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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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Abstract base class representing a mutable molecular graph that owns and manages its atoms and bonds. More...
Inheritance diagram for CDPL.Chem.Molecule:Classes | |
| class | AtomSequence |
| class | BondSequence |
Public Member Functions | |
| None | __init__ () |
Initializes the Molecule instance. | |
| 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 | 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 (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... | |
| None | remove (MolecularGraph molgraph) |
Removes atoms and bonds referenced by the molecular graph molgraph that are part of this Molecule instance. More... | |
| Molecule | 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... | |
| Molecule | 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... | |
| 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 | __iadd__ (Molecule mol) |
| Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol. More... | |
| Molecule | __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... | |
| 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) |
Static Public Member Functions | |
| None | registerCopyPostprocessingFunction (VoidMoleculeMolecularGraphFunctor func) |
| Registers a new copy postprocessing function in the global registry. More... | |
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) | |
Abstract base class representing a mutable molecular graph that owns and manages its atoms and bonds.
Extends the Chem.MolecularGraph interface with editing methods (addAtom(), addBond(), removeAtom(), removeBond(), copy(), append(), remove()) and supports a global registry of copy postprocessing functions invoked after copying/append operations to properly transform properties referencing atoms and bonds of the source molecular graph.
| None CDPL.Chem.Molecule.reserveMemoryForAtoms | ( | int | num_atoms | ) |
Reserves memory for num_atoms atoms.
Allows implementors to speed up the creation of molecules with a known large number of atoms.
| num_atoms | The expected number of atoms for which memory shall be allocated in advance. |
| None CDPL.Chem.Molecule.reserveMemoryForBonds | ( | int | num_bonds | ) |
Reserves memory for num_bonds bonds.
Allows implementors to speed up the creation of molecules with a known large number of bonds.
| num_bonds | The expected number of bonds for which memory shall be allocated in advance. |
| Atom CDPL.Chem.Molecule.addAtom | ( | ) |
Creates a new atom and adds it to the molecule.
Note that this method does not create any bonds - the returned atom is always unconnected.
| Bond CDPL.Chem.Molecule.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.
If a bond between the specified atoms already exists then the existing bond will be returned. If a bond does not yet exist, a new bond will be created. The atom specified by atom1_idx becomes the start atom and the atom specified by atom2_idx the end atom of the newly created bond.
| atom1_idx | The zero-based index of the first atom of the bond. |
| atom2_idx | The zero-based index of the second atom of the bond. |
| Base.IndexError | if atom1_idx and/or atom2_idx is not in the range [0, getNumAtoms()). |
| None CDPL.Chem.Molecule.removeAtom | ( | int | idx | ) |
Removes the atom at the specified index.
If the specified atom is connected to any other atoms of the molecule then the connecting bonds will also be removed.
| idx | The index of the atom to remove. |
| Base.IndexError | if idx is not in the range [0, getNumAtoms()). |
| None CDPL.Chem.Molecule.removeBond | ( | int | idx | ) |
Removes the bond at the specified index.
| idx | The zero-based index of the bond to remove. |
| Base.IndexError | if idx is not in the range [0, getNumBonds()). |
| None CDPL.Chem.Molecule.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 in CDPL.Chem.BasicMolecule.
| None CDPL.Chem.Molecule.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 in CDPL.Chem.BasicMolecule.
| None CDPL.Chem.Molecule.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 in CDPL.Chem.BasicMolecule.
| None CDPL.Chem.Molecule.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 in CDPL.Chem.BasicMolecule.
| None CDPL.Chem.Molecule.remove | ( | MolecularGraph | molgraph | ) |
Removes atoms and bonds referenced by the molecular graph molgraph that are part of this Molecule instance.
| molgraph | The molecular graph specifying the atoms and bonds to remove. |
this != &molgraph. 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 in CDPL.Chem.BasicMolecule.
| Molecule CDPL.Chem.Molecule.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 in CDPL.Chem.BasicMolecule.
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static |
Registers a new copy postprocessing function in the global registry.
