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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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A canonicalized molecular fragment with an associated hash code, used as the key for fragment-library lookup in conformer generation. More...
Inheritance diagram for CDPL.ConfGen.CanonicalFragment:Classes | |
| class | AtomMapping |
| Maps each atom of the fragment (in canonical order) to the corresponding atom of the parent molecular graph. More... | |
Public Member Functions | |
| None | __init__ () |
Constructs an empty CanonicalFragment instance. | |
| None | __init__ (Chem.MolecularGraph molgraph, Chem.MolecularGraph parent) |
Constructs a CanonicalFragment instance from the fragment molgraph of the parent molecular graph parent. More... | |
| None | __init__ (CanonicalFragment frag) |
Constructs a copy of the CanonicalFragment instance frag. More... | |
| int | getObjectID () |
| Returns the numeric identifier (ID) of the wrapped C++ class instance. More... | |
| CanonicalFragment | assign (CanonicalFragment frag) |
| Replaces the contents of this fragment with a copy of frag. More... | |
| None | create (Chem.MolecularGraph molgraph, Chem.MolecularGraph parent, bool modify=True, bool strip_aro_subst=True) |
| Builds the canonical fragment from the fragment molgraph of the parent molecular graph parent. More... | |
| int | getHashCode () |
| Returns the hash code of the fragment. More... | |
| None | clear () |
| Removes all atoms and bonds and resets the hash code. | |
| Chem.AtomMapping | getAtomMapping () |
| Returns the atom mapping from this fragment to the parent molecular graph. More... | |
| Public Member Functions inherited from CDPL.Chem.MolecularGraph | |
| AtomSequence | getAtoms () |
| BondSequence | getBonds () |
| 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 (BoolAtom2Functor 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 () |
| 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__ (Bond bond) |
Returns the result of the membership test operation bond 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 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.BondContainer | |
| Bond | __getitem__ (int idx) |
| Public Member Functions inherited from CDPL.Base.PropertyContainer | |
| 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 | |
| objectID = property(getObjectID) | |
| hashCode = property(getHashCode) | |
| atomMapping = property(getAtomMapping) | |
| 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) | |
A canonicalized molecular fragment with an associated hash code, used as the key for fragment-library lookup in conformer generation.
A CanonicalFragment is constructed from a fragment of a parent molecular graph and stores a canonicalized copy of the fragment's atoms and bonds. Canonicalization yields a stable atom ordering and an associated hash code that uniquely identifies the topology (and, optionally, the stereochemistry) of the fragment.
| None CDPL.ConfGen.CanonicalFragment.__init__ | ( | Chem.MolecularGraph | molgraph, |
| Chem.MolecularGraph | parent | ||
| ) |
Constructs a CanonicalFragment instance from the fragment molgraph of the parent molecular graph parent.
| molgraph | The molecular graph defining the fragment to canonicalize. |
| parent | The parent molecular graph the fragment was derived from. |
| None CDPL.ConfGen.CanonicalFragment.__init__ | ( | CanonicalFragment | frag | ) |
Constructs a copy of the CanonicalFragment instance frag.
| frag | The CanonicalFragment to copy. |
| int CDPL.ConfGen.CanonicalFragment.getObjectID | ( | ) |
Returns the numeric identifier (ID) of the wrapped C++ class instance.
Different Python CanonicalFragment 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 CanonicalFragment 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.Base.PropertyContainer.
| CanonicalFragment CDPL.ConfGen.CanonicalFragment.assign | ( | CanonicalFragment | frag | ) |
Replaces the contents of this fragment with a copy of frag.
| frag | The source CanonicalFragment. |
| None CDPL.ConfGen.CanonicalFragment.create | ( | Chem.MolecularGraph | molgraph, |
| Chem.MolecularGraph | parent, | ||
| bool | modify = True, |
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| bool | strip_aro_subst = True |
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| ) |
Builds the canonical fragment from the fragment molgraph of the parent molecular graph parent.
| molgraph | The molecular graph defining the fragment to canonicalize. |
| parent | The parent molecular graph the fragment was derived from. |
| modify | If True, the fragment is modified prior to canonicalization (e.g. ring perception, hydrogenization). |
| strip_aro_subst | If True, aromatic-ring substituents are stripped during fragment construction. |
| int CDPL.ConfGen.CanonicalFragment.getHashCode | ( | ) |
Returns the hash code of the fragment.
| Chem.AtomMapping CDPL.ConfGen.CanonicalFragment.getAtomMapping | ( | ) |
Returns the atom mapping from this fragment to the parent molecular graph.
1.9.1