prf::DihedralGroup Class Reference

The dihedral group or boomerang. More...

#include <DihedralGroup.hh>

Inheritance diagram for prf::DihedralGroup:

Public Member Functions
void	Initialize ()
	Initialize the node, possibly pre-calculate anything that can be.
void	SetTheta (double x0, double x1)
	Base-Root-Junction, and the only other theta angle in this case.
void	SetBondLengths (double x0, double x1, double x2)
	All bond lengths.
void	Create ()
	Assign coordinates to atoms attached to outgoing bonds.
Public Member Functions inherited from prf::Node
void	ReCreate ()
	Recursive Create. Self followed by subnodes.
virtual void	AssignPhi (double)
	assign to the dof of the Node.
double	Phi ()
	retrieve the torsional angle
void	LockPhi (double xx)
	Lock the torsional dof of the Node to value xx.
int	Locked () const
	if it is really a dof
Atom &	ATOM (int i)
	Reference to i'th atom.
Atom &	atom (int i)
	Reference to i'th atom.
void	AddSubnode (Node *nd)
	Make another node a subnode.
void	AtomOffset (int i)
void	RevertPhi (double)
	Revert the torsional angle to a given value.
virtual void	ExportConnections (ConnectionsMatrix &aa)
	Export connection information to an external ConnectionsMatrix.
virtual void	LocPairs (std::deque< std::pair< int, int > > &lcp)
	List pairs of member atoms which are connected by 3 covalent bonds.
virtual void	BuildConnections ()
	Assign proper Bases to subnodes and call BuildConnections on them.
virtual void	SetBase (Atom &ap)
	Set a new atom as one Base.
void	SetBase (Atom &, Atom &, Atom &)
	be careful: This actually means set Base, Root and Junction
void	set_bases (Atom &b1, Atom &b2, Atom &b3)
	And this means set all bases.
void	MobileAtoms (int &r1, int &r2)
	Atoms that move when the node turns.
void	SetMobileAtoms (int i, int j)
	Set what range should be returned as the mobile atoms.
virtual void	AssignAtoms (Atom &a0, Atom &a1, Atom &a2, std::vector< Atom > &att, int st)
virtual void	AssignAtoms (Atom &a0, Atom &a1, Atom &a2, Atom &a3)
virtual void	AssignAtoms (Atom &a0, Atom &a1, Atom &a2, Atom &a3, Atom &a4)
virtual void	AssignAtoms (Atom &a0, Atom &a1, Atom &a2, Atom &a3, Atom &a4, Atom &a5)
virtual void	SetRelPhi (double, double)
Public Member Functions inherited from prf::Named
	Named ()
	Create an object with name "unnamed".
	Named (const char *st)
	Create an object with name st given as a C string.
	Named (std::string st)
	Create an object with a name given as a string.
std::string	Name () const
	Retrive the name of an object.
void	Name (std::string gnm)
	Assign a new name to an object.

Detailed Description

This group with only one outgoing bond only occurs in Methionine, Serine Threonine and Tyrosine

Member Function Documentation

void DihedralGroup::Create ( )

virtual

*Using the position of Base, Root and Junction, and the state of the degree of freedom associated with the node, find the coordinates of all other atoms in the node.

Reimplemented from prf::Node.

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The documentation for this class was generated from the following files:

• model/Elements/DihedralGroup.hh
• model/Elements/DihedralGroup.cc