PROFASI  Version 1.5
Public Member Functions | List of all members
prf::ATetGroup Class Reference

Asymmetric Tetrahedral Group. More...

#include <ATetGroup.hh>

Inheritance diagram for prf::ATetGroup:
Inheritance graph
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Public Member Functions

void SetTheta (double t0, double t1, double t2, double t3)
 Assign individually the bond angle for each outgoing bond.
 
void SetPhi (double pab, double pac)
 Adjust the locations of the Branches around the incoming bond.
 
void Initialize ()
 Initialize the node, possibly pre-calculate anything that can be.
 
void SetBondAngles (double, double, double, double)
 Set the bondangles base-root-junction and root-junction-branch1,2,3.
 
void SetRelPhi (double, double)
 Set the phi angle separation between brances 1-2 and 1-3.
 
void SetBranchLength (int i, double x)
 Set bondlength for branch 0,1 or 2.
 
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
 
AtomATOM (int i)
 Reference to i'th atom.
 
Atomatom (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)
 
- 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

Mainly represents the CH2 groups in side chains. But it is meant to be any atom connected to 4 others. The three outgoing bonds could have different kinds of atoms, and hence different bondlengths and bond angles.

Member Function Documentation

void ATetGroup::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.

void prf::ATetGroup::SetTheta ( double  t0,
double  t1,
double  t2,
double  t3 
)
inline

The first parameter is the Base-Root-Junction angle, the other 3 are Root-Junction-Branch_i angles


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

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2