schrodinger.seam.coders module

exception schrodinger.seam.coders.UnserializableMolError

Bases: Exception

class schrodinger.seam.coders.MolToSmilesCoder

Bases: apache_beam.coders.coders.Coder

encode(mol: rdkit.Chem.rdchem.Mol) → bytes

Encodes the given object into a byte string.

decode(smiles_bytes: bytes) → rdkit.Chem.rdchem.Mol

Decodes the given byte string into the corresponding object.

is_deterministic()

Whether this coder is guaranteed to encode values deterministically.

A deterministic coder is required for key coders in GroupByKey operations to produce consistent results.

For example, note that the default coder, the PickleCoder, is not deterministic: the ordering of picked entries in maps may vary across executions since there is no defined order, and such a coder is not in general suitable for usage as a key coder in GroupByKey operations, since each instance of the same key may be encoded differently.

Returns:

Whether coder is deterministic.

estimate_size(mol: rdkit.Chem.rdchem.Mol) → int

Estimates the encoded size of the given value, in bytes.

Dataflow estimates the encoded size of a PCollection processed in a pipeline step by using the estimated size of a random sample of