PROFASI  Version 1.5
Public Member Functions | List of all members
PopulationHandler Class Reference

Helper class for configuring the protein population. More...

#include <PopulationHandler.hh>

Inherits HandlerBase.

Public Member Functions

 PopulationHandler ()
 Default constructor.
Populationpopulation ()
 Retrieve pointer to population.
int read_xml_pop (std::string xmlfile)
 Set up a population from an XML population description file.
int read_pdb_pop (std::string pdbfilename, std::string sel)
 Set up a population from a PDB file and selection.
int parseCommand (InstructionString s)
 Parse commands passed as a deque of InstructionString objects.
void boxSize (double xx, bool usbit=true)
 Set size of the periodic box.
- Public Member Functions inherited from HandlerBase
virtual void parseCommands (std::list< InstructionString > &cmds, int argc, char *argv[])
 Parse commands passed as a deque of InstructionString objects.

Detailed Description

The population handler owns a population object, and provides a broader interface to it. The idea is to reduce the Population class to a simple container of proteins, and provide well defined catetories of functionality in small helper classes like this one. At the present, PopulationHandler is only responsible for initializing the population: either from a ProFASi XML structure file, or (through a set of settings file commands) from sequence alone, or from a PDB file.

Member Function Documentation

void PopulationHandler::boxSize ( double  xx,
bool  usbit = true 

PROFASI simulations are always done in a periodic box. Here we set the box size. If the user does not provide a box size, a sensible default is calculated by analyzing the population. The parameter usbit is used to distinguish a box size set up promted by a user choice (settings file etc) from an automatic calculation for the case when such a choice is not given. Values specified by the user have priority.

int PopulationHandler::read_pdb_pop ( std::string  pdbfilename,
std::string  sel 

This function will import a selection from a given PDB file as the population. This means, any pre-existing chains in the population will be lost. The selections are given in the usual method ProFASi PDB handling: Selections and Filters .

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