RWMol is a molecule class that is intended to be edited. More...

#include <RWMol.h>

Inheritance diagram for RDKit::RWMol:

Public Member Functions
	RWMol ()

	RWMol (const ROMol &other, bool quickCopy=false, int confId=-1)
	copy constructor with a twist

	RWMol (const RWMol &other)

RWMol &	operator= (const RWMol &)

	RWMol (RWMol &&other) noexcept

RWMol &	operator= (RWMol &&other) noexcept

void	insertMol (const ROMol &other)
	insert the atoms and bonds from `other` into this molecule

void	clear ()
	removes all atoms, bonds, properties, bookmarks, etc.

void	beginBatchEdit ()

void	rollbackBatchEdit ()

void	commitBatchEdit ()

Atoms
unsigned int	addAtom (bool updateLabel=true)
	adds an empty Atom to our collection

unsigned int	addAtom (Atom *atom, bool updateLabel=true, bool takeOwnership=false)
	adds an Atom to our collection

void	replaceAtom (unsigned int idx, Atom *atom, bool updateLabel=false, bool preserveProps=false)
	adds an Atom to our collection

Atom *	getLastAtom ()
	returns a pointer to the highest-numbered Atom

Atom *	getActiveAtom ()
	returns a pointer to the "active" Atom

void	setActiveAtom (Atom *atom)
	sets our `activeAtom`

void	setActiveAtom (unsigned int idx)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

void	removeAtom (unsigned int idx)
	removes an Atom from the molecule

void	removeAtom (Atom *atom)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

void	removeAtom (Atom *atom, bool clearProps)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Bonds
unsigned int	addBond (unsigned int beginAtomIdx, unsigned int endAtomIdx, Bond::BondType order=Bond::UNSPECIFIED)
	adds a Bond between the indicated Atoms

unsigned int	addBond (Atom beginAtom, Atom endAtom, Bond::BondType order=Bond::UNSPECIFIED)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

unsigned int	addBond (Bond *bond, bool takeOwnership=false)
	adds a Bond to our collection

Bond *	createPartialBond (unsigned int beginAtomIdx, Bond::BondType order=Bond::UNSPECIFIED)
	starts a Bond and sets its beginAtomIdx

unsigned int	finishPartialBond (unsigned int endAtomIdx, int bondBookmark, Bond::BondType order=Bond::UNSPECIFIED)
	finishes a partially constructed bond

void	removeBond (unsigned int beginAtomIdx, unsigned int endAtomIdx)
	removes a bond from the molecule

void	replaceBond (unsigned int idx, Bond *bond, bool preserveProps=false, bool keepSGroups=true)
	replaces a particular Bond

Public Member Functions inherited from RDKit::ROMol
CXXAtomIterator< MolGraph, Atom * >	atoms ()
	C++11 Range iterator.

CXXAtomIterator< const MolGraph, Atom *const >	atoms () const

CXXAtomIterator< const MolGraph, Atom *const, MolGraph::adjacency_iterator >	atomNeighbors (Atom const *at) const

CXXAtomIterator< MolGraph, Atom *, MolGraph::adjacency_iterator >	atomNeighbors (Atom const *at)

CXXBondIterator< const MolGraph, Bond *const, MolGraph::out_edge_iterator >	atomBonds (Atom const *at) const

CXXBondIterator< MolGraph, Bond *, MolGraph::out_edge_iterator >	atomBonds (Atom const *at)

CXXBondIterator< MolGraph, Bond * >	bonds ()

CXXBondIterator< const MolGraph, Bond *const >	bonds () const

	ROMol ()

	ROMol (const ROMol &other, bool quickCopy=false, int confId=-1)
	copy constructor with a twist

	ROMol (const std::string &binStr)
	construct a molecule from a pickle string

	ROMol (const std::string &binStr, unsigned int propertyFlags)
	construct a molecule from a pickle string

	ROMol (ROMol &&o) noexcept

ROMol &	operator= (ROMol &&o) noexcept

ROMol &	operator= (const ROMol &)=delete

virtual	~ROMol ()

