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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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Concrete Chem.Molecule implementation that owns Chem.BasicAtom and Chem.BasicBond instances. 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 mol. More... | |
| None | copy (Molecule mol) |
| Replaces the current set of atoms, bonds and properties by a copy of mol. More... | |
| None | copy (MolecularGraph molgraph) |
| Replaces the current set of atoms, bonds and properties by a copy of molgraph. More... | |
| None | append (BasicMolecule mol) |
| Extends the current set of atoms and bonds by a copy of those in mol. More... | |
| None | append (Molecule mol) |
| Extends the current set of atoms and bonds by a copy of those in mol. More... | |
| None | append (MolecularGraph molgraph) |
| Extends the current set of atoms and bonds by a copy of those in 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 in the molecule mol. More... | |
| BasicMolecule | __iadd__ (Molecule mol) |
| Extends the current set of atoms and bonds by a copy of the atoms and bonds in the molecule mol. More... | |
| BasicMolecule | __iadd__ (MolecularGraph molgraph) |
| Extends the current set of atoms and bonds by a copy of the atoms and bonds in 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. 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 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 (BoolAtom2Functor 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) |
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 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) | |
Concrete Chem.Molecule implementation that owns Chem.BasicAtom and Chem.BasicBond instances.
BasicMolecule provides the default in-memory representation of a molecular graph: atoms and bonds are allocated from internal object pools and accessed through random-access iterators. The class implements the full editing interface inherited from Chem.Molecule (addAtom, addBond, removeAtom, removeBond, copy, append, remove, reserveMemoryForAtoms, reserveMemoryForBonds) and is the standard concrete type used by readers and downstream algorithms throughout CDPKit.
| None CDPL.Chem.BasicMolecule.__init__ | ( | BasicMolecule | mol | ) |
Constructs a copy of the Chem.Molecule instance mol.
| mol | The other Chem.Molecule instance to copy. |
| None CDPL.Chem.BasicMolecule.__init__ | ( | Molecule | mol | ) |
Constructs a copy of the Chem.Molecule instance mol.
| mol | The other Chem.Molecule instance to copy. |
| None CDPL.Chem.BasicMolecule.__init__ | ( | MolecularGraph | molgraph | ) |
Constructs a BasicMolecule instance with copies of the atoms and bonds of the Chem.MolecularGraph instance molgraph.
| molgraph | The Chem.MolecularGraph instance providing the atoms and bonds to copy. |
| None CDPL.Chem.BasicMolecule.copy | ( | BasicMolecule | mol | ) |
Replaces the current set of atoms, bonds and properties by a copy of mol.
| mol | The source molecule. |
| None CDPL.Chem.BasicMolecule.copy | ( | Molecule | mol | ) |
Replaces the current set of atoms, bonds and properties by a copy of mol.
| mol | The source molecule. |
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 molgraph.
| molgraph | The source molecular graph. |
Reimplemented from CDPL.Chem.Molecule.
| None CDPL.Chem.BasicMolecule.append | ( | BasicMolecule | mol | ) |
Extends the current set of atoms and bonds by a copy of those in mol.
| mol | The source molecule. |
| None CDPL.Chem.BasicMolecule.append | ( | Molecule | mol | ) |
Extends the current set of atoms and bonds by a copy of those in mol.
| mol | The source molecule. |
Reimplemented from CDPL.Chem.Molecule.
| None CDPL.Chem.BasicMolecule.append | ( | MolecularGraph | molgraph | ) |
Extends the current set of atoms and bonds by a copy of those in molgraph.
| molgraph | The source molecular graph. |
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 in 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 in 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 in 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