molprop.pyg_molgraph.MultiGraphData

class molprop.pyg_molgraph.MultiGraphData(x_size_dict=None, **kwargs)

Bases: Data

Methods

__init__
apply	Applies the function func, either to all attributes or only the ones given in *args.
apply_	Applies the in-place function func, either to all attributes or only the ones given in *args.
clone	Performs cloning of tensors, either for all attributes or only the ones given in *args.
coalesce	Sorts and removes duplicated entries from edge indices edge_index.
concat	Concatenates self with another data object.
contains_isolated_nodes
contains_self_loops
contiguous	Ensures a contiguous memory layout, either for all attributes or only the ones given in *args.
coo	Returns the edge indices in the GraphStore in COO format.
cpu	Copies attributes to CPU memory, either for all attributes or only the ones given in *args.
csc	Returns the edge indices in the GraphStore in CSC format.
csr	Returns the edge indices in the GraphStore in CSR format.
cuda	Copies attributes to CUDA memory, either for all attributes or only the ones given in *args.
debug
detach	Detaches attributes from the computation graph by creating a new tensor, either for all attributes or only the ones given in *args.
detach_	Detaches attributes from the computation graph, either for all attributes or only the ones given in *args.
edge_attrs	Returns all edge-level tensor attribute names.
edge_subgraph	Returns the induced subgraph given by the edge indices subset.
from_dict	Creates a Data object from a dictionary.
generate_ids	Generates and sets n_id and e_id attributes to assign each node and edge to a continuously ascending and unique ID.
get_all_edge_attrs	Returns all registered edge attributes.
get_all_tensor_attrs	Obtains all feature attributes stored in Data.
get_edge_index	Synchronously obtains an edge_index tuple from the GraphStore.
get_tensor	Synchronously obtains a tensor from the FeatureStore.
get_tensor_size	Obtains the size of a tensor given its TensorAttr, or None if the tensor does not exist.
has_isolated_nodes	Returns True if the graph contains isolated nodes.
has_self_loops	Returns True if the graph contains self-loops.
is_coalesced	Returns True if edge indices edge_index are sorted and do not contain duplicate entries.
is_directed	Returns True if graph edges are directed.
is_edge_attr	Returns True if the object at key key denotes an edge-level tensor attribute.
is_node_attr	Returns True if the object at key key denotes a node-level tensor attribute.
is_sorted	Returns True if edge indices edge_index are sorted.
is_sorted_by_time	Returns True if time is sorted.
is_undirected	Returns True if graph edges are undirected.
keys	Returns a list of all graph attribute names.
multi_get_tensor	Synchronously obtains a list of tensors from the FeatureStore for each tensor associated with the attributes in attrs.
node_attrs	Returns all node-level tensor attribute names.
pin_memory	Copies attributes to pinned memory, either for all attributes or only the ones given in *args.
put_edge_index	Synchronously adds an edge_index tuple to the GraphStore.
put_tensor	Synchronously adds a tensor to the FeatureStore.
record_stream	Ensures that the tensor memory is not reused for another tensor until all current work queued on stream has been completed, either for all attributes or only the ones given in *args.
remove_edge_index	Synchronously deletes an edge_index tuple from the GraphStore.
remove_tensor	Removes a tensor from the FeatureStore.
requires_grad_	Tracks gradient computation, either for all attributes or only the ones given in *args.
share_memory_	Moves attributes to shared memory, either for all attributes or only the ones given in *args.
size	Returns the size of the adjacency matrix induced by the graph.
snapshot	Returns a snapshot of data to only hold events that occurred in period [start_time, end_time].
sort	Sorts edge indices edge_index and their corresponding edge features.
sort_by_time	Sorts data associated with time according to time.
stores_as
subgraph	Returns the induced subgraph given by the node indices subset.
to	Performs tensor device conversion, either for all attributes or only the ones given in *args.
to_dict	Returns a dictionary of stored key/value pairs.
to_heterogeneous	Converts a Data object to a heterogeneous HeteroData object.
to_namedtuple	Returns a NamedTuple of stored key/value pairs.
up_to	Returns a snapshot of data to only hold events that occurred up to end_time (inclusive of edge_time).
update	Updates the data object with the elements from another data object.
update_tensor	Updates a tensor in the FeatureStore with a new value.
validate	Validates the correctness of the data.
view	Returns a view of the FeatureStore given a not yet fully-specified TensorAttr.