Atom *	operator[] (const vertex_descriptor &v)

const Atom *	operator[] (const vertex_descriptor &v) const

Bond *	operator[] (const edge_descriptor &e)

const Bond *	operator[] (const edge_descriptor &e) const

const std::vector< StereoGroup > &	getStereoGroups () const
	Gets a reference to the groups of atoms with relative stereochemistry.

void	setStereoGroups (std::vector< StereoGroup > stereo_groups)
	Sets groups of atoms with relative stereochemistry.

unsigned int	getNumAtoms () const
	returns our number of atoms

unsigned int	getNumAtoms (bool onlyExplicit) const

unsigned int	getNumHeavyAtoms () const
	returns our number of heavy atoms (atomic number > 1)

Atom *	getAtomWithIdx (unsigned int idx)
	returns a pointer to a particular Atom

const Atom *	getAtomWithIdx (unsigned int idx) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<class U>
Atom *	getAtomWithIdx (const U idx)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<class U>
const Atom *	getAtomWithIdx (const U idx) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

unsigned int	getAtomDegree (const Atom *at) const
	returns the degree (number of neighbors) of an Atom in the graph

unsigned int	getNumBonds (bool onlyHeavy=1) const
	returns our number of Bonds

Bond *	getBondWithIdx (unsigned int idx)
	returns a pointer to a particular Bond

const Bond *	getBondWithIdx (unsigned int idx) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<class U>
Bond *	getBondWithIdx (const U idx)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<class U>
const Bond *	getBondWithIdx (const U idx) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Bond *	getBondBetweenAtoms (unsigned int idx1, unsigned int idx2)
	returns a pointer to the bond between two atoms, Null on failure

const Bond *	getBondBetweenAtoms (unsigned int idx1, unsigned int idx2) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<class U, class V>
Bond *	getBondBetweenAtoms (const U idx1, const V idx2)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<class U, class V>
const Bond *	getBondBetweenAtoms (const U idx1, const V idx2) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

void	setAtomBookmark (Atom *at, int mark)
	associates an Atom pointer with a bookmark

void	replaceAtomBookmark (Atom *at, int mark)
	associates an Atom pointer with a bookmark

Atom *	getAtomWithBookmark (int mark)
	returns the first Atom associated with the `bookmark` provided

Atom *	getUniqueAtomWithBookmark (int mark)

ATOM_PTR_LIST &	getAllAtomsWithBookmark (int mark)
	returns all Atoms associated with the `bookmark` provided

void	clearAtomBookmark (int mark)
	removes a `bookmark` from our collection

void	clearAtomBookmark (int mark, const Atom *atom)
	removes a particular Atom from the list associated with the `bookmark`

void	clearAllAtomBookmarks ()
	blows out all atomic `bookmarks`

bool	hasAtomBookmark (int mark) const
	queries whether or not any atoms are associated with a `bookmark`

ATOM_BOOKMARK_MAP *	getAtomBookmarks ()
	returns a pointer to all of our atom `bookmarks`

void	setBondBookmark (Bond *bond, int mark)
	associates a Bond pointer with a bookmark

Bond *	getBondWithBookmark (int mark)
	returns the first Bond associated with the `bookmark` provided

Bond *	getUniqueBondWithBookmark (int mark)

BOND_PTR_LIST &	getAllBondsWithBookmark (int mark)
	returns all bonds associated with the `bookmark` provided

void	clearBondBookmark (int mark)
	removes a `bookmark` from our collection

void	clearBondBookmark (int mark, const Bond *bond)
	removes a particular Bond from the list associated with the `bookmark`

void	clearAllBondBookmarks ()
	blows out all bond `bookmarks`

bool	hasBondBookmark (int mark) const
	queries whether or not any bonds are associated with a `bookmark`

BOND_BOOKMARK_MAP *	getBondBookmarks ()
	returns a pointer to all of our bond `bookmarks`

const Conformer &	getConformer (int id=-1) const

Conformer &	getConformer (int id=-1)

void	removeConformer (unsigned int id)
	Delete the conformation with the specified ID.

void	clearConformers ()
	Clear all the conformations on the molecule.

unsigned int	addConformer (Conformer *conf, bool assignId=false)
	Add a new conformation to the molecule.

