Chemical Data Processing Library Python API - Version 1.1.1
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Classes | |
class | AtomSequence |
class | BondSequence |
Public Member Functions | |
None | __init__ () |
Initializes the Atom instance. | |
Molecule | getMolecule () |
Returns a reference to the parent molecule. More... | |
Bond | getBondToAtom (Atom atom) |
Returns a reference to the Chem.Bond object that connects this atom to the argument atom. More... | |
Bond | findBondToAtom (Atom atom) |
Returns a reference to the Chem.Bond object that connects this atom to the argument atom. More... | |
int | getIndex () |
Returns the index of the atom in its parent molecule. More... | |
Atom | assign (Atom atom) |
Assignment operator that replaces the current set of properties with the properties of atom;. More... | |
object | getAtoms () |
object | getBonds () |
Atom | getAtom (int idx) |
Returns a reference to the connected atom at index idx. More... | |
bool | containsAtom (Atom atom) |
Tells whether this atom and the argument atom are connected by a bond. More... | |
int | getAtomIndex (Atom atom) |
Returns the index of the specified connected atom. More... | |
int | getNumAtoms () |
Returns the number of connected atoms. More... | |
None | orderAtoms (ForceField.InteractionFilterFunction2 func) |
Entity3D | getEntity (int idx) |
int | getNumEntities () |
Bond | getBond (int idx) |
Returns a reference to the incident bond at index idx. More... | |
bool | containsBond (Bond bond) |
Tells whether the specified bond is incident to this atom. More... | |
None | orderBonds (BoolBond2Functor func) |
int | getBondIndex (Bond bond) |
Returns the index of the specified incident bond. More... | |
int | getNumBonds () |
Returns the number of incident bonds. More... | |
bool | __contains__ (Atom atom) |
Returns the result of the membership test operation atom in self . More... | |
bool | __contains__ (Bond bond) |
Returns the result of the membership test operation bond in self . More... | |
bool | __contains__ (Base.LookupKey key) |
Returns the result of the membership test operation key in self . More... | |
Base.Any | __getitem__ (Base.LookupKey key) |
None | __setitem__ (Base.LookupKey key, Base.Any value) |
bool | __delitem__ (Base.LookupKey key) |
int | __len__ () |
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) |
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) |
Properties | |
molecule = property(getMolecule) | |
index = property(getIndex) | |
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) | |
Atom.
Molecule CDPL.Chem.Atom.getMolecule | ( | ) |
Returns a reference to the parent molecule.
Returns a reference to the Chem.Bond object that connects this atom to the argument atom.
atom | The adjacent atom for which to return the connecting bond. |
Base.ItemNotFound | if the argument atom is not connected to this atom. |
Returns a reference to the Chem.Bond object that connects this atom to the argument atom.
atom | The adjacent atom for which to return a reference to the connecting bond. |
int CDPL.Chem.Atom.getIndex | ( | ) |
Returns the index of the atom in its parent molecule.
Assignment operator that replaces the current set of properties with the properties of atom;.
atom | The atom whose properties get copied. |
Reimplemented in CDPL.Chem.BasicAtom.
object CDPL.Chem.Atom.getAtoms | ( | ) |
object CDPL.Chem.Atom.getBonds | ( | ) |
Atom CDPL.Chem.Atom.getAtom | ( | int | idx | ) |
Returns a reference to the connected atom at index idx.
idx | The index of the atom to return. |
Base.IndexError | if idx is not in the range [0, getNumAtoms() - 1]. |
Reimplemented from CDPL.Chem.AtomContainer.
bool CDPL.Chem.Atom.containsAtom | ( | Atom | atom | ) |
Tells whether this atom and the argument atom are connected by a bond.
atom | The atom to test for adjacency. |
True
if the argument atom is connected to this atom, and False
otherwise. Reimplemented from CDPL.Chem.AtomContainer.
int CDPL.Chem.Atom.getAtomIndex | ( | Atom | atom | ) |
Returns the index of the specified connected atom.
atom | The connected atom for which to return the index. |
Base.ItemNotFound | if the specified atom is not connected to this atom. |
Reimplemented from CDPL.Chem.AtomContainer.
int CDPL.Chem.Atom.getNumAtoms | ( | ) |
Returns the number of connected atoms.
Equivalent to getNumBonds().
Reimplemented from CDPL.Chem.AtomContainer.
None CDPL.Chem.Atom.orderAtoms | ( | ForceField.InteractionFilterFunction2 | func | ) |
func |
Reimplemented from CDPL.Chem.AtomContainer.
Entity3D CDPL.Chem.Atom.getEntity | ( | int | idx | ) |
int CDPL.Chem.Atom.getNumEntities | ( | ) |
Reimplemented from CDPL.Chem.AtomContainer.
Bond CDPL.Chem.Atom.getBond | ( | int | idx | ) |
Returns a reference to the incident bond at index idx.
idx | The index of the incident bond to return. |
Base.IndexError | if idx is not in the range [0, getNumBonds() - 1]. |
Reimplemented from CDPL.Chem.BondContainer.
bool CDPL.Chem.Atom.containsBond | ( | Bond | bond | ) |
Tells whether the specified bond is incident to this atom.
bond | The bond to test for incidence. |
True
if the argument bond is incident to this atom, and False
otherwise. Reimplemented from CDPL.Chem.BondContainer.
None CDPL.Chem.Atom.orderBonds | ( | BoolBond2Functor | func | ) |
func |
Reimplemented from CDPL.Chem.BondContainer.
int CDPL.Chem.Atom.getBondIndex | ( | Bond | bond | ) |
Returns the index of the specified incident bond.
bond | The bond for which to return the index. |
Base.ItemNotFound | if the specified bond is not incident to this atom. |
Reimplemented from CDPL.Chem.BondContainer.
int CDPL.Chem.Atom.getNumBonds | ( | ) |
Returns the number of incident bonds.
Equivalent to getNumAtoms().
Reimplemented from CDPL.Chem.BondContainer.
bool CDPL.Chem.Atom.__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.
bool CDPL.Chem.Atom.__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.BondContainer.
bool CDPL.Chem.Atom.__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.Entity3D.
Base.Any CDPL.Chem.Atom.__getitem__ | ( | Base.LookupKey | key | ) |
None CDPL.Chem.Atom.__setitem__ | ( | Base.LookupKey | key, |
Base.Any | value | ||
) |
key | |
value |
Reimplemented from CDPL.Chem.Entity3D.
bool CDPL.Chem.Atom.__delitem__ | ( | Base.LookupKey | key | ) |
int CDPL.Chem.Atom.__len__ | ( | ) |
Reimplemented from CDPL.Chem.AtomContainer.