Faunus::MoleculeData Class Reference

General properties for molecules. More...

#include <molecule.h>

Collaboration diagram for Faunus::MoleculeData:

Public Types
using	index_type = int

Public Member Functions
index_type &	id ()
	Type id.
const index_type &	id () const
	Type id.
void	createMolecularConformations (const json &j)
	Add conformations if appropriate.
void	setConformationWeights (const json &j)
	Add weights for conformations.
size_t	numConformations () const
	Number of conformations.
	MoleculeData (const std::string &name, const ParticleVector &particles, const BasePointerVector< pairpotential::BondData > &bonds)
bool	isImplicit () const
	Is molecule implicit and explicitly absent from simulation cell?
bool	isPairExcluded (int i, int j) const
bool	isMolecular () const
bool	isAtomic () const
void	setInserter (std::shared_ptr< MoleculeInserter > ins)
	Specify function to be used when inserting into space. More...
ParticleVector	getRandomConformation (Geometry::GeometryBase &geo, const ParticleVector &otherparticles=ParticleVector())
	Get random conformation that fits in container. More...

Public Attributes
std::shared_ptr< MoleculeInserter >	inserter = nullptr
	Functor for insertion into space.
std::string	name
	Molecule name.
bool	atomic = false
	True if atomic group (salt etc.)
bool	compressible
	True if compressible group (scales internally upon volume change) More...
bool	rigid = false
	True if particle should be considered as rigid.
double	activity = 0.0
	Chemical activity (mol/l)
std::vector< AtomData::index_type >	atoms
	Sequence of atoms in molecule (atom id's)
BasePointerVector< pairpotential::BondData >	bonds
WeightedDistribution< ParticleVector >	conformations
	Conformations of molecule.

Protected Attributes
ExclusionsVicinity	exclusions
	Implementation of isPairExcluded; various implementation can be provided in the future.

Friends
class	MoleculeBuilder
void	to_json (json &j, const MoleculeData &a)
void	from_json (const json &j, MoleculeData &a)

Detailed Description

General properties for molecules.

Member Function Documentation

getRandomConformation()

ParticleVector Faunus::MoleculeData::getRandomConformation	(	Geometry::GeometryBase &	geo,
		const ParticleVector &	otherparticles = ParticleVector()
	)

Get random conformation that fits in container.

Parameters

geo	Geometry
otherparticles	Typically spc.p is insertion depends on other particle

By default the molecule is placed at a random position and orientation with no container overlap using the RandomInserter class. This behavior can be changed by specifying another inserter using setInserter().

setInserter()

void Faunus::MoleculeData::setInserter

(

std::shared_ptr< MoleculeInserter >

ins

)

Specify function to be used when inserting into space.

By default a random position and orientation is generator and overlap with container is avoided.

Member Data Documentation

compressible

bool Faunus::MoleculeData::compressible

Initial value:

=
        false

True if compressible group (scales internally upon volume change)

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The documentation for this class was generated from the following files:

• src/molecule.h
• src/molecule.cpp