unsigned int	getNumConformers () const

RingInfo *	getRingInfo () const

ADJ_ITER_PAIR	getAtomNeighbors (Atom const *at) const
	provides access to all neighbors around an Atom

OBOND_ITER_PAIR	getAtomBonds (Atom const *at) const
	provides access to all Bond objects connected to an Atom

ATOM_ITER_PAIR	getVertices ()
	returns an iterator pair for looping over all Atoms

BOND_ITER_PAIR	getEdges ()
	returns an iterator pair for looping over all Bonds

ATOM_ITER_PAIR	getVertices () const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

BOND_ITER_PAIR	getEdges () const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

MolGraph const &	getTopology () const
	brief returns a pointer to our underlying BGL object

AtomIterator	beginAtoms ()
	get an AtomIterator pointing at our first Atom

ConstAtomIterator	beginAtoms () const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

AtomIterator	endAtoms ()
	get an AtomIterator pointing at the end of our Atoms

ConstAtomIterator	endAtoms () const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

BondIterator	beginBonds ()
	get a BondIterator pointing at our first Bond

ConstBondIterator	beginBonds () const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

BondIterator	endBonds ()
	get a BondIterator pointing at the end of our Bonds

ConstBondIterator	endBonds () const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

AromaticAtomIterator	beginAromaticAtoms ()
	get an AtomIterator pointing at our first aromatic Atom

ConstAromaticAtomIterator	beginAromaticAtoms () const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

AromaticAtomIterator	endAromaticAtoms ()
	get an AtomIterator pointing at the end of our Atoms

ConstAromaticAtomIterator	endAromaticAtoms () const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

HeteroatomIterator	beginHeteros ()
	get an AtomIterator pointing at our first hetero Atom

ConstHeteroatomIterator	beginHeteros () const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

HeteroatomIterator	endHeteros ()
	get an AtomIterator pointing at the end of our Atoms

ConstHeteroatomIterator	endHeteros () const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

bool	hasQuery () const
	if the Mol has any Query atoms or bonds

QueryAtomIterator	beginQueryAtoms (QueryAtom const *query)
	get an AtomIterator pointing at our first Atom that matches `query`

ConstQueryAtomIterator	beginQueryAtoms (QueryAtom const *) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

QueryAtomIterator	endQueryAtoms ()
	get an AtomIterator pointing at the end of our Atoms

ConstQueryAtomIterator	endQueryAtoms () const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

MatchingAtomIterator	beginMatchingAtoms (bool(query)(Atom ))
	get an AtomIterator pointing at our first Atom that matches `query`

ConstMatchingAtomIterator	beginMatchingAtoms (bool(query)(const Atom )) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

MatchingAtomIterator	endMatchingAtoms ()
	get an AtomIterator pointing at the end of our Atoms

ConstMatchingAtomIterator	endMatchingAtoms () const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

ConformerIterator	beginConformers ()

ConformerIterator	endConformers ()

ConstConformerIterator	beginConformers () const

ConstConformerIterator	endConformers () const

void	clearComputedProps (bool includeRings=true) const
	clears all of our `computed` `properties`

void	updatePropertyCache (bool strict=true)
	calculates any of our lazy `properties`

bool	needsUpdatePropertyCache () const

void	clearPropertyCache ()

void	debugMol (std::ostream &str) 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::ROMol
unsigned int	numBonds {0}

Protected Attributes inherited from RDKit::RDProps
Dict	d_props

Detailed Description

RWMol is a molecule class that is intended to be edited.

See documentation for ROMol for general remarks

Definition at line 32 of file RWMol.h.

Constructor & Destructor Documentation

◆ RWMol() [1/4]

RDKit::RWMol::RWMol ( )

inline

Definition at line 34 of file RWMol.h.

References RDKit::ROMol::ROMol().

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

◆ RWMol() [2/4]

RDKit::RWMol::RWMol	(	const ROMol &	other,
		bool	quickCopy = false,
		int	confId = -1 )

inline

copy constructor with a twist

Parameters

other	the molecule to be copied
quickCopy	(optional) if this is true, the resulting ROMol will not copy any of the properties or bookmarks and conformers from `other`. This can make the copy substantially faster (thus the name).
confId	if this is >=0, the resulting ROMol will contain only the specified conformer from `other`.

