Chemical Data Processing Library Python API - Version 1.1.1
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Describes an electron system of a molecule in terms of involved atoms and their electron contributions. More...
Public Member Functions | |
None | __init__ () |
Constructs an empty ElectronSystem instance. | |
None | __init__ (ElectronSystem elec_sys) |
Initializes a copy of the ElectronSystem instance elec_sys. More... | |
int | getObjectID () |
Returns the numeric identifier (ID) of the wrapped C++ class instance. More... | |
ElectronSystem | assign (ElectronSystem elec_sys) |
Replaces the current state of self with a copy of the state of the ElectronSystem instance elec_sys. More... | |
bool | addAtom (Atom atom, int elec_contrib) |
Extends the electron system by the specified atom and its electron contributions. More... | |
bool | addAtoms (ElectronSystem elec_sys) |
Adds the atoms and associated electron contributions in the electron system elec_sys to this system. More... | |
None | removeAtom (int idx) |
Removes the atom at the specified index. More... | |
bool | removeAtom (Atom atom) |
Removes the specified atom. More... | |
None | clear () |
Removes all atoms. | |
None | swap (ElectronSystem elec_sys) |
Exchanges the state of this electron system with the state of the system elec_sys. More... | |
int | getNumElectrons () |
Returns the total number of electrons contributed by the involved atoms. More... | |
int | getElectronContrib (Atom atom) |
Returns the number of electrons contributed by the specified atom. More... | |
int | getElectronContrib (int atom) |
Returns the number of electrons contributed by the specified atom. More... | |
None | setElectronContrib (Atom atom, int elec_contrib) |
Changes the number of electrons that are contributed by the specified atom. More... | |
None | setElectronContrib (int atom, int elec_contrib) |
Changes the number of electrons that are contributed by the specified atom. More... | |
None | merge (ElectronSystem elec_sys) |
Merges the atoms and associated electron contributions in the electron system elec_sys with this system. More... | |
bool | overlaps (ElectronSystem elec_sys) |
Checks if the electron system shares at least one atom with the system elec_sys. More... | |
bool | contains (ElectronSystem elec_sys) |
Checks if all atoms in the electron system elec_sys are also part of this electron system. More... | |
bool | connected (ElectronSystem elec_sys, BondContainer bonds) |
Checks if the atom sets of the electron systems do not intersect but are linked by at least one bond. More... | |
bool | __contains__ (Atom atom) |
Returns the result of the membership test operation atom in self . More... | |
Atom | __getitem__ (int idx) |
int | __len__ () |
Public Member Functions inherited from CDPL.Chem.AtomContainer | |
Atom | getAtom (int idx) |
Returns a reference to the atom at index idx. More... | |
bool | containsAtom (Atom atom) |
Tells whether the specified Chem.Atom instance is stored in this container. More... | |
int | getAtomIndex (Atom atom) |
Returns the index of the specified Chem.Atom instance in this container. More... | |
int | getNumAtoms () |
Returns the number of stored Chem.Atom objects. More... | |
None | orderAtoms (ForceField.InteractionFilterFunction2 func) |
Orders the stored 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... | |
Properties | |
objectID = property(getObjectID) | |
numElectrons = property(getNumElectrons) | |
Properties inherited from CDPL.Chem.AtomContainer | |
numAtoms = property(getNumAtoms) | |
Properties inherited from CDPL.Chem.Entity3DContainer | |
objectID = property(getObjectID) | |
numEntities = property(getNumEntities) | |
Describes an electron system of a molecule in terms of involved atoms and their electron contributions.
None CDPL.Chem.ElectronSystem.__init__ | ( | ElectronSystem | elec_sys | ) |
Initializes a copy of the ElectronSystem instance elec_sys.
elec_sys | The ElectronSystem instance to copy. |
int CDPL.Chem.ElectronSystem.getObjectID | ( | ) |
Returns the numeric identifier (ID) of the wrapped C++ class instance.
Different Python ElectronSystem instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b
thus cannot tell reliably whether the two ElectronSystem instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID()
.
Reimplemented from CDPL.Chem.Entity3DContainer.
