Classes
class	AnalysisTool

class	BaseBead
	information about a base bead More...

class	Bead
	information about a bead More...

class	BeadList

class	BeadMap

class	BeadMotif
	Designed determine what kind of structure a beadstructure has. More...

class	BeadMotifConnector
	Simple class for storing the connections between motifs and the underlying beads that are part of the connection. More...

class	BeadPair
	A particle pair. More...

class	BeadStructure
	Designed to determine if the structure beads passed in. More...

class	BeadTriple
	A triplet of tree Beads. More...

class	BondBead

class	BondedStatistics
	Class calculates data associated with bond interactions. More...

class	BoundaryCondition
	Class keeps track of how the boundaries of the system are handled. More...

class	CGEngine
	coarse graining engine More...

class	CGMoleculeDef
	definition of a coarse grained molecule More...

class	CGObserver
	Observer class for analysis hook. More...

class	CsgApplication

class	CsgUnits
	Class keeps track csgs default units, for when unit conversions are necessarry. More...

class	DLPOLYTopologyReader
	class for reading dlpoly topology files More...

class	DLPOLYTrajectoryReader
	class for reading dlpoly trajectory and configuration files More...

class	DLPOLYTrajectoryWriter
	class for writing dlpoly trajectory and configuration files More...

class	ExclusionList

class	FileFormatFactory

class	GMXTopologyReader
	reader for gromacs topology files More...

class	GMXTrajectoryReader
	class for reading gromacs trajectory files More...

class	GMXTrajectoryWriter

class	GROReader
	reader for gro files More...

class	GROWriter

class	H5MDTrajectoryReader
	class for reading H5MD trajectory. More...

class	IAngle
	angle interaction More...

class	IBond
	bond interaction More...

class	IDihedral
	dihedral interaction More...

class	Imc
	class to calculate distribution functions and cross correlations for inverse monte carlo More...

class	IMCNBSearchHandler

class	Interaction
	base class for all interactions More...

class	LAMMPSDataReader
	class for reading lammps data files More...

class	LAMMPSDumpReader
	class for reading lammps dump files More...

class	LAMMPSDumpWriter

class	Map

class	Map_Ellipsoid

class	Map_Sphere

class	Molecule
	information about molecules More...

class	MoleculeItem

class	MotifDeconstructor_
	This is an internal class meant to deconstruct bead motifs into their simple forms. More...

class	NBList
	Neighbour list class. More...

class	NBList_3Body
	Neighbour list class for 3 body interactions. More...

class	NBListGrid

class	NBListGrid_3Body

class	NematicOrder

class	OpenBox

class	OrthorhombicBox

class	PairList

class	PDBReader

class	PDBWriter

class	PotentialFunction

class	PotentialFunctionCBSPL

class	PotentialFunctionLJ126

class	PotentialFunctionLJG

class	RDFCalculator
	class to calculate distribution functions and cross correlations for inverse monte carlo More...

class	Residue
	class for a residue More...

class	StdAnalysis

class	TabulatedPotential
	Tabulated Potential calculates histograms of bead interactions. More...

class	Topology
	topology of the whole system More...

class	TopologyMap

class	TopologyReader

class	TrajectoryReader
	trajectoryreader interface More...

class	TrajectoryWriter

class	TriclinicBox

class	TripleList

class	XMLBead

class	XMLMolecule

class	XMLTopologyReader

class	XYZReader
	class for reading xyz files More...

class	XYZWriter

Typedefs
typedef boost::bimap< boost::bimaps::multiset_of< tools::Edge >, boost::bimaps::set_of< tools::Edge > >	reduced_edge_to_edges_map
	Maps a reduced edge to all the edges that make up the reduced edge.

typedef boost::container::deque_options< boost::container::block_size< sizeof(Residue) *4 > >::type	block_residue_x4_t

typedef boost::container::deque_options< boost::container::block_size< sizeof(Molecule) *4 > >::type	block_molecule_4x_t

typedef boost::container::deque_options< boost::container::block_size< sizeof(Bead) *4 > >::type	block_bead_x4_t

using	MoleculeContainer = boost::container::deque< Molecule, void, block_molecule_4x_t >

using	BeadContainer = boost::container::deque< Bead, void, block_bead_x4_t >

using	ResidueContainer = boost::container::deque< Residue, void, block_residue_x4_t >

using	InteractionContainer = std::vector< Interaction * >

typedef std::pair< Index, BeadMotif >	IdMotif

using	element = reduced_edge_to_edges_map::value_type

using	group_matrix = Eigen::MatrixXd

Enumerations
enum class	BeadMapType { Spherical , Ellipsoidal }

Functions
template<class T >
T	breakIntoMotifs (BeadStructure &beadstructure)
	breaks a beadstructure into individual motifs.

