Graph Representation
The chem_mat_data package provides various chemical property prediction datasets in a pre-processed format,
in which molecules are mapped to graph structures that represent the atoms as nodes and the bonds as corresponding
edges.
Graph Dict Structure
Practically, this graph structure is represented as a native python dict object with a set of specific attributes.
Generally, the graph dict structure follows the following naming convention
- Prefix
node_for node-level attributes with shape \((V, ?)\) - Prefix
edge_for edge-level attributes with shape \((E, ?)\) - Prefix
graph_for graph-level attributes with shape \((?, )\)
More specifically, each graph dict object has the following minimal set of attributes:
| Attribute | Description |
|---|---|
node_indices |
Integer numpy array of shape \((V, )\) where \(V\) is the number of nodes in the graph. Contains the unique integer indices of the graph nodes. |
node_attributes |
Float numpy array of shape \((V, N)\) where \(V\) is the number of nodes and \(N\) is the number of numeric node features. Contains the numeric feature vectors that represent each node. |
edge_indices |
Integer numpy array of shape \((E, 2)\) where \(E\) is the number of edges in the graph. Contains tuples \((i, j)\) of node indices that indicate the existence of an edge between nodes \(i\) and \(j\). |
edge_attributes |
Float numpy array of shape \((E, M)\) where \(E\) is the number of edges in the graph and \(M\) is the number of values in the graph. |
graph_labels |
Float numpy array of shape \((T, )\) where \(T\) is the number of target values associated with each element of the dataset. The target values can either be continuous regression targets such as [1.43, -9.4] or could be one-hot classification labels such as [0, 1, 0]. |
graph_repr |
The string numpy array of shape \((1, )\) containing the string SMILES representation of the original molecule. |
Depending on the dataset, the graph dict representation may contain additional attributes that represent custom properties such as the 3D coordinates of nodes/atoms, for exmaple.
Default Features
The graph representations that can be downloaded already come with a pre-defined encoding of numeric node and edge feature vectors that encode specific information about the atoms and bonds of the molecular graphs. The selection of which attributes are included here is pre-determined to be a basic selection of attributes which will be explained in detail in the following sections.
All features were calculated based on the rdkit.Mol representation of the corresponding elements.
If the default feature selection is for some reason insufficient for a given task, there is the option to define custom pre-processing classes with a custom selection of features. Custom Pre-Processing
Node Features
The standard node features are the following:
| Feature Index | Name | Description |
|---|---|---|
| \(0\) | is Carbon (C)? | Integer one-hot label if the node represents a carbon atom. |
| \(1\) | is Oxygen (O)? | Integer one-hot label if the node represents an oxygen atom. |
| \(2\) | is Nitrogen (N)? | Integer one-hot label if the node represents a nitrogen atom. |
| \(3\) | is Sulfur (S)? | Integer one-hot label if the node represents a sulfur atom. |
| \(4\) | is Phosphorus (P)? | Integer one-hot label if the node represents a phosphorus atom. |
| \(5\) | is Fluorine (F)? | Integer one-hot label if the node represents a fluorine atom. |
| \(6\) | is Chlorine (Cl)? | Integer one-hot label if the node represents a chlorine atom. |
| \(7\) | is Bromine (Br)? | Integer one-hot label if the node represents a bromine atom. |
| \(8\) | is Iodine (I)? | Integer one-hot label if the node represents an iodine atom. |
| \(9\) | is Silicon (Si)? | Integer one-hot label if the node represents a silicon atom. |
| \(10\) | is Boron (B)? | Integer one-hot label if the node represents a boron atom. |
