RDKit::MacroMol Class Reference

#include <MacroMol.h>

Inheritance diagram for RDKit::MacroMol:

Public Member Functions
	MacroMol ()
	Constructs a MacroMol with an empty local template library.
	MacroMol (std::unique_ptr< MacroMolTemplateLibrary > localTemplateLibrary)
	Constructs a MacroMol that takes ownership of a local template library.
	MacroMol (const MacroMol &other)
MacroMol &	operator= (const MacroMol &other)
	MacroMol (MacroMol &&other) noexcept=default
MacroMol &	operator= (MacroMol &&other) noexcept=default
void	setLocalTemplateLibrary (std::unique_ptr< MacroMolTemplateLibrary > newTemplateLibrary)
	Replaces the local template library and takes ownership of it.
MacroMolTemplateLibrary &	getLocalTemplateLibrary ()
	Returns this molecule's local template library.
const MacroMolTemplateLibrary &	getLocalTemplateLibrary () const
	Returns this molecule's local template library.
bool	checkLocalTemplateReferences () const
	Checks that every macro atom resolves in the local template library.
unsigned int	addMacroAtom (std::string symbol, MonomerClass monomerClass)
	Adds a new macro atom to the molecule.
unsigned int	addMacroBond (unsigned int beginAtomIdx, unsigned int endAtomIdx, int beginAttachPt, int endAttachPt, Bond::BondType bondType=Bond::SINGLE)
	Adds a bond between two macro atoms.
unsigned int	addAtomToMacroAtomBond (unsigned int beginAtomIdx, unsigned int endMacroAtomIdx, int endAttachPt, Bond::BondType bondType=Bond::BondType::SINGLE)
	Adds a bond from a regular atom to a macro atom.
unsigned int	addMacroAtomToAtomBond (unsigned int beginMacroAtomIdx, unsigned int endAtomIdx, int beginAttachPt, Bond::BondType bondType=Bond::BondType::SINGLE)
	Adds a bond from a macro atom to a regular atom.
unsigned int	addBond (unsigned int beginAtomIdx, unsigned int endAtomIdx, Bond::BondType bondType=Bond::SINGLE)
	Adds a bond between two regular atoms.
unsigned int	addBond (Atom *beginAtom, Atom *endAtom, Bond::BondType bondType=Bond::SINGLE)
	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)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
Public Member Functions inherited from RDKit::RWMol
	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 ()
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.
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< MolGraph, Atom *, MolGraph::vertex_iterator, true >	checkedAtoms ()
CXXAtomIterator< const MolGraph, Atom *const, MolGraph::vertex_iterator, true >	checkedAtoms () 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)
CXXAtomIterator< const MolGraph, Atom *const, MolGraph::adjacency_iterator, true, true >	checkedAtomNeighbors (Atom const *at) const
CXXAtomIterator< MolGraph, Atom *, MolGraph::adjacency_iterator, true, true >	checkedAtomNeighbors (Atom const *at)
CXXBondIterator< const MolGraph, Bond *const, MolGraph::out_edge_iterator, true >	checkedAtomBonds (Atom const *at) const
CXXBondIterator< MolGraph, Bond *, MolGraph::out_edge_iterator, true >	checkedAtomBonds (Atom const *at)
CXXBondIterator< MolGraph, Bond * >	bonds ()
CXXBondIterator< const MolGraph, Bond *const >	bonds () const
CXXBondIterator< MolGraph, Bond *, MolGraph::edge_iterator, true >	checkedBonds ()
CXXBondIterator< const MolGraph, Bond *const, MolGraph::edge_iterator, true >	checkedBonds () 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 (Atom const *query)
	get an AtomIterator pointing at our first Atom that matches query
ConstQueryAtomIterator	beginQueryAtoms (Atom const *query) 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	setName (const std::string &name) const
	sets the molecule name/title; equivalent to setting the _Name property
std::string	getName () 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_view key, T val, bool computed=false) const
	sets a property value
template<typename T>
void	getProp (const std::string_view key, T &res) const
	allows retrieval of a particular property value
template<typename T>
T	getProp (const std::string_view 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_view key, T &res) const
bool	hasProp (const std::string_view 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_view 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

Definition at line 23 of file MacroMol.h.

Constructor & Destructor Documentation

MacroMol() [1/4]

RDKit::MacroMol::MacroMol

(

)

Constructs a MacroMol with an empty local template library.

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

MacroMol() [2/4]

RDKit::MacroMol::MacroMol ( std::unique_ptr< MacroMolTemplateLibrary > localTemplateLibrary )

explicit

Constructs a MacroMol that takes ownership of a local template library.

Parameters

localTemplateLibrary

the non-null library to take ownership of

MacroMol() [3/4]

RDKit::MacroMol::MacroMol

(

const MacroMol &

other

)

References MacroMol().

