The class for representing SubstanceGroups. More...

#include <SubstanceGroup.h>

Inheritance diagram for RDKit::SubstanceGroup:

Classes
struct	AttachPoint

struct	CState

Public Types
enum class	BondType { XBOND , CBOND }
	Bond type (see V3000 spec) More...

typedef std::array< RDGeom::Point3D, 3 >	Bracket

Public Member Functions
	SubstanceGroup ()=delete
	No default constructor.

	SubstanceGroup (ROMol *owning_mol, const std::string &type)

	SubstanceGroup (const SubstanceGroup &other)=default

SubstanceGroup &	operator= (const SubstanceGroup &other)=default

	SubstanceGroup (SubstanceGroup &&other) noexcept

SubstanceGroup &	operator= (SubstanceGroup &&other) noexcept

	~SubstanceGroup ()=default
	Destructor.

bool	hasOwningMol () const
	returns whether or not this belongs to a molecule

ROMol &	getOwningMol () const
	Get the molecule that owns this instance.

bool	getIsValid () const

void	setIsValid (bool isValid)
	set whether or not this group is valid; invalid groups must be ignored.

unsigned int	getIndexInMol () const

void	addAtomWithIdx (unsigned int idx)

void	addParentAtomWithIdx (unsigned int idx)

void	addBondWithIdx (unsigned int idx)

void	addAtomWithBookmark (int mark)

void	addParentAtomWithBookmark (int mark)

void	addBondWithBookmark (int mark)

void	removeAtomWithIdx (unsigned int idx)

void	removeParentAtomWithIdx (unsigned int idx)

void	removeBondWithIdx (unsigned int idx)

void	addBracket (const Bracket &bracket)

void	addCState (unsigned int bondIdx, const RDGeom::Point3D &vector)

void	addAttachPoint (unsigned int aIdx, int lvIdx, const std::string &idStr)

BondType	getBondType (unsigned int bondIdx) const

const std::vector< unsigned int > &	getAtoms () const

const std::vector< unsigned int > &	getParentAtoms () const

const std::vector< unsigned int > &	getBonds () const

void	setAtoms (std::vector< unsigned int > atoms)

void	setParentAtoms (std::vector< unsigned int > patoms)

void	setBonds (std::vector< unsigned int > bonds)

const std::vector< Bracket > &	getBrackets () const

const std::vector< CState > &	getCStates () const

const std::vector< AttachPoint > &	getAttachPoints () const

std::vector< Bracket > &	getBrackets ()

std::vector< CState > &	getCStates ()

std::vector< AttachPoint > &	getAttachPoints ()

void	clearBrackets ()

void	clearCStates ()

void	clearAttachPoints ()

bool	adjustToRemovedAtom (unsigned int atomIdx)

bool	includesAtom (unsigned int atomIdx) const

bool	adjustToRemovedBond (unsigned int bondIdx)

bool	includesBond (unsigned int bondIdx) const

void	setOwningMol (ROMol *mol)

bool	operator== (const SubstanceGroup &other) const

Public Member Functions inherited from RDKit::RDProps
	RDProps ()

	RDProps (const RDProps &rhs)

RDProps &	operator= (const RDProps &rhs)

	RDProps (RDProps &&o) noexcept=default

RDProps &	operator= (RDProps &&rhs) noexcept=default

void	clear ()

const Dict &	getDict () const
	gets the underlying Dictionary

Dict &	getDict ()

STR_VECT	getPropList (bool includePrivate=true, bool includeComputed=true) const
	returns a list with the names of our `properties`

template<typename T>
void	setProp (const std::string &key, T val, bool computed=false) const
	sets a `property` value

template<typename T>
void	getProp (const std::string &key, T &res) const
	allows retrieval of a particular property value

template<typename T>
T	getProp (const std::string &key) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<typename T>
bool	getPropIfPresent (const std::string &key, T &res) const

bool	hasProp (const std::string &key) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

void	clearProp (const std::string &key) const
	clears the value of a `property`

void	clearComputedProps () const
	clears all of our `computed` `properties`

void	updateProps (const RDProps &source, bool preserveExisting=false)
	update the properties from another

Additional Inherited Members
Protected Attributes inherited from RDKit::RDProps
Dict	d_props

Detailed Description

The class for representing SubstanceGroups.

Notes:

These are inspired by the SGroups in the MDL formats
Implementation is based on 2010 MDL SD specification: http://infochim.u-strasbg.fr/recherche/Download/Fragmentor/MDL_SDF.pdf
See SGroups.md for further, more comprehensive notes.

Definition at line 54 of file SubstanceGroup.h.

Member Typedef Documentation

◆ Bracket

typedef std::array<RDGeom::Point3D, 3> RDKit::SubstanceGroup::Bracket

Definition at line 62 of file SubstanceGroup.h.

Member Enumeration Documentation

◆ BondType

enum class RDKit::SubstanceGroup::BondType

strong

Bond type (see V3000 spec)

Enumerator
XBOND
CBOND

Definition at line 57 of file SubstanceGroup.h.

