Chemical Data Processing Library Python API - Version 1.1.1
Classes | Public Member Functions | Properties | List of all members
CDPL.Chem.MolecularGraph Class Reference

MolecularGraph. More...

+ Inheritance diagram for CDPL.Chem.MolecularGraph:

Classes

class  AtomSequence
 
class  BondSequence
 

Public Member Functions

None __init__ ()
 Initializes the MolecularGraph instance.
 
AtomSequence getAtoms ()
 
BondSequence getBonds ()
 
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 ()
 
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__ ()
 
- 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.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

MolecularGraph.

Member Function Documentation

◆ getAtoms()

AtomSequence CDPL.Chem.MolecularGraph.getAtoms ( )
Returns

Reimplemented in CDPL.Chem.Molecule, and CDPL.Chem.Fragment.

◆ getBonds()

BondSequence CDPL.Chem.MolecularGraph.getBonds ( )
Returns

Reimplemented in CDPL.Chem.Molecule, and CDPL.Chem.Fragment.

◆ clone()

MolecularGraph CDPL.Chem.MolecularGraph.clone ( )

Creates a copy of the molecular graph.

Returns
A smart reference to the copy of the molecular graph.

◆ getAtom()

Atom CDPL.Chem.MolecularGraph.getAtom ( int  idx)
Parameters
idx
Returns

Reimplemented from CDPL.Chem.AtomContainer.

Reimplemented in CDPL.Chem.Molecule.

◆ containsAtom()

bool CDPL.Chem.MolecularGraph.containsAtom ( Atom  atom)
Parameters
atom
Returns

Reimplemented from CDPL.Chem.AtomContainer.

Reimplemented in CDPL.Chem.Molecule.

◆ getAtomIndex()

int CDPL.Chem.MolecularGraph.getAtomIndex ( Atom  atom)
Parameters
atom
Returns

Reimplemented from CDPL.Chem.AtomContainer.

Reimplemented in CDPL.Chem.Molecule.

◆ getNumAtoms()

int CDPL.Chem.MolecularGraph.getNumAtoms ( )
Returns

Reimplemented from CDPL.Chem.AtomContainer.

Reimplemented in CDPL.Chem.Molecule.

◆ orderAtoms()

None CDPL.Chem.MolecularGraph.orderAtoms ( ForceField.InteractionFilterFunction2  func)
Parameters
func

Reimplemented from CDPL.Chem.AtomContainer.

Reimplemented in CDPL.Chem.Molecule.

◆ getEntity()

Entity3D CDPL.Chem.MolecularGraph.getEntity ( int  idx)
Parameters
idx
Returns

Reimplemented from CDPL.Chem.AtomContainer.

Reimplemented in CDPL.Chem.Molecule.

◆ getNumEntities()

int CDPL.Chem.MolecularGraph.getNumEntities ( )
Returns

Reimplemented from CDPL.Chem.AtomContainer.

Reimplemented in CDPL.Chem.Molecule.

◆ getBond()

Bond CDPL.Chem.MolecularGraph.getBond ( int  idx)
Parameters
idx
Returns

Reimplemented from CDPL.Chem.BondContainer.

Reimplemented in CDPL.Chem.Molecule.

◆ containsBond()

bool CDPL.Chem.MolecularGraph.containsBond ( Bond  bond)
Parameters
bond
Returns

Reimplemented from CDPL.Chem.BondContainer.

Reimplemented in CDPL.Chem.Molecule.

◆ orderBonds()

None CDPL.Chem.MolecularGraph.orderBonds ( BoolBond2Functor  func)
Parameters
func

Reimplemented from CDPL.Chem.BondContainer.

Reimplemented in CDPL.Chem.Molecule.

◆ getBondIndex()

int CDPL.Chem.MolecularGraph.getBondIndex ( Bond  bond)
Parameters
bond
Returns

Reimplemented from CDPL.Chem.BondContainer.

Reimplemented in CDPL.Chem.Molecule.

◆ getNumBonds()

int CDPL.Chem.MolecularGraph.getNumBonds ( )
Returns

Reimplemented from CDPL.Chem.BondContainer.

Reimplemented in CDPL.Chem.Molecule.

◆ __contains__() [1/3]

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

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

Parameters
atomThe value to test for membership.
Returns
The result of the membership test operation.

Reimplemented from CDPL.Chem.AtomContainer.

Reimplemented in CDPL.Chem.Molecule, and CDPL.Chem.Fragment.

◆ __contains__() [2/3]

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

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

Parameters
bondThe value to test for membership.
Returns
The result of the membership test operation.

Reimplemented from CDPL.Chem.BondContainer.

Reimplemented in CDPL.Chem.Molecule, and CDPL.Chem.Fragment.

◆ __contains__() [3/3]

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

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

Parameters
keyThe value to test for membership.
Returns
The result of the membership test operation.

Reimplemented in CDPL.Chem.Molecule, and CDPL.Chem.Fragment.

◆ __getitem__()

Base.Any CDPL.Chem.MolecularGraph.__getitem__ ( Base.LookupKey  key)
Parameters
key
Returns

Reimplemented in CDPL.Chem.Molecule, and CDPL.Chem.Fragment.

◆ __setitem__()

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

Reimplemented in CDPL.Chem.Molecule, and CDPL.Chem.Fragment.

◆ __delitem__()

bool CDPL.Chem.MolecularGraph.__delitem__ ( Base.LookupKey  key)
Parameters
key
Returns

Reimplemented in CDPL.Chem.Molecule, and CDPL.Chem.Fragment.

◆ __len__()

int CDPL.Chem.MolecularGraph.__len__ ( )