apply(func: Callable, *args: str)

Applies the function func, either to all attributes or only the ones given in *args.

apply_(func: Callable, *args: str)

Applies the in-place function func, either to all attributes or only the ones given in *args.

clone(*args: str)

Performs cloning of tensors, either for all attributes or only the ones given in *args.

coalesce() → Self

Sorts and removes duplicated entries from edge indices edge_index.

concat(data: Self) → Self

Concatenates self with another data object. All values needs to have matching shapes at non-concat dimensions.

contiguous(*args: str)

Ensures a contiguous memory layout, either for all attributes or only the ones given in *args.

coo(edge_types: List[Any] | None = None, store: bool = False) → Tuple[Dict[Tuple[str, str, str], Tensor], Dict[Tuple[str, str, str], Tensor], Dict[Tuple[str, str, str], Tensor | None]]

Returns the edge indices in the GraphStore in COO format.

Parameters:

• edge_types (List[Any], optional) – The edge types of edge indices to obtain. If set to None, will return the edge indices of all existing edge types. (default: None)

• store (bool, optional) – Whether to store converted edge indices in the GraphStore. (default: False)

cpu(*args: str)

Copies attributes to CPU memory, either for all attributes or only the ones given in *args.

csc(edge_types: List[Any] | None = None, store: bool = False) → Tuple[Dict[Tuple[str, str, str], Tensor], Dict[Tuple[str, str, str], Tensor], Dict[Tuple[str, str, str], Tensor | None]]

Returns the edge indices in the GraphStore in CSC format.

Parameters:

• edge_types (List[Any], optional) – The edge types of edge indices to obtain. If set to None, will return the edge indices of all existing edge types. (default: None)

• store (bool, optional) – Whether to store converted edge indices in the GraphStore. (default: False)

csr(edge_types: List[Any] | None = None, store: bool = False) → Tuple[Dict[Tuple[str, str, str], Tensor], Dict[Tuple[str, str, str], Tensor], Dict[Tuple[str, str, str], Tensor | None]]

Returns the edge indices in the GraphStore in CSR format.

Parameters:

• edge_types (List[Any], optional) – The edge types of edge indices to obtain. If set to None, will return the edge indices of all existing edge types. (default: None)

• store (bool, optional) – Whether to store converted edge indices in the GraphStore. (default: False)

cuda(device: int | str | None = None, *args: str, non_blocking: bool = False)

Copies attributes to CUDA memory, either for all attributes or only the ones given in *args.

detach(*args: str)

Detaches attributes from the computation graph by creating a new tensor, either for all attributes or only the ones given in *args.

detach_(*args: str)

Detaches attributes from the computation graph, either for all attributes or only the ones given in *args.

edge_attrs() → List[str]

Returns all edge-level tensor attribute names.

edge_subgraph(subset: Tensor) → Self

Returns the induced subgraph given by the edge indices subset. Will currently preserve all the nodes in the graph, even if they are isolated after subgraph computation.

Parameters:

subset (LongTensor or BoolTensor) – The edges to keep.

classmethod from_dict(mapping: Dict[str, Any]) → Self

Creates a Data object from a dictionary.

generate_ids()

Generates and sets n_id and e_id attributes to assign each node and edge to a continuously ascending and unique ID.

get_all_edge_attrs() → List[EdgeAttr]

Returns all registered edge attributes.

get_all_tensor_attrs() → List[TensorAttr]

Obtains all feature attributes stored in Data.

get_edge_index(*args, **kwargs) → Tuple[Tensor, Tensor]

Synchronously obtains an edge_index tuple from the GraphStore.

Parameters:

• *args – Arguments passed to EdgeAttr.

• **kwargs – Keyword arguments passed to EdgeAttr.

Raises:

KeyError – If the edge_index corresponding to the input EdgeAttr was not found.

get_tensor(*args, convert_type: bool = False, **kwargs) → Tensor | ndarray

Synchronously obtains a tensor from the FeatureStore.