Registered functions are invoked in registration order typically after copy/append operations that populate a Chem.Molecule instance with atoms and bonds from a source Chem.MolecularGraph instance.
| func | The callback function to register. |
| None CDPL.Chem.Molecule.invokeCopyPostprocessingFunctions | ( | MolecularGraph | src_molgraph | ) |
Invokes all registered copy postprocessing functions on this molecule with src_molgraph as the source molecular graph.
| src_molgraph | The source molecular graph that provided the copied atoms and bonds. |
| Atom CDPL.Chem.Molecule.getAtom | ( | int | idx | ) |
Returns a reference to the atom at index idx.
| idx | The zero-based index of the atom to return. |
| Base.IndexError | if idx is not in the range [0, getNumAtoms()). |
Reimplemented from CDPL.Chem.MolecularGraph.
| bool CDPL.Chem.Molecule.containsAtom | ( | Atom | atom | ) |
Tells whether the specified atom is part of the atom sequence.
| atom | The atom to look for. |
True if atom is part of the sequence, and False otherwise. Reimplemented from CDPL.Chem.MolecularGraph.
| int CDPL.Chem.Molecule.getAtomIndex | ( | Atom | atom | ) |
Returns the index of the specified atom.
| atom | The atom for which to return the index. |
| Base.ItemNotFound | if the specified atom could not be found. |
Reimplemented from CDPL.Chem.MolecularGraph.
| int CDPL.Chem.Molecule.getNumAtoms | ( | ) |
Returns the number of atoms.
Reimplemented from CDPL.Chem.MolecularGraph.
| None CDPL.Chem.Molecule.orderAtoms | ( | BoolAtom2Functor | func | ) |
Orders the atoms according to criteria implemented by the provided atom comparison function.
| func | The atom comparison function implementing the applied ordering criteria. |
Reimplemented from CDPL.Chem.MolecularGraph.
| Entity3D CDPL.Chem.Molecule.getEntity | ( | int | idx | ) |
Returns a reference to the entity at index idx.
Forwards to getAtom() and exists to satisfy the Chem.Entity3DContainer interface.
| idx | The zero-based entity index. |
| Base.IndexError | if idx is not in the range [0, getNumAtoms()). |
Reimplemented from CDPL.Chem.MolecularGraph.
| int CDPL.Chem.Molecule.getNumEntities | ( | ) |
Returns the number of stored Chem.Entity3D objects.
Forwards to getNumAtoms() and exists to satisfy the Chem.Entity3DContainer interface.
Reimplemented from CDPL.Chem.MolecularGraph.
| Bond CDPL.Chem.Molecule.getBond | ( | int | idx | ) |
Returns a reference to the bond at index idx.
| idx | The zero-based index of the bond to return. |
| Base.IndexError | if idx is not in the range [0, getNumBonds()). |
Reimplemented from CDPL.Chem.MolecularGraph.
| bool CDPL.Chem.Molecule.containsBond | ( | Bond | bond | ) |
Tells whether the specified bond is part of the bond sequence.
| bond | The bond to look for. |
True if bond is part of the sequence, and False otherwise. Reimplemented from CDPL.Chem.MolecularGraph.
| None CDPL.Chem.Molecule.orderBonds | ( | BoolBond2Functor | func | ) |
Orders the bonds according to criteria implemented by the provided bond comparison function.
| func | The bond comparison function implementing the applied ordering criteria. |
Reimplemented from CDPL.Chem.MolecularGraph.
| int CDPL.Chem.Molecule.getBondIndex | ( | Bond | bond | ) |
Returns the index of the specified bond.
| bond | The bond for which to return the index. |
| Base.ItemNotFound | if the specified bond could not be found. |
Reimplemented from CDPL.Chem.MolecularGraph.
| int CDPL.Chem.Molecule.getNumBonds | ( | ) |
Returns the number of bonds.
Reimplemented from CDPL.Chem.MolecularGraph.
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 in CDPL.Chem.BasicMolecule.
| Molecule CDPL.Chem.Molecule.__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 in CDPL.Chem.BasicMolecule.
| Molecule CDPL.Chem.Molecule.__isub__ | ( | MolecularGraph | molgraph | ) |
Removes atoms and bonds referenced by the molecular graph molgraph that are part of this Molecule instance.
Internally calls remove() to perform the actual work.
| molgraph | The Chem.MolecularGraph instance specifying the atoms and bonds to remove. |
| bool CDPL.Chem.Molecule.__contains__ | ( | Base.LookupKey | key | ) |
Returns the result of the membership test operation key in self.
| key | The value to test for membership. |
Reimplemented from CDPL.Chem.MolecularGraph.
| bool CDPL.Chem.Molecule.__contains__ | ( | Bond | bond | ) |
Returns the result of the membership test operation bond in self.
| bond | The value to test for membership. |
Reimplemented from CDPL.Chem.MolecularGraph.
| bool CDPL.Chem.Molecule.__contains__ | ( | Atom | atom | ) |
Returns the result of the membership test operation atom in self.
| atom | The value to test for membership. |
Reimplemented from CDPL.Chem.MolecularGraph.
1.9.1