topology of the whole system More...

#include <topology.h>

Collaboration diagram for votca::csg::Topology:

[legend]

Public Member Functions
	Topology ()
	constructor

	~Topology ()

void	Cleanup ()
	Cleans up all the stored data.

Bead *	CreateBead (Bead::Symmetry symmetry, std::string name, std::string type, Index resnr, double m, double q)
	Creates a new Bead.

Molecule *	CreateMolecule (std::string name)
	Creates a new molecule.

void	CheckMoleculeNaming (void)
	checks weather molecules with the same name really contain the same number of beads

Residue &	CreateResidue (std::string name)
	Create a new resiude.

Residue &	CreateResidue (std::string name, Index id)

void	CreateMoleculesByRange (std::string name, Index first, Index nbeads, Index nmolecules)
	create molecules based on blocks of atoms

Index	MoleculeCount () const
	number of molecules in the system

Index	BeadCount () const

Index	ResidueCount () const

Molecule *	MoleculeByIndex (Index index)

BeadContainer &	Beads ()

ResidueContainer &	Residues ()

const ResidueContainer &	Residues () const

MoleculeContainer &	Molecules ()

const MoleculeContainer &	Molecules () const

InteractionContainer &	BondedInteractions ()

const InteractionContainer &	BondedInteractions () const

void	AddBondedInteraction (Interaction *ic)

std::vector< Interaction * >	InteractionsInGroup (const std::string &group)

bool	BeadTypeExist (std::string type) const
	Determine if a bead type exists.

void	RegisterBeadType (std::string type)
	Register the bead type with the topology object.

Index	getBeadTypeId (std::string type) const
	Given a bead type this method returns the id associated with the type.

Bead *	getBead (const Index i)
	Returns a pointer to the bead with index i.

const Bead *	getBead (const Index i) const

Residue &	getResidue (const Index i)

const Residue &	getResidue (const Index i) const

Molecule *	getMolecule (const Index i)

const Molecule *	getMolecule (const Index i) const

void	ClearMoleculeList ()

void	CopyTopologyData (Topology *top)
	copy topology data of different topology

void	RenameMolecules (std::string range, std::string name)
	rename all the molecules in range

void	RenameBeadType (std::string name, std::string newname)
	rename all the bead types

void	SetBeadTypeMass (std::string name, double value)
	set the mass of all the beads of a certain type

void	setBox (const Eigen::Matrix3d &box, BoundaryCondition::eBoxtype boxtype=BoundaryCondition::typeAuto)

const Eigen::Matrix3d &	getBox () const

const BoundaryCondition &	getBoundary () const
	Return the boundary condition object.

void	setTime (double t)

double	getTime () const

void	setStep (Index s)

Index	getStep () const

void	setParticleGroup (std::string particle_group)

std::string	getParticleGroup () const

Eigen::Vector3d	getDist (Index bead1, Index bead2) const
	pbc correct distance of two beads

Eigen::Vector3d	BCShortestConnection (const Eigen::Vector3d &r_i, const Eigen::Vector3d &r_j) const
	calculate shortest vector connecting two points

double	ShortestBoxSize () const
	return the shortest box size

double	BoxVolume () const

void	RebuildExclusions ()

ExclusionList &	getExclusions ()

const ExclusionList &	getExclusions () const

BoundaryCondition::eBoxtype	getBoxType () const

template<typename iteratable >
void	InsertExclusion (Bead *bead1, iteratable &l)

bool	HasVel ()

void	SetHasVel (const bool v)

bool	HasForce ()

void	SetHasForce (const bool v)

Protected Member Functions
BoundaryCondition::eBoxtype	autoDetectBoxType (const Eigen::Matrix3d &box) const

Protected Attributes
std::unique_ptr< BoundaryCondition >	bc_

std::unordered_map< std::string, Index >	beadtypes_
	bead types in the topology

BeadContainer	beads_
	beads in the topology

MoleculeContainer	molecules_
	molecules in the topology

ResidueContainer	residues_
	residues in the topology

InteractionContainer	interactions_
	bonded interactions in the topology

ExclusionList	exclusions_

std::map< std::string, Index >	interaction_groups_

std::map< std::string, std::vector< Interaction * > >	interactions_by_group_

double	time_ = 0.0

Index	step_ = 0

bool	has_vel_ = false

bool	has_force_ = false

std::string	particle_group_ = "unassigned"
	The particle group (For H5MD file format)

Detailed Description

topology of the whole system

The Topology class stores the topology of the system like the beads, bonds, molecules and residues.