Constructor & Destructor Documentation

◆ SubstanceGroup() [1/4]

RDKit::SubstanceGroup::SubstanceGroup ( )

delete

No default constructor.

Referenced by operator=(), operator=(), operator==(), SubstanceGroup(), and SubstanceGroup().

◆ SubstanceGroup() [2/4]

RDKit::SubstanceGroup::SubstanceGroup	(	ROMol *	owning_mol,
		const std::string &	type )

Main Constructor. Ownership is only set on this side of the relationship: mol->addSubstanceGroup(sgroup) still needs to be called to get ownership on the other side.

◆ SubstanceGroup() [3/4]

RDKit::SubstanceGroup::SubstanceGroup ( const SubstanceGroup & other )

default

References SubstanceGroup().

◆ SubstanceGroup() [4/4]

RDKit::SubstanceGroup::SubstanceGroup ( SubstanceGroup && other )

inlinenoexcept

Definition at line 101 of file SubstanceGroup.h.

References RDKit::RDProps::RDProps(), and SubstanceGroup().

◆ ~SubstanceGroup()

RDKit::SubstanceGroup::~SubstanceGroup ( )

default

Destructor.

Member Function Documentation

◆ addAtomWithBookmark()

void RDKit::SubstanceGroup::addAtomWithBookmark ( int mark )

◆ addAtomWithIdx()

void RDKit::SubstanceGroup::addAtomWithIdx ( unsigned int idx )

◆ addAttachPoint()

void RDKit::SubstanceGroup::addAttachPoint	(	unsigned int	aIdx,
		int	lvIdx,
		const std::string &	idStr )

◆ addBondWithBookmark()

void RDKit::SubstanceGroup::addBondWithBookmark ( int mark )

◆ addBondWithIdx()

void RDKit::SubstanceGroup::addBondWithIdx ( unsigned int idx )

◆ addBracket()

void RDKit::SubstanceGroup::addBracket ( const Bracket & bracket )

◆ addCState()

void RDKit::SubstanceGroup::addCState	(	unsigned int	bondIdx,
		const RDGeom::Point3D &	vector )

◆ addParentAtomWithBookmark()

void RDKit::SubstanceGroup::addParentAtomWithBookmark ( int mark )

◆ addParentAtomWithIdx()

void RDKit::SubstanceGroup::addParentAtomWithIdx ( unsigned int idx )

◆ adjustToRemovedAtom()

bool RDKit::SubstanceGroup::adjustToRemovedAtom ( unsigned int atomIdx )

adjusts our atom IDs to reflect that an atom has been removed from the parent molecule decrements all atom IDs that are higher than atomIdx raises a SubstanceGroupException if atomIdx is actually part of this substance group

Returns: whether or not anything was changed

◆ adjustToRemovedBond()

bool RDKit::SubstanceGroup::adjustToRemovedBond ( unsigned int bondIdx )

adjusts our bond IDs to reflect that a bond has been removed from the parent molecule decrements all bond IDs that are higher than bondIdx raises a SubstanceGroupException if bondIdx is actually part of this substance group

Returns: whether or not anything was changed

◆ clearAttachPoints()

void RDKit::SubstanceGroup::clearAttachPoints ( )

inline

Definition at line 187 of file SubstanceGroup.h.

◆ clearBrackets()

void RDKit::SubstanceGroup::clearBrackets ( )

inline

Definition at line 185 of file SubstanceGroup.h.

◆ clearCStates()

void RDKit::SubstanceGroup::clearCStates ( )

inline

Definition at line 186 of file SubstanceGroup.h.

◆ getAtoms()

const std::vector< unsigned int > & RDKit::SubstanceGroup::getAtoms ( ) const

inline

Definition at line 169 of file SubstanceGroup.h.

◆ getAttachPoints() [1/2]

std::vector< AttachPoint > & RDKit::SubstanceGroup::getAttachPoints ( )

inline

Definition at line 183 of file SubstanceGroup.h.

◆ getAttachPoints() [2/2]

const std::vector< AttachPoint > & RDKit::SubstanceGroup::getAttachPoints ( ) const

inline

Definition at line 179 of file SubstanceGroup.h.

◆ getBonds()

const std::vector< unsigned int > & RDKit::SubstanceGroup::getBonds ( ) const

inline

Definition at line 171 of file SubstanceGroup.h.

◆ getBondType()

BondType RDKit::SubstanceGroup::getBondType ( unsigned int bondIdx ) const

◆ getBrackets() [1/2]

std::vector< Bracket > & RDKit::SubstanceGroup::getBrackets ( )

inline

Definition at line 181 of file SubstanceGroup.h.

◆ getBrackets() [2/2]

const std::vector< Bracket > & RDKit::SubstanceGroup::getBrackets ( ) const

inline

Definition at line 177 of file SubstanceGroup.h.

◆ getCStates() [1/2]

std::vector< CState > & RDKit::SubstanceGroup::getCStates ( )

inline

Definition at line 182 of file SubstanceGroup.h.

