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

BasicMolecule. More...

+ Inheritance diagram for CDPL.Chem.BasicMolecule:

Public Member Functions

None __init__ ()
 Constructs an empty BasicMolecule instance.
 
None __init__ (BasicMolecule mol)
 Constructs a copy of the Chem.Molecule instance mol. More...
 
None __init__ (Molecule mol)
 Constructs a copy of the Chem.Molecule instance mol. More...
 
None __init__ (MolecularGraph molgraph)
 Constructs a BasicMolecule instance with copies of the atoms and bonds of the Chem.MolecularGraph instance molgraph. More...
 
None copy (BasicMolecule mol)
 Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol. More...
 
None copy (Molecule mol)
 Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol. More...
 
None copy (MolecularGraph molgraph)
 Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecular graph molgraph. More...
 
None append (BasicMolecule mol)
 Extends the current set of atoms and bonds by a copy of the atoms and bonds in the molecule mol. More...
 
None append (Molecule mol)
 Extends the current set of atoms and bonds by a copy of the atoms and bonds in the molecule mol. More...
 
None append (MolecularGraph molgraph)
 Extends the current set of atoms and bonds by a copy of the atoms and bonds in the molecular graph molgraph. More...
 
BasicMolecule assign (BasicMolecule mol)
 Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol. More...
 
BasicMolecule assign (Molecule mol)
 Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol. More...
 
BasicMolecule assign (MolecularGraph molgraph)
 Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecular graph molgraph. More...
 
BasicMolecule __iadd__ (BasicMolecule mol)
 Performs the in-place addition operation self += mol. More...
 
BasicMolecule __iadd__ (Molecule mol)
 Performs the in-place addition operation self += mol. More...
 
BasicMolecule __iadd__ (MolecularGraph molgraph)
 Performs the in-place addition operation self += molgraph. More...
 
- Public Member Functions inherited from CDPL.Chem.Molecule
None reserveMemoryForAtoms (int num_atoms)
 Reserves memory for num_atoms atoms. More...
 
None reserveMemoryForBonds (int num_bonds)
 Reserves memory for num_bonds bonds. More...
 
None clear ()
 Removes all atoms and bonds and clears all properties of the molecule.
 
Atom addAtom ()
 Creates a new atom and adds it to the molecule. More...
 
Bond addBond (int atom1_idx, int atom2_idx)
 Creates a new or returns an already existing bond between the atoms specified by atom1_idx and atom2_idx. More...
 
None removeAtom (int idx)
 Removes the atom at the specified index. More...
 
None removeBond (int idx)
 Removes the bond at the specified index. More...
 
None remove (MolecularGraph molgraph)
 Removes atoms and bonds referenced by the molecular graph molgraph that are part of this Molecule instance. More...
 
AtomSequence getAtoms ()
 
BondSequence getBonds ()
 
None invokeCopyPostprocessingFunctions (MolecularGraph src_molgraph)
 
Atom getAtom (int idx)
 Returns a reference to the atom at index idx. More...
 
bool containsAtom (Atom atom)
 Tells whether the specified atom is part of this molecule. More...
 
int getAtomIndex (Atom atom)
 Returns the index of the specified atom. More...
 
int getNumAtoms ()
 Returns the number of explicit atoms. More...
 
None orderAtoms (ForceField.InteractionFilterFunction2 func)
 
Entity3D getEntity (int idx)
 
int getNumEntities ()
 
Bond getBond (int idx)
 Returns a reference to the bond at index idx. More...
 
bool containsBond (Bond bond)
 Tells whether the specified bond is part of this molecule. More...
 
None orderBonds (BoolBond2Functor func)
 
int getBondIndex (Bond bond)
 Returns the index of the specified bond. More...
 
int getNumBonds ()
 Returns the number of explicit bonds. More...
 
tuple __getstate__ ()
 
Molecule __isub__ (MolecularGraph molgraph)
 Performs the in-place subtraction operation self -= molgraph. More...
 
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.MolecularGraph
MolecularGraph clone ()
 Creates a copy of the molecular graph. More...
 
