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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 chemical bond between two atoms (represented by Chem.Atom instances). More...
Inheritance diagram for CDPL.Chem.Bond:Classes | |
| class | AtomSequence |
Public Member Functions | |
| None | __init__ () |
Contructs the Bond instance. | |
| Atom | getNeighbor (Atom atom) |
| Returns the connected neighbor of the argument atom. More... | |
| Atom | getBegin () |
| Returns the start atom of the bond. More... | |
| Atom | getEnd () |
| Returns the end atom of the bond. More... | |
| Molecule | getMolecule () |
| Returns the parent molecule. More... | |
| int | getIndex () |
| Returns the index of the bond in its parent molecule. More... | |
| Bond | assign (Bond bond) |
| Assignment operator that replaces the current set of properties with the properties of bond. More... | |
| AtomSequence | getAtoms () |
| Atom | getAtom (int idx) |
| Returns the atom at index idx. More... | |
| bool | containsAtom (Atom atom) |
| Tells whether the bond is incident to the specified atom. More... | |
| int | getAtomIndex (Atom atom) |
| Returns the index of the specified atom. More... | |
| int | getNumAtoms () |
| Returns the number of atoms connected by the bond. More... | |
| None | orderAtoms (BoolAtom2Functor func) |
| Orders the atoms according to criteria implemented by the provided atom comparison function. More... | |
| Entity3D | getEntity (int idx) |
| Returns the entity at index idx. More... | |
| int | getNumEntities () |
| Returns the number of stored Chem.Entity3D instances. 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__ (Atom atom) |
Returns the result of the membership test operation atom in self. More... | |
| None | __setitem__ (Base.LookupKey key, Base.Any val) |
| bool | __delitem__ (Base.LookupKey key) |
| int | __len__ () |
| Returns the number of property entries. 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.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_val) |
| Returns the value of the property specified by key , or the default value def_val if an entry does not exist. More... | |
| list | getPropertyKeys () |
| Returns a list containing the keys of the current property entries. More... | |
| list | getPropertyValues () |
| Returns a list containing the values of the current property entries. More... | |
| list | getProperties () |
| Returns a reference to itself. More... | |
| None | setProperty (LookupKey key, Any val) |
| Sets the value of the property specified by key to val. More... | |
| bool | removeProperty (LookupKey key) |
| Removes the entry for 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 () |
| Erases all container entries. | |
| None | addProperties (PropertyContainer cntnr) |
Adds the property entries of the PropertyContainer instance cntnr. More... | |
| None | copyProperties (PropertyContainer cntnr) |
| Replaces the current property entries by a copy of the entries in cntnr. More... | |
| None | swap (PropertyContainer cntnr) |
| Exchanges the property entries of this container with the ones of cntnr. More... | |
| Any | __getitem__ (LookupKey key) |
| Returns the value of the property specified by key. More... | |
| bool | __contains__ (LookupKey key) |
| Tells whether or not a value has been assigned to the property specified by key. More... | |
| None | __setitem__ (LookupKey key, Any val) |
| Sets the value of the property specified by key to val. More... | |
| bool | __delitem__ (LookupKey key) |
| Removes the entry for the property specified by key. More... | |
Properties | |
| begin = property(getBegin) | |
| end = property(getEnd) | |
| molecule = property(getMolecule) | |
| index = property(getIndex) | |
| atoms = property(getAtoms) | |
| 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.Base.PropertyContainer | |
| objectID = property(getObjectID) | |
| propertyKeys = property(getPropertyKeys) | |
| propertyValues = property(getPropertyValues) | |
| properties = property(getProperties) | |
| numProperties = property(getNumProperties) | |
Abstract base class representing a chemical bond between two atoms (represented by Chem.Atom instances).
Bond combines the per-bond property storage inherited from Base.PropertyContainer with a fixed-size (always two atoms) Chem.AtomContainer interface that yields the bond's begin and end atoms. Concrete implementation (Chem.BasicBond) instances are created, owned and managed by a parent Chem.Molecule instance.
Returns the connected neighbor of the argument atom.
| atom | The atom for which to return the connected neighbor atom. |
| Base.ItemNotFound | if the bond is not incident to the specified atom. |
| Atom CDPL.Chem.Bond.getBegin | ( | ) |
Returns the start atom of the bond.
Equivalent to calling getAtom(0).
| Atom CDPL.Chem.Bond.getEnd | ( | ) |
Returns the end atom of the bond.
Equivalent to calling getAtom(1).
| Molecule CDPL.Chem.Bond.getMolecule | ( | ) |
Returns the parent molecule.
| int CDPL.Chem.Bond.getIndex | ( | ) |
Returns the index of the bond in its parent molecule.
Assignment operator that replaces the current set of properties with the properties of bond.
| bond | The bond whose properties get copied. |
Reimplemented in CDPL.Chem.BasicBond.
| Atom CDPL.Chem.Bond.getAtom | ( | int | idx | ) |
Returns the atom at index idx.
The index 0 specifies the start atom (see getBegin() const) and 1 the end atom of the bond (see getEnd() const).
| idx | The index of the atom to return. |
| Base.IndexError | if idx is not in the range [0, 1]. |
Reimplemented from CDPL.Chem.AtomContainer.
| bool CDPL.Chem.Bond.containsAtom | ( | Atom | atom | ) |
Tells whether the bond is incident to the specified atom.
| atom | The atom to check. |
True if the bond is incident to the specified atom, and False otherwise. Reimplemented from CDPL.Chem.AtomContainer.
| int CDPL.Chem.Bond.getAtomIndex | ( | Atom | atom | ) |
Returns the index of the specified atom.
If the specified atom is the start atom of the bond, the index 0 is returned. For the end atom of the bond, the value 1 will be returned.
| atom | The atom for which to return the index. |
| Base.ItemNotFound | if the bond is not incident to the specified atom. |
Reimplemented from CDPL.Chem.AtomContainer.
| int CDPL.Chem.Bond.getNumAtoms | ( | ) |
Returns the number of atoms connected by the bond.
Since a bond connects exactly two atoms, the return value is always 2.
Reimplemented from CDPL.Chem.AtomContainer.
| None CDPL.Chem.Bond.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.AtomContainer.
| Entity3D CDPL.Chem.Bond.getEntity | ( | int | idx | ) |
Returns 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.AtomContainer.
| int CDPL.Chem.Bond.getNumEntities | ( | ) |
Returns the number of stored Chem.Entity3D instances.
Forwards to getNumAtoms() and exists to satisfy the Chem.Entity3DContainer interface.
Reimplemented from CDPL.Chem.AtomContainer.
| bool CDPL.Chem.Bond.__contains__ | ( | Base.LookupKey | key | ) |
Returns the result of the membership test operation key in self.
| key | The value to test for membership. |
| bool CDPL.Chem.Bond.__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.AtomContainer.
| int CDPL.Chem.Bond.__len__ | ( | ) |
Returns the number of property entries.
Reimplemented from CDPL.Base.PropertyContainer.
1.9.1