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

#include <SeriesJacobians.hh>

Inheritance diagram for core::kinematics::jacobian::SeriesJacobians:

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 ()
	get residues that make up the chain More...

void	update_Jacobian_matrices (core::conformation::Conformation const &conformation)
	update all Jacobian matrices in the chain More...

Public Attributes
utility::vector1 < core::kinematics::jacobian::ModuleType1OP >	modules_
	vector with 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_
	reference atom in which all vectors are expressed More...

Detailed Description

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

Author: teunhoevenaars (teunh.nosp@m.oeve.nosp@m.naars.nosp@m.@gma.nosp@m.il.co.nosp@m.m)

Member Typedef Documentation

typedef utility::vector1<core::Size> core::kinematics::jacobian::SeriesJacobians::residue_series

typedef a vector containing a series of residue numbers

Constructor & Destructor Documentation

core::kinematics::jacobian::SeriesJacobians::SeriesJacobians ( )

delete

No default constructor because SeriesJacobian is not used on its own, but always as part of a JacobianStructure.

core::kinematics::jacobian::SeriesJacobians::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.

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::CANONICAL_AA, determine_residue_series_type(), init_modules_amino_acids(), modules_, number_dofs_, ref_atom_, and residue_set_.

core::kinematics::jacobian::SeriesJacobians::SeriesJacobians ( SeriesJacobians const & src )

default

Copy constructor.

Copy constructor. Keep default unless deep copying is needed (and in that case, consider using DeepCopyOPs.)

core::kinematics::jacobian::SeriesJacobians::~SeriesJacobians ( )

override

Destructor.

Member Function Documentation

SeriesJacobiansOP core::kinematics::jacobian::SeriesJacobians::clone ( ) const

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

SeriesJacobianTypeEnum core::kinematics::jacobian::SeriesJacobians::determine_residue_series_type	(	core::conformation::Conformation const &	conformation,
		residue_series const &	res_numbers
	)

private

function to determine the type of the residues that make up the series

References core::kinematics::jacobian::CANONICAL_AA, core::chemical::ResidueType::is_canonical_aa(), and core::conformation::Conformation::residue_type().

Referenced by SeriesJacobians().

utility::vector1< core::Size > core::kinematics::jacobian::SeriesJacobians::get_residues ( )

inline

get residues that make up the chain

References residue_set_.

utility::vector1< core::kinematics::jacobian::ModuleType1OP > core::kinematics::jacobian::SeriesJacobians::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 number_dofs_, ref_atom_, and residue_set_.

Referenced by SeriesJacobians().

void core::kinematics::jacobian::SeriesJacobians::update_Jacobian_matrices ( core::conformation::Conformation const & conformation )

update all Jacobian matrices in the chain

update all Jacobian matrices in the series chain

References modules_.