- 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)
 

Additional Inherited Members

- Static Public Member Functions inherited from CDPL.Chem.Molecule
None registerCopyPostprocessingFunction (VoidMoleculeMolecularGraphFunctor func)
 
- Properties inherited from CDPL.Chem.Molecule
 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

BasicMolecule.

Constructor & Destructor Documentation

◆ __init__() [1/3]

None CDPL.Chem.BasicMolecule.__init__ ( BasicMolecule  mol)

Constructs a copy of the Chem.Molecule instance mol.

Parameters
molThe other Chem.Molecule instance to copy.

◆ __init__() [2/3]

None CDPL.Chem.BasicMolecule.__init__ ( Molecule  mol)

Constructs a copy of the Chem.Molecule instance mol.

Parameters
molThe other Chem.Molecule instance to copy.

◆ __init__() [3/3]

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

Constructs a BasicMolecule instance with copies of the atoms and bonds of the Chem.MolecularGraph instance molgraph.

Parameters
molgraphThe Chem.MolecularGraph instance providing the atoms and bonds to copy.

Member Function Documentation

◆ copy() [1/3]

None CDPL.Chem.BasicMolecule.copy ( BasicMolecule  mol)

Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol.

Parameters
molThe molecule to copy.

◆ copy() [2/3]

None CDPL.Chem.BasicMolecule.copy ( Molecule  mol)

Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol.

Parameters
molThe molecule to copy.

Reimplemented from CDPL.Chem.Molecule.

◆ copy() [3/3]

None CDPL.Chem.BasicMolecule.copy ( MolecularGraph  molgraph)

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

Parameters
molgraphThe Chem.MolecularGraph instance providing the atoms, bonds and properties to copy.

Reimplemented from CDPL.Chem.Molecule.

◆ append() [1/3]

None CDPL.Chem.BasicMolecule.append ( BasicMolecule  mol)

Extends the current set of atoms and bonds by a copy of the atoms and bonds in the molecule mol.

Parameters
molThe molecule providing the atoms and bonds to append.
Note
Does not affect any properties.

◆ append() [2/3]

None CDPL.Chem.BasicMolecule.append ( Molecule  mol)

Extends the current set of atoms and bonds by a copy of the atoms and bonds in the molecule mol.

Parameters
molThe molecule providing the atoms and bonds to append.
Note
Does not affect any properties.

Reimplemented from CDPL.Chem.Molecule.

◆ append() [3/3]

None CDPL.Chem.BasicMolecule.append ( MolecularGraph  molgraph)

Extends the current set of atoms and bonds by a copy of the atoms and bonds in the molecular graph molgraph.

Parameters
molgraphThe Chem.MolecularGraph instance providing the atoms and bonds to append.
Note
Does not affect any properties.

Reimplemented from CDPL.Chem.Molecule.

◆ assign() [1/3]

BasicMolecule CDPL.Chem.BasicMolecule.assign ( BasicMolecule  mol)

Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol.

Internally calls copy() to perform the actual work.

Parameters
molThe molecule to copy.
Returns
self

◆ assign() [2/3]

BasicMolecule CDPL.Chem.BasicMolecule.assign ( Molecule  mol)

Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol.

Internally calls copy() to perform the actual work.

Parameters
molThe molecule to copy.
Returns
self

Reimplemented from CDPL.Chem.Molecule.

◆ assign() [3/3]

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

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

Internally calls copy() to perform the actual work.

Parameters
molgraphThe Chem.MolecularGraph instance providing the atoms and bonds to copy.
Returns
self

Reimplemented from CDPL.Chem.Molecule.

◆ __iadd__() [1/3]

BasicMolecule CDPL.Chem.BasicMolecule.__iadd__ ( BasicMolecule  mol)

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

Parameters
molSpecifies the second addend.
Returns
The updated BasicMolecule instance self.

◆ __iadd__() [2/3]

BasicMolecule CDPL.Chem.BasicMolecule.__iadd__ ( Molecule  mol)

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

Parameters
molSpecifies the second addend.
Returns
The updated BasicMolecule instance self.

Reimplemented from CDPL.Chem.Molecule.

◆ __iadd__() [3/3]

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

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

Parameters
molgraphSpecifies the second addend.
Returns
The updated BasicMolecule instance self.

Reimplemented from CDPL.Chem.Molecule.