Data structure representing a canonicalized molecular fragment. More...

Inheritance diagram for CDPL.ConfGen.CanonicalFragment:

Classes
class	AtomMapping
	Maps each atom of the fragment (in canonical order) to the corresponding atom of the parent molecular graph. More...

Public Member Functions
None	__init__ ()
	Constructs an empty `CanonicalFragment` instance.

None	__init__ (Chem.MolecularGraph molgraph, Chem.MolecularGraph parent)
	Constructs a `CanonicalFragment` instance from the fragment molgraph of the parent molecular graph parent. More...

None	__init__ (CanonicalFragment frag)
	Constructs a copy of the `CanonicalFragment` instance frag. More...

int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

CanonicalFragment	assign (CanonicalFragment frag)
	Replaces the contents of this fragment with a copy of frag. More...

None	create (Chem.MolecularGraph molgraph, Chem.MolecularGraph parent, bool modify=True, bool strip_aro_subst=True)
	Builds the canonical fragment from the fragment molgraph of the parent molecular graph parent. More...

int	getHashCode ()
	Returns the hash code of the fragment. More...

None	clear ()
	Removes all atoms and bonds and resets the hash code.

Chem.AtomMapping	getAtomMapping ()
	Returns the atom mapping from this fragment to the parent molecular graph. More...

Public Member Functions inherited from CDPL.Chem.MolecularGraph
AtomSequence	getAtoms ()

BondSequence	getBonds ()

MolecularGraph	clone ()
	Creates a deep copy of the molecular graph. More...

Atom	getAtom (int idx)
	Returns the atom at index idx. More...

bool	containsAtom (Atom atom)
	Tells whether the specified atom is part of the atom sequence. More...

int	getAtomIndex (Atom atom)
	Returns the index of the specified atom. More...

int	getNumAtoms ()
	Returns the number of atoms. More...

None	orderAtoms (BoolAtom2Functor func)
	Orders the atoms according to criteria implemented by the provided atom comparison function. More...

Entity3D	getEntity (int idx)
	Returns the entity at index idx. More...

int	getNumEntities ()
	Returns the number of stored Chem.Entity3D instances. More...

Bond	getBond (int idx)
	Returns the bond at index idx. More...

bool	containsBond (Bond bond)
	Tells whether the specified bond is part of the bond sequence. More...

None	orderBonds (BoolBond2Functor func)
	Orders the bonds according to criteria implemented by the provided bond comparison function. More...

int	getBondIndex (Bond bond)
	Returns the index of the specified bond. More...

int	getNumBonds ()
	Returns the number of bonds. More...

Base.Any	__getitem__ (Base.LookupKey key)

bool	__contains__ (Base.LookupKey key)
	Returns the result of the membership test operation `key in self`. More...

bool	__contains__ (Bond bond)
	Returns the result of the membership test operation `bond in self`. More...

bool	__contains__ (Atom atom)
	Returns the result of the membership test operation `atom in self`. More...

None	__setitem__ (Base.LookupKey key, Base.Any val)

bool	__delitem__ (Base.LookupKey key)

int	__len__ ()
	Returns the number of property entries. More...

Public Member Functions inherited from CDPL.Chem.AtomContainer
Atom	__getitem__ (int idx)

Public Member Functions inherited from CDPL.Chem.BondContainer
Bond	__getitem__ (int idx)

Public Member Functions inherited from CDPL.Base.PropertyContainer
int	getNumProperties ()
	Returns the number of property entries. More...

Any	getPropertyOrDefault (LookupKey key, Any def_val)
	Returns the value of the property specified by key , or the default value def_val if an entry does not exist. More...

list	getPropertyKeys ()
	Returns a list containing the keys of the current property entries. More...

list	getPropertyValues ()
	Returns a list containing the values of the current property entries. More...

list	getProperties ()
	Returns a reference to itself. More...

None	setProperty (LookupKey key, Any val)
	Sets the value of the property specified by key to val. More...

bool	removeProperty (LookupKey key)
	Removes the entry for the property specified by key. More...

Any	getProperty (LookupKey key, bool throw_=False)
	Returns the value of the property specified by key. More...

bool	isPropertySet (LookupKey key)
	Tells whether or not a value has been assigned to the property specified by key. More...

None	clearProperties ()
	Erases all container entries.

None	addProperties (PropertyContainer cntnr)
	Adds the property entries of the `PropertyContainer` instance cntnr. More...

None	copyProperties (PropertyContainer cntnr)
	Replaces the current property entries by a copy of the entries in cntnr. More...