Parameters:

• *args – Arguments passed to TensorAttr.

• convert_type (bool, optional) – Whether to convert the type of the output tensor to the type of the attribute index. (default: False)

• **kwargs – Keyword arguments passed to TensorAttr.

Raises:

ValueError – If the input TensorAttr is not fully specified.

get_tensor_size(*args, **kwargs) → Tuple[int, ...] | None

Obtains the size of a tensor given its TensorAttr, or None if the tensor does not exist.

has_isolated_nodes() → bool

Returns True if the graph contains isolated nodes.

has_self_loops() → bool

Returns True if the graph contains self-loops.

is_coalesced() → bool

Returns True if edge indices edge_index are sorted and do not contain duplicate entries.

property is_cuda: bool

Returns True if any torch.Tensor attribute is stored on the GPU, False otherwise.

is_directed() → bool

Returns True if graph edges are directed.

is_edge_attr(key: str) → bool

Returns True if the object at key key denotes an edge-level tensor attribute.

is_node_attr(key: str) → bool

Returns True if the object at key key denotes a node-level tensor attribute.

is_sorted(sort_by_row: bool = True) → bool

Returns True if edge indices edge_index are sorted.

Parameters:

sort_by_row (bool, optional) – If set to False, will require column-wise order/by destination node order of edge_index. (default: True)

is_sorted_by_time() → bool

Returns True if time is sorted.

is_undirected() → bool

Returns True if graph edges are undirected.

keys() → List[str]

Returns a list of all graph attribute names.

multi_get_tensor(attrs: List[TensorAttr], convert_type: bool = False) → List[Tensor | ndarray]

Synchronously obtains a list of tensors from the FeatureStore for each tensor associated with the attributes in attrs.

Note

The default implementation simply iterates over all calls to get_tensor(). Implementor classes that can provide additional, more performant functionality are recommended to to override this method.

Parameters:

• attrs (List[TensorAttr]) – A list of input TensorAttr objects that identify the tensors to obtain.

• convert_type (bool, optional) – Whether to convert the type of the output tensor to the type of the attribute index. (default: False)

Raises:

ValueError – If any input TensorAttr is not fully specified.

node_attrs() → List[str]

Returns all node-level tensor attribute names.

property num_edge_features: int

Returns the number of features per edge in the graph.

property num_edge_types: int

Returns the number of edge types in the graph.

property num_edges: int

Returns the number of edges in the graph. For undirected graphs, this will return the number of bi-directional edges, which is double the amount of unique edges.

property num_faces: int | None

Returns the number of faces in the mesh.

property num_features: int

Returns the number of features per node in the graph. Alias for num_node_features.

property num_node_features: int

Returns the number of features per node in the graph.

property num_node_types: int

Returns the number of node types in the graph.

property num_nodes: int | None

Returns the number of nodes in the graph.

Note

The number of nodes in the data object is automatically inferred in case node-level attributes are present, e.g., data.x. In some cases, however, a graph may only be given without any node-level attributes. :pyg:`PyG` then guesses the number of nodes according to edge_index.max().item() + 1. However, in case there exists isolated nodes, this number does not have to be correct which can result in unexpected behavior. Thus, we recommend to set the number of nodes in your data object explicitly via data.num_nodes = .... You will be given a warning that requests you to do so.

pin_memory(*args: str)

Copies attributes to pinned memory, either for all attributes or only the ones given in *args.

put_edge_index(edge_index: Tuple[Tensor, Tensor], *args, **kwargs) → bool

Synchronously adds an edge_index tuple to the GraphStore. Returns whether insertion was successful.

Parameters:

• edge_index (Tuple[torch.Tensor, torch.Tensor]) – The edge_index tuple in a format specified in EdgeAttr.

• *args – Arguments passed to EdgeAttr.

• **kwargs – Keyword arguments passed to EdgeAttr.

put_tensor(tensor: Tensor | ndarray, *args, **kwargs) → bool

Synchronously adds a tensor to the FeatureStore. Returns whether insertion was successful.

Parameters:

• tensor (torch.Tensor or np.ndarray) – The feature tensor to be added.