Definition at line 45 of file RWMol.h.

References RDKit::ROMol::ROMol().

◆ RWMol() [3/4]

RDKit::RWMol::RWMol ( const RWMol & other )

inline

Definition at line 47 of file RWMol.h.

References RDKit::ROMol::ROMol(), and RWMol().

◆ RWMol() [4/4]

RDKit::RWMol::RWMol ( RWMol && other )

inlinenoexcept

Definition at line 49 of file RWMol.h.

References RDKit::ROMol::ROMol(), and RWMol().

Member Function Documentation

◆ addAtom() [1/2]

unsigned int RDKit::RWMol::addAtom	(	Atom *	atom,
		bool	updateLabel = true,
		bool	takeOwnership = false )

inline

adds an Atom to our collection

Parameters

atom	pointer to the Atom to add
updateLabel	(optional) if this is true, the new Atom will be our `activeAtom`
takeOwnership	(optional) if this is true, we take ownership of `atom` instead of copying it.

Returns: the index of the added atom

Definition at line 82 of file RWMol.h.

◆ addAtom() [2/2]

unsigned int RDKit::RWMol::addAtom ( bool updateLabel = true )

adds an empty Atom to our collection

Parameters

updateLabel (optional) if this is true, the new Atom will be our activeAtom

Returns: the index of the added atom

Referenced by RDKit::SLNParse::addAtomToMol(), and RDKit::SLNParse::startMol().

◆ addBond() [1/3]

unsigned int RDKit::RWMol::addBond	(	Atom *	beginAtom,
		Atom *	endAtom,
		Bond::BondType	order = Bond::UNSPECIFIED )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

References RDKit::Bond::UNSPECIFIED.

◆ addBond() [2/3]

unsigned int RDKit::RWMol::addBond	(	Bond *	bond,
		bool	takeOwnership = false )

inline

adds a Bond to our collection

Parameters

bond	pointer to the Bond to add
takeOwnership	(optional) if this is true, we take ownership of `bond` instead of copying it.

Returns: the new number of bonds

Definition at line 143 of file RWMol.h.

◆ addBond() [3/3]

unsigned int RDKit::RWMol::addBond	(	unsigned int	beginAtomIdx,
		unsigned int	endAtomIdx,
		Bond::BondType	order = Bond::UNSPECIFIED )

adds a Bond between the indicated Atoms

Returns: the number of Bonds

References RDKit::Bond::UNSPECIFIED.

Referenced by RDKit::SLNParse::addAtomToMol(), and RDKit::SLNParse::startMol().

◆ beginBatchEdit()

void RDKit::RWMol::beginBatchEdit ( )

◆ clear()

void RDKit::RWMol::clear ( )

inline

removes all atoms, bonds, properties, bookmarks, etc.

Definition at line 203 of file RWMol.h.

References RDKit::ROMol::numBonds.

◆ commitBatchEdit()

void RDKit::RWMol::commitBatchEdit ( )

◆ createPartialBond()

Bond * RDKit::RWMol::createPartialBond	(	unsigned int	beginAtomIdx,
		Bond::BondType	order = Bond::UNSPECIFIED )

starts a Bond and sets its beginAtomIdx

Returns: a pointer to the new bond

The caller should set a bookmark to the returned Bond in order to be able to later complete it:

  Bond *pBond = mol->createPartialBond(1);
  mol->setBondBookmark(pBond,666);
  ... do some other stuff ...
  mol->finishPartialBond(2,666,Bond::SINGLE);
  mol->clearBondBookmark(666,pBond);

or, if we want to set the BondType initially:

  Bond *pBond = mol->createPartialBond(1,Bond::DOUBLE);
  mol->setBondBookmark(pBond,666);
  ... do some other stuff ...
  mol->finishPartialBond(2,666);
  mol->clearBondBookmark(666,pBond);

the call to finishPartialBond() will take priority if you set the BondType in both calls.

References RDKit::Bond::UNSPECIFIED.

