#include <segmentmapper.h>

Collaboration diagram for votca::xtp::SegmentMapper< AtomContainer >:

[legend]

Classes
struct	FragInfo

struct	Seginfo

Public Member Functions
	SegmentMapper (Logger &log)

void	LoadMappingFile (const std::string &mapfile)

AtomContainer	map (const Segment &seg, const SegId &segid) const

AtomContainer	map (const Segment &seg, QMState state) const

AtomContainer	map (const Segment &seg, const std::string &coordfilename) const

Private Types
using	mapAtom = typename AtomContainer::Atom_Type

using	atom_id = std::pair< Index, std::string >

Private Member Functions
Index	FindVectorIndexFromAtomId (Index atomid, const std::vector< mapAtom * > &fragment_mapatoms) const

void	ParseFragment (Seginfo &seginfo, const tools::Property &frag)

template<typename T >
Eigen::Vector3d	CalcWeightedPos (const std::vector< double > &weights, const T &atoms) const

void	PlaceMapAtomonMD (const std::vector< mapAtom * > &fragment_mapatoms, const std::vector< const Atom * > &fragment_mdatoms) const

void	MapMapAtomonMD (const FragInfo &frag, const std::vector< mapAtom * > &fragment_mapatoms, const std::vector< const Atom * > &fragment_mdatoms) const

std::pair< Index, Index >	CalcAtomIdRange (const Segment &seg) const

std::pair< Index, Index >	CalcAtomIdRange (const std::vector< Index > &seg) const

atom_id	StringToMapIndex (const std::string &map_string) const

atom_id	StringToMDIndex (const std::string &md_string) const

Index	getRank (const mapAtom &atom) const

std::vector< double >	getWeights (const tools::Property &frag) const

std::string	getFrame (const tools::Property &frag) const

void	FillMap ()

void	FillMap ()

Index	getRank (const QMAtom &) const

Private Attributes
std::map< std::string, std::string >	mapatom_xml_

std::map< std::string, Seginfo >	segment_info_

Logger &	log_

Detailed Description

template<class AtomContainer>
class votca::xtp::SegmentMapper< AtomContainer >

Definition at line 39 of file segmentmapper.h.

Member Typedef Documentation

◆ atom_id

template<class AtomContainer >

using votca::xtp::SegmentMapper< AtomContainer >::atom_id = std::pair<Index, std::string>

private

Definition at line 54 of file segmentmapper.h.

◆ mapAtom

template<class AtomContainer >

using votca::xtp::SegmentMapper< AtomContainer >::mapAtom = typename AtomContainer::Atom_Type

private

Definition at line 52 of file segmentmapper.h.

Constructor & Destructor Documentation

◆ SegmentMapper()

template<class AtomContainer >

votca::xtp::SegmentMapper< AtomContainer >::SegmentMapper ( Logger & log )

Definition at line 30 of file segmentmapper.cc.

Member Function Documentation

◆ CalcAtomIdRange() [1/2]

template<class AtomContainer >

std::pair< Index, Index > votca::xtp::SegmentMapper< AtomContainer >::CalcAtomIdRange ( const Segment & seg ) const

private

Definition at line 267 of file segmentmapper.cc.

◆ CalcAtomIdRange() [2/2]

template<class AtomContainer >

std::pair< Index, Index > votca::xtp::SegmentMapper< AtomContainer >::CalcAtomIdRange ( const std::vector< Index > & seg ) const

private

Definition at line 260 of file segmentmapper.cc.

◆ CalcWeightedPos()

template<class AtomContainer >

template<typename T >

Eigen::Vector3d votca::xtp::SegmentMapper< AtomContainer >::CalcWeightedPos	(	const std::vector< double > &	weights,
		const T &	atoms
	)		const

private

Definition at line 52 of file segmentmapper.cc.

◆ FillMap() [1/2]

template<class AtomContainer >

void votca::xtp::SegmentMapper< AtomContainer >::FillMap ( )

inlineprivate

Definition at line 111 of file segmentmapper.h.

◆ FillMap() [2/2]

void votca::xtp::SegmentMapper< QMMolecule >::FillMap ( )

inlineprivate

Definition at line 122 of file segmentmapper.h.

◆ FindVectorIndexFromAtomId()

template<class AtomContainer >

Index votca::xtp::SegmentMapper< AtomContainer >::FindVectorIndexFromAtomId	(	Index	atomid,
		const std::vector< mapAtom * > &	fragment_mapatoms
	)		const

private

Definition at line 295 of file segmentmapper.cc.

◆ getFrame()

template<class AtomContainer >

std::string votca::xtp::SegmentMapper< AtomContainer >::getFrame ( const tools::Property & frag ) const

inlineprivate

Definition at line 104 of file segmentmapper.h.