• *args – Arguments passed to TensorAttr.

• **kwargs – Keyword arguments passed to TensorAttr.

Raises:

ValueError – If the input TensorAttr is not fully specified.

record_stream(stream: Stream, *args: str)

Ensures that the tensor memory is not reused for another tensor until all current work queued on stream has been completed, either for all attributes or only the ones given in *args.

remove_edge_index(*args, **kwargs) → bool

Synchronously deletes an edge_index tuple from the GraphStore. Returns whether deletion was successful.

Parameters:

• *args – Arguments passed to EdgeAttr.

• **kwargs – Keyword arguments passed to EdgeAttr.

remove_tensor(*args, **kwargs) → bool

Removes a tensor from the FeatureStore. Returns whether deletion was successful.

Parameters:

• *args – Arguments passed to TensorAttr.

• **kwargs – Keyword arguments passed to TensorAttr.

Raises:

ValueError – If the input TensorAttr is not fully specified.

requires_grad_(*args: str, requires_grad: bool = True)

Tracks gradient computation, either for all attributes or only the ones given in *args.

share_memory_(*args: str)

Moves attributes to shared memory, either for all attributes or only the ones given in *args.

size(dim: int | None = None) → Tuple[int | None, int | None] | int | None

Returns the size of the adjacency matrix induced by the graph.

snapshot(start_time: float | int, end_time: float | int, attr: str = 'time') → Self

Returns a snapshot of data to only hold events that occurred in period [start_time, end_time].

sort(sort_by_row: bool = True) → Self

Sorts edge indices edge_index and their corresponding edge features.

Parameters:

sort_by_row (bool, optional) – If set to False, will sort edge_index in column-wise order/by destination node. (default: True)

sort_by_time() → Self

Sorts data associated with time according to time.

subgraph(subset: Tensor) → Self

Returns the induced subgraph given by the node indices subset.

Parameters:

subset (LongTensor or BoolTensor) – The nodes to keep.

to(device: int | str, *args: str, non_blocking: bool = False)

Performs tensor device conversion, either for all attributes or only the ones given in *args.

to_dict() → Dict[str, Any]

Returns a dictionary of stored key/value pairs.

to_heterogeneous(node_type: Tensor | None = None, edge_type: Tensor | None = None, node_type_names: List[str] | None = None, edge_type_names: List[Tuple[str, str, str]] | None = None)

Converts a Data object to a heterogeneous HeteroData object. For this, node and edge attributes are splitted according to the node-level and edge-level vectors node_type and edge_type, respectively. node_type_names and edge_type_names can be used to give meaningful node and edge type names, respectively. That is, the node_type 0 is given by node_type_names[0]. If the Data object was constructed via to_homogeneous(), the object can be reconstructed without any need to pass in additional arguments.

Parameters:

• node_type (torch.Tensor, optional) – A node-level vector denoting the type of each node. (default: None)

• edge_type (torch.Tensor, optional) – An edge-level vector denoting the type of each edge. (default: None)

• node_type_names (List[str], optional) – The names of node types. (default: None)

• edge_type_names (List[Tuple[str, str, str]], optional) – The names of edge types. (default: None)

to_namedtuple() → NamedTuple

Returns a NamedTuple of stored key/value pairs.

up_to(end_time: float | int) → Self

Returns a snapshot of data to only hold events that occurred up to end_time (inclusive of edge_time).

update(data: Self | Dict[str, Any]) → Self

Updates the data object with the elements from another data object. Added elements will override existing ones (in case of duplicates).

update_tensor(tensor: Tensor | ndarray, *args, **kwargs) → bool

Updates a tensor in the FeatureStore with a new value. Returns whether the update was succesful.

Note

Implementor classes can choose to define more efficient update methods; the default performs a removal and insertion.

Parameters:

• tensor (torch.Tensor or np.ndarray) – The feature tensor to be updated.

• *args – Arguments passed to TensorAttr.

• **kwargs – Keyword arguments passed to TensorAttr.

validate(raise_on_error: bool = True) → bool

Validates the correctness of the data.

view(*args, **kwargs) → AttrView

Returns a view of the FeatureStore given a not yet fully-specified TensorAttr.