ProtoMol - an object-oriented component based framework for Molecular Dynamics simulations.
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ProtoMol::Molecule Struct Reference

#include <Molecule.h>

List of all members.

Public Member Functions

 Molecule ()
size_t size ()
int operator[] (int i)

Public Attributes

Real mass
Vector3D position
Vector3D momentum
std::vector< int > atoms
std::vector< PairInt > pairs
bool water
unsigned int type
unsigned int newtype
Real lambda
std::vector< int > bondList
std::vector< int > angleList
std::vector< int > dihedralList
std::vector< int > improperList

Detailed Description

This class defines the information for one molecule. It contains the mass of the molecule, its center of mass position and momentum, and a list of the atoms on the molecule.

Constructor & Destructor Documentation

ProtoMol::Molecule::Molecule (   )  [inline]
 

Member Function Documentation

int ProtoMol::Molecule::operator[] (  int  i  )  [inline]
 

Return atom number.

size_t ProtoMol::Molecule::size (   )  [inline]
 

Return number of atoms of this molecule.

Member Data Documentation

std::vector<int> ProtoMol::Molecule::angleList
 

std::vector<int> ProtoMol::Molecule::atoms
 

List of the ID#s of the atoms on the molecule.

std::vector<int> ProtoMol::Molecule::bondList
 

std::vector<int> ProtoMol::Molecule::dihedralList
 

std::vector<int> ProtoMol::Molecule::improperList
 

list of the index #s of each bond, angle, dihedral, and improper on this molecule...may not need this because of pairs above!!!!

Real ProtoMol::Molecule::lambda
 

Parameter controlling the identity (or type) of the molecule.

Real ProtoMol::Molecule::mass
 

The mass of the molecule.

Vector3D ProtoMol::Molecule::momentum
 

The xyz momentum of the molecule's center of mass.

unsigned int ProtoMol::Molecule::newtype
 

Type of the molecule...needed for ISG simulations type is the molecule's type in the Lambda = 0 state; newtype is the molecule's type in the Lambda = 1 state;

std::vector<PairInt> ProtoMol::Molecule::pairs
 

List of pairs (bond, angle, dihedral and improper).

Vector3D ProtoMol::Molecule::position
 

The xyz coordinate of the molecule's center of mass.

unsigned int ProtoMol::Molecule::type
 

bool ProtoMol::Molecule::water
 

If molecule is a water molecule.

The documentation for this struct was generated from the following file: Last update: . GNU GENERAL PUBLIC LICENSE, copyrighted by the University of Notre Dame and the University of Bergen, Norway.