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 More...

RWMol &	operator= (const RWMol &)

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

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

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

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

unsigned int	addAtom (ATOM_SPTR atom, bool updateLabel=true)
	adds an Atom to our collection More...

void	replaceAtom (unsigned int idx, Atom *atom, bool updateLabel=false)
	replaces a particular Atom More...

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

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

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

void	setActiveAtom (unsigned int idx)

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

void	removeAtom (Atom *atom)

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

unsigned int	addBond (ATOM_SPTR beginAtom, ATOM_SPTR endAtom, Bond::BondType order=Bond::UNSPECIFIED)

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

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

unsigned int	addBond (BOND_SPTR bsp)
	adds a Bond to our collection More...

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

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

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

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

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

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

virtual	~ROMol ()

ATOM_SPTR	operator[] (const vertex_descriptor &v)

const ATOM_SPTR	operator[] (const vertex_descriptor &v) const

BOND_SPTR	operator[] (const edge_descriptor &e)

const BOND_SPTR	operator[] (const edge_descriptor &e) const

unsigned int	getNumAtoms (bool onlyExplicit=1) const
	returns our number of atoms More...

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

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

const Atom *	getAtomWithIdx (unsigned int idx) const

template<class U >
Atom *	getAtomWithIdx (const U idx)

template<class U >
const Atom *	getAtomWithIdx (const U idx) const

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

unsigned int	getAtomDegree (ATOM_SPTR at) const

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

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

const Bond *	getBondWithIdx (unsigned int idx) const

template<class U >
Bond *	getBondWithIdx (const U idx)

template<class U >
const Bond *	getBondWithIdx (const U idx) const

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

const Bond *	getBondBetweenAtoms (unsigned int idx1, unsigned int idx2) const

template<class U , class V >
Bond *	getBondBetweenAtoms (const U idx1, const V idx2)

template<class U , class V >
const Bond *	getBondBetweenAtoms (const U idx1, const V idx2) const

void	setAtomBookmark (ATOM_SPTR at, int mark)
	associates an Atom pointer with a bookmark More...

void	setAtomBookmark (Atom *at, int mark)

void	replaceAtomBookmark (ATOM_SPTR at, int mark)
	associates an Atom pointer with a bookmark More...

void	replaceAtomBookmark (Atom *at, int mark)

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

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

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

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

void	clearAtomBookmark (const int mark, ATOM_SPTR atom)

void	clearAllAtomBookmarks ()
	blows out all atomic `bookmarks` More...

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

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

void	setBondBookmark (BOND_SPTR bond, int mark)
	associates a Bond pointer with a bookmark More...

void	setBondBookmark (Bond *bond, int mark)

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

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

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

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

void	clearBondBookmark (int mark, BOND_SPTR bond)

void	clearAllBondBookmarks ()
	blows out all bond `bookmarks` More...

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

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

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

Conformer &	getConformer (int id=-1)

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

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

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

unsigned int	getNumConformers () const

RingInfo *	getRingInfo () const

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

ADJ_ITER_PAIR	getAtomNeighbors (ATOM_SPTR at) const

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

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

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

ATOM_ITER_PAIR	getVertices () const

BOND_ITER_PAIR	getEdges () const

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

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

ConstAtomIterator	beginAtoms () const

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

ConstAtomIterator	endAtoms () const

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

ConstBondIterator	beginBonds () const

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

ConstBondIterator	endBonds () const

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

ConstAromaticAtomIterator	beginAromaticAtoms () const

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

ConstAromaticAtomIterator	endAromaticAtoms () const

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

ConstHeteroatomIterator	beginHeteros () const

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

ConstHeteroatomIterator	endHeteros () const

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

ConstQueryAtomIterator	beginQueryAtoms (QueryAtom const *) const

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

ConstQueryAtomIterator	endQueryAtoms () const

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

ConstMatchingAtomIterator	beginMatchingAtoms (bool(query)(const Atom )) const

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

ConstMatchingAtomIterator	endMatchingAtoms () const

ConformerIterator	beginConformers ()

ConformerIterator	endConformers ()

ConstConformerIterator	beginConformers () const

ConstConformerIterator	endConformers () const

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

template<typename T >
void	setProp (const char *key, T val, bool computed=false) const
	sets a `property` value More...

