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Chemical Data Processing Library Python API - Version 1.2.3
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Chemical Data Processing Library Python API - Version 1.2.3
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Inheritance diagram for CDPL.Chem.Fragment:Classes | |
| class | AtomSequence |
| class | BondSequence |
Public Member Functions | |
| None | __init__ () |
Constructs an empty Fragment instance. | |
| None | __init__ (Fragment frag) |
Constructs a copy of the Fragment instance frag. More... | |
| None | __init__ (MolecularGraph molgraph) |
Constructs a Fragment instance storing the atoms, bonds and properties of the molecular graph molgraph. More... | |
| Fragment | assign (Fragment frag) |
| Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the fragment frag. More... | |
| Fragment | assign (MolecularGraph molgraph) |
| Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the molecular graph molgraph. More... | |
| bool | addAtom (Atom atom) |
| Extends the fragment by the specified atom. More... | |
| None | removeAtom (int idx) |
| Removes the atom at the specified index. More... | |
| bool | removeAtom (Atom atom) |
| Removes the specified atom. More... | |
| bool | addBond (Bond bond) |
| Extends the fragment by the specified bond. More... | |
| None | removeBond (int idx) |
| Removes the bond at the specified index. More... | |
| bool | removeBond (Bond bond) |
| Removes the specified bond. More... | |
| None | clear () |
| Removes all atoms and bonds. | |
| None | swap (Fragment frag) |
| Exchanges the atoms, bonds and properties of this fragment with the atoms, bonds and properties of the fragment frag. More... | |
| AtomSequence | getAtoms () |
| BondSequence | getBonds () |
| None | reserveMemoryForAtoms (int num_atoms) |
| None | reserveMemoryForBonds (int num_bonds) |
| 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__ () |
| Fragment | __iadd__ (MolecularGraph molgraph) |
Performs the in-place addition operation self += molgraph. More... | |
| Fragment | __isub__ (MolecularGraph molgraph) |
Performs the in-place subtraction operation self -= molgraph. More... | |
| Public Member Functions inherited from CDPL.Chem.MolecularGraph | |
| MolecularGraph | clone () |
| Creates a copy of the molecular graph. More... | |
| Atom | getAtom (int idx) |
| bool | containsAtom (Atom atom) |
| int | getAtomIndex (Atom atom) |
| int | getNumAtoms () |
| None | orderAtoms (ForceField.InteractionFilterFunction2 func) |
| Entity3D | getEntity (int idx) |
| int | getNumEntities () |
| Bond | getBond (int idx) |
| bool | containsBond (Bond bond) |
| None | orderBonds (BoolBond2Functor func) |
| int | getBondIndex (Bond bond) |
| int | getNumBonds () |
| 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 | |
| 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) | |
| None CDPL.Chem.Fragment.__init__ | ( | Fragment | frag | ) |
| None CDPL.Chem.Fragment.__init__ | ( | MolecularGraph | molgraph | ) |
Constructs a Fragment instance storing the atoms, bonds and properties of the molecular graph molgraph.
| molgraph | The Chem.MolecularGraph instance providing the atoms, bonds and properties to store. |
Reimplemented in CDPL.Chem.CyclicSubstructure, and CDPL.Chem.AromaticSubstructure.
Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the fragment frag.
| frag | The fragment to copy. |
| Fragment CDPL.Chem.Fragment.assign | ( | MolecularGraph | molgraph | ) |
Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the molecular graph molgraph.
| molgraph | The Chem.MolecularGraph instance providing the atoms, bonds and properties to copy. |
| bool CDPL.Chem.Fragment.addAtom | ( | Atom | atom | ) |
Extends the fragment by the specified atom.
| atom | The atom to add. |
True if the atom was not already a part of the fragment, and False otherwise. | None CDPL.Chem.Fragment.removeAtom | ( | int | idx | ) |
Removes the atom at the specified index.
If the specified atom is connected to any other atoms of the fragment, the connecting bonds will also be removed.
| 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.Fragment.removeAtom | ( | Atom | atom | ) |
Removes the specified atom.
If the specified atom is connected to any other atoms of the fragment, the connecting bonds will also be removed.
| atom | The atom to remove. |
True if the atom was part of the fragment and has been removed, and False otherwise. | bool CDPL.Chem.Fragment.addBond | ( | Bond | bond | ) |
Extends the fragment by the specified bond.
If the atoms of the bond are not already part of the fragment, they will be added automatically.
| bond | The bond to add. |
True if the bond was not already a part of the fragment, and False otherwise. | None CDPL.Chem.Fragment.removeBond | ( | int | idx | ) |
Removes the bond at the specified index.
| idx | The zero-based index of the bond to remove. |
| Base.IndexError | if the number of bonds is zero or idx is not in the range [0, getNumBonds() - 1]. |
| bool CDPL.Chem.Fragment.removeBond | ( | Bond | bond | ) |
Removes the specified bond.
| bond | The bond to remove. |
True if the bond was removed, and False otherwise. | None CDPL.Chem.Fragment.swap | ( | Fragment | frag | ) |
Exchanges the atoms, bonds and properties of this fragment with the atoms, bonds and properties of the fragment frag.
| frag | The fragment the atoms, bonds and properties get exchanged with. |
| AtomSequence CDPL.Chem.Fragment.getAtoms | ( | ) |
Reimplemented from CDPL.Chem.MolecularGraph.
| BondSequence CDPL.Chem.Fragment.getBonds | ( | ) |
Reimplemented from CDPL.Chem.MolecularGraph.
| None CDPL.Chem.Fragment.reserveMemoryForAtoms | ( | int | num_atoms | ) |
| num_atoms |
| None CDPL.Chem.Fragment.reserveMemoryForBonds | ( | int | num_bonds | ) |
| num_bonds |
| bool CDPL.Chem.Fragment.__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.
| bool CDPL.Chem.Fragment.__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.Fragment.__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.
| Base.Any CDPL.Chem.Fragment.__getitem__ | ( | Base.LookupKey | key | ) |
| None CDPL.Chem.Fragment.__setitem__ | ( | Base.LookupKey | key, |
| Base.Any | value | ||
| ) |
| key | |
| value |
Reimplemented from CDPL.Chem.MolecularGraph.
| bool CDPL.Chem.Fragment.__delitem__ | ( | Base.LookupKey | key | ) |
| int CDPL.Chem.Fragment.__len__ | ( | ) |
Reimplemented from CDPL.Chem.MolecularGraph.
Reimplemented in CDPL.Biomol.HierarchyViewModel, and CDPL.Biomol.HierarchyViewChain.
| Fragment CDPL.Chem.Fragment.__iadd__ | ( | MolecularGraph | molgraph | ) |
Performs the in-place addition operation self += molgraph.
| molgraph | Specifies the second addend. |
Fragment instance self. | Fragment CDPL.Chem.Fragment.__isub__ | ( | MolecularGraph | molgraph | ) |
Performs the in-place subtraction operation self -= molgraph.
| molgraph | Specifies the subtrahend. |
Fragment instance self. 
1.9.1