jacobian¶

Bindings for core::kinematics::jacobian namespace

class pyrosetta.rosetta.core.kinematics.jacobian.JacobianStructure¶

Bases: pybind11_object

The JacobianStructure class is the upper-level wrapper of the Jacobian analysis of a protein’s kinematics relations.

teunhoevenaars (teunhoevenaars.com)

assign(self: pyrosetta.rosetta.core.kinematics.jacobian.JacobianStructure, : pyrosetta.rosetta.core.kinematics.jacobian.JacobianStructure) → pyrosetta.rosetta.core.kinematics.jacobian.JacobianStructure¶: C++: core::kinematics::jacobian::JacobianStructure::operator=(const class core::kinematics::jacobian::JacobianStructure &) –> class core::kinematics::jacobian::JacobianStructure &

clone(self: pyrosetta.rosetta.core.kinematics.jacobian.JacobianStructure) → pyrosetta.rosetta.core.kinematics.jacobian.JacobianStructure¶

Clone operation: make a copy of this object, and return an owning pointer to the copy.

C++: core::kinematics::jacobian::JacobianStructure::clone() const –> class std::shared_ptr<class core::kinematics::jacobian::JacobianStructure>

get_single_chain(self: pyrosetta.rosetta.core.kinematics.jacobian.JacobianStructure, index: int) → core::kinematics::jacobian::SeriesJacobians¶

get one serial chain of the structure

C++: core::kinematics::jacobian::JacobianStructure::get_single_chain(unsigned long) –> const class std::shared_ptr<class core::kinematics::jacobian::SeriesJacobians>

class pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1¶

Bases: pybind11_object

The ModuleType1 class covers the Jacobian analysis at the lower-level for type-1 systems, which have internal DoFs that can be organized as three sets of two torsion angles with intersecting axes.

teunhoevenaars (teunhoevenaars.com)

apply_delta_torsion_values(self: pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1, conformation: pyrosetta.rosetta.core.conformation.Conformation, dq: pyrosetta.rosetta.numeric.MathVector_double_t) → None¶

apply vector of delta angles to the torsion angles that are associated to this instance

dq must have dimension 6 and all delta angles must be in radians

C++: core::kinematics::jacobian::ModuleType1::apply_delta_torsion_values(class core::conformation::Conformation &, const class numeric::MathVector<double> &) –> void

assign(self: pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1, : pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1) → pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1¶: C++: core::kinematics::jacobian::ModuleType1::operator=(const class core::kinematics::jacobian::ModuleType1 &) –> class core::kinematics::jacobian::ModuleType1 &

clone(self: pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1) → pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1¶

Clone operation: make a copy of this object, and return an owning pointer to the copy.

C++: core::kinematics::jacobian::ModuleType1::clone() const –> class std::shared_ptr<class core::kinematics::jacobian::ModuleType1>

free_residues(self: pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the number of DoFs of which this module represents the differential equations

C++: core::kinematics::jacobian::ModuleType1::free_residues() –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_jacobian_matrices(self: pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1, conformation: pyrosetta.rosetta.core.conformation.Conformation) → core::kinematics::jacobian::ModuleType1::jacobian_struct¶

calculate all Jacobian matrices for the instantaneous conformation

C++: core::kinematics::jacobian::ModuleType1::get_jacobian_matrices(const class core::conformation::Conformation &) –> struct core::kinematics::jacobian::ModuleType1::jacobian_struct

get_number_dofs(self: pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1) → int¶

Returns the number of DoFs of which this module represents the differential equations

C++: core::kinematics::jacobian::ModuleType1::get_number_dofs() –> unsigned long

get_torsion_ids(self: pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID¶

Returns the residues that make up the Jacobian module. N.B. this vector always contains six residue numbers,: but only the first < number_dofs_ > torsion IDs are free to move. The remaining torsions represent constrained motions

C++: core::kinematics::jacobian::ModuleType1::get_torsion_ids() –> class utility::vector1<class core::id::TorsionID, class std::allocator<class core::id::TorsionID> >

get_torsion_values(self: pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1, conformation: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.numeric.MathVector_double_t¶