None	swap (PropertyContainer cntnr)
	Exchanges the property entries of this container with the ones of cntnr. More...

Any	__getitem__ (LookupKey key)
	Returns the value of the property specified by key. More...

bool	__contains__ (LookupKey key)
	Tells whether or not a value has been assigned to the property specified by key. More...

None	__setitem__ (LookupKey key, Any val)
	Sets the value of the property specified by key to val. More...

bool	__delitem__ (LookupKey key)
	Removes the entry for the property specified by key. More...

Properties
	objectID = property(getObjectID)

	hashCode = property(getHashCode)

	atomMapping = property(getAtomMapping)

Properties inherited from CDPL.Chem.MolecularGraph
	atoms = property(getAtoms)

	bonds = property(getBonds)

Properties inherited from CDPL.Chem.AtomContainer
	numAtoms = property(getNumAtoms)

Properties inherited from CDPL.Chem.Entity3DContainer
	objectID = property(getObjectID)

	numEntities = property(getNumEntities)

Properties inherited from CDPL.Chem.BondContainer
	objectID = property(getObjectID)

	numBonds = property(getNumBonds)

Properties inherited from CDPL.Base.PropertyContainer
	objectID = property(getObjectID)

	propertyKeys = property(getPropertyKeys)

	propertyValues = property(getPropertyValues)

	properties = property(getProperties)

	numProperties = property(getNumProperties)

Detailed Description

Data structure representing a canonicalized molecular fragment.

A CanonicalFragment is constructed from a fragment of a parent molecular graph and stores a canonicalized copy of the fragment's atoms and bonds. Canonicalization yields a stable atom ordering and an associated hash code that uniquely identifies the topology (and, optionally, the stereochemistry) of the fragment.

See also: ConfGen.FragmentLibrary

Constructor & Destructor Documentation

◆ init() [1/2]

None CDPL.ConfGen.CanonicalFragment.__init__	(	Chem.MolecularGraph	molgraph,
		Chem.MolecularGraph	parent
	)

Constructs a CanonicalFragment instance from the fragment molgraph of the parent molecular graph parent.

Parameters

molgraph	The molecular graph defining the fragment to canonicalize.
parent	The parent molecular graph the fragment was derived from.

◆ init() [2/2]

None CDPL.ConfGen.CanonicalFragment.__init__ ( CanonicalFragment frag )

Constructs a copy of the CanonicalFragment instance frag.

Parameters

frag	The `CanonicalFragment` to copy.

Member Function Documentation

◆ getObjectID()

int CDPL.ConfGen.CanonicalFragment.getObjectID ( )

Returns the numeric identifier (ID) of the wrapped C++ class instance.

Different Python CanonicalFragment instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two CanonicalFragment instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().

Returns: The numeric ID of the internally referenced C++ class instance.

Reimplemented from CDPL.Base.PropertyContainer.

◆ assign()

CanonicalFragment CDPL.ConfGen.CanonicalFragment.assign ( CanonicalFragment frag )

Replaces the contents of this fragment with a copy of frag.

Parameters

frag	The source `CanonicalFragment`.

Returns: self.

◆ create()

None CDPL.ConfGen.CanonicalFragment.create	(	Chem.MolecularGraph	molgraph,
		Chem.MolecularGraph	parent,
		bool	modify = `True`,
		bool	strip_aro_subst = `True`
	)

Builds the canonical fragment from the fragment molgraph of the parent molecular graph parent.

Parameters

molgraph	The molecular graph defining the fragment to canonicalize.
parent	The parent molecular graph the fragment was derived from.
modify	If `True`, the fragment is modified prior to canonicalization (e.g. ring perception, hydrogenization).
strip_aro_subst	If `True`, aromatic-ring substituents are stripped during fragment construction.

◆ getHashCode()

int CDPL.ConfGen.CanonicalFragment.getHashCode ( )

Returns the hash code of the fragment.

Returns: The fragment hash code (0 if not yet computed).

◆ getAtomMapping()

Chem.AtomMapping CDPL.ConfGen.CanonicalFragment.getAtomMapping ( )

Returns the atom mapping from this fragment to the parent molecular graph.

Returns: The atom mapping.

Classes

Public Member Functions

Properties

Detailed Description

Constructor & Destructor Documentation

◆ __init__() [1/2]

◆ __init__() [2/2]

Member Function Documentation

◆ getObjectID()

◆ assign()

◆ create()

◆ getHashCode()

◆ getAtomMapping()

◆ init() [1/2]

◆ init() [2/2]