scoring_grid::GridSet::average_score(class utility::vector1<class core::conformation::UltraLightResidue, class std::allocator<class core::conformation::UltraLightResidue> > &) const –> double

chain(*args, **kwargs)

Overloaded function.

1. chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, chain: str) -> None

set ligand chain (must be done before initialization)

C++: protocols::qsar::scoring_grid::GridSet::chain(char) –> void

2. chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet) -> str

get ligand chain

C++: protocols::qsar::scoring_grid::GridSet::chain() const –> char

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet

C++: protocols::qsar::scoring_grid::GridSet::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridSet>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, data: pyrosetta.rosetta.std.vector_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize the JSON object to a map.

C++: protocols::qsar::scoring_grid::GridSet::deserialize(class std::vector<class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, class std::allocator<class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > >) –> void

get_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, name: str) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::GridSet::get_grid(const std::string &) const –> class std::shared_ptr<const class protocols::qsar::scoring_grid::GridBase>

get_grid_names(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet) → pyrosetta.rosetta.utility.vector1_std_string

get a list of grid names

C++: protocols::qsar::scoring_grid::GridSet::get_grid_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

grid_scores(*args, **kwargs)

Overloaded function.

1. grid_scores(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, residue: pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.std.map_std_string_double

C++: protocols::qsar::scoring_grid::GridSet::grid_scores(const class core::conformation::Residue &) const –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

2. grid_scores(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.std.map_std_string_double

C++: protocols::qsar::scoring_grid::GridSet::grid_scores(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

has_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, name: str) → bool

Returns true if we already have a grid with the given name.

C++: protocols::qsar::scoring_grid::GridSet::has_grid(const std::string &) const –> bool

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet) → str

Return a string representing the settings of this GridSet

This should encapsulate everything that doesn’t change with a call to reinitialize() The string is not meant to be interpretable.

C++: protocols::qsar::scoring_grid::GridSet::hash_fingerprint() const –> std::string

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, residues: pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue) -> bool

check if all atoms in all the ligands are in grid

C++: protocols::qsar::scoring_grid::GridSet::is_in_grid(const class utility::vector1<class core::conformation::UltraLightResidue, class std::allocator<class core::conformation::UltraLightResidue> > &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

check to see if all atoms in the ligand are in the grid

C++: protocols::qsar::scoring_grid::GridSet::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

3. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

check to see if all atoms in the ligand are in the grid

C++: protocols::qsar::scoring_grid::GridSet::is_in_grid(const class core::conformation::Residue &) const –> bool

is_normalization_enabled(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet) → bool

is normalization applied during scoring?

C++: protocols::qsar::scoring_grid::GridSet::is_normalization_enabled() const –> bool

is_qsar_map_attached(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet) → bool

is a qsar map attached to the grid manager?

C++: protocols::qsar::scoring_grid::GridSet::is_qsar_map_attached() const –> bool

make_new_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, tag: pyrosetta.rosetta.utility.tag.Tag) → None

make a new grid from grid tag, and insert it into the grid manager

C++: protocols::qsar::scoring_grid::GridSet::make_new_grid(class std::shared_ptr<const class utility::tag::Tag>) –> void

reinitialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Reinitialize the included grids with the given information

C++: protocols::qsar::scoring_grid::GridSet::reinitialize(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

resolution(*args, **kwargs)

Overloaded function.

1. resolution(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, resolution: float) -> None

set resolution (must be done before initialization)

C++: protocols::qsar::scoring_grid::GridSet::resolution(double) –> void

2. resolution(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet) -> float

get grid resoultion

C++: protocols::qsar::scoring_grid::GridSet::resolution() const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize the current map to a JSON object.

C++: protocols::qsar::scoring_grid::GridSet::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_normalization_function(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, norm_function_name: str) → None

set normalization function

C++: protocols::qsar::scoring_grid::GridSet::set_normalization_function(std::string) –> void

set_qsar_map(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) → None

set the qsar_map

C++: protocols::qsar::scoring_grid::GridSet::set_qsar_map(class std::shared_ptr<const class protocols::qsar::qsarMap>) –> void

size(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet) → int

return the number of grids

C++: protocols::qsar::scoring_grid::GridSet::size() const –> unsigned long

total_score(*args, **kwargs)

Overloaded function.

1. total_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> float

return the total score of a residue on the grid

C++: protocols::qsar::scoring_grid::GridSet::total_score(const class core::conformation::UltraLightResidue &) const –> double

2. total_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, residue: pyrosetta.rosetta.core.conformation.Residue) -> float

return the total score of a residue on the grid

C++: protocols::qsar::scoring_grid::GridSet::total_score(const class core::conformation::Residue &) const –> double

3. total_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, pose: pyrosetta.rosetta.core.pose.Pose, chain_id: int) -> float

return the total score of a chain on the grid

C++: protocols::qsar::scoring_grid::GridSet::total_score(const class core::pose::Pose &, const unsigned long) const –> double

4. total_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> float

return the total score for a set of residues on the grid

C++: protocols::qsar::scoring_grid::GridSet::total_score(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> double

width(*args, **kwargs)

Overloaded function.

1. width(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, width: float) -> None

set width (must be done before initialization)

C++: protocols::qsar::scoring_grid::GridSet::width(double) –> void

2. width(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet) -> float

get grid width

C++: protocols::qsar::scoring_grid::GridSet::width() const –> double

write_grids(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet, prefix: str) → None

write all grids out using the BRIX format

C++: protocols::qsar::scoring_grid::GridSet::write_grids(std::string) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid

Bases: SingleGrid

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid, : pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid

C++: protocols::qsar::scoring_grid::HbaGrid::operator=(const class protocols::qsar::scoring_grid::HbaGrid &) –> class protocols::qsar::scoring_grid::HbaGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::HbaGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::HbaGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::HbaGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json_spirit object to a SingleGrid

C++: protocols::qsar::scoring_grid::HbaGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

diffuse_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, width: float, magnitude: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, prefix: str) → None

C++: protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(const std::string &) const –> void

fill_with_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, : float) → None

the entire grid with some value

C++: protocols::qsar::scoring_grid::SingleGrid::fill_with_value(double) –> void

get_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

get the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_center() const –> class numeric::xyzVector<double>

get_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

get the chain around which the grid is calculated

C++: protocols::qsar::scoring_grid::SingleGrid::get_chain() –> char

get_dimensions(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t

get dimensions of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_dimensions() –> class numeric::xyzVector<unsigned long>

get_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.core.grid.CartGrid_double_t

return a constant reference to the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_grid() const –> const class core::grid::CartGrid<double> &

get_max_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the minimum score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_max_value() const –> double

get_min_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the max score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_min_value() const –> double

get_pdb_coords(*args, **kwargs)

Overloaded function.

1. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: int, y: int, z: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(int, int, int) –> class numeric::xyzVector<double>

2. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, gridpt: pyrosetta.rosetta.numeric.xyzVector_int_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(class numeric::xyzVector<int>) –> class numeric::xyzVector<double>

get_point(*args, **kwargs)

Overloaded function.

1. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: float, y: float, z: float) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(double, double, double) const –> double

2. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(class numeric::xyzVector<double>) const –> double

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

return the grids type

C++: protocols::qsar::scoring_grid::SingleGrid::get_type() const –> std::string

static grid_name() → str

C++: protocols::qsar::scoring_grid::HbaGrid::grid_name() –> std::string

grid_to_kin(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.utility.io.ozstream, min_val: float, max_val: float, stride: int) → None

C++: protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(class utility::io::ozstream &, double, double, unsigned long) –> void

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid) → str

C++: protocols::qsar::scoring_grid::HbaGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::SingleGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

C++: protocols::qsar::scoring_grid::HbaGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::HbaGrid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_id_to_exclude: int) -> None

C++: protocols::qsar::scoring_grid::HbaGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::qsar::scoring_grid::HbaGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_ids_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::qsar::scoring_grid::HbaGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::HbaGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

C++: protocols::qsar::scoring_grid::HbaGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize the SingleGrid to a json_spirit object

C++: protocols::qsar::scoring_grid::HbaGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

set the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_center(class numeric::xyzVector<double>) –> void

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, chain: str) → None

set the chain around which to calculate the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_chain(char) –> void

set_distance_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, atom_shell: float, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(const double &, const class numeric::xyzVector<double> &, double) –> void

set_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_point(const class numeric::xyzVector<double> &, double) –> void

set_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, inner_radius: float, outer_radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

set_score_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, lj_spline: pyrosetta.rosetta.numeric.interpolation.spline.Interpolator, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(class std::shared_ptr<const class numeric::interpolation::spline::Interpolator>, const class numeric::xyzVector<double> &, double) –> void

set_sphere(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_sphere(const class numeric::xyzVector<double> &, double, double) –> void

set_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, type: str) → None

set the grid type

C++: protocols::qsar::scoring_grid::SingleGrid::set_type(std::string) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::SingleGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGridCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGridCreator

C++: protocols::qsar::scoring_grid::HbaGridCreator::operator=(const class protocols::qsar::scoring_grid::HbaGridCreator &) –> class protocols::qsar::scoring_grid::HbaGridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::HbaGridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::HbaGridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGridCreator) → str

C++: protocols::qsar::scoring_grid::HbaGridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::HbaGridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid

Bases: SingleGrid

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid, : pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid

C++: protocols::qsar::scoring_grid::HbdGrid::operator=(const class protocols::qsar::scoring_grid::HbdGrid &) –> class protocols::qsar::scoring_grid::HbdGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::HbdGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::HbdGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::HbdGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json_spirit object to a SingleGrid

C++: protocols::qsar::scoring_grid::HbdGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

diffuse_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, width: float, magnitude: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, prefix: str) → None

C++: protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(const std::string &) const –> void

fill_with_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, : float) → None

the entire grid with some value

C++: protocols::qsar::scoring_grid::SingleGrid::fill_with_value(double) –> void

get_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

get the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_center() const –> class numeric::xyzVector<double>

get_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

get the chain around which the grid is calculated

C++: protocols::qsar::scoring_grid::SingleGrid::get_chain() –> char

get_dimensions(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t

get dimensions of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_dimensions() –> class numeric::xyzVector<unsigned long>

get_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.core.grid.CartGrid_double_t

return a constant reference to the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_grid() const –> const class core::grid::CartGrid<double> &

get_max_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the minimum score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_max_value() const –> double

get_min_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the max score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_min_value() const –> double

get_pdb_coords(*args, **kwargs)

Overloaded function.

1. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: int, y: int, z: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(int, int, int) –> class numeric::xyzVector<double>

2. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, gridpt: pyrosetta.rosetta.numeric.xyzVector_int_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(class numeric::xyzVector<int>) –> class numeric::xyzVector<double>

get_point(*args, **kwargs)

Overloaded function.

1. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: float, y: float, z: float) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(double, double, double) const –> double

2. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(class numeric::xyzVector<double>) const –> double

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

return the grids type

C++: protocols::qsar::scoring_grid::SingleGrid::get_type() const –> std::string

static grid_name() → str

C++: protocols::qsar::scoring_grid::HbdGrid::grid_name() –> std::string

grid_to_kin(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.utility.io.ozstream, min_val: float, max_val: float, stride: int) → None

C++: protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(class utility::io::ozstream &, double, double, unsigned long) –> void

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid) → str

C++: protocols::qsar::scoring_grid::HbdGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::SingleGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

C++: protocols::qsar::scoring_grid::HbdGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::HbdGrid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_id_to_exclude: int) -> None

C++: protocols::qsar::scoring_grid::HbdGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::qsar::scoring_grid::HbdGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_ids_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::qsar::scoring_grid::HbdGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::HbdGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

C++: protocols::qsar::scoring_grid::HbdGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize the SingleGrid to a json_spirit object

C++: protocols::qsar::scoring_grid::HbdGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

set the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_center(class numeric::xyzVector<double>) –> void

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, chain: str) → None

set the chain around which to calculate the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_chain(char) –> void

set_distance_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, atom_shell: float, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(const double &, const class numeric::xyzVector<double> &, double) –> void

set_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_point(const class numeric::xyzVector<double> &, double) –> void

set_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, inner_radius: float, outer_radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

set_score_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, lj_spline: pyrosetta.rosetta.numeric.interpolation.spline.Interpolator, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(class std::shared_ptr<const class numeric::interpolation::spline::Interpolator>, const class numeric::xyzVector<double> &, double) –> void

set_sphere(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_sphere(const class numeric::xyzVector<double> &, double, double) –> void

set_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, type: str) → None

set the grid type

C++: protocols::qsar::scoring_grid::SingleGrid::set_type(std::string) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::SingleGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGridCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGridCreator

C++: protocols::qsar::scoring_grid::HbdGridCreator::operator=(const class protocols::qsar::scoring_grid::HbdGridCreator &) –> class protocols::qsar::scoring_grid::HbdGridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::HbdGridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::HbdGridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGridCreator) → str

C++: protocols::qsar::scoring_grid::HbdGridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::HbdGridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.HeavyAtomNormalization

Bases: ScoreNormalization

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HeavyAtomNormalization, : pyrosetta.rosetta.protocols.qsar.scoring_grid.HeavyAtomNormalization) → pyrosetta.rosetta.protocols.qsar.scoring_grid.HeavyAtomNormalization

C++: protocols::qsar::scoring_grid::HeavyAtomNormalization::operator=(const class protocols::qsar::scoring_grid::HeavyAtomNormalization &) –> class protocols::qsar::scoring_grid::HeavyAtomNormalization &

get_name(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.HeavyAtomNormalization) → str

C++: protocols::qsar::scoring_grid::HeavyAtomNormalization::get_name() const –> std::string

class pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore

Bases: ConstantScoreBase

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore, : pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore) → pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore

C++: protocols::qsar::scoring_grid::LigandPropertyScore::operator=(const class protocols::qsar::scoring_grid::LigandPropertyScore &) –> class protocols::qsar::scoring_grid::LigandPropertyScore &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.core.conformation.UltraLightResidue, : int, : pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::ConstantScoreBase::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.core.conformation.Residue, : int, : pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::ConstantScoreBase::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::LigandPropertyScore::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json spirit Value into a GridBase object

C++: protocols::qsar::scoring_grid::LigandPropertyScore::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : str) → None

output a BRIX formatted grid. This really does not work well but is being left for legacy purposes

C++: protocols::qsar::scoring_grid::ConstantScoreBase::dump_BRIX(const std::string &) const –> void

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore) → str

get the type of the grid

C++: protocols::qsar::scoring_grid::LigandPropertyScore::get_type() const –> std::string

static grid_name() → str

C++: protocols::qsar::scoring_grid::LigandPropertyScore::grid_name() –> std::string

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore) → str

C++: protocols::qsar::scoring_grid::LigandPropertyScore::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.numeric.xyzVector_double_t, : float, : float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::ConstantScoreBase::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

determine if all residue atoms are in a grid

C++: protocols::qsar::scoring_grid::ConstantScoreBase::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.core.conformation.Residue) -> bool

determine if all residue atoms are in a grid

C++: protocols::qsar::scoring_grid::ConstantScoreBase::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore, tag: pyrosetta.rosetta.utility.tag.Tag) → None

C++: protocols::qsar::scoring_grid::LigandPropertyScore::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::LigandPropertyScore::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.numeric.xyzVector_double_t, : int) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::ConstantScoreBase::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::ConstantScoreBase::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::ConstantScoreBase::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::LigandPropertyScore::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of a residue using the current grid

C++: protocols::qsar::scoring_grid::LigandPropertyScore::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

Serialize the GridBase object into a json_spirit Value

C++: protocols::qsar::scoring_grid::LigandPropertyScore::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase, : str) → None

set the chain the grid applies to

C++: protocols::qsar::scoring_grid::ConstantScoreBase::set_chain(char) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::LigandPropertyScore::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScoreCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScoreCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScoreCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScoreCreator

C++: protocols::qsar::scoring_grid::LigandPropertyScoreCreator::operator=(const class protocols::qsar::scoring_grid::LigandPropertyScoreCreator &) –> class protocols::qsar::scoring_grid::LigandPropertyScoreCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScoreCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::LigandPropertyScoreCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScoreCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::LigandPropertyScoreCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScoreCreator) → str

C++: protocols::qsar::scoring_grid::LigandPropertyScoreCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScoreCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::LigandPropertyScoreCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid

Bases: SingleGrid

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid, : pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid

C++: protocols::qsar::scoring_grid::LipidMemGrid::operator=(const class protocols::qsar::scoring_grid::LipidMemGrid &) –> class protocols::qsar::scoring_grid::LipidMemGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the LipidMemGrid

C++: protocols::qsar::scoring_grid::LipidMemGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the LipidMemGrid

C++: protocols::qsar::scoring_grid::LipidMemGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::LipidMemGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json spirit Value into a LipidMemGrid object

C++: protocols::qsar::scoring_grid::LipidMemGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

diffuse_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, width: float, magnitude: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, prefix: str) → None

C++: protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(const std::string &) const –> void

fill_with_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, : float) → None

the entire grid with some value

C++: protocols::qsar::scoring_grid::SingleGrid::fill_with_value(double) –> void

get_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

get the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_center() const –> class numeric::xyzVector<double>

get_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

get the chain around which the grid is calculated

C++: protocols::qsar::scoring_grid::SingleGrid::get_chain() –> char

get_dimensions(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t

get dimensions of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_dimensions() –> class numeric::xyzVector<unsigned long>

get_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.core.grid.CartGrid_double_t

return a constant reference to the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_grid() const –> const class core::grid::CartGrid<double> &

get_max_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the minimum score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_max_value() const –> double

get_min_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the max score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_min_value() const –> double

get_pdb_coords(*args, **kwargs)

Overloaded function.

1. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: int, y: int, z: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(int, int, int) –> class numeric::xyzVector<double>

2. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, gridpt: pyrosetta.rosetta.numeric.xyzVector_int_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(class numeric::xyzVector<int>) –> class numeric::xyzVector<double>

get_point(*args, **kwargs)

Overloaded function.

1. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: float, y: float, z: float) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(double, double, double) const –> double

2. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(class numeric::xyzVector<double>) const –> double

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

return the grids type

C++: protocols::qsar::scoring_grid::SingleGrid::get_type() const –> std::string

static grid_name() → str

C++: protocols::qsar::scoring_grid::LipidMemGrid::grid_name() –> std::string

grid_to_kin(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.utility.io.ozstream, min_val: float, max_val: float, stride: int) → None

C++: protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(class utility::io::ozstream &, double, double, unsigned long) –> void

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid) → str

Return a string representing the settings which don’t change based on reinitialization

C++: protocols::qsar::scoring_grid::LipidMemGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::SingleGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

a LipidMemGrid based on RosettaScripts input

C++: protocols::qsar::scoring_grid::LipidMemGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::LipidMemGrid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_id_to_exclude: int) -> None

populate the grid with LipidMemGrid values in vector based on a passed pose

C++: protocols::qsar::scoring_grid::LipidMemGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_ids_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

populate the grid with LipidMemGrid values in vector based on a passed pose

C++: protocols::qsar::scoring_grid::LipidMemGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

populate the grids in the vector with Membrane ligand values based on a passed pose

C++: protocols::qsar::scoring_grid::LipidMemGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the LipidMemGrid

C++: protocols::qsar::scoring_grid::LipidMemGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of a residue using the LipidMemGrid

C++: protocols::qsar::scoring_grid::LipidMemGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

Serialize the LipidMemGrid object into a json_spirit Value

C++: protocols::qsar::scoring_grid::LipidMemGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

set the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_center(class numeric::xyzVector<double>) –> void

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, chain: str) → None

set the chain around which to calculate the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_chain(char) –> void

set_distance_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, atom_shell: float, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(const double &, const class numeric::xyzVector<double> &, double) –> void

set_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_point(const class numeric::xyzVector<double> &, double) –> void

set_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, inner_radius: float, outer_radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

set_score_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, lj_spline: pyrosetta.rosetta.numeric.interpolation.spline.Interpolator, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(class std::shared_ptr<const class numeric::interpolation::spline::Interpolator>, const class numeric::xyzVector<double> &, double) –> void

set_sphere(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_sphere(const class numeric::xyzVector<double> &, double, double) –> void

set_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, type: str) → None

set the grid type

C++: protocols::qsar::scoring_grid::SingleGrid::set_type(std::string) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::LipidMemGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGridCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGridCreator

C++: protocols::qsar::scoring_grid::LipidMemGridCreator::operator=(const class protocols::qsar::scoring_grid::LipidMemGridCreator &) –> class protocols::qsar::scoring_grid::LipidMemGridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::LipidMemGridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::LipidMemGridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGridCreator) → str

C++: protocols::qsar::scoring_grid::LipidMemGridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::LipidMemGridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.MolecularWeightNormalization

Bases: ScoreNormalization

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.MolecularWeightNormalization, : pyrosetta.rosetta.protocols.qsar.scoring_grid.MolecularWeightNormalization) → pyrosetta.rosetta.protocols.qsar.scoring_grid.MolecularWeightNormalization

C++: protocols::qsar::scoring_grid::MolecularWeightNormalization::operator=(const class protocols::qsar::scoring_grid::MolecularWeightNormalization &) –> class protocols::qsar::scoring_grid::MolecularWeightNormalization &

get_name(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.MolecularWeightNormalization) → str

C++: protocols::qsar::scoring_grid::MolecularWeightNormalization::get_name() const –> std::string

class pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid

Bases: GridBase

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, rhs: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid

copy assignment

C++: protocols::qsar::scoring_grid::PCSMultiGrid::operator=(const class protocols::qsar::scoring_grid::PCSMultiGrid &) –> class protocols::qsar::scoring_grid::PCSMultiGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current PCSMultiGrid

C++: protocols::qsar::scoring_grid::PCSMultiGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current PCSMultiGrid

C++: protocols::qsar::scoring_grid::PCSMultiGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::PCSMultiGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json_spirit object to a PCSMultiGrid

C++: protocols::qsar::scoring_grid::PCSMultiGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, prefix: str) → None

output a BRIX formatted grid. This really does not work well but is being left for legacy purposes

C++: protocols::qsar::scoring_grid::PCSMultiGrid::dump_BRIX(const std::string &) const –> void

get_number_pcs_grids(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid) → int

C++: protocols::qsar::scoring_grid::PCSMultiGrid::get_number_pcs_grids() const –> unsigned long

get_pcs_grids(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_qsar_scoring_grid_SingleGrid_t

C++: protocols::qsar::scoring_grid::PCSMultiGrid::get_pcs_grids() –> class utility::vector1<class std::shared_ptr<class protocols::qsar::scoring_grid::SingleGrid>, class std::allocator<class std::shared_ptr<class protocols::qsar::scoring_grid::SingleGrid> > > &

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid) → str

get the type of the grid

C++: protocols::qsar::scoring_grid::PCSMultiGrid::get_type() const –> std::string

get_weight(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid) → float

C++: protocols::qsar::scoring_grid::PCSMultiGrid::get_weight() const –> double

static grid_name() → str

C++: protocols::qsar::scoring_grid::PCSMultiGrid::grid_name() –> std::string

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid) → str

C++: protocols::qsar::scoring_grid::PCSMultiGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

setup a vector of PCSSingleGrid objects

initialize each PCSSingleGrid with a given center point, width and resolution (in angstroms) and set grid values to zero.

