SeriesJacobians.cc File Reference

class that handles the Jacobian analysis of atoms connected in series More...

#include <core/kinematics/jacobian/SeriesJacobians.hh>
#include <basic/Tracer.hh>
#include <utility/pointer/memory.hh>
#include <core/kinematics/jacobian/ModuleType1.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/conformation/Conformation.hh>
#include <core/id/TorsionID.hh>

Namespaces
	core
	A class for reading in the atom type properties.
	core::kinematics
	core::kinematics::jacobian

Functions
static basic::Tracer	TR ("core.kinematics.jacobian.SeriesJacobians")

Detailed Description

class that handles the Jacobian analysis of atoms connected in series

Author

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

Function Documentation

TR()

static basic::Tracer TR ( "core.kinematics.jacobian.SeriesJacobians"  )

static

This class handles the Jacobian analysis of a single series of atoms. A full Jacobian analysis consists of one or more sets of such series, as described in jacobian_structure_class. A series of atoms (represented by a series of residues) in a protein can have any length, and therefore any number of internal Degrees of Freedom (DoFs) However, the number of Cartesian DoFs of the final atom in the chain are by definition 6. Therefore, the maximum number of independent internal DoFs to describe six differential Cartesian DoFs is 6. Jacobian analysis relies on orthogonal vectors, which means that a Jacobian analysis can only be done for blocks of maximum six internal DoFs. To deal with this, the SeriesJacobians class splits up a series of atoms (taken from input residues) into blocks that have six internal DoFs.