std::pair< std::unordered_map< Index, BeadMotif >, BeadMotifConnector >	breakIntoSimpleMotifs (BeadMotif bead_motif)
	This function will take a beadmotif and break it into its simple motifs.

std::vector< BeadStructure >	breakIntoStructures (BeadStructure &beadstructure)

std::ostream &	operator<< (std::ostream &out, ExclusionList &exl)

void	imcio_write_dS (const std::string &file, const tools::Table &dS, const std::list< Index > *list=nullptr)

void	imcio_write_matrix (const std::string &file, const Eigen::MatrixXd &gmc, const std::list< Index > *list=nullptr)

void	imcio_write_index (const std::string &file, const std::vector< std::pair< std::string, tools::RangeParser > > &ranges)

Eigen::MatrixXd	imcio_read_matrix (const std::string &filename)

std::vector< std::pair< std::string, tools::RangeParser > >	imcio_read_index (const std::string &filename)

FileFormatFactory< TopologyReader > &	TopReaderFactory ()

FileFormatFactory< TrajectoryReader > &	TrjReaderFactory ()

FileFormatFactory< TrajectoryWriter > &	TrjWriterFactory ()

void	HelpTextHeader (const std::string &tool_name)

void	removeAllEdgesConnectedToVertex_ (Index junction, Graph &full_graph, unordered_map< Edge, bool > &remove_edges)
	Determines which edges are connected to the junction and stored them in the remove_edges map.

Index	determineEdgesOfBranchesWithSingleConnectionToJunction_ (Index junction, ReducedGraph &reduced_graph, unordered_map< Edge, bool > &remove_edges, unordered_map< Index, vector< Edge > > contracted_branch_edges_connected_to_junction)

void	calculateEdgesToRemove_ (Graph &full_graph, unordered_map< Edge, bool > &remove_edges)
	Calculates which edges to remove from a graph, in order to split it up correctly into simple motif types.

bool	compareAtomIdiExclusionList (const ExclusionList::exclusion_t a, const ExclusionList::exclusion_t b)

bool	compareAtomIdBeadList (const Bead a, const Bead b)

std::vector< std::string >	TrimCommentsFrom_ (std::vector< std::string > fields)

std::pair< std::string, std::string >	getNames (const Molecule &mol)

bool	is_digits (const std::string &str)

Variables
const Index	unassigned_id = -1

static Index	motif_index = 0

Typedef Documentation

◆ BeadContainer

using votca::csg::BeadContainer = typedef boost::container::deque<Bead, void, block_bead_x4_t>

Definition at line 69 of file topology.h.

◆ block_bead_x4_t

typedef boost::container::deque_options<boost::container::block_size<sizeof(Bead)*4>>::type votca::csg::block_bead_x4_t

Definition at line 65 of file topology.h.

◆ block_molecule_4x_t

typedef boost::container::deque_options<boost::container::block_size<sizeof(Molecule)*4>>::type votca::csg::block_molecule_4x_t

Definition at line 63 of file topology.h.

◆ block_residue_x4_t

typedef boost::container::deque_options<boost::container::block_size<sizeof(Residue)*4>>::type votca::csg::block_residue_x4_t

Definition at line 60 of file topology.h.

◆ element

using votca::csg::element = typedef reduced_edge_to_edges_map::value_type

Definition at line 27 of file beadmotifconnector.cc.

◆ group_matrix

using votca::csg::group_matrix = typedef Eigen::MatrixXd

Definition at line 39 of file imcio.cc.

◆ IdMotif

typedef std::pair<Index, BeadMotif> votca::csg::IdMotif

Definition at line 50 of file beadmotifalgorithms.cc.

◆ InteractionContainer

using votca::csg::InteractionContainer = typedef std::vector<Interaction *>

Definition at line 72 of file topology.h.