Definition at line 81 of file topology.h.

Constructor & Destructor Documentation

◆ Topology()

votca::csg::Topology::Topology ( )

inline

constructor

Definition at line 84 of file topology.h.

◆ ~Topology()

votca::csg::Topology::~Topology ( )

Definition at line 47 of file topology.cc.

Member Function Documentation

◆ AddBondedInteraction()

void votca::csg::Topology::AddBondedInteraction ( Interaction * ic )

Definition at line 188 of file topology.cc.

◆ autoDetectBoxType()

BoundaryCondition::eBoxtype votca::csg::Topology::autoDetectBoxType ( const Eigen::Matrix3d & box ) const

protected

Definition at line 252 of file topology.cc.

◆ BCShortestConnection()

Eigen::Vector3d votca::csg::Topology::BCShortestConnection	(	const Eigen::Vector3d &	r_i,
		const Eigen::Vector3d &	r_j
	)		const

calculate shortest vector connecting two points

Parameters

r_i	first point
r_j	second point

Returns: distance vector

calculates the smallest distance between two points with correct treatment of pbc

Definition at line 238 of file topology.cc.

◆ BeadCount()

Index votca::csg::Topology::BeadCount ( ) const

inline

number of beads in the system

Returns: number of beads in the system

Definition at line 150 of file topology.h.

◆ Beads()

BeadContainer & votca::csg::Topology::Beads ( )

inline

access containter with all beads

Returns: bead container

Definition at line 169 of file topology.h.

◆ BeadTypeExist()

bool votca::csg::Topology::BeadTypeExist ( std::string type ) const

Determine if a bead type exists.

Returns: bool true if it has been registered

Definition at line 210 of file topology.cc.

◆ BondedInteractions() [1/2]

InteractionContainer & votca::csg::Topology::BondedInteractions ( )

inline

access containter with all bonded interactions

Returns: bonded interaction container

Definition at line 189 of file topology.h.

◆ BondedInteractions() [2/2]

const InteractionContainer & votca::csg::Topology::BondedInteractions ( ) const

inline

Definition at line 190 of file topology.h.

◆ BoxVolume()

double votca::csg::Topology::BoxVolume ( ) const

calculates the box volume

Returns: box volume

Definition at line 248 of file topology.cc.

◆ CheckMoleculeNaming()

void votca::csg::Topology::CheckMoleculeNaming ( void )

checks weather molecules with the same name really contain the same number of beads

Definition at line 169 of file topology.cc.

◆ Cleanup()

void votca::csg::Topology::Cleanup ( )

Cleans up all the stored data.

Definition at line 49 of file topology.cc.

◆ ClearMoleculeList()

void votca::csg::Topology::ClearMoleculeList ( )

inline

delete all molecule information

Definition at line 237 of file topology.h.

◆ CopyTopologyData()

void votca::csg::Topology::CopyTopologyData ( Topology * top )

copy topology data of different topology

Parameters

top	topology to copy from

Definition at line 102 of file topology.cc.

◆ CreateBead()

Bead * votca::csg::Topology::CreateBead	(	Bead::Symmetry	symmetry,
		std::string	name,
		std::string	type,
		Index	resnr,
		double	m,
		double	q
	)

inline

Creates a new Bead.

Parameters

[in]	symmetry	symmetry of the bead, 1: spherical 3: ellipsoidal
[in]	name	name of the bead
[in]	type	bead type
[in]	resnr	residue number
[in]	m	mass
[in]	q	charge

Returns: pointer to created bead

The function creates a new bead and adds it to the list of beads.

Definition at line 441 of file topology.h.

◆ CreateMolecule()

Molecule * votca::csg::Topology::CreateMolecule ( std::string name )

inline

Creates a new molecule.

Parameters

[in] name name of the molecule

Returns: pointer to created molecule

Definition at line 449 of file topology.h.

