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

Represents the phenyl ring with attached hydrogens. More...

#include <PhenylGroup.hh>

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

void Initialize ()
 Ininitalize now calculates geometrical constants for phenyl ring.
 
void SetRootLengths (double x0, double x1)
 Base-Root and Root-Junction lengths.
 
void SetRootAngle (double x)
 Base-Root-Junction angle.
 
void Create ()
 Assign coordinates to atoms attached to outgoing bonds.
 
void ExportConnections (ConnectionsMatrix &aa)
 Export connection information to an external ConnectionsMatrix.
 
void LocPairs (std::deque< std::pair< int, int > > &lcp)
 List pairs of member atoms which are connected by 3 covalent 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 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)
 
virtual void SetBranchLength (int i, double x)
 
- 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

The Phenyl ring with all attached hydrogens is regarded as one rigid block. So, it is easy to calculate positions of all these atoms when the position of two of the carbon atoms in the ring is fixed. It is therefore just one node even if there are many junctions where bonds meet. Root here is the external atom to which the ring is attached. Junction is the Carbon on the ring attached to the Root. There is no branch. The whole ring is regarded as the outgoing part.

Member Function Documentation

void PhenylGroup::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.


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