C++: protocols::qsar::scoring_grid::PCSMultiGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

determine if all residue atoms are in a grid

C++: protocols::qsar::scoring_grid::PCSMultiGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

determine if all residue atoms are in a grid

C++: protocols::qsar::scoring_grid::PCSMultiGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

setup a PCSMultiGrid based on RosettaScripts input

C++: protocols::qsar::scoring_grid::PCSMultiGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::PCSMultiGrid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

populate grids in the vector with PCS values based on a passed pose

C++: protocols::qsar::scoring_grid::PCSMultiGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_id_to_exclude: int) -> None

populate grids in the vector with PCS values based on a passed pose

C++: protocols::qsar::scoring_grid::PCSMultiGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_ids_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

populate grids in the vector with PCS values based on a passed pose

C++: protocols::qsar::scoring_grid::PCSMultiGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current PCSMultiGrid

C++: protocols::qsar::scoring_grid::PCSMultiGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of a residue using the current PCSMultiGrid

C++: protocols::qsar::scoring_grid::PCSMultiGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize the PCSMultiGrid to a json_spirit object

C++: protocols::qsar::scoring_grid::PCSMultiGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, chain: str) → None

set the chain the grid applies to

C++: protocols::qsar::scoring_grid::PCSMultiGrid::set_chain(char) –> void

set_weight(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, w: float) → None

C++: protocols::qsar::scoring_grid::PCSMultiGrid::set_weight(double) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::PCSMultiGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGridCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGridCreator

C++: protocols::qsar::scoring_grid::PCSMultiGridCreator::operator=(const class protocols::qsar::scoring_grid::PCSMultiGridCreator &) –> class protocols::qsar::scoring_grid::PCSMultiGridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::PCSMultiGridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::PCSMultiGridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGridCreator) → str

C++: protocols::qsar::scoring_grid::PCSMultiGridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::PCSMultiGridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid

Bases: SingleGrid

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid, rhs: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid

copy assignment

C++: protocols::qsar::scoring_grid::PCSSingleGrid::operator=(const class protocols::qsar::scoring_grid::PCSSingleGrid &) –> class protocols::qsar::scoring_grid::PCSSingleGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current PCSSingleGrid

C++: protocols::qsar::scoring_grid::PCSSingleGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current PCSSingleGrid

C++: protocols::qsar::scoring_grid::PCSSingleGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::PCSSingleGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json_spirit object to a PCSSingleGrid

C++: protocols::qsar::scoring_grid::PCSSingleGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

diffuse_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, width: float, magnitude: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, prefix: str) → None

C++: protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(const std::string &) const –> void

fill_with_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, : float) → None

the entire grid with some value

C++: protocols::qsar::scoring_grid::SingleGrid::fill_with_value(double) –> void

get_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

get the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_center() const –> class numeric::xyzVector<double>

get_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

get the chain around which the grid is calculated

C++: protocols::qsar::scoring_grid::SingleGrid::get_chain() –> char

get_dimensions(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t

get dimensions of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_dimensions() –> class numeric::xyzVector<unsigned long>

get_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.core.grid.CartGrid_double_t

return a constant reference to the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_grid() const –> const class core::grid::CartGrid<double> &

get_max_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the minimum score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_max_value() const –> double

get_min_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the max score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_min_value() const –> double

get_pcs_values(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_nmr_pcs_PCSSingle_t

C++: protocols::qsar::scoring_grid::PCSSingleGrid::get_pcs_values() const –> const class utility::vector1<class std::shared_ptr<class core::scoring::nmr::pcs::PCSSingle>, class std::allocator<class std::shared_ptr<class core::scoring::nmr::pcs::PCSSingle> > > &

get_pdb_coords(*args, **kwargs)

Overloaded function.

1. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: int, y: int, z: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(int, int, int) –> class numeric::xyzVector<double>

2. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, gridpt: pyrosetta.rosetta.numeric.xyzVector_int_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(class numeric::xyzVector<int>) –> class numeric::xyzVector<double>

get_point(*args, **kwargs)

Overloaded function.

1. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: float, y: float, z: float) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(double, double, double) const –> double

2. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(class numeric::xyzVector<double>) const –> double

get_tensor(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid) → pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor

C++: protocols::qsar::scoring_grid::PCSSingleGrid::get_tensor() const –> class std::shared_ptr<const class core::scoring::nmr::pcs::PCSTensor>

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

return the grids type

C++: protocols::qsar::scoring_grid::SingleGrid::get_type() const –> std::string

get_weight(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid) → float

C++: protocols::qsar::scoring_grid::PCSSingleGrid::get_weight() const –> double

static grid_name() → str

C++: protocols::qsar::scoring_grid::PCSSingleGrid::grid_name() –> std::string

grid_to_kin(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.utility.io.ozstream, min_val: float, max_val: float, stride: int) → None

C++: protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(class utility::io::ozstream &, double, double, unsigned long) –> void

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid) → str

C++: protocols::qsar::scoring_grid::PCSSingleGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::SingleGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

setup a PCSSingleGrid based on RosettaScripts input

C++: protocols::qsar::scoring_grid::PCSSingleGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::PCSSingleGrid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

populate the grid with PCS values based on a passed pose

C++: protocols::qsar::scoring_grid::PCSSingleGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_id_to_exclude: int) -> None

populate the grid with PCS values based on a passed pose

C++: protocols::qsar::scoring_grid::PCSSingleGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_ids_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

populate the grid with PCS values based on a passed pose

C++: protocols::qsar::scoring_grid::PCSSingleGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current PCSSingleGrid

C++: protocols::qsar::scoring_grid::PCSSingleGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of a residue using the current PCSSingleGrid

C++: protocols::qsar::scoring_grid::PCSSingleGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize the PCSSingleGrid to a json_spirit object

C++: protocols::qsar::scoring_grid::PCSSingleGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

set the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_center(class numeric::xyzVector<double>) –> void

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, chain: str) → None

set the chain around which to calculate the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_chain(char) –> void

set_distance_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, atom_shell: float, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(const double &, const class numeric::xyzVector<double> &, double) –> void

set_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_point(const class numeric::xyzVector<double> &, double) –> void

set_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, inner_radius: float, outer_radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

set_score_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, lj_spline: pyrosetta.rosetta.numeric.interpolation.spline.Interpolator, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(class std::shared_ptr<const class numeric::interpolation::spline::Interpolator>, const class numeric::xyzVector<double> &, double) –> void

set_sphere(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_sphere(const class numeric::xyzVector<double> &, double, double) –> void

set_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, type: str) → None

set the grid type

C++: protocols::qsar::scoring_grid::SingleGrid::set_type(std::string) –> void

set_weight(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid, w: float) → None

C++: protocols::qsar::scoring_grid::PCSSingleGrid::set_weight(double) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::SingleGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGridCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGridCreator

C++: protocols::qsar::scoring_grid::PCSSingleGridCreator::operator=(const class protocols::qsar::scoring_grid::PCSSingleGridCreator &) –> class protocols::qsar::scoring_grid::PCSSingleGridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::PCSSingleGridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::PCSSingleGridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGridCreator) → str

C++: protocols::qsar::scoring_grid::PCSSingleGridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::PCSSingleGridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid

Bases: SingleGrid

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid, : pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid

C++: protocols::qsar::scoring_grid::RepGrid::operator=(const class protocols::qsar::scoring_grid::RepGrid &) –> class protocols::qsar::scoring_grid::RepGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::RepGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json_spirit object to a SingleGrid

C++: protocols::qsar::scoring_grid::RepGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

diffuse_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, width: float, magnitude: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, prefix: str) → None

C++: protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(const std::string &) const –> void

fill_with_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, : float) → None

the entire grid with some value

C++: protocols::qsar::scoring_grid::SingleGrid::fill_with_value(double) –> void

get_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

get the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_center() const –> class numeric::xyzVector<double>

get_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

get the chain around which the grid is calculated

C++: protocols::qsar::scoring_grid::SingleGrid::get_chain() –> char

get_dimensions(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t

get dimensions of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_dimensions() –> class numeric::xyzVector<unsigned long>

get_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.core.grid.CartGrid_double_t

return a constant reference to the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_grid() const –> const class core::grid::CartGrid<double> &

get_max_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the minimum score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_max_value() const –> double

get_min_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the max score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_min_value() const –> double

get_pdb_coords(*args, **kwargs)

Overloaded function.

1. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: int, y: int, z: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(int, int, int) –> class numeric::xyzVector<double>

2. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, gridpt: pyrosetta.rosetta.numeric.xyzVector_int_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(class numeric::xyzVector<int>) –> class numeric::xyzVector<double>

get_point(*args, **kwargs)

Overloaded function.

1. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: float, y: float, z: float) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(double, double, double) const –> double

2. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(class numeric::xyzVector<double>) const –> double

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

return the grids type

C++: protocols::qsar::scoring_grid::SingleGrid::get_type() const –> std::string

static grid_name() → str

C++: protocols::qsar::scoring_grid::RepGrid::grid_name() –> std::string

grid_to_kin(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.utility.io.ozstream, min_val: float, max_val: float, stride: int) → None

C++: protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(class utility::io::ozstream &, double, double, unsigned long) –> void

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid) → str

C++: protocols::qsar::scoring_grid::RepGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::SingleGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

C++: protocols::qsar::scoring_grid::RepGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::RepGrid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_id_to_exclude: int) -> None

C++: protocols::qsar::scoring_grid::RepGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::qsar::scoring_grid::RepGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_ids_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::qsar::scoring_grid::RepGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of a residue using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize the SingleGrid to a json_spirit object

C++: protocols::qsar::scoring_grid::RepGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

set the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_center(class numeric::xyzVector<double>) –> void

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, chain: str) → None

set the chain around which to calculate the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_chain(char) –> void

set_distance_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, atom_shell: float, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(const double &, const class numeric::xyzVector<double> &, double) –> void

set_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_point(const class numeric::xyzVector<double> &, double) –> void

set_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, inner_radius: float, outer_radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

set_score_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, lj_spline: pyrosetta.rosetta.numeric.interpolation.spline.Interpolator, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(class std::shared_ptr<const class numeric::interpolation::spline::Interpolator>, const class numeric::xyzVector<double> &, double) –> void

set_sphere(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_sphere(const class numeric::xyzVector<double> &, double, double) –> void

set_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, type: str) → None

set the grid type

C++: protocols::qsar::scoring_grid::SingleGrid::set_type(std::string) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::SingleGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGridCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGridCreator

C++: protocols::qsar::scoring_grid::RepGridCreator::operator=(const class protocols::qsar::scoring_grid::RepGridCreator &) –> class protocols::qsar::scoring_grid::RepGridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::RepGridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::RepGridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGridCreator) → str

C++: protocols::qsar::scoring_grid::RepGridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::RepGridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoreNormalization

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoreNormalization, : pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoreNormalization) → pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoreNormalization

C++: protocols::qsar::scoring_grid::ScoreNormalization::operator=(const class protocols::qsar::scoring_grid::ScoreNormalization &) –> class protocols::qsar::scoring_grid::ScoreNormalization &

get_name(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoreNormalization) → str

C++: protocols::qsar::scoring_grid::ScoreNormalization::get_name() const –> std::string

class pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader

Bases: DataLoader

A class for loading ScoringGrids into the XML parser’s basic::datacache::DataMap.

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader, : pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader) → pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader

C++: protocols::qsar::scoring_grid::ScoringGridLoader::operator=(const class protocols::qsar::scoring_grid::ScoringGridLoader &) –> class protocols::qsar::scoring_grid::ScoringGridLoader &

load_data(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

The ScoringGridLoader will create named ScoringGrids and load them into the basic::datacache::DataMap

C++: protocols::qsar::scoring_grid::ScoringGridLoader::load_data(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> void

static loader_name() → str

C++: protocols::qsar::scoring_grid::ScoringGridLoader::loader_name() –> std::string

parse_gridset_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader, tag: pyrosetta.rosetta.utility.tag.Tag, parent: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Utility function for load_data(), which only takes tags for a single GridSet

C++: protocols::qsar::scoring_grid::ScoringGridLoader::parse_gridset_tag(class std::shared_ptr<const class utility::tag::Tag>, class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::ScoringGridLoader::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static scoring_grid_loader_ct_namer(element_name: str) → str

C++: protocols::qsar::scoring_grid::ScoringGridLoader::scoring_grid_loader_ct_namer(const std::string &) –> std::string

class pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoaderCreator

Bases: DataLoaderCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoaderCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoaderCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoaderCreator

C++: protocols::qsar::scoring_grid::ScoringGridLoaderCreator::operator=(const class protocols::qsar::scoring_grid::ScoringGridLoaderCreator &) –> class protocols::qsar::scoring_grid::ScoringGridLoaderCreator &

create_loader(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoaderCreator) → pyrosetta.rosetta.protocols.parser.DataLoader

C++: protocols::qsar::scoring_grid::ScoringGridLoaderCreator::create_loader() const –> class std::shared_ptr<class protocols::parser::DataLoader>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoaderCreator) → str

C++: protocols::qsar::scoring_grid::ScoringGridLoaderCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoaderCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::ScoringGridLoaderCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

schema_ct_naming_function(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoaderCreator) → std::function<std::string (std::string const&)>

C++: protocols::qsar::scoring_grid::ScoringGridLoaderCreator::schema_ct_naming_function() const –> class std::function<std::string (const std::string &)>

class pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid

Bases: SingleGrid

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid, : pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid

C++: protocols::qsar::scoring_grid::ShapeGrid::operator=(const class protocols::qsar::scoring_grid::ShapeGrid &) –> class protocols::qsar::scoring_grid::ShapeGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::ShapeGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::ShapeGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::ShapeGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize the grid information

C++: protocols::qsar::scoring_grid::ShapeGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

diffuse_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, width: float, magnitude: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, prefix: str) → None

C++: protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(const std::string &) const –> void

fill_with_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, : float) → None

the entire grid with some value

C++: protocols::qsar::scoring_grid::SingleGrid::fill_with_value(double) –> void

get_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

get the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_center() const –> class numeric::xyzVector<double>

get_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

get the chain around which the grid is calculated

C++: protocols::qsar::scoring_grid::SingleGrid::get_chain() –> char

get_dimensions(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t

get dimensions of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_dimensions() –> class numeric::xyzVector<unsigned long>

get_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.core.grid.CartGrid_double_t

return a constant reference to the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_grid() const –> const class core::grid::CartGrid<double> &

get_max_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the minimum score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_max_value() const –> double

get_min_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the max score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_min_value() const –> double

get_pdb_coords(*args, **kwargs)

Overloaded function.

1. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: int, y: int, z: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(int, int, int) –> class numeric::xyzVector<double>

2. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, gridpt: pyrosetta.rosetta.numeric.xyzVector_int_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(class numeric::xyzVector<int>) –> class numeric::xyzVector<double>

get_point(*args, **kwargs)

Overloaded function.

1. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: float, y: float, z: float) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(double, double, double) const –> double

2. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(class numeric::xyzVector<double>) const –> double

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

return the grids type

C++: protocols::qsar::scoring_grid::SingleGrid::get_type() const –> std::string

static grid_name() → str

C++: protocols::qsar::scoring_grid::ShapeGrid::grid_name() –> std::string

grid_to_kin(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.utility.io.ozstream, min_val: float, max_val: float, stride: int) → None

C++: protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(class utility::io::ozstream &, double, double, unsigned long) –> void

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid) → str

C++: protocols::qsar::scoring_grid::ShapeGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::SingleGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

C++: protocols::qsar::scoring_grid::ShapeGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::ShapeGrid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, : int) -> None

C++: protocols::qsar::scoring_grid::ShapeGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::qsar::scoring_grid::ShapeGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::qsar::scoring_grid::ShapeGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::ShapeGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

C++: protocols::qsar::scoring_grid::ShapeGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize the grid information

C++: protocols::qsar::scoring_grid::ShapeGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

set the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_center(class numeric::xyzVector<double>) –> void

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, chain: str) → None

set the chain around which to calculate the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_chain(char) –> void

set_distance_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, atom_shell: float, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(const double &, const class numeric::xyzVector<double> &, double) –> void

set_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_point(const class numeric::xyzVector<double> &, double) –> void

set_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, inner_radius: float, outer_radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

set_score_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, lj_spline: pyrosetta.rosetta.numeric.interpolation.spline.Interpolator, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(class std::shared_ptr<const class numeric::interpolation::spline::Interpolator>, const class numeric::xyzVector<double> &, double) –> void

set_sphere(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_sphere(const class numeric::xyzVector<double> &, double, double) –> void

set_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, type: str) → None

set the grid type

C++: protocols::qsar::scoring_grid::SingleGrid::set_type(std::string) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::SingleGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGridCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGridCreator

C++: protocols::qsar::scoring_grid::ShapeGridCreator::operator=(const class protocols::qsar::scoring_grid::ShapeGridCreator &) –> class protocols::qsar::scoring_grid::ShapeGridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::ShapeGridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::ShapeGridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGridCreator) → str

C++: protocols::qsar::scoring_grid::ShapeGridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::ShapeGridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid

Bases: GridBase

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, : pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid

C++: protocols::qsar::scoring_grid::SingleGrid::operator=(const class protocols::qsar::scoring_grid::SingleGrid &) –> class protocols::qsar::scoring_grid::SingleGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::SingleGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json_spirit object to a SingleGrid

C++: protocols::qsar::scoring_grid::SingleGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

diffuse_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, width: float, magnitude: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, prefix: str) → None

C++: protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(const std::string &) const –> void

fill_with_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, : float) → None

the entire grid with some value

C++: protocols::qsar::scoring_grid::SingleGrid::fill_with_value(double) –> void

get_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

get the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_center() const –> class numeric::xyzVector<double>

get_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

get the chain around which the grid is calculated

C++: protocols::qsar::scoring_grid::SingleGrid::get_chain() –> char

get_dimensions(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t

get dimensions of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_dimensions() –> class numeric::xyzVector<unsigned long>

get_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.core.grid.CartGrid_double_t

return a constant reference to the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_grid() const –> const class core::grid::CartGrid<double> &

get_max_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the minimum score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_max_value() const –> double

get_min_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the max score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_min_value() const –> double

get_pdb_coords(*args, **kwargs)

Overloaded function.

1. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: int, y: int, z: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(int, int, int) –> class numeric::xyzVector<double>

2. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, gridpt: pyrosetta.rosetta.numeric.xyzVector_int_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(class numeric::xyzVector<int>) –> class numeric::xyzVector<double>

get_point(*args, **kwargs)

Overloaded function.

1. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: float, y: float, z: float) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(double, double, double) const –> double

2. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(class numeric::xyzVector<double>) const –> double

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

return the grids type

C++: protocols::qsar::scoring_grid::SingleGrid::get_type() const –> std::string

grid_to_kin(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.utility.io.ozstream, min_val: float, max_val: float, stride: int) → None

C++: protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(class utility::io::ozstream &, double, double, unsigned long) –> void

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

Return a string representing the settings which don’t change based on reinitialization

C++: protocols::qsar::scoring_grid::SingleGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::SingleGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

setup a grid based on RosettaScripts input

C++: protocols::qsar::scoring_grid::SingleGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_id_to_exclude: int) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::SingleGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_ids_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::SingleGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::SingleGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of a residue using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize the SingleGrid to a json_spirit object

C++: protocols::qsar::scoring_grid::SingleGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

set the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_center(class numeric::xyzVector<double>) –> void

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, chain: str) → None

set the chain around which to calculate the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_chain(char) –> void

set_distance_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, atom_shell: float, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(const double &, const class numeric::xyzVector<double> &, double) –> void

set_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_point(const class numeric::xyzVector<double> &, double) –> void

set_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, inner_radius: float, outer_radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

set_score_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, lj_spline: pyrosetta.rosetta.numeric.interpolation.spline.Interpolator, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(class std::shared_ptr<const class numeric::interpolation::spline::Interpolator>, const class numeric::xyzVector<double> &, double) –> void

set_sphere(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_sphere(const class numeric::xyzVector<double> &, double, double) –> void

set_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, type: str) → None

set the grid type

C++: protocols::qsar::scoring_grid::SingleGrid::set_type(std::string) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::SingleGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid

Bases: SingleGrid

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid, : pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid

C++: protocols::qsar::scoring_grid::SiteGrid::operator=(const class protocols::qsar::scoring_grid::SiteGrid &) –> class protocols::qsar::scoring_grid::SiteGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::SiteGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json_spirit object to a SingleGrid

C++: protocols::qsar::scoring_grid::SiteGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

diffuse_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, width: float, magnitude: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, prefix: str) → None

C++: protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(const std::string &) const –> void

fill_with_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, : float) → None

the entire grid with some value

C++: protocols::qsar::scoring_grid::SingleGrid::fill_with_value(double) –> void

get_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

get the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_center() const –> class numeric::xyzVector<double>

get_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

get the chain around which the grid is calculated

C++: protocols::qsar::scoring_grid::SingleGrid::get_chain() –> char

get_dimensions(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t

get dimensions of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_dimensions() –> class numeric::xyzVector<unsigned long>

get_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.core.grid.CartGrid_double_t

return a constant reference to the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_grid() const –> const class core::grid::CartGrid<double> &

get_max_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the minimum score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_max_value() const –> double

get_min_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the max score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_min_value() const –> double

get_pdb_coords(*args, **kwargs)

Overloaded function.

1. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: int, y: int, z: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(int, int, int) –> class numeric::xyzVector<double>

2. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, gridpt: pyrosetta.rosetta.numeric.xyzVector_int_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(class numeric::xyzVector<int>) –> class numeric::xyzVector<double>

get_point(*args, **kwargs)

Overloaded function.

1. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: float, y: float, z: float) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(double, double, double) const –> double

2. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(class numeric::xyzVector<double>) const –> double

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

return the grids type

C++: protocols::qsar::scoring_grid::SingleGrid::get_type() const –> std::string

static grid_name() → str

C++: protocols::qsar::scoring_grid::SiteGrid::grid_name() –> std::string

grid_to_kin(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.utility.io.ozstream, min_val: float, max_val: float, stride: int) → None

C++: protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(class utility::io::ozstream &, double, double, unsigned long) –> void

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid) → str

C++: protocols::qsar::scoring_grid::SiteGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::SingleGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

C++: protocols::qsar::scoring_grid::SiteGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::SiteGrid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_id_to_exclude: int) -> None

C++: protocols::qsar::scoring_grid::SiteGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::qsar::scoring_grid::SiteGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_ids_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::qsar::scoring_grid::SiteGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of a residue using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize the SingleGrid to a json_spirit object

C++: protocols::qsar::scoring_grid::SiteGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

set the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_center(class numeric::xyzVector<double>) –> void

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, chain: str) → None

set the chain around which to calculate the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_chain(char) –> void

set_distance_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, atom_shell: float, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(const double &, const class numeric::xyzVector<double> &, double) –> void

set_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_point(const class numeric::xyzVector<double> &, double) –> void

set_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, inner_radius: float, outer_radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

set_score_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, lj_spline: pyrosetta.rosetta.numeric.interpolation.spline.Interpolator, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(class std::shared_ptr<const class numeric::interpolation::spline::Interpolator>, const class numeric::xyzVector<double> &, double) –> void

set_sphere(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_sphere(const class numeric::xyzVector<double> &, double, double) –> void

set_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, type: str) → None

set the grid type

C++: protocols::qsar::scoring_grid::SingleGrid::set_type(std::string) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::SingleGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGridCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGridCreator

C++: protocols::qsar::scoring_grid::SiteGridCreator::operator=(const class protocols::qsar::scoring_grid::SiteGridCreator &) –> class protocols::qsar::scoring_grid::SiteGridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::SiteGridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::SiteGridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGridCreator) → str

C++: protocols::qsar::scoring_grid::SiteGridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::SiteGridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid

Bases: SingleGrid

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid, : pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid

C++: protocols::qsar::scoring_grid::SolvationGrid::operator=(const class protocols::qsar::scoring_grid::SolvationGrid &) –> class protocols::qsar::scoring_grid::SolvationGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::SolvationGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json_spirit object to a Interpolator

C++: protocols::qsar::scoring_grid::SolvationGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

diffuse_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, width: float, magnitude: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, prefix: str) → None

C++: protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(const std::string &) const –> void

fill_with_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, : float) → None

the entire grid with some value

C++: protocols::qsar::scoring_grid::SingleGrid::fill_with_value(double) –> void

get_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

get the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_center() const –> class numeric::xyzVector<double>

get_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

get the chain around which the grid is calculated

C++: protocols::qsar::scoring_grid::SingleGrid::get_chain() –> char

get_dimensions(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t

get dimensions of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_dimensions() –> class numeric::xyzVector<unsigned long>

get_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.core.grid.CartGrid_double_t

return a constant reference to the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_grid() const –> const class core::grid::CartGrid<double> &

get_max_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the minimum score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_max_value() const –> double

get_min_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the max score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_min_value() const –> double

get_pdb_coords(*args, **kwargs)

Overloaded function.

1. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: int, y: int, z: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(int, int, int) –> class numeric::xyzVector<double>

2. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, gridpt: pyrosetta.rosetta.numeric.xyzVector_int_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(class numeric::xyzVector<int>) –> class numeric::xyzVector<double>

get_point(*args, **kwargs)

Overloaded function.

1. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: float, y: float, z: float) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(double, double, double) const –> double

2. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(class numeric::xyzVector<double>) const –> double

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

return the grids type

C++: protocols::qsar::scoring_grid::SingleGrid::get_type() const –> std::string

static grid_name() → str

C++: protocols::qsar::scoring_grid::SolvationGrid::grid_name() –> std::string

grid_to_kin(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.utility.io.ozstream, min_val: float, max_val: float, stride: int) → None

C++: protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(class utility::io::ozstream &, double, double, unsigned long) –> void

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid) → str

C++: protocols::qsar::scoring_grid::SolvationGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::SingleGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

C++: protocols::qsar::scoring_grid::SolvationGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::SolvationGrid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, : int) -> None

C++: protocols::qsar::scoring_grid::SolvationGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::qsar::scoring_grid::SolvationGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::qsar::scoring_grid::SolvationGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of a residue using the current grid

C++: protocols::qsar::scoring_grid::SingleGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize the Interpolator to a json_spirit object

C++: protocols::qsar::scoring_grid::SolvationGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

set the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_center(class numeric::xyzVector<double>) –> void

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, chain: str) → None

set the chain around which to calculate the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_chain(char) –> void

set_distance_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, atom_shell: float, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(const double &, const class numeric::xyzVector<double> &, double) –> void

set_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_point(const class numeric::xyzVector<double> &, double) –> void

set_probe_atom_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid, atom_type: int) → None

C++: protocols::qsar::scoring_grid::SolvationGrid::set_probe_atom_type(const unsigned short &) –> void

set_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, inner_radius: float, outer_radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

set_score_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, lj_spline: pyrosetta.rosetta.numeric.interpolation.spline.Interpolator, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(class std::shared_ptr<const class numeric::interpolation::spline::Interpolator>, const class numeric::xyzVector<double> &, double) –> void

set_sphere(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_sphere(const class numeric::xyzVector<double> &, double, double) –> void

set_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, type: str) → None

set the grid type

C++: protocols::qsar::scoring_grid::SingleGrid::set_type(std::string) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::SingleGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGridCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGridCreator

C++: protocols::qsar::scoring_grid::SolvationGridCreator::operator=(const class protocols::qsar::scoring_grid::SolvationGridCreator &) –> class protocols::qsar::scoring_grid::SolvationGridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::SolvationGridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::SolvationGridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGridCreator) → str

C++: protocols::qsar::scoring_grid::SolvationGridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::SolvationGridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid

Bases: GridBase

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, : pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::operator=(const class protocols::qsar::scoring_grid::SolvationMetaGrid &) –> class protocols::qsar::scoring_grid::SolvationMetaGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json spirit Value into a GridBase object

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, prefix: str) → None

output a BRIX formatted grid. This really does not work well but is being left for legacy purposes

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::dump_BRIX(const std::string &) const –> void

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid) → str

get the type of the grid

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::get_type() const –> std::string

static grid_name() → str

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::grid_name() –> std::string

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid) → str

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

determine if all residue atoms are in a grid

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

determine if all residue atoms are in a grid

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

a grid based on RosettaScripts input

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_id_to_exclude: int) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_ids_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

populate the grid with values based on a passed pose

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of a residue using the current grid

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

Serialize the GridBase object into a json_spirit Value

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, chain: str) → None

set the chain the grid applies to

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::set_chain(char) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::SolvationMetaGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGridCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGridCreator

C++: protocols::qsar::scoring_grid::SolvationMetaGridCreator::operator=(const class protocols::qsar::scoring_grid::SolvationMetaGridCreator &) –> class protocols::qsar::scoring_grid::SolvationMetaGridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::SolvationMetaGridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::SolvationMetaGridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGridCreator) → str

C++: protocols::qsar::scoring_grid::SolvationMetaGridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::SolvationMetaGridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid

Bases: SingleGrid

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid, : pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid

C++: protocols::qsar::scoring_grid::VdwGrid::operator=(const class protocols::qsar::scoring_grid::VdwGrid &) –> class protocols::qsar::scoring_grid::VdwGrid &

atom_score(*args, **kwargs)

Overloaded function.

1. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::VdwGrid::atom_score(const class core::conformation::UltraLightResidue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. atom_score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid, residue: pyrosetta.rosetta.core.conformation.Residue, atomno: int, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an atom using the current grid

C++: protocols::qsar::scoring_grid::VdwGrid::atom_score(const class core::conformation::Residue &, unsigned long, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

clone(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid) → pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

Make a copy of the grid, respecting the subclassing.

C++: protocols::qsar::scoring_grid::VdwGrid::clone() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

deserialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid, data: pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t) → None

deserialize a json_spirit object to a Interpolator

C++: protocols::qsar::scoring_grid::VdwGrid::deserialize(class std::map<std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_map<std::string > > > > >) –> void

diffuse_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, width: float, magnitude: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

dump_BRIX(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, prefix: str) → None

C++: protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(const std::string &) const –> void

fill_with_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, : float) → None

the entire grid with some value

C++: protocols::qsar::scoring_grid::SingleGrid::fill_with_value(double) –> void

get_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

get the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_center() const –> class numeric::xyzVector<double>

get_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

get the chain around which the grid is calculated

C++: protocols::qsar::scoring_grid::SingleGrid::get_chain() –> char

get_dimensions(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t

get dimensions of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_dimensions() –> class numeric::xyzVector<unsigned long>

get_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → pyrosetta.rosetta.core.grid.CartGrid_double_t

return a constant reference to the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_grid() const –> const class core::grid::CartGrid<double> &

get_max_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the minimum score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_max_value() const –> double

get_min_value(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → float

get the max score value in the grid

C++: protocols::qsar::scoring_grid::SingleGrid::get_min_value() const –> double

get_pdb_coords(*args, **kwargs)

Overloaded function.

1. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: int, y: int, z: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(int, int, int) –> class numeric::xyzVector<double>

2. get_pdb_coords(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, gridpt: pyrosetta.rosetta.numeric.xyzVector_int_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

get the pdb coordinates based on grid point coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(class numeric::xyzVector<int>) –> class numeric::xyzVector<double>

get_point(*args, **kwargs)

Overloaded function.

1. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, x: float, y: float, z: float) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(double, double, double) const –> double

2. get_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

get the value of a single point in the grid based on pdb coordinates

C++: protocols::qsar::scoring_grid::SingleGrid::get_point(class numeric::xyzVector<double>) const –> double

get_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid) → str

return the grids type

C++: protocols::qsar::scoring_grid::SingleGrid::get_type() const –> std::string

static grid_name() → str

C++: protocols::qsar::scoring_grid::VdwGrid::grid_name() –> std::string

grid_to_kin(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.utility.io.ozstream, min_val: float, max_val: float, stride: int) → None

C++: protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(class utility::io::ozstream &, double, double, unsigned long) –> void

hash_fingerprint(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid) → str

C++: protocols::qsar::scoring_grid::VdwGrid::hash_fingerprint() const –> std::string

initialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, width: float, resolution: float) → None

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

C++: protocols::qsar::scoring_grid::SingleGrid::initialize(const class numeric::xyzVector<double> &, double, double) –> void

is_in_grid(*args, **kwargs)

Overloaded function.

1. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::UltraLightResidue &) const –> bool

2. is_in_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

check to see if residue is in grid

C++: protocols::qsar::scoring_grid::SingleGrid::is_in_grid(const class core::conformation::Residue &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid, tag: pyrosetta.rosetta.utility.tag.Tag) → None

C++: protocols::qsar::scoring_grid::VdwGrid::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::VdwGrid::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

refresh(*args, **kwargs)

Overloaded function.

1. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, : int) -> None

C++: protocols::qsar::scoring_grid::VdwGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> void

2. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::qsar::scoring_grid::VdwGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> void

3. refresh(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::qsar::scoring_grid::VdwGrid::refresh(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

return the current score of an UltraLightResidue using the current grid

C++: protocols::qsar::scoring_grid::VdwGrid::score(const class core::conformation::UltraLightResidue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

2. score(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid, residue: pyrosetta.rosetta.core.conformation.Residue, max_score: float, qsar_map: pyrosetta.rosetta.protocols.qsar.qsarMap) -> float

C++: protocols::qsar::scoring_grid::VdwGrid::score(const class core::conformation::Residue &, const double, class std::shared_ptr<const class protocols::qsar::qsarMap>) const –> double

serialize(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid) → pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t

serialize the Interpolator to a json_spirit object

C++: protocols::qsar::scoring_grid::VdwGrid::serialize() const –> class utility::json_spirit::Value_impl<struct utility::json_spirit::Config_vector<std::string > >

set_center(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

set the center of the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_center(class numeric::xyzVector<double>) –> void

set_chain(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, chain: str) → None

set the chain around which to calculate the grid

C++: protocols::qsar::scoring_grid::SingleGrid::set_chain(char) –> void

set_distance_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, atom_shell: float, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(const double &, const class numeric::xyzVector<double> &, double) –> void

set_point(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_point(const class numeric::xyzVector<double> &, double) –> void

set_ring(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, inner_radius: float, outer_radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_ring(const class numeric::xyzVector<double> &, double, double, double) –> void

set_score_sphere_for_atom(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, lj_spline: pyrosetta.rosetta.numeric.interpolation.spline.Interpolator, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, cutoff: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(class std::shared_ptr<const class numeric::interpolation::spline::Interpolator>, const class numeric::xyzVector<double> &, double) –> void

set_sphere(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, radius: float, value: float) → None

C++: protocols::qsar::scoring_grid::SingleGrid::set_sphere(const class numeric::xyzVector<double> &, double, double) –> void

set_type(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, type: str) → None

set the grid type

C++: protocols::qsar::scoring_grid::SingleGrid::set_type(std::string) –> void

show(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid, out: pyrosetta.rosetta.std.ostream) → None

Print a brief summary about this grid to the provided output stream

C++: protocols::qsar::scoring_grid::SingleGrid::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGridCreator

Bases: GridCreator

assign(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGridCreator, : pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGridCreator) → pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGridCreator

C++: protocols::qsar::scoring_grid::VdwGridCreator::operator=(const class protocols::qsar::scoring_grid::VdwGridCreator &) –> class protocols::qsar::scoring_grid::VdwGridCreator &

create_grid(*args, **kwargs)

Overloaded function.

1. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGridCreator, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::VdwGridCreator::create_grid(class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

2. create_grid(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGridCreator) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase

C++: protocols::qsar::scoring_grid::VdwGridCreator::create_grid() const –> class std::shared_ptr<class protocols::qsar::scoring_grid::GridBase>

keyname(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGridCreator) → str

C++: protocols::qsar::scoring_grid::VdwGridCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGridCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::qsar::scoring_grid::VdwGridCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.protocols.qsar.scoring_grid.attributes_for_parse_grid_set_from_tag(*args, **kwargs)

Overloaded function.

1. attributes_for_parse_grid_set_from_tag(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None

2. attributes_for_parse_grid_set_from_tag(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, description: str) -> None

3. attributes_for_parse_grid_set_from_tag(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, description: str, option_name: str) -> None

Append the attributes read by parse_grid_set_from_tag()

C++: protocols::qsar::scoring_grid::attributes_for_parse_grid_set_from_tag(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const std::string &, const std::string &) –> void

pyrosetta.rosetta.protocols.qsar.scoring_grid.attributes_for_parse_optional_grid_set_from_tag(*args, **kwargs)

Overloaded function.

1. attributes_for_parse_optional_grid_set_from_tag(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None

2. attributes_for_parse_optional_grid_set_from_tag(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, description: str) -> None

3. attributes_for_parse_optional_grid_set_from_tag(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, description: str, option_name: str) -> None

Append the attributes read by parse_optional_grid_set_from_tag()

C++: protocols::qsar::scoring_grid::attributes_for_parse_optional_grid_set_from_tag(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const std::string &, const std::string &) –> void

pyrosetta.rosetta.protocols.qsar.scoring_grid.complex_type_name_for_scoring_grid(element_name: str) → str

Used to name the xs:complexType for a scoring grid that is

created with the given element name

C++: protocols::qsar::scoring_grid::complex_type_name_for_scoring_grid(const std::string &) –> std::string

pyrosetta.rosetta.protocols.qsar.scoring_grid.get_score_normalization_function(norm_tag: str) → protocols::qsar::scoring_grid::ScoreNormalization

C++: protocols::qsar::scoring_grid::get_score_normalization_function(const std::string &) –> class std::shared_ptr<class protocols::qsar::scoring_grid::ScoreNormalization>

pyrosetta.rosetta.protocols.qsar.scoring_grid.parse_grid_set_from_tag(*args, **kwargs)

Overloaded function.

1. parse_grid_set_from_tag(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet

2. parse_grid_set_from_tag(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, option_name: str) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet

Get a GridSet from the datamap, using the option_name attribute of the tag.

C++: protocols::qsar::scoring_grid::parse_grid_set_from_tag(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &, const std::string &) –> class std::shared_ptr<const class protocols::qsar::scoring_grid::GridSet>

pyrosetta.rosetta.protocols.qsar.scoring_grid.parse_optional_grid_set_from_tag(*args, **kwargs)

Overloaded function.

1. parse_optional_grid_set_from_tag(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet

2. parse_optional_grid_set_from_tag(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, option_name: str) -> pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet

Get a GridSet from the datamap, using the option_name attribute of the tag.

If a GridSet hasn’t been specified, return a nullptr

C++: protocols::qsar::scoring_grid::parse_optional_grid_set_from_tag(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &, const std::string &) –> class std::shared_ptr<const class protocols::qsar::scoring_grid::GridSet>

pyrosetta.rosetta.protocols.qsar.scoring_grid.xsd_type_definition_w_attributes(xsd: utility::tag::XMLSchemaDefinition, scoring_grid_name: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

Define the XML schema definition for a scoring grid that has no

subelements but does have a set of attributes (aka options).

C++: protocols::qsar::scoring_grid::xsd_type_definition_w_attributes(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void