Inheritance diagram for CDPL.Chem.Fragment:

Classes
class	AtomSequence

class	BondSequence

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

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

None	__init__ (MolecularGraph molgraph)
	Constructs a `Fragment` instance storing the atoms, bonds and properties of the molecular graph molgraph. More...

Fragment	assign (Fragment frag)
	Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the fragment frag. More...

Fragment	assign (MolecularGraph molgraph)
	Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the molecular graph molgraph. More...

bool	addAtom (Atom atom)
	Extends the fragment by the specified atom. More...

None	removeAtom (int idx)
	Removes the atom at the specified index. More...

bool	removeAtom (Atom atom)
	Removes the specified atom. More...

bool	addBond (Bond bond)
	Extends the fragment by the specified bond. More...

None	removeBond (int idx)
	Removes the bond at the specified index. More...

bool	removeBond (Bond bond)
	Removes the specified bond. More...

None	clear ()
	Removes all atoms and bonds.

None	swap (Fragment frag)
	Exchanges the atoms, bonds and properties of this fragment with the atoms, bonds and properties of the fragment frag. More...

AtomSequence	getAtoms ()

BondSequence	getBonds ()

None	reserveMemoryForAtoms (int num_atoms)

None	reserveMemoryForBonds (int num_bonds)

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

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

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

Base.Any	__getitem__ (Base.LookupKey key)

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

bool	__delitem__ (Base.LookupKey key)

int	__len__ ()

Fragment	__iadd__ (MolecularGraph molgraph)
	Performs the in-place addition operation `self += molgraph`. More...

Fragment	__isub__ (MolecularGraph molgraph)
	Performs the in-place subtraction operation `self -= molgraph`. More...

Public Member Functions inherited from CDPL.Chem.MolecularGraph
MolecularGraph	clone ()
	Creates a copy of the molecular graph. More...

Atom	getAtom (int idx)

bool	containsAtom (Atom atom)

int	getAtomIndex (Atom atom)

int	getNumAtoms ()

None	orderAtoms (ForceField.InteractionFilterFunction2 func)

Entity3D	getEntity (int idx)

int	getNumEntities ()

Bond	getBond (int idx)

bool	containsBond (Bond bond)

None	orderBonds (BoolBond2Functor func)

int	getBondIndex (Bond bond)

int	getNumBonds ()

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

Public Member Functions inherited from CDPL.Chem.Entity3DContainer
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

Public Member Functions inherited from CDPL.Chem.BondContainer
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

Bond	__getitem__ (int idx)

Public Member Functions inherited from CDPL.Base.PropertyContainer
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

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

Any	getPropertyOrDefault (LookupKey key, Any def_value)

list	getPropertyKeys ()

list	getPropertyValues ()

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

None	setProperty (LookupKey key, Any value)

bool	removeProperty (LookupKey key)
	Clears the value of 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 ()
	Clears all property values.

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

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

None	swap (PropertyContainer cntnr)
	Exchanges the properties of this container with the properties of the container cntnr. More...

Any	__getitem__ (LookupKey key)

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

None	__setitem__ (LookupKey key, Any value)

bool	__delitem__ (LookupKey key)

Properties
	atoms = property(getAtoms)

	bonds = property(getBonds)

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

Fragment.

Constructor & Destructor Documentation

◆ init() [1/2]

None CDPL.Chem.Fragment.__init__ ( Fragment frag )

Constructs a copy of the Fragment instance frag.

Parameters

frag	The other `Fragment` instance to copy.

◆ init() [2/2]

None CDPL.Chem.Fragment.__init__ ( MolecularGraph molgraph )

Constructs a Fragment instance storing the atoms, bonds and properties of the molecular graph molgraph.

Parameters

molgraph The Chem.MolecularGraph instance providing the atoms, bonds and properties to store.

Reimplemented in CDPL.Chem.CyclicSubstructure, and CDPL.Chem.AromaticSubstructure.

Member Function Documentation

◆ assign() [1/2]

Fragment CDPL.Chem.Fragment.assign ( Fragment frag )

Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the fragment frag.

Parameters

frag	The fragment to copy.

Returns: self

◆ assign() [2/2]

Fragment CDPL.Chem.Fragment.assign ( MolecularGraph molgraph )

Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the molecular graph molgraph.

Parameters

molgraph The Chem.MolecularGraph instance providing the atoms, bonds and properties to copy.

Returns: self

◆ addAtom()

bool CDPL.Chem.Fragment.addAtom ( Atom atom )

Extends the fragment by the specified atom.

Parameters

atom	The atom to add.

Returns: True if the atom was not already a part of the fragment, and False otherwise.

◆ removeAtom() [1/2]

None CDPL.Chem.Fragment.removeAtom ( int idx )

Removes the atom at the specified index.

If the specified atom is connected to any other atoms of the fragment, the connecting bonds will also be removed.

Parameters

idx	The zero-based index of the atom to remove.

Exceptions

Base.IndexError if the number of atoms is zero or idx is not in the range [0, getNumAtoms() - 1].

◆ removeAtom() [2/2]

bool CDPL.Chem.Fragment.removeAtom ( Atom atom )

Removes the specified atom.

If the specified atom is connected to any other atoms of the fragment, the connecting bonds will also be removed.