◆ MoleculeContainer

using votca::csg::MoleculeContainer = typedef boost::container::deque<Molecule, void, block_molecule_4x_t>

Definition at line 67 of file topology.h.

◆ reduced_edge_to_edges_map

typedef boost::bimap<boost::bimaps::multiset_of<tools::Edge>, boost::bimaps::set_of<tools::Edge> > votca::csg::reduced_edge_to_edges_map

Maps a reduced edge to all the edges that make up the reduced edge.

Reduced edge

0 - 4

Will point to explicit edges:

0 - 1 - 2 - 3 - 4

Each of these explicit edges will point back to the reduced edge

Explicit Edges Reduced Edge

 0 - 1      ->       0 - 4
 1 - 2      ->       0 - 4
 2 - 3      ->       0 - 4
 3 - 4      ->       0 - 4

Definition at line 59 of file beadmotifconnector.h.

◆ ResidueContainer

using votca::csg::ResidueContainer = typedef boost::container::deque<Residue, void, block_residue_x4_t>

Definition at line 70 of file topology.h.

Enumeration Type Documentation

◆ BeadMapType

enum class votca::csg::BeadMapType

strong

Enumerator
Spherical
Ellipsoidal

Definition at line 37 of file map.h.

Function Documentation

◆ breakIntoMotifs()

template<class T >

T votca::csg::breakIntoMotifs ( BeadStructure & beadstructure )

breaks a beadstructure into individual motifs.

Will essentially take structures that are indenpendent of each other and break them into separate beadmotifs.

Parameters

[in] beadstructure - reference to beadstructure

Returns: - a container of beadmotifs

Definition at line 40 of file beadmotifalgorithms.h.

◆ breakIntoSimpleMotifs()

pair< unordered_map< Index, BeadMotif >, BeadMotifConnector > votca::csg::breakIntoSimpleMotifs ( BeadMotif bead_motif )

This function will take a beadmotif and break it into its simple motifs.

A simple motif is one of four types: single_bead line loop fused_ring

So given a beadmotif like this:

  H1               H1
  |
  C1          =>   C1
 /  \
H2  H3           H2   H3

This structure which is originally of type 'single_structure' will be broken up into 4 singles of type 'single_bead'

Something like this:

C1 - C2 C1 - C2 | | => | | C3 - C4 - C5 - H1 C3 - C4 C5 - H1

This structure is of type 'single_structure' will be broken up into two separate structures 1 of type 'loop' and the other of type line.

Definition at line 403 of file beadmotifalgorithms.cc.

◆ breakIntoStructures()

vector< BeadStructure > votca::csg::breakIntoStructures ( BeadStructure & beadstructure )

Definition at line 30 of file beadstructurealgorithms.cc.

◆ calculateEdgesToRemove_()

void votca::csg::calculateEdgesToRemove_	(	Graph &	full_graph,
		unordered_map< Edge, bool > &	remove_edges
	)

Calculates which edges to remove from a graph, in order to split it up correctly into simple motif types.

This will depend on the number of junctions and the number of edges of each branch that is connected to each of the junctions.

Definition at line 122 of file beadmotifalgorithms.cc.

◆ compareAtomIdBeadList()

bool votca::csg::compareAtomIdBeadList	(	const Bead *	a,
		const Bead *	b
	)

Definition at line 148 of file exclusionlist.cc.

◆ compareAtomIdiExclusionList()

bool votca::csg::compareAtomIdiExclusionList	(	const ExclusionList::exclusion_t *	a,
		const ExclusionList::exclusion_t *	b
	)

Definition at line 143 of file exclusionlist.cc.

◆ determineEdgesOfBranchesWithSingleConnectionToJunction_()

Index votca::csg::determineEdgesOfBranchesWithSingleConnectionToJunction_	(	Index	junction,
		ReducedGraph &	reduced_graph,
		unordered_map< Edge, bool > &	remove_edges,
		unordered_map< Index, vector< Edge > >	contracted_branch_edges_connected_to_junction
	)

The purpose of this function is to determine which edges connected to the starting vertex in the full graph were explored for a branch. We are starting with a contracted edge from the reduced graph. So it must first be expanded and then it can be explored.

Definition at line 78 of file beadmotifalgorithms.cc.

