RDKit::SubstanceGroup Class Reference

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 55 of file SubstanceGroup.h.

Member Typedef Documentation

Bracket

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

Definition at line 63 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 58 of file SubstanceGroup.h.

Constructor & Destructor Documentation

SubstanceGroup() [1/4]

RDKit::SubstanceGroup::SubstanceGroup ( )

delete

No default constructor.

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

SubstanceGroup() [4/4]

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

inlinenoexcept

Definition at line 102 of file SubstanceGroup.h.

~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 188 of file SubstanceGroup.h.

clearBrackets()

void RDKit::SubstanceGroup::clearBrackets ( )

inline

Definition at line 186 of file SubstanceGroup.h.

clearCStates()

void RDKit::SubstanceGroup::clearCStates ( )

inline

Definition at line 187 of file SubstanceGroup.h.

getAtoms()

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

inline

Definition at line 170 of file SubstanceGroup.h.

getAttachPoints() [1/2]

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

inline

Definition at line 184 of file SubstanceGroup.h.

getAttachPoints() [2/2]

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

inline

Definition at line 180 of file SubstanceGroup.h.

getBonds()

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

inline

Definition at line 172 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 182 of file SubstanceGroup.h.

getBrackets() [2/2]

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

inline

Definition at line 178 of file SubstanceGroup.h.

getCStates() [1/2]

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

inline

Definition at line 183 of file SubstanceGroup.h.

getCStates() [2/2]

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

inline

Definition at line 179 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 141 of file SubstanceGroup.h.

getOwningMol()

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

inline

Get the molecule that owns this instance.

Definition at line 134 of file SubstanceGroup.h.

References PRECONDITION.

getParentAtoms()

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

inline

Definition at line 171 of file SubstanceGroup.h.

hasOwningMol()

bool RDKit::SubstanceGroup::hasOwningMol ( ) const

inline

returns whether or not this belongs to a molecule

Definition at line 131 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

operator=() [2/2]

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

inlinenoexcept

Definition at line 112 of file SubstanceGroup.h.

operator==()

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

inline

Definition at line 220 of file SubstanceGroup.h.

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 144 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