Parameters

atom	The atom to remove.

Returns: True if the atom was part of the fragment and has been removed, and False otherwise.

◆ addBond()

bool CDPL.Chem.Fragment.addBond ( Bond bond )

Extends the fragment by the specified bond.

If the atoms of the bond are not already part of the fragment, they will be added automatically.

Parameters

bond	The bond to add.

Returns: True if the bond was not already a part of the fragment, and False otherwise.

◆ removeBond() [1/2]

None CDPL.Chem.Fragment.removeBond ( int idx )

Removes the bond at the specified index.

Parameters

idx	The zero-based index of the bond to remove.

Exceptions

Base.IndexError if the number of bonds is zero or idx is not in the range [0, getNumBonds() - 1].

◆ removeBond() [2/2]

bool CDPL.Chem.Fragment.removeBond ( Bond bond )

Removes the specified bond.

Parameters

bond	The bond to remove.

Returns: True if the bond was removed, and False otherwise.

◆ swap()

None CDPL.Chem.Fragment.swap ( Fragment frag )

Exchanges the atoms, bonds and properties of this fragment with the atoms, bonds and properties of the fragment frag.

Parameters

frag	The fragment the atoms, bonds and properties get exchanged with.

◆ getAtoms()

AtomSequence CDPL.Chem.Fragment.getAtoms ( )

Returns

Reimplemented from CDPL.Chem.MolecularGraph.

◆ getBonds()

BondSequence CDPL.Chem.Fragment.getBonds ( )

Returns

Reimplemented from CDPL.Chem.MolecularGraph.

◆ reserveMemoryForAtoms()

None CDPL.Chem.Fragment.reserveMemoryForAtoms ( int num_atoms )

Parameters

num_atoms

◆ reserveMemoryForBonds()

None CDPL.Chem.Fragment.reserveMemoryForBonds ( int num_bonds )

Parameters

num_bonds

◆ contains() [1/3]

bool CDPL.Chem.Fragment.__contains__ ( Atom atom )

Returns the result of the membership test operation atom in self.

Parameters

atom	The value to test for membership.

Returns: The result of the membership test operation.

Reimplemented from CDPL.Chem.MolecularGraph.

◆ contains() [2/3]

bool CDPL.Chem.Fragment.__contains__ ( Bond bond )

Returns the result of the membership test operation bond in self.

Parameters

bond	The value to test for membership.

Returns: The result of the membership test operation.

Reimplemented from CDPL.Chem.MolecularGraph.

◆ contains() [3/3]

bool CDPL.Chem.Fragment.__contains__ ( Base.LookupKey key )

Returns the result of the membership test operation key in self.

Parameters

key	The value to test for membership.

Returns: The result of the membership test operation.

Reimplemented from CDPL.Chem.MolecularGraph.

◆ getitem()

Base.Any CDPL.Chem.Fragment.__getitem__ ( Base.LookupKey key )

Parameters

key

Returns

Reimplemented from CDPL.Chem.MolecularGraph.

◆ setitem()

None CDPL.Chem.Fragment.__setitem__	(	Base.LookupKey	key,
		Base.Any	value
	)

Parameters

key
value

Reimplemented from CDPL.Chem.MolecularGraph.

◆ delitem()

bool CDPL.Chem.Fragment.__delitem__ ( Base.LookupKey key )

Parameters

key

Returns

Reimplemented from CDPL.Chem.MolecularGraph.

◆ len()

int CDPL.Chem.Fragment.__len__ ( )

Returns

Reimplemented from CDPL.Chem.MolecularGraph.

Reimplemented in CDPL.Biomol.HierarchyViewModel, and CDPL.Biomol.HierarchyViewChain.

◆ iadd()

Fragment CDPL.Chem.Fragment.__iadd__ ( MolecularGraph molgraph )

Performs the in-place addition operation self += molgraph.

Parameters

molgraph Specifies the second addend.

Returns: The updated Fragment instance self.

◆ isub()

Fragment CDPL.Chem.Fragment.__isub__ ( MolecularGraph molgraph )

Performs the in-place subtraction operation self -= molgraph.

Parameters

molgraph Specifies the subtrahend.

Returns: The updated Fragment instance self.

Classes

Public Member Functions

Properties

Detailed Description

Constructor & Destructor Documentation

◆ __init__() [1/2]

◆ __init__() [2/2]

Member Function Documentation

◆ assign() [1/2]

◆ assign() [2/2]

◆ addAtom()

◆ removeAtom() [1/2]

◆ removeAtom() [2/2]

◆ addBond()

◆ removeBond() [1/2]

◆ removeBond() [2/2]

◆ swap()

◆ getAtoms()

◆ getBonds()

◆ reserveMemoryForAtoms()

◆ reserveMemoryForBonds()

◆ __contains__() [1/3]

◆ __contains__() [2/3]

◆ __contains__() [3/3]

◆ __getitem__()

◆ __setitem__()

◆ __delitem__()

◆ __len__()

◆ __iadd__()

◆ __isub__()

◆ init() [1/2]

◆ init() [2/2]

◆ contains() [1/3]

◆ contains() [2/3]

◆ contains() [3/3]

◆ getitem()

◆ setitem()

◆ delitem()

◆ len()

◆ iadd()

◆ isub()