rdkit.ML.KNN.KNNModel.KNNModel:
This is a base class used by KNNClassificationModel
and KNNRegressionModel to represent a k-nearest neighbor predictor.
rdkit.Chem.Pharm2D.SigFactory.SigFactory:
SigFactory's are used by creating one, setting the relevant
parameters, then calling the GetSignature() method each time a
signature is required.
dict:
dict() -> new empty dictionary
dict(mapping) -> new dictionary initialized from a mapping object's
(key, value) pairs
dict(iterable) -> new dictionary initialized as if via:
d = {}
for k, v in iterable:
d[k] = v
dict(**kwargs) -> new dictionary initialized with the name=value pairs
in the keyword argument list.
rdkit.ML.InfoTheory.rdInfoTheory.BitCorrMatGenerator:
A class to generate a pariwise correlation matrix between a list of bits
The mode of operation for this class is something like this
>>> cmg = BitCorrMatGenerator()
>>> cmg.SetBitList(blist)
>>> for fp in fpList:
>>> cmg.CollectVotes(fp)
>>> corrMat = cmg.GetCorrMatrix()
rdkit.Chem.rdChemReactions.EvenSamplePairsStrategy:
Randomly sample Pairs evenly from a collection of building blocks
This is a good strategy for choosing a relatively small selection
of building blocks from a larger set.
rdkit.Chem.rdfiltercatalog.FilterHierarchyMatcher:
Hierarchical Filter
basic constructors:
FilterHierarchyMatcher( matcher )
where can be any FilterMatcherBase (SmartsMatcher, etc)
FilterHierarchyMatcher's have children and can form matching
trees.
rdkit.Chem.rdSubstructLibrary.CachedSmilesMolHolder:
Holds molecules as smiles string
This allows more molecules to be held in memory at a time
AddMol(mol) -> adds a molecule to the molecule holder, returns index of molecule
AddSmiles(smiles) -> adds a smiles string to the molecule holder, returns index of molecule
The smiles is stored as-is, no checking is done for validity.
rdkit.Chem.rdSubstructLibrary.CachedTrustedSmilesMolHolder:
Holds molecules as trusted smiles string
This allows more molecules to be held in memory at a time and avoids RDKit sanitization
overhead
See: http://rdkit.blogspot.com/2016/09/avoiding-unnecessary-work-and.html
AddMol(mol) -> adds a molecule to the molecule holder, returns index of molecule
AddSmiles(smiles) -> adds a smiles string to the molecule holder, returns index of molecule
The smiles is stored as-is, no checking is done for validity.
rdkit.Geometry.rdGeometry.Point3D:
A class to represent a three-dimensional point
The x, y, and z coordinates can be read and written using either attributes
(i.e.
rdkit.Chem.rdRGroupDecomposition.RGroupDecomposition:
RGroupDecompositionParameters controls how the RGroupDecomposition sets labelling and matches structures
OPTIONS:
- RGroupCoreAlignment: can be one of RGroupCoreAlignment.None or RGroupCoreAlignment.MCS
If set to MCS, cores labels are mapped to each other using their
Maximum common substructure overlap.
rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters:
RGroupDecompositionParameters controls how the RGroupDecomposition sets labelling and matches structures
OPTIONS:
- RGroupCoreAlignment: can be one of RGroupCoreAlignment.None or RGroupCoreAlignment.MCS
If set to MCS, cores labels are mapped to each other using their
Maximum common substructure overlap.
rdkit.Chem.rdSubstructLibrary.SubstructLibrary:
SubstructLibrary: This provides a simple API for substructure searching large datasets
The SubstructLibrary takes full advantage of available threads during the search operation.