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

template<typename T >
void	getProp (const char *key, T &res) const
	allows retrieval of a particular property value More...

template<typename T >
void	getProp (const std::string &key, T &res) const

template<typename T >
T	getProp (const char *key) const

template<typename T >
T	getProp (const std::string &key) const

template<typename T >
bool	getPropIfPresent (const char *key, T &res) const

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

bool	hasProp (const char *key) const
	returns whether or not we have a `property` with name `key` More...

bool	hasProp (const std::string &key) const

void	clearProp (const char *key) const
	clears the value of a `property` More...

void	clearProp (const std::string &key) const

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

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

bool	needsUpdatePropertyCache () const

void	debugMol (std::ostream &str) const
	sends some debugging info to a stream More...

Detailed Description

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

See documentation for ROMol for general remarks

Definition at line 30 of file RWMol.h.

Constructor & Destructor Documentation

◆ RWMol() [1/2]

RDKit::RWMol::RWMol ( )

inline

Definition at line 32 of file RWMol.h.

◆ RWMol() [2/2]

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 44 of file RWMol.h.

References addAtom(), insertMol(), and operator=().

Member Function Documentation

◆ addAtom() [1/3]

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 new number of atoms

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

◆ addAtom() [2/3]

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 new number of atoms

Definition at line 77 of file RWMol.h.

◆ addAtom() [3/3]

unsigned int RDKit::RWMol::addAtom	(	ATOM_SPTR	atom,
		bool	updateLabel = `true`
	)

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`

Returns: the new number of atoms

Note: since this is using a smart pointer, we don't need to worry about issues of ownership.

Definition at line 96 of file RWMol.h.

References replaceAtom().

◆ addBond() [1/5]

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

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

◆ addBond() [2/5]

unsigned int RDKit::RWMol::addBond	(	ATOM_SPTR	beginAtom,
		ATOM_SPTR	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.

◆ addBond() [3/5]

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.

◆ addBond() [4/5]

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 153 of file RWMol.h.

◆ addBond() [5/5]

unsigned int RDKit::RWMol::addBond ( BOND_SPTR bsp )

inline

adds a Bond to our collection

Parameters

bsp	smart pointer to the Bond to add

Returns: the new number of bonds

Note: since this is using a smart pointer, we don't need to worry about issues of ownership.

Definition at line 166 of file RWMol.h.

References createPartialBond(), finishPartialBond(), removeBond(), and RDKit::Bond::UNSPECIFIED.

◆ clear()

void RDKit::RWMol::clear ( )

inline

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

Definition at line 212 of file RWMol.h.

References detail::computedPropName.

◆ 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.

Referenced by addBond().

◆ 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

Referenced by addBond().

◆ 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 getLastAtom().

◆ getLastAtom()

Atom* RDKit::RWMol::getLastAtom ( )

inline

returns a pointer to the highest-numbered Atom

Definition at line 110 of file RWMol.h.

References addBond(), getActiveAtom(), RDKit::ROMol::getAtomWithIdx(), RDKit::ROMol::getNumAtoms(), removeAtom(), setActiveAtom(), and RDKit::Bond::UNSPECIFIED.

◆ insertMol()

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

insert the atoms and bonds from other into this molecule

Referenced by RWMol().

◆ operator=()

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

Referenced by RWMol().

◆ removeAtom() [1/2]

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

removes an Atom from the molecule

Referenced by getLastAtom().

◆ removeAtom() [2/2]

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.

◆ removeBond()

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

removes a bond from the molecule

Referenced by addBond().

◆ replaceAtom()

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

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`

Referenced by addAtom().

◆ setActiveAtom() [1/2]

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

sets our activeAtom

Referenced by getLastAtom().

◆ 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

Detailed Description

Constructor & Destructor Documentation

◆ RWMol() [1/2]

◆ RWMol() [2/2]

Member Function Documentation

◆ addAtom() [1/3]

◆ addAtom() [2/3]

◆ addAtom() [3/3]

◆ addBond() [1/5]

◆ addBond() [2/5]

◆ addBond() [3/5]

◆ addBond() [4/5]

◆ addBond() [5/5]

◆ clear()

◆ createPartialBond()

◆ finishPartialBond()

◆ getActiveAtom()

◆ getLastAtom()

◆ insertMol()

◆ operator=()

◆ removeAtom() [1/2]

◆ removeAtom() [2/2]

◆ removeBond()

◆ replaceAtom()

◆ setActiveAtom() [1/2]

◆ setActiveAtom() [2/2]