|
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 the atoms, bonds and properties of the molecule mol. 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 (BasicMolecule mol) |
| Extends the current set of atoms and bonds by a copy of the atoms and bonds in the molecule mol. More...
|
|
None | append (Molecule mol) |
| Extends the current set of atoms and bonds by a copy of the atoms and bonds in the molecule mol. More...
|
|
None | append (MolecularGraph molgraph) |
| Extends the current set of atoms and bonds by a copy of the atoms and bonds in the molecular graph 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) |
| Performs the in-place addition operation self += mol . More...
|
|
BasicMolecule | __iadd__ (Molecule mol) |
| Performs the in-place addition operation self += mol . More...
|
|
BasicMolecule | __iadd__ (MolecularGraph molgraph) |
| Performs the in-place addition operation self += molgraph . More...
|
|
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) |
|
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 (ForceField.InteractionFilterFunction2 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) |
| Performs the in-place subtraction operation self -= molgraph . 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__ () |
|
MolecularGraph | clone () |
| Creates a copy of the molecular graph. More...
|
|
Atom | __getitem__ (int idx) |
|
int | getObjectID () |
| Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
|
|
int | getObjectID () |
| Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
|
|
Bond | __getitem__ (int idx) |
|
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) |
|