The SeriesJacobians class is the mid-level of the Jacobian analysis of a protein's kinematics relations. More...
#include <SeriesJacobians.hh>
Public Types | |
| typedef utility::vector1< core::Size > | residue_series |
| typedef a vector containing a series of residue numbers More... | |
Public Member Functions | |
| SeriesJacobians ()=delete | |
| No default constructor because SeriesJacobian is not used on its own, but always as part of a JacobianStructure. More... | |
| SeriesJacobians (core::conformation::Conformation const &conformation, residue_series const &residue_set, core::id::AtomID const &ref_atom) | |
| Constructor based on a vector containing a series of residues. More... | |
| SeriesJacobians (SeriesJacobians const &src) | |
| Copy constructor. More... | |
| ~SeriesJacobians () override | |
| Destructor. More... | |
| SeriesJacobiansOP | clone () const |
| Clone operation: make a copy of this object, and return an owning pointer to the copy. More... | |
| utility::vector1< core::Size > | get_residues () const |
| get residues that make up the chain More... | |
| core::Size | num_dofs () const |
| get amount of DoFs of the chain More... | |
| core::kinematics::MoveMapOP | move_map () const |
| get pointer to movemap More... | |
| core::id::AtomID | get_ref_atom_ID () const |
| get reference atom used to express all vectors in all modules More... | |
| utility::vector1< ModuleType1::jacobian_struct > | get_Jacobian_matrices (core::conformation::Conformation const &conformation) const |
| update all Jacobian matrices in the chain More... | |
Public Attributes | |
| utility::vector1< core::kinematics::jacobian::ModuleType1OP > | modules_ |
| vector with pointers to Jacobian modules More... | |
Private Member Functions | |
| utility::vector1< core::kinematics::jacobian::ModuleType1OP > | init_modules_amino_acids () |
| function that initializes the low-level Jacobian modules for a series of canonical amino acids More... | |
| SeriesJacobianTypeEnum | determine_residue_series_type (core::conformation::Conformation const &conformation, residue_series const &res_numbers) |
| function to determine the type of the residues that make up the series More... | |
Private Attributes | |
| utility::vector1< core::Size > | residue_set_ |
| vector with residue series whose internal DoFs are free to move More... | |
| core::Size | number_dofs_ |
| number of dofs of the serial chain More... | |
| core::id::AtomID | ref_atom_ID_ |
| reference atom in which all vectors are expressed More... | |
| core::kinematics::MoveMapOP | move_map_ {nullptr} |
| movemap of the series More... | |
Detailed Description
The SeriesJacobians class is the mid-level of the Jacobian analysis of a protein's kinematics relations.
Member Typedef Documentation
◆ residue_series
| typedef utility::vector1<core::Size> core::kinematics::jacobian::SeriesJacobians::residue_series |
typedef a vector containing a series of residue numbers
Constructor & Destructor Documentation
◆ SeriesJacobians() [1/3]
|
delete |
No default constructor because SeriesJacobian is not used on its own, but always as part of a JacobianStructure.
◆ SeriesJacobians() [2/3]
| core::kinematics::jacobian::SeriesJacobians::SeriesJacobians | ( | core::conformation::Conformation const & | conformation, |
| residue_series const & | residue_set, | ||
| core::id::AtomID const & | ref_atom_ID | ||
| ) |
Constructor based on a vector containing a series of residues.
This function constructs SeriesJacobians object based on a series of residues. First it is determined what kind of residues the series consists of, because this determines which Jacobian modules need to be initialized.
- Parameters
-
[in] residue_set the provided vector with residue numbers needs to be in ascending order, but may contain gaps (e.g. a vector with residues [16, 17, 19, 23, 24, 25, 26] is fine).
References core::kinematics::jacobian::ALPHA_AA, determine_residue_series_type(), init_modules_amino_acids(), modules_, number_dofs_, ref_atom_ID_, and residue_set_.
◆ SeriesJacobians() [3/3]
|
default |
Copy constructor.
Copy constructor. Keep default unless deep copying is needed (and in that case, consider using DeepCopyOPs.)
◆ ~SeriesJacobians()
|
override |
Destructor.
Member Function Documentation
◆ clone()
| SeriesJacobiansOP core::kinematics::jacobian::SeriesJacobians::clone | ( | ) | const |
Clone operation: make a copy of this object, and return an owning pointer to the copy.
◆ determine_residue_series_type()
|
private |
function to determine the type of the residues that make up the series
References core::kinematics::jacobian::ALPHA_AA, core::chemical::ResidueType::is_alpha_aa(), and core::conformation::Conformation::residue_type().
Referenced by SeriesJacobians().
◆ get_Jacobian_matrices()
| utility::vector1< ModuleType1::jacobian_struct > core::kinematics::jacobian::SeriesJacobians::get_Jacobian_matrices | ( | core::conformation::Conformation const & | conformation | ) | const |
update all Jacobian matrices in the chain
obtain vector of structs with all Jacobian matrices in the series chain
References modules_.
◆ get_ref_atom_ID()
|
inline |
get reference atom used to express all vectors in all modules
References ref_atom_ID_.
◆ get_residues()
|
inline |
get residues that make up the chain
References residue_set_.
◆ init_modules_amino_acids()
|
private |
function that initializes the low-level Jacobian modules for a series of canonical amino acids
For canonical amino acids the internal DoFs are the phi and psi torsion angles. That knowledge is used to initialize the underlying Jacobian modules. First, the total number of DoFs in the residue series is calculated, and subsequently the residue series is complemented with "assisting residues" such that the series can be split up in modules of six torsion axes. This means that some of the torsion axes in the last module are actually constrained, which is captured by the variable dofs_module.
References core::id::BB, move_map_, number_dofs_, ref_atom_ID_, and residue_set_.
Referenced by SeriesJacobians().
◆ move_map()
|
inline |
get pointer to movemap
References move_map_.
◆ num_dofs()
|
inline |
get amount of DoFs of the chain
References number_dofs_.
Member Data Documentation
◆ modules_
| utility::vector1< core::kinematics::jacobian::ModuleType1OP > core::kinematics::jacobian::SeriesJacobians::modules_ |
vector with pointers to Jacobian modules
Referenced by get_Jacobian_matrices(), and SeriesJacobians().
◆ move_map_
|
private |
movemap of the series
Referenced by init_modules_amino_acids(), and move_map().
◆ number_dofs_
|
private |
number of dofs of the serial chain
Referenced by init_modules_amino_acids(), num_dofs(), and SeriesJacobians().
◆ ref_atom_ID_
|
private |
reference atom in which all vectors are expressed
Referenced by get_ref_atom_ID(), init_modules_amino_acids(), and SeriesJacobians().
◆ residue_set_
|
private |
vector with residue series whose internal DoFs are free to move
Referenced by get_residues(), init_modules_amino_acids(), and SeriesJacobians().
The documentation for this class was generated from the following files:
- src/core/kinematics/jacobian/SeriesJacobians.hh
- src/core/kinematics/jacobian/SeriesJacobians.cc