◆ getRank() [1/2]

template<class AtomContainer >

Index votca::xtp::SegmentMapper< AtomContainer >::getRank ( const mapAtom & atom ) const

inlineprivate

Definition at line 100 of file segmentmapper.h.

◆ getRank() [2/2]

Index votca::xtp::SegmentMapper< QMMolecule >::getRank ( const QMAtom & ) const

inlineprivate

Definition at line 132 of file segmentmapper.h.

◆ getWeights()

template<class AtomContainer >

std::vector< double > votca::xtp::SegmentMapper< AtomContainer >::getWeights ( const tools::Property & frag ) const

private

Definition at line 64 of file segmentmapper.cc.

◆ LoadMappingFile()

template<class AtomContainer >

void votca::xtp::SegmentMapper< AtomContainer >::LoadMappingFile ( const std::string & mapfile )

Definition at line 181 of file segmentmapper.cc.

◆ map() [1/3]

template<class AtomContainer >

AtomContainer votca::xtp::SegmentMapper< AtomContainer >::map	(	const Segment &	seg,
		const SegId &	segid
	)		const

Definition at line 35 of file segmentmapper.cc.

◆ map() [2/3]

template<class AtomContainer >

AtomContainer votca::xtp::SegmentMapper< AtomContainer >::map	(	const Segment &	seg,
		const std::string &	coordfilename
	)		const

Definition at line 408 of file segmentmapper.cc.

◆ map() [3/3]

template<class AtomContainer >

AtomContainer votca::xtp::SegmentMapper< AtomContainer >::map	(	const Segment &	seg,
		QMState	state
	)		const

Definition at line 388 of file segmentmapper.cc.

◆ MapMapAtomonMD()

template<class AtomContainer >

void votca::xtp::SegmentMapper< AtomContainer >::MapMapAtomonMD	(	const FragInfo &	frag,
		const std::vector< mapAtom * > &	fragment_mapatoms,
		const std::vector< const Atom * > &	fragment_mdatoms
	)		const

private

Definition at line 306 of file segmentmapper.cc.

◆ ParseFragment()

template<class AtomContainer >

void votca::xtp::SegmentMapper< AtomContainer >::ParseFragment	(	Seginfo &	seginfo,
		const tools::Property &	frag
	)

private

Definition at line 101 of file segmentmapper.cc.

◆ PlaceMapAtomonMD()

template<class AtomContainer >

void votca::xtp::SegmentMapper< AtomContainer >::PlaceMapAtomonMD	(	const std::vector< mapAtom * > &	fragment_mapatoms,
		const std::vector< const Atom * > &	fragment_mdatoms
	)		const

private

Definition at line 284 of file segmentmapper.cc.

◆ StringToMapIndex()

template<class AtomContainer >

std::pair< Index, std::string > votca::xtp::SegmentMapper< AtomContainer >::StringToMapIndex ( const std::string & map_string ) const

private

Definition at line 230 of file segmentmapper.cc.

◆ StringToMDIndex()

template<class AtomContainer >

std::pair< Index, std::string > votca::xtp::SegmentMapper< AtomContainer >::StringToMDIndex ( const std::string & md_string ) const

private

Definition at line 241 of file segmentmapper.cc.

Member Data Documentation

◆ log_

template<class AtomContainer >

Logger& votca::xtp::SegmentMapper< AtomContainer >::log_

private

Definition at line 92 of file segmentmapper.h.

◆ mapatom_xml_

template<class AtomContainer >

std::map<std::string, std::string> votca::xtp::SegmentMapper< AtomContainer >::mapatom_xml_

private

Definition at line 73 of file segmentmapper.h.

◆ segment_info_

template<class AtomContainer >

std::map<std::string, Seginfo> votca::xtp::SegmentMapper< AtomContainer >::segment_info_

private

Definition at line 74 of file segmentmapper.h.

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

xtp/include/votca/xtp/segmentmapper.h
xtp/src/libxtp/segmentmapper.cc

Classes

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ atom_id

◆ mapAtom

Constructor & Destructor Documentation

◆ SegmentMapper()

Member Function Documentation

◆ CalcAtomIdRange() [1/2]

◆ CalcAtomIdRange() [2/2]

◆ CalcWeightedPos()

◆ FillMap() [1/2]

◆ FillMap() [2/2]

◆ FindVectorIndexFromAtomId()

◆ getFrame()

◆ getRank() [1/2]

◆ getRank() [2/2]

◆ getWeights()

◆ LoadMappingFile()

◆ map() [1/3]

◆ map() [2/3]

◆ map() [3/3]

◆ MapMapAtomonMD()

◆ ParseFragment()

◆ PlaceMapAtomonMD()

◆ StringToMapIndex()

◆ StringToMDIndex()

Member Data Documentation

◆ log_

◆ mapatom_xml_

◆ segment_info_