◆ getCStates() [2/2]

const std::vector< CState > & RDKit::SubstanceGroup::getCStates ( ) const

inline

Definition at line 178 of file SubstanceGroup.h.

◆ getIndexInMol()

unsigned int RDKit::SubstanceGroup::getIndexInMol ( ) const

get the index of this sgroup in dp_mol's sgroups vector (do not mistake this by the ID!)

◆ getIsValid()

bool RDKit::SubstanceGroup::getIsValid ( ) const

inline

returns whether or not this group is valid; invalid groups must be ignored.

Definition at line 140 of file SubstanceGroup.h.

◆ getOwningMol()

ROMol & RDKit::SubstanceGroup::getOwningMol ( ) const

inline

Get the molecule that owns this instance.

Definition at line 133 of file SubstanceGroup.h.

References PRECONDITION.

◆ getParentAtoms()

const std::vector< unsigned int > & RDKit::SubstanceGroup::getParentAtoms ( ) const

inline

Definition at line 170 of file SubstanceGroup.h.

◆ hasOwningMol()

bool RDKit::SubstanceGroup::hasOwningMol ( ) const

inline

returns whether or not this belongs to a molecule

Definition at line 130 of file SubstanceGroup.h.

◆ includesAtom()

bool RDKit::SubstanceGroup::includesAtom ( unsigned int atomIdx ) const

Returns: whether or not anything the specified atom is part of the definition of this substance group

◆ includesBond()

bool RDKit::SubstanceGroup::includesBond ( unsigned int bondIdx ) const

Returns: whether or not anything the specified bond is part of the definition of this substance group

◆ operator=() [1/2]

SubstanceGroup & RDKit::SubstanceGroup::operator= ( const SubstanceGroup & other )

default

References SubstanceGroup().

◆ operator=() [2/2]

SubstanceGroup & RDKit::SubstanceGroup::operator= ( SubstanceGroup && other )

inlinenoexcept

Definition at line 111 of file SubstanceGroup.h.

References RDKit::RDProps::operator=(), and SubstanceGroup().

◆ operator==()

bool RDKit::SubstanceGroup::operator== ( const SubstanceGroup & other ) const

inline

Definition at line 219 of file SubstanceGroup.h.

References SubstanceGroup().

◆ removeAtomWithIdx()

void RDKit::SubstanceGroup::removeAtomWithIdx ( unsigned int idx )

◆ removeBondWithIdx()

void RDKit::SubstanceGroup::removeBondWithIdx ( unsigned int idx )

◆ removeParentAtomWithIdx()

void RDKit::SubstanceGroup::removeParentAtomWithIdx ( unsigned int idx )

◆ setAtoms()

void RDKit::SubstanceGroup::setAtoms ( std::vector< unsigned int > atoms )

◆ setBonds()

void RDKit::SubstanceGroup::setBonds ( std::vector< unsigned int > bonds )

◆ setIsValid()

void RDKit::SubstanceGroup::setIsValid ( bool isValid )

inline

set whether or not this group is valid; invalid groups must be ignored.

Definition at line 143 of file SubstanceGroup.h.

◆ setOwningMol()

void RDKit::SubstanceGroup::setOwningMol ( ROMol * mol )

Set owning molecule This only updates atoms and bonds; parent sgroup has to be updated independently, since parent might not exist at the time this is called.

◆ setParentAtoms()

void RDKit::SubstanceGroup::setParentAtoms ( std::vector< unsigned int > patoms )

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

SubstanceGroup.h

Classes

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Bracket

Member Enumeration Documentation

◆ BondType

Constructor & Destructor Documentation

◆ SubstanceGroup() [1/4]

◆ SubstanceGroup() [2/4]

◆ SubstanceGroup() [3/4]

◆ SubstanceGroup() [4/4]

◆ ~SubstanceGroup()

Member Function Documentation

◆ addAtomWithBookmark()

◆ addAtomWithIdx()

◆ addAttachPoint()

◆ addBondWithBookmark()

◆ addBondWithIdx()

◆ addBracket()

◆ addCState()

◆ addParentAtomWithBookmark()

◆ addParentAtomWithIdx()

◆ adjustToRemovedAtom()

◆ adjustToRemovedBond()

◆ clearAttachPoints()

◆ clearBrackets()

◆ clearCStates()

◆ getAtoms()

◆ getAttachPoints() [1/2]

◆ getAttachPoints() [2/2]

◆ getBonds()

◆ getBondType()

◆ getBrackets() [1/2]

◆ getBrackets() [2/2]

◆ getCStates() [1/2]

◆ getCStates() [2/2]

◆ getIndexInMol()

◆ getIsValid()

◆ getOwningMol()

◆ getParentAtoms()

◆ hasOwningMol()

◆ includesAtom()

◆ includesBond()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ removeAtomWithIdx()

◆ removeBondWithIdx()

◆ removeParentAtomWithIdx()

◆ setAtoms()

◆ setBonds()

◆ setIsValid()

◆ setOwningMol()

◆ setParentAtoms()