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Chemical Data Processing Library Python API - Version 1.4.0
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Chemical Data Processing Library Python API - Version 1.4.0
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Default implementation of the Chem.Molecule interface. More...
Inheritance diagram for CDPL.Chem.BasicMolecule:Public Member Functions | |
| None | __init__ () |
Constructs an empty BasicMolecule instance. | |
| None | __init__ (BasicMolecule mol) |
Constructs a BasicMolecule instance that is a copy of the molecule mol. More... | |
| None | __init__ (Molecule mol) |
Constructs a BasicMolecule instance that is a copy of the molecule mol. More... | |
| None | __init__ (MolecularGraph molgraph) |
Constructs a BasicMolecule instance with copies of the atoms, bonds and properties provided by the molecular graph 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 of the molecule mol. More... | |
| None | append (Molecule mol) |
| Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol. More... | |
| None | append (MolecularGraph molgraph) |
| Extends the current set of atoms and bonds by a copy of the atoms and bonds of 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) |
| Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol. More... | |
| BasicMolecule | __iadd__ (Molecule mol) |
| Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol. More... | |
| BasicMolecule | __iadd__ (MolecularGraph molgraph) |
| Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecular graph 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) |
| Invokes all registered copy postprocessing functions on this molecule with src_molgraph as the source molecular graph. More... | |
| 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 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 a reference to the entity at index idx. More... | |
| int | getNumEntities () |
| Returns the number of stored Chem.Entity3D objects. More... | |
| 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 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... | |
| tuple | __getstate__ () |
| Molecule | __isub__ (MolecularGraph molgraph) |
Removes atoms and bonds referenced by the molecular graph molgraph that are part of this Molecule instance. 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 value) |
| bool | __delitem__ (Base.LookupKey key) |
| int | __len__ () |
| Public Member Functions inherited from CDPL.Chem.MolecularGraph | |
| MolecularGraph | clone () |
| Creates a deep 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) |
| Returns the value of the property specified by key. More... | |
| 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) |
| Registers a new copy postprocessing function in the global registry. More... | |
| 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) | |
Default implementation of the Chem.Molecule interface.
BasicMolecule implements the full editing interface inherited from Chem.Molecule and is the standard concrete type used for the creation, manipulation and processing of molecule/molecular graph data throughout the CDPL.
| None CDPL.Chem.BasicMolecule.__init__ | ( | BasicMolecule | mol | ) |
Constructs a BasicMolecule instance that is a copy of the molecule mol.
| mol | The other molecule to copy. |
| None CDPL.Chem.BasicMolecule.__init__ | ( | Molecule | mol | ) |
Constructs a BasicMolecule instance that is a copy of the molecule mol.
| mol | The other molecule to copy. |
| None CDPL.Chem.BasicMolecule.__init__ | ( | MolecularGraph | molgraph | ) |
Constructs a BasicMolecule instance with copies of the atoms, bonds and properties provided by the molecular graph molgraph.
| molgraph | The molecular graph providing the atoms, bonds and properties to copy. |
| 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.
| mol | The molecule to copy. |
| 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.
| mol | The molecule to copy. |
Reimplemented from CDPL.Chem.Molecule.
| 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.
| molgraph | The molecular graph providing the atoms, bonds and properties to copy. |
Reimplemented from CDPL.Chem.Molecule.
| None CDPL.Chem.BasicMolecule.append | ( | BasicMolecule | mol | ) |
Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol.
| mol | The molecule providing the atoms and bonds to append. |
| None CDPL.Chem.BasicMolecule.append | ( | Molecule | mol | ) |
Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol.
| mol | The molecule providing the atoms and bonds to append. |
Reimplemented from CDPL.Chem.Molecule.
| None CDPL.Chem.BasicMolecule.append | ( | MolecularGraph | molgraph | ) |
Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecular graph molgraph.
| molgraph | The molecular graph providing the atoms and bonds to append. |
Reimplemented from CDPL.Chem.Molecule.
| 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.
| mol | The molecule to copy. |
| 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.
| mol | The molecule to copy. |
Reimplemented from CDPL.Chem.Molecule.
| 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.
| molgraph | The Chem.MolecularGraph instance providing the atoms and bonds to copy. |
Reimplemented from CDPL.Chem.Molecule.
| BasicMolecule CDPL.Chem.BasicMolecule.__iadd__ | ( | BasicMolecule | mol | ) |
Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol.
Internally calls append() to perform the actual work.
| mol | The molecule providing the atoms and bonds to append. |
| BasicMolecule CDPL.Chem.BasicMolecule.__iadd__ | ( | Molecule | mol | ) |
Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol.
Internally calls append() to perform the actual work.
| mol | The molecule providing the atoms and bonds to append. |
Reimplemented from CDPL.Chem.Molecule.
| BasicMolecule CDPL.Chem.BasicMolecule.__iadd__ | ( | MolecularGraph | molgraph | ) |
Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecular graph molgraph.
Internally calls append() to perform the actual work.
| molgraph | The Chem.MolecularGraph instance providing the atoms and bonds to append. |
Reimplemented from CDPL.Chem.Molecule.
1.9.1