MacroMol() [4/4]

RDKit::MacroMol::MacroMol ( MacroMol && other )

defaultnoexcept

References MacroMol().

Member Function Documentation

addAtomToMacroAtomBond()

unsigned int RDKit::MacroMol::addAtomToMacroAtomBond	(	unsigned int	beginAtomIdx,
		unsigned int	endMacroAtomIdx,
		int	endAttachPt,
		Bond::BondType	bondType = Bond::BondType::SINGLE )

Adds a bond from a regular atom to a macro atom.

The graph bond's bond type is unspecified; use MacroBondInfo for the macro bond type.

Parameters

beginAtomIdx	index of the regular atom where the bond begins
endMacroAtomIdx	index of the macro atom where the bond ends
endAttachPt	the attachment point on the end (macro) atom
bondType	the type of the bond

Returns

the new number of bonds

References RDKit::Bond::SINGLE.

addBond() [1/3]

unsigned int RDKit::MacroMol::addBond	(	Atom *	beginAtom,
		Atom *	endAtom,
		Bond::BondType	bondType = Bond::SINGLE )

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::SINGLE.

addBond() [2/3]

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

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::SINGLE.

addBond() [3/3]

unsigned int RDKit::MacroMol::addBond	(	unsigned int	beginAtomIdx,
		unsigned int	endAtomIdx,
		Bond::BondType	bondType = Bond::SINGLE )

Adds a bond between two regular atoms.

Note: neither atom may be a macro atom; use addMacroBond(), addAtomToMacroAtomBond(), or addMacroAtomToAtomBond() for bonds involving macro atoms.

Parameters

beginAtomIdx	index of the atom where the bond begins
endAtomIdx	index of the atom where the bond ends
bondType	the type of the bond

Returns

the new number of bonds

References RDKit::Bond::SINGLE.

addMacroAtom()

unsigned int RDKit::MacroMol::addMacroAtom	(	std::string	symbol,
		MonomerClass	monomerClass )

Adds a new macro atom to the molecule.

Parameters

symbol	the symbol (dummy label) used to identify the monomer
monomerClass	the class of monomer the macro atom represents

Returns

the index of the newly added atom

References symbol.

addMacroAtomToAtomBond()

unsigned int RDKit::MacroMol::addMacroAtomToAtomBond	(	unsigned int	beginMacroAtomIdx,
		unsigned int	endAtomIdx,
		int	beginAttachPt,
		Bond::BondType	bondType = Bond::BondType::SINGLE )

Adds a bond from a macro atom to a regular atom.

The graph bond's bond type is unspecified; use MacroBondInfo for the macro bond type.

Parameters

beginMacroAtomIdx	index of the macro atom where the bond begins
endAtomIdx	index of the regular atom where the bond ends
beginAttachPt	the attachment point on the begin (macro) atom
bondType	the type of the bond

Returns

the new number of bonds

References RDKit::Bond::SINGLE.

addMacroBond()

unsigned int RDKit::MacroMol::addMacroBond	(	unsigned int	beginAtomIdx,
		unsigned int	endAtomIdx,
		int	beginAttachPt,
		int	endAttachPt,
		Bond::BondType	bondType = Bond::SINGLE )

Adds a bond between two macro atoms.

Both atoms must be macro atoms. The graph bond's bond type is unspecified; use MacroBondInfo for the macro bond type.

Parameters

beginAtomIdx	index of the atom where the bond begins
endAtomIdx	index of the atom where the bond ends
beginAttachPt	the attachment point on the begin (macro) atom
endAttachPt	the attachment point on the end (macro) atom
bondType	the type of the bond

Returns

the new number of bonds

References RDKit::Bond::SINGLE.

checkLocalTemplateReferences()

bool RDKit::MacroMol::checkLocalTemplateReferences

(

)

const

Checks that every macro atom resolves in the local template library.

Macro atoms are looked up by monomer class and symbol, then by monomer class and template name. Ordinary atoms are ignored.

getLocalTemplateLibrary() [1/2]

MacroMolTemplateLibrary & RDKit::MacroMol::getLocalTemplateLibrary

(

)

Returns this molecule's local template library.

getLocalTemplateLibrary() [2/2]

const MacroMolTemplateLibrary & RDKit::MacroMol::getLocalTemplateLibrary

(

)

const

Returns this molecule's local template library.

operator=() [1/2]

MacroMol & RDKit::MacroMol::operator=

(

const MacroMol &

other

)

References MacroMol().

operator=() [2/2]

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

defaultnoexcept

References MacroMol().

setLocalTemplateLibrary()

void RDKit::MacroMol::setLocalTemplateLibrary

(

std::unique_ptr< MacroMolTemplateLibrary >

newTemplateLibrary

)

Replaces the local template library and takes ownership of it.

Parameters

newTemplateLibrary

the non-null library to take ownership of

---

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

• MacroMol.h