| \(11\) | is Sodium (Na)? | Integer one-hot label if the node represents a sodium atom. |
| \(12\) | is Magnesium (Mg)? | Integer one-hot label if the node represents a magnesium atom. |
| \(13\) | is Calcium (Ca)? | Integer one-hot label if the node represents a calcium atom. |
| \(14\) | is Iron (Fe)? | Integer one-hot label if the node represents an iron atom. |
| \(15\) | is Aluminum (Al)? | Integer one-hot label if the node represents an aluminum atom. |
| \(16\) | is Copper (Cu)? | Integer one-hot label if the node represents a copper atom. |
| \(17\) | is Zinc (Zn)? | Integer one-hot label if the node represents a zinc atom. |
| \(18\) | is Potassium (K)? | Integer one-hot label if the node represents a potassium atom. |
| \(19\) | is Uknown atom? | Integer one-hot label for an unknown atom type not covered by the above list of atoms. |
| \(20\) | S hybrid | Integer one-hot label if the atom has S hybridization. |
| \(21\) | SP hybrid | Integer one-hot label if the atom has SP hybridization. |
| \(22\) | SP2 hybrid | Integer one-hot label if the atom has SP2 hybridization. |
| \(23\) | SP3 hybrid | Integer one-hot label if the atom has SP3 hybridization. |
| \(24\) | SP2D hybrid | Integer one-hot label if the atom has SP2D hybridization. |
| \(25\) | SP3D hybrid | Integer one-hot label if the atom has SP3D hybridization. |
| \(26\) | Unknown hybridization | Integer one-hot label for an unknown hybridization type not covered by the above list. |
| \(27\) | 0 Neighbors | Integer one-hot label if the atom has 0 neighbors. |
| \(28\) | 1 Neighbor | Integer one-hot label if the atom has 1 neighbor. |
| \(29\) | 2 Neighbors | Integer one-hot label if the atom has 2 neighbors. |
| \(30\) | 3 Neighbors | Integer one-hot label if the atom has 3 neighbors. |
| \(31\) | 4 Neighbors | Integer one-hot label if the atom has 4 neighbors. |
| \(32\) | 5 Neighbors | Integer one-hot label if the atom has 5 neighbors. |
| \(33\) | 0 Hydrogens | Integer one-hot label if the atom has 0 attached hydrogen atoms. |
| \(34\) | 1 Hydrogen | Integer one-hot label if the atom has 1 attached hydrogen atom. |
| \(35\) | 2 Hydrogens | Integer one-hot label if the atom has 2 attached hydrogen atoms. |
| \(36\) | 3 Hydrogens | Integer one-hot label if the atom has 3 attached hydrogen atoms. |
| \(37\) | 4 Hydrogens | Integer one-hot label if the atom has 4 attached hydrogen atoms. |
| \(38\) | Mass | Float value representing the mass of the atom. |
| \(39\) | Charge | Integer value representing the electrical charge of the atom. |
| \(40\) | Is Aromatic? | Integer one-hot label if the atom is aromatic. |
| \(41\) | Is in Ring? | Integer one-hot label if the atom is in a ring. |
| \(42\) | Crippen Contributions | Float value representing the Crippen logP contributions of the atom as computed by RDKit. |
Edge Features
The standard edge features are the following:
| Feature Index | Name | Description |
|---|---|---|
| \(0\) | Single Bond | One hot encoding if the bond is a single bond. |
| \(1\) | Double Bond | One hot encoding if the bond is a double bond. |
| \(2\) | Triple Bond | One hot encoding if the bond is a triple bond. |
| \(3\) | Aromatic Bond | One hot encoding if the bond is an aromatic bond. |
| \(4\) | Ionic Bond | One hot encoding if the bond is an ionic bond. |
| \(5\) | Hydrogen Bond | One hot encoding if the bond is a hydrogen bond. |
| \(6\) | Unknown Bond | One hot encoding if the bond type is unknown. |
| \(7\) | Stereo None | One hot encoding if the bond has no stereo property. |
| \(8\) | Stereo Any | One hot encoding if the bond has any stereo property. |
| \(9\) | Stereo Z | One hot encoding if the bond has Z stereo property. |
| \(10\) | Stereo E | One hot encoding if the bond has E stereo property. |
| \(11\) | Is Aromatic | Integer flag if the bond is aromatic. |
| \(12\) | Is in Ring | Integer flag if the bond is part of a ring. |
| \(13\) | Is Conjugated | Integer flag if the bond is conjugated. |