◆ getNames()

std::pair< std::string, std::string > votca::csg::getNames ( const Molecule & mol )

Definition at line 154 of file lammpsdatareader.cc.

◆ HelpTextHeader()

void votca::csg::HelpTextHeader ( const std::string & tool_name )

Definition at line 41 of file version.cc.

◆ imcio_read_index()

std::vector< std::pair< std::string, tools::RangeParser > > votca::csg::imcio_read_index ( const std::string & filename )

Definition at line 147 of file imcio.cc.

◆ imcio_read_matrix()

Eigen::MatrixXd votca::csg::imcio_read_matrix ( const std::string & filename )

Definition at line 113 of file imcio.cc.

◆ imcio_write_dS()

void votca::csg::imcio_write_dS	(	const std::string &	file,
		const tools::Table &	dS,
		const std::list< Index > *	list = `nullptr`
	)

Definition at line 42 of file imcio.cc.

◆ imcio_write_index()

void votca::csg::imcio_write_index	(	const std::string &	file,
		const std::vector< std::pair< std::string, tools::RangeParser > > &	ranges
	)

Definition at line 95 of file imcio.cc.

◆ imcio_write_matrix()

void votca::csg::imcio_write_matrix	(	const std::string &	file,
		const Eigen::MatrixXd &	gmc,
		const std::list< Index > *	list = `nullptr`
	)

Definition at line 66 of file imcio.cc.

◆ is_digits()

bool votca::csg::is_digits ( const std::string & str )

Definition at line 43 of file topology.cc.

◆ operator<<()

std::ostream & votca::csg::operator<<	(	std::ostream &	out,
		ExclusionList &	exl
	)

Definition at line 152 of file exclusionlist.cc.

◆ removeAllEdgesConnectedToVertex_()

void votca::csg::removeAllEdgesConnectedToVertex_	(	Index	junction,
		Graph &	full_graph,
		unordered_map< Edge, bool > &	remove_edges
	)

Determines which edges are connected to the junction and stored them in the remove_edges map.

Definition at line 64 of file beadmotifalgorithms.cc.

◆ TopReaderFactory()

FileFormatFactory< TopologyReader > & votca::csg::TopReaderFactory ( )

inline

Definition at line 41 of file topologyreader.h.

◆ TrimCommentsFrom_()

std::vector< std::string > votca::csg::TrimCommentsFrom_ ( std::vector< std::string > fields )

Definition at line 49 of file lammpsdatareader.cc.

◆ TrjReaderFactory()

FileFormatFactory< TrajectoryReader > & votca::csg::TrjReaderFactory ( )

inline

Definition at line 53 of file trajectoryreader.h.

◆ TrjWriterFactory()

FileFormatFactory< TrajectoryWriter > & votca::csg::TrjWriterFactory ( )

inline

Definition at line 47 of file trajectorywriter.h.

Variable Documentation

◆ motif_index

Index votca::csg::motif_index = 0

static

Definition at line 54 of file beadmotifalgorithms.cc.

◆ unassigned_id

const Index votca::csg::unassigned_id = -1

Definition at line 52 of file beadmotifalgorithms.cc.

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ BeadContainer

◆ block_bead_x4_t

◆ block_molecule_4x_t

◆ block_residue_x4_t

◆ element

◆ group_matrix

◆ IdMotif

◆ InteractionContainer

◆ MoleculeContainer

◆ reduced_edge_to_edges_map

◆ ResidueContainer

Enumeration Type Documentation

◆ BeadMapType

Function Documentation

◆ breakIntoMotifs()

◆ breakIntoSimpleMotifs()

◆ breakIntoStructures()

◆ calculateEdgesToRemove_()

◆ compareAtomIdBeadList()

◆ compareAtomIdiExclusionList()

◆ determineEdgesOfBranchesWithSingleConnectionToJunction_()

◆ getNames()

◆ HelpTextHeader()

◆ imcio_read_index()

◆ imcio_read_matrix()

◆ imcio_write_dS()

◆ imcio_write_index()

◆ imcio_write_matrix()

◆ is_digits()

◆ operator<<()

◆ removeAllEdgesConnectedToVertex_()

◆ TopReaderFactory()

◆ TrimCommentsFrom_()

◆ TrjReaderFactory()

◆ TrjWriterFactory()

Variable Documentation

◆ motif_index

◆ unassigned_id