ElectronSystem CDPL.Chem.ElectronSystem.assign | ( | ElectronSystem | elec_sys | ) |
Replaces the current state of self with a copy of the state of the ElectronSystem instance elec_sys.
elec_sys | The ElectronSystem instance to copy. |
bool CDPL.Chem.ElectronSystem.addAtom | ( | Atom | atom, |
int | elec_contrib | ||
) |
Extends the electron system by the specified atom and its electron contributions.
atom | The atom to add. |
elec_contrib | The number of electrons contributed by the added atom. |
True
if the atom was not already involved in this electron system and False
, otherwise.bool CDPL.Chem.ElectronSystem.addAtoms | ( | ElectronSystem | elec_sys | ) |
Adds the atoms and associated electron contributions in the electron system elec_sys to this system.
The method is equivalent to repeatedly calling addAtom() for each atom in elec_sys.
elec_sys | The electron system to add. |
True
if the electron system was extended by atoms from elec_sys and False
, otherwise. None CDPL.Chem.ElectronSystem.removeAtom | ( | int | idx | ) |
Removes the atom at the specified index.
idx | The zero-based index of the atom to remove. |
Base.IndexError | if the number of atoms is zero or idx is not in the range [0, getNumAtoms() - 1]. |
bool CDPL.Chem.ElectronSystem.removeAtom | ( | Atom | atom | ) |
Removes the specified atom.
atom | The atom to remove. |
True
if the atom was part of the electron system and has been removed, and False
otherwise. None CDPL.Chem.ElectronSystem.swap | ( | ElectronSystem | elec_sys | ) |
Exchanges the state of this electron system with the state of the system elec_sys.
elec_sys | The other ElectronSystem instance. |
int CDPL.Chem.ElectronSystem.getNumElectrons | ( | ) |
Returns the total number of electrons contributed by the involved atoms.
int CDPL.Chem.ElectronSystem.getElectronContrib | ( | Atom | atom | ) |
Returns the number of electrons contributed by the specified atom.
atom | The atom for which to return the contributed electron count. |
Base.ItemNotFound | if the specified atom is not part of the electron system. |
int CDPL.Chem.ElectronSystem.getElectronContrib | ( | int | atom | ) |
Returns the number of electrons contributed by the specified atom.
atom | The atom for which to return the contributed electron count. |
Base.ItemNotFound | if the specified atom is not part of the electron system. |
None CDPL.Chem.ElectronSystem.setElectronContrib | ( | Atom | atom, |
int | elec_contrib | ||
) |
Changes the number of electrons that are contributed by the specified atom.
atom | The atom for which to update the electron contribution. |
elec_contrib | The number of electrons contributed by the specified atom. |
Base.ItemNotFound | if the specified atom is not part of the electron system. |
None CDPL.Chem.ElectronSystem.setElectronContrib | ( | int | atom, |
int | elec_contrib | ||
) |
Changes the number of electrons that are contributed by the specified atom.
atom | The atom for which to update the electron contribution. |
elec_contrib | The number of electrons contributed by the specified atom. |
Base.ItemNotFound | if the specified atom is not part of the electron system. |
None CDPL.Chem.ElectronSystem.merge | ( | ElectronSystem | elec_sys | ) |
Merges the atoms and associated electron contributions in the electron system elec_sys with this system.
For atoms that are present in both electron systems, the resulting electron contribution will be the sum of their contributions to the respective systems!
elec_sys | The electron system to merge. |
bool CDPL.Chem.ElectronSystem.overlaps | ( | ElectronSystem | elec_sys | ) |
Checks if the electron system shares at least one atom with the system elec_sys.
elec_sys | The electron system to check for atom set intersection. |
True
if at least one atom in elec_sys is also part of this electron system and False
, otherwise. bool CDPL.Chem.ElectronSystem.contains | ( | ElectronSystem | elec_sys | ) |
Checks if all atoms in the electron system elec_sys are also part of this electron system.
elec_sys | The electron system to check for atom set containment. |
True
if all atoms in elec_sys are also part of this electron system and False
, otherwise. bool CDPL.Chem.ElectronSystem.connected | ( | ElectronSystem | elec_sys, |
BondContainer | bonds | ||
) |
Checks if the atom sets of the electron systems do not intersect but are linked by at least one bond.
elec_sys | The electron system to check. |
bonds | The set of available bonds. |
True
if the electron systems do not share any atoms but are linked by at least one bond and False
, otherwise. bool CDPL.Chem.ElectronSystem.__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.
Atom CDPL.Chem.ElectronSystem.__getitem__ | ( | int | idx | ) |
int CDPL.Chem.ElectronSystem.__len__ | ( | ) |
Reimplemented from CDPL.Chem.AtomContainer.