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

A structure with 8 integers to characterize a degree of freedom. More...

#include <DOF_Info.hh>

Public Member Functions

 DOF_Info ()
 Default constructor.
 
 DOF_Info (const DOF_Info &)
 Copy constructor.
 
DOF_Infooperator= (const DOF_Info &d)
 Assignment operator.
 
void assign (int kind, int ch_no, int grp_no, int glob_idx, int idx_in_chn, int sp_idx_in_grp, int sp_glob_idx, int sp_idx_in_chn)
 Assign to all fields.
 
std::string str () const
 Make a string representation.
 

Public Attributes

int dof_kind
 An enumeration of different kinds of coordinates.
 
int chain
 Which chain the DOF belongs to.
 
int group
 Which group the DOF belongs to (when it makes sense)
 
int global_index
 Global index among all DOFs in the system.
 
int index_in_chain
 Index among all DOFs in the protein chain.
 
int specific_index_in_group
 Index among DOFs of the same kind in the particular residue.
 
int specific_global_index
 Global index among DOFs of the same kind in the population.
 
int specific_index_in_chain
 Index among DOFs of the same kind in the chain.
 

Detailed Description

A degree of freedom in ProFASi is either a torsional angle, or a rigid body coordinate. By convention, information about the overall location and orientation of a protein is specified through the Cartessian coordinates of the first three atoms on the backbone seen from the N-terminus. ProFASi 1.5 provides a unified interface to all degrees of freedom in the system. This small class stores useful information about a particular DOF in one place, like which chain or residue it belongs to. All members are public. It is important that these are 8 integers: we intend to build a heavily accessed array of a large number of these objects.

Member Data Documentation

int prf::DOF_Info::index_in_chain

This is the answer to the question: what is the index of this DOF in this chain ? It's relation to the group_index member below is complicated. The protein class may rearrange DOFs from all constituent amino acids for convenience.

int prf::DOF_Info::specific_index_in_group

This is the index of a particular DOF of a certain kind in a residue. There may be rigid body DOFs assigned to a group with group indexes from 0 to 8. There could be one or two backbone DOF with group indexes starting from 0. This goes for side chain DOF as well. The variable specific_index_in_group enumerates DOFs of a certain kind in the residue.


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