PROFASI  Version 1.5
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prf::Translation Class Reference

Rigid body translation of a whole chain. More...

#include <Translation.hh>

Inheritance diagram for prf::Translation:
Inheritance graph

Additional Inherited Members

- Public Member Functions inherited from prf::Update
void set_RandomNumberGenerator (RandomNumberBase *rn)
 An update needs a random number generator.
void set_sequencial_sweep (bool sw=true)
 Sweep through the DOFs sequencially rather than randomly.
void connect (Population *pl)
 An update must be connected with a population.
virtual void init ()
 Initialize update for use.
int perform (int itm)
 Make a move in the conformation space.
virtual int accept ()
 Finalizes a proposed update.
virtual int revert ()
 Reverts the proposed update.
virtual void print_setup (std::string &st)
 Print info about any departure from default behaviour.
size_t n_relevant_dof () const
 The number of DOF in the system which may be touched by the update.
double get_weight_of_dof (int idof)
 Weight of a particular DOF.
void set_weight_of_dof (int idof, double vl)
 Set weight of a DOF.
virtual void configure (prf_xml::XML_Node *nd)
 Configure update using options provided in an XML node.
size_t get_site_of_dof (DOF_Info &dof)
 get site index of a given DOF
bool sidechain_update () const
bool rigid_chain_update () const
bool backbone_update () const
bool multichain_update () const
bool local_update () const
unsigned num_changes ()
dof_change_typechange (unsigned i)
void current_atoms (int &istr, int &iend)
 The first and last atoms affected by the update.
int begin_atom ()
 First affected atom.
int end_atom ()
 One past the last atom, like the end() in standard containers.
int begin_flexible_part ()
 Start of the flexible part of the update.
int end_flexible_part ()
 End of the flexible part, once again, one past the last ...
virtual double intrinsic_weight () const
 Additional weight for Metropolis-Hastings updates.
int n_residue_rigid_ranges () const
 Makes list of ranges of changed residues.
void residue_rigid_range (int i, int &r1, int &r2)
 i'th rigid range returned as ligand indices in r1 and r2
std::vector< std::pair< int,
int > > * 
residue_rigid_ranges ()
 Pointer to the vector of rigid ranges.
int n_atom_rigid_ranges () const
void atom_rigid_range (int i, int &r1, int &r2)
std::vector< std::pair< int,
int > > * 
atom_rigid_ranges ()

Detailed Description

Simple block translation of a whole chain by a random vector. The size of the translation vector is kept small compared to the box size.

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