◆ CreateMoleculesByRange()

void votca::csg::Topology::CreateMoleculesByRange	(	std::string	name,
		Index	first,
		Index	nbeads,
		Index	nmolecules
	)

create molecules based on blocks of atoms

Parameters

[in]	name	molecule name
[in]	first	first bead
[in]	nbeads	number of beads per molecule
[in]	nmolecules	number of molecules

Todo:: implement checking, only used in xml topology reader

Definition at line 72 of file topology.cc.

◆ CreateResidue() [1/2]

Residue & votca::csg::Topology::CreateResidue ( std::string name )

inline

Create a new resiude.

Parameters

[in] name residue name

Returns: created residue

Definition at line 462 of file topology.h.

◆ CreateResidue() [2/2]

Residue & votca::csg::Topology::CreateResidue	(	std::string	name,
		Index	id
	)

inline

Definition at line 454 of file topology.h.

◆ getBead() [1/2]

Bead * votca::csg::Topology::getBead ( const Index i )

inline

Returns a pointer to the bead with index i.

Parameters

[in] i the id of the bead

Returns: Bead * is a pointer to the bead

Definition at line 227 of file topology.h.

◆ getBead() [2/2]

const Bead * votca::csg::Topology::getBead ( const Index i ) const

inline

Definition at line 228 of file topology.h.

◆ getBeadTypeId()

Index votca::csg::Topology::getBeadTypeId ( std::string type ) const

Given a bead type this method returns the id associated with the type.

Parameters

[in] type string name of the type

Returns: Index the id of the type

Definition at line 133 of file topology.cc.

◆ getBoundary()

const BoundaryCondition & votca::csg::Topology::getBoundary ( ) const

inline

Return the boundary condition object.

Definition at line 303 of file topology.h.

◆ getBox()

const Eigen::Matrix3d & votca::csg::Topology::getBox ( ) const

inline

get the simulation box

Returns: triclinic box matrix

Definition at line 298 of file topology.h.

◆ getBoxType()

BoundaryCondition::eBoxtype votca::csg::Topology::getBoxType ( ) const

inline

Definition at line 394 of file topology.h.

◆ getDist()

Eigen::Vector3d votca::csg::Topology::getDist	(	Index	bead1,
		Index	bead2
	)		const

pbc correct distance of two beads

Parameters

bead1	index of first bead
bead2	index of second bead

Returns: distance vector

calculates the smallest distance between two beads with correct treatment of pbc

Definition at line 243 of file topology.cc.

◆ getExclusions() [1/2]

ExclusionList & votca::csg::Topology::getExclusions ( )

inline

access exclusion list

Returns: exclusion list

Definition at line 391 of file topology.h.

◆ getExclusions() [2/2]

const ExclusionList & votca::csg::Topology::getExclusions ( ) const

inline

Definition at line 392 of file topology.h.

◆ getMolecule() [1/2]

Molecule * votca::csg::Topology::getMolecule ( const Index i )

inline

Definition at line 231 of file topology.h.

◆ getMolecule() [2/2]

const Molecule * votca::csg::Topology::getMolecule ( const Index i ) const

inline

Definition at line 232 of file topology.h.

◆ getParticleGroup()

std::string votca::csg::Topology::getParticleGroup ( ) const

inline

Gets the particle group.

Returns: The name of a particle group.

Definition at line 343 of file topology.h.

◆ getResidue() [1/2]

Residue & votca::csg::Topology::getResidue ( const Index i )

inline

Definition at line 229 of file topology.h.

◆ getResidue() [2/2]

const Residue & votca::csg::Topology::getResidue ( const Index i ) const

inline

Definition at line 230 of file topology.h.

◆ getStep()

Index votca::csg::Topology::getStep ( ) const

inline

get the step number of current frame

Returns: step number

Definition at line 329 of file topology.h.

◆ getTime()

double votca::csg::Topology::getTime ( ) const

inline

get the time of current frame

Returns: simulation time in ns

Definition at line 317 of file topology.h.

◆ HasForce()

bool votca::csg::Topology::HasForce ( )

inline

Definition at line 402 of file topology.h.

◆ HasVel()

bool votca::csg::Topology::HasVel ( )

inline

Definition at line 399 of file topology.h.

◆ InsertExclusion()

template<typename iteratable >

void votca::csg::Topology::InsertExclusion	(	Bead *	bead1,
		iteratable &	l
	)

inline

Definition at line 475 of file topology.h.