◆ finishPartialBond()

unsigned int RDKit::RWMol::finishPartialBond	(	unsigned int	endAtomIdx,
		int	bondBookmark,
		Bond::BondType	order = Bond::UNSPECIFIED )

finishes a partially constructed bond

Returns: the final number of Bonds

See the documentation for createPartialBond() for more details

References RDKit::Bond::UNSPECIFIED.

◆ getActiveAtom()

Atom * RDKit::RWMol::getActiveAtom ( )

returns a pointer to the "active" Atom

If we have an activeAtom, it will be returned, otherwise the results of getLastAtom() will be returned.

Referenced by RDKit::SLNParse::addAtomToMol(), RDKit::SLNParse::addBranchToMol(), and RDKit::SLNParse::closeRingBond().

◆ getLastAtom()

Atom * RDKit::RWMol::getLastAtom ( )

inline

returns a pointer to the highest-numbered Atom

Definition at line 101 of file RWMol.h.

References RDKit::ROMol::getAtomWithIdx(), and RDKit::ROMol::getNumAtoms().

◆ insertMol()

void RDKit::RWMol::insertMol ( const ROMol & other )

insert the atoms and bonds from other into this molecule

References RDKit::ROMol::ROMol().

Referenced by RDKit::SLNParse::addBranchToMol().

◆ operator=() [1/2]

RWMol & RDKit::RWMol::operator= ( const RWMol & )

References RWMol().

◆ operator=() [2/2]

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

inlinenoexcept

Definition at line 50 of file RWMol.h.

References RDKit::ROMol::operator=(), and RWMol().

◆ removeAtom() [1/3]

void RDKit::RWMol::removeAtom ( Atom * atom )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ removeAtom() [2/3]

void RDKit::RWMol::removeAtom	(	Atom *	atom,
		bool	clearProps )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ removeAtom() [3/3]

void RDKit::RWMol::removeAtom ( unsigned int idx )

removes an Atom from the molecule

◆ removeBond()

void RDKit::RWMol::removeBond	(	unsigned int	beginAtomIdx,
		unsigned int	endAtomIdx )

removes a bond from the molecule

◆ replaceAtom()

void RDKit::RWMol::replaceAtom	(	unsigned int	idx,
		Atom *	atom,
		bool	updateLabel = false,
		bool	preserveProps = false )

adds an Atom to our collection

replaces a particular Atom

Parameters

idx	the index of the Atom to replace
atom	the new atom, which will be copied.
updateLabel	(optional) if this is true, the new Atom will be our `activeAtom`
preserveProps	if true preserve the original atom property data

◆ replaceBond()

void RDKit::RWMol::replaceBond	(	unsigned int	idx,
		Bond *	bond,
		bool	preserveProps = false,
		bool	keepSGroups = true )

replaces a particular Bond

Parameters

idx	the index of the Bond to replace
bond	the new bond, which will be copied.
preserveProps	if true preserve the original bond property data
keepSGroups	if true, keep Substance groups referencing the bond

◆ rollbackBatchEdit()

void RDKit::RWMol::rollbackBatchEdit ( )

inline

Definition at line 211 of file RWMol.h.

◆ setActiveAtom() [1/2]

void RDKit::RWMol::setActiveAtom ( Atom * atom )

sets our activeAtom

Referenced by RDKit::SLNParse::addBranchToMol().

◆ setActiveAtom() [2/2]

void RDKit::RWMol::setActiveAtom ( unsigned int idx )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

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

RWMol.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RWMol() [1/4]

◆ RWMol() [2/4]

◆ RWMol() [3/4]

◆ RWMol() [4/4]

Member Function Documentation

◆ addAtom() [1/2]

◆ addAtom() [2/2]

◆ addBond() [1/3]

◆ addBond() [2/3]

◆ addBond() [3/3]

◆ beginBatchEdit()

◆ clear()

◆ commitBatchEdit()

◆ createPartialBond()

◆ finishPartialBond()

◆ getActiveAtom()

◆ getLastAtom()

◆ insertMol()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ removeAtom() [1/3]

◆ removeAtom() [2/3]

◆ removeAtom() [3/3]

◆ removeBond()

◆ replaceAtom()

◆ replaceBond()

◆ rollbackBatchEdit()

◆ setActiveAtom() [1/2]

◆ setActiveAtom() [2/2]