RDKit::RWMol Class Reference

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

#include <RWMol.h>

Inheritance diagram for RDKit::RWMol:

List of all members.

Public Member Functions
	RWMol ()
	RWMol (const ROMol &other, bool quickCopy=false)
	copy constructor with a twist
void	insertMol (const ROMol &other)
	insert the atoms and bonds from other into this molecule
unsigned int	addAtom (bool updateLabel=true)
	adds an empty Atom to our collection
void	replaceAtom (unsigned int idx, Atom *atom, bool updateLabel=false)
	replaces a particular Atom
GRAPH_NODE_TYPE	getLastAtom ()
	returns a pointer to the highest-numbered Atom
GRAPH_NODE_TYPE	getActiveAtom ()
	returns a pointer to the "active" Atom
void	setActiveAtom (Atom *atom)
	sets our activeAtom
void	setActiveAtom (unsigned int idx)
void	removeAtom (unsigned int idx)
	removes an Atom from the molecule
void	removeAtom (Atom *atom)
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_SPTR beginAtom, ATOM_SPTR endAtom, Bond::BondType order=Bond::UNSPECIFIED)
unsigned int	addBond (Atom *beginAtom, Atom *endAtom, Bond::BondType order=Bond::UNSPECIFIED)
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

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Detailed Description

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

See documentation for ROMol for general remarks

Definition at line 20 of file RWMol.h.

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Constructor & Destructor Documentation

RDKit::RWMol::RWMol

(

)

[inline]

Definition at line 26 of file RWMol.h.

RDKit::RWMol::RWMol	(	const ROMol &	other,
		bool	quickCopy = false
	)			[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).

Definition at line 35 of file RWMol.h.

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Member Function Documentation

void RDKit::RWMol::insertMol

(

const ROMol &

other

)

insert the atoms and bonds from other into this molecule

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

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

GRAPH_NODE_TYPE RDKit::RWMol::getLastAtom

(

)

[inline]

returns a pointer to the highest-numbered Atom

Definition at line 67 of file RWMol.h.

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

GRAPH_NODE_TYPE 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.

void RDKit::RWMol::setActiveAtom

(

Atom *

atom

)

sets our activeAtom

void RDKit::RWMol::setActiveAtom

(

unsigned int

idx

)

void RDKit::RWMol::removeAtom

(

unsigned int

idx

)

removes an Atom from the molecule

void RDKit::RWMol::removeAtom

(

Atom *

atom

)

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

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

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

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.

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

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

removes a bond from the molecule

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

• RWMol.h

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