◆ InteractionsInGroup()

std::vector< Interaction * > votca::csg::Topology::InteractionsInGroup ( const std::string & group )

Definition at line 201 of file topology.cc.

◆ MoleculeByIndex()

Molecule * votca::csg::Topology::MoleculeByIndex ( Index index )

inline

get molecule by index

Parameters

index molecule number

Returns: pointer to molecule

Definition at line 470 of file topology.h.

◆ MoleculeCount()

Index votca::csg::Topology::MoleculeCount ( ) const

inline

number of molecules in the system

Returns: number of molecule in topology

Definition at line 144 of file topology.h.

◆ Molecules() [1/2]

MoleculeContainer & votca::csg::Topology::Molecules ( )

inline

access containter with all molecules

Returns: molecule container

Definition at line 182 of file topology.h.

◆ Molecules() [2/2]

const MoleculeContainer & votca::csg::Topology::Molecules ( ) const

inline

Definition at line 183 of file topology.h.

◆ RebuildExclusions()

void votca::csg::Topology::RebuildExclusions ( )

rebuild exclusion list

Definition at line 250 of file topology.cc.

◆ RegisterBeadType()

void votca::csg::Topology::RegisterBeadType ( std::string type )

Register the bead type with the topology object.

Records are kept of the different bead types in the topology object. This method stores the bead type.

Definition at line 214 of file topology.cc.

◆ RenameBeadType()

void votca::csg::Topology::RenameBeadType	(	std::string	name,
		std::string	newname
	)

rename all the bead types

Parameters

name	current rame of the bead type
newname	new name of bead type

Definition at line 150 of file topology.cc.

◆ RenameMolecules()

void votca::csg::Topology::RenameMolecules	(	std::string	range,
		std::string	name
	)

rename all the molecules in range

Parameters

range	range string of type 1:2:10 = 1, 3, 5, 7, ...
name	new name of molecule range is a string which is parsed by RangeParser,

Definition at line 138 of file topology.cc.

◆ ResidueCount()

Index votca::csg::Topology::ResidueCount ( ) const

inline

number of residues in the system

Returns: number of residues

Definition at line 156 of file topology.h.

◆ Residues() [1/2]

ResidueContainer & votca::csg::Topology::Residues ( )

inline

access containter with all residues

Returns: bead container

Definition at line 175 of file topology.h.

◆ Residues() [2/2]

const ResidueContainer & votca::csg::Topology::Residues ( ) const

inline

Definition at line 176 of file topology.h.

◆ SetBeadTypeMass()

void votca::csg::Topology::SetBeadTypeMass	(	std::string	name,
		double	value
	)

set the mass of all the beads of a certain type

Parameters

name	the bead type
value	mass value

Definition at line 160 of file topology.cc.

◆ setBox()

void votca::csg::Topology::setBox	(	const Eigen::Matrix3d &	box,
		BoundaryCondition::eBoxtype	boxtype = `BoundaryCondition::typeAuto`
	)

inline

set the simulation box

Parameters

box	triclinic box matrix
boxtype	type of the box (triclinic, orthorhombic, open)

Definition at line 272 of file topology.h.

◆ SetHasForce()

void votca::csg::Topology::SetHasForce ( const bool v )

inline

Definition at line 403 of file topology.h.

◆ SetHasVel()

void votca::csg::Topology::SetHasVel ( const bool v )

inline

Definition at line 400 of file topology.h.

◆ setParticleGroup()

void votca::csg::Topology::setParticleGroup ( std::string particle_group )

inline

Sets the particle group. (For the H5MD file format)

Parameters

particle_group The name of a particle group.

Definition at line 335 of file topology.h.

◆ setStep()

void votca::csg::Topology::setStep ( Index s )

inline

set the step number of current frame

Parameters

s	step number

Definition at line 323 of file topology.h.

◆ setTime()

void votca::csg::Topology::setTime ( double t )

inline

set the time of current frame

Parameters

t	simulation time in ns

Definition at line 311 of file topology.h.

◆ ShortestBoxSize()

double votca::csg::Topology::ShortestBoxSize ( ) const

return the shortest box size

Returns: shortest size

Calculates the shortest length to connect two sides of the box

Definition at line 268 of file topology.cc.

