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

Modified Phenyl Group. More...

#include <MPhenylGroup.hh>

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

void Initialize ()
 Initialize the node, possibly pre-calculate anything that can be.
 
void Create ()
 Assign coordinates to atoms attached to outgoing bonds.
 
void ExportConnections (ConnectionsMatrix &aa)
 Export connection information to an external ConnectionsMatrix.
 
void BuildConnections ()
 Assign proper Bases to subnodes and call BuildConnections on them.
 
void LocPairs (std::deque< std::pair< int, int > > &lcp)
 List pairs of member atoms which are connected by 3 covalent bonds.
 
void SetBranchLength (int i, double x)
 Length of the bond connecting the i'th attachment to the ring.
 
- 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 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

Almost identical to the PhenylGroup, but all atoms attached to the ring can now be different. They could be located at different distances. Useful to construct the ring of the Tyrosine. In principle this class could serve to represent PhenylGroup as well. But to keep open this possibility of different atoms is more expensive. So, it should be used only when required.

Member Function Documentation

void MPhenylGroup::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