Get variables that are associated to this instance

C++: core::kinematics::jacobian::ModuleType1::get_torsion_values(const class core::conformation::Conformation &) –> class numeric::MathVector<double>

class jacobian_struct¶

Bases: pybind11_object

Struct to pass around all variations of Jacobian matrices

fw_dofs is the Jacobian matrix that maps differential torsion angles [rad/s] or [delta rad] on Cartesian reference frame fw_cons is the 6x6 Jacobian matrix that maps virtual (helper, constrained) torsion angles [rad/s] or [delta rad] on Cartesian reference frame fw_all is the 6x6 Jacobian matrix that maps all six torsion angles (real and virtual) [rad/s] or [delta rad] on Cartesian reference frame inv_dofs is the 6x6 Jacobian matrix that maps twist from Cartesian ref. frame onto torsion angles inv_cons is the 6x6 Jacobian matrix that maps twist from Cartesian ref. frame onto virtual torsion angles that represent the modules constraints inv_all is the 6x6 Jacobian matrix that maps twist from Cartesian ref. frame onto all torsion angles (real and virtual)

property fw_all¶

property fw_cons¶

property fw_dofs¶

property inv_all¶

property inv_cons¶

property inv_dofs¶

class screw_construct_struct¶

Bases: pybind11_object

struct with the different linear algebra objects that are needed to express the twists and wrenches to calculate the instantaneous Jacobian matrices of the module

Hmatrices vector with the homogeneous matrices that describe the homogeneous transformations between the reference atom (ref_atom_) and the first atom in key_atoms_IDs_, followed by the homogeneous transformations between the subsequent atoms in key_atoms_IDs_. s_vectors is a vector1 with screw axis vectors r_vectorss is a vector1 with moment arm vectors for screw definitions

property Hmatrices¶

property r_vectors¶

property s_vectors¶

set_torsion_values(self: pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1, conformation: pyrosetta.rosetta.core.conformation.Conformation, vars: pyrosetta.rosetta.numeric.MathVector_double_t) → None¶

Set the variables that are associated to this module

C++: core::kinematics::jacobian::ModuleType1::set_torsion_values(class core::conformation::Conformation &, const class numeric::MathVector<double> &) –> void

class pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobianTypeEnum¶

Bases: pybind11_object

List of supported residue types in the loop that is to be represented by a series Jacobian

Members:

ALPHA_AA

OTHER

num_types

ALPHA_AA = <SeriesJacobianTypeEnum.ALPHA_AA: 1>¶

OTHER = <SeriesJacobianTypeEnum.OTHER: 2>¶

property name¶

num_types = <SeriesJacobianTypeEnum.OTHER: 2>¶

property value¶

class pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians¶

Bases: pybind11_object

The SeriesJacobians class is the mid-level of the Jacobian analysis of a protein’s kinematics relations.

teunhoevenaars (teunhoevenaars.com)

assign(self: pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians, : pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians) → pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians¶: C++: core::kinematics::jacobian::SeriesJacobians::operator=(const class core::kinematics::jacobian::SeriesJacobians &) –> class core::kinematics::jacobian::SeriesJacobians &

clone(self: pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians) → pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians¶

Clone operation: make a copy of this object, and return an owning pointer to the copy.

C++: core::kinematics::jacobian::SeriesJacobians::clone() const –> class std::shared_ptr<class core::kinematics::jacobian::SeriesJacobians>

get_ref_atom_ID(self: pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians) → pyrosetta.rosetta.core.id.AtomID¶

get reference atom used to express all vectors in all modules

C++: core::kinematics::jacobian::SeriesJacobians::get_ref_atom_ID() const –> class core::id::AtomID

get_residues(self: pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

get residues that make up the chain

C++: core::kinematics::jacobian::SeriesJacobians::get_residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

property modules_¶

move_map(self: pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians) → pyrosetta.rosetta.core.kinematics.MoveMap¶

get pointer to movemap

C++: core::kinematics::jacobian::SeriesJacobians::move_map() const –> class std::shared_ptr<class core::kinematics::MoveMap>

num_dofs(self: pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians) → int¶

get amount of DoFs of the chain

C++: core::kinematics::jacobian::SeriesJacobians::num_dofs() const –> unsigned long

pyrosetta.rosetta.core.kinematics.jacobian.calculate_error_twist(RT_current: pyrosetta.rosetta.core.kinematics.RT, RT_target: pyrosetta.rosetta.core.kinematics.RT) → Tuple[pyrosetta.rosetta.numeric.xyzVector_double_t, pyrosetta.rosetta.numeric.xyzVector_double_t]¶

calculates the error twist between two RT objects, i.e. the linearised dual vector between them

C++: core::kinematics::jacobian::calculate_error_twist(const class core::kinematics::RT, const class core::kinematics::RT) –> struct std::pair<class numeric::xyzVector<double>, class numeric::xyzVector<double> >

pyrosetta.rosetta.core.kinematics.jacobian.project_ZYX_euler_on_cart(euler_angles: pyrosetta.rosetta.numeric.xyzVector_double_t, euler_error: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

projects intrinsic Euler angles onto extrinsic Euler angles in order XYZ (i.e. projected onto Cartesian unit vectors)

C++: core::kinematics::jacobian::project_ZYX_euler_on_cart(const class numeric::xyzVector<double>, const class numeric::xyzVector<double>) –> class numeric::xyzVector<double>