Member Data Documentation

◆ bc_

std::unique_ptr<BoundaryCondition> votca::csg::Topology::bc_

protected

Definition at line 406 of file topology.h.

◆ beads_

BeadContainer votca::csg::Topology::beads_

protected

beads in the topology

Definition at line 415 of file topology.h.

◆ beadtypes_

std::unordered_map<std::string, Index> votca::csg::Topology::beadtypes_

protected

bead types in the topology

Definition at line 412 of file topology.h.

◆ exclusions_

ExclusionList votca::csg::Topology::exclusions_

protected

Definition at line 426 of file topology.h.

◆ has_force_

bool votca::csg::Topology::has_force_ = false

protected

Definition at line 435 of file topology.h.

◆ has_vel_

bool votca::csg::Topology::has_vel_ = false

protected

Definition at line 434 of file topology.h.

◆ interaction_groups_

std::map<std::string, Index> votca::csg::Topology::interaction_groups_

protected

Definition at line 428 of file topology.h.

◆ interactions_

InteractionContainer votca::csg::Topology::interactions_

protected

bonded interactions in the topology

Definition at line 424 of file topology.h.

◆ interactions_by_group_

std::map<std::string, std::vector<Interaction *> > votca::csg::Topology::interactions_by_group_

protected

Definition at line 430 of file topology.h.

◆ molecules_

MoleculeContainer votca::csg::Topology::molecules_

protected

molecules in the topology

Definition at line 418 of file topology.h.

◆ particle_group_

std::string votca::csg::Topology::particle_group_ = "unassigned"

protected

The particle group (For H5MD file format)

Definition at line 438 of file topology.h.

◆ residues_

ResidueContainer votca::csg::Topology::residues_

protected

residues in the topology

Definition at line 421 of file topology.h.

◆ step_

Index votca::csg::Topology::step_ = 0

protected

Definition at line 433 of file topology.h.

◆ time_

double votca::csg::Topology::time_ = 0.0

protected

Definition at line 432 of file topology.h.

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

csg/include/votca/csg/topology.h
csg/src/libcsg/topology.cc

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Topology()

◆ ~Topology()

Member Function Documentation

◆ AddBondedInteraction()

◆ autoDetectBoxType()

◆ BCShortestConnection()

◆ BeadCount()

◆ Beads()

◆ BeadTypeExist()

◆ BondedInteractions() [1/2]

◆ BondedInteractions() [2/2]

◆ BoxVolume()

◆ CheckMoleculeNaming()

◆ Cleanup()

◆ ClearMoleculeList()

◆ CopyTopologyData()

◆ CreateBead()

◆ CreateMolecule()

◆ CreateMoleculesByRange()

◆ CreateResidue() [1/2]

◆ CreateResidue() [2/2]

◆ getBead() [1/2]

◆ getBead() [2/2]

◆ getBeadTypeId()

◆ getBoundary()

◆ getBox()

◆ getBoxType()

◆ getDist()

◆ getExclusions() [1/2]

◆ getExclusions() [2/2]

◆ getMolecule() [1/2]

◆ getMolecule() [2/2]

◆ getParticleGroup()

◆ getResidue() [1/2]

◆ getResidue() [2/2]

◆ getStep()

◆ getTime()

◆ HasForce()

◆ HasVel()

◆ InsertExclusion()

◆ InteractionsInGroup()

◆ MoleculeByIndex()

◆ MoleculeCount()

◆ Molecules() [1/2]

◆ Molecules() [2/2]

◆ RebuildExclusions()

◆ RegisterBeadType()

◆ RenameBeadType()

◆ RenameMolecules()

◆ ResidueCount()

◆ Residues() [1/2]

◆ Residues() [2/2]

◆ SetBeadTypeMass()

◆ setBox()

◆ SetHasForce()

◆ SetHasVel()

◆ setParticleGroup()

◆ setStep()

◆ setTime()

◆ ShortestBoxSize()

Member Data Documentation

◆ bc_

◆ beads_

◆ beadtypes_

◆ exclusions_

◆ has_force_

◆ has_vel_

◆ interaction_groups_

◆ interactions_

◆ interactions_by_group_

◆ molecules_

◆ particle_group_

◆ residues_

◆ step_

◆ time_