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

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

unsigned int addAtom (ATOM_SPTR atom, bool updateLabel=true)

adds an Atom to our collection

void replaceAtom (unsigned int idx, Atom *atom, bool updateLabel=false)

replaces a particular Atom

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)

void removeAtom (unsigned int idx)

removes an Atom from the molecule

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

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

unsigned int addBond (BOND_SPTR bsp)

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

Detailed Description

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

See documentation for ROMol for general remarks

Definition at line 25 of file RWMol.h.

Constructor & Destructor Documentation

RDKit::RWMol::RWMol ( ) [inline]

Definition at line 28 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 37 of file RWMol.h.

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

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

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

Reimplemented from RDKit::ROMol.

Definition at line 67 of file RWMol.h.

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.

Reimplemented from RDKit::ROMol.

Definition at line 84 of file RWMol.h.

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`

Atom* RDKit::RWMol::getLastAtom ( ) [inline]

returns a pointer to the highest-numbered Atom

Definition at line 98 of file RWMol.h.

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

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.

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

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

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`
	)

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

Reimplemented from RDKit::ROMol.

Definition at line 142 of file RWMol.h.

unsigned int RDKit::RWMol::addBond ( BOND_SPTR bsp ) [inline]

adds a Bond to our collection

Parameters:

bond

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.

Reimplemented from RDKit::ROMol.

Definition at line 154 of file RWMol.h.

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

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

RWMol.h


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
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
unsigned int	addAtom (ATOM_SPTR atom, bool updateLabel=true)
	adds an Atom to our collection
void	replaceAtom (unsigned int idx, Atom *atom, bool updateLabel=false)
	replaces a particular Atom
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)
void	removeAtom (unsigned int idx)
	removes an Atom from the molecule
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
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
unsigned int	addBond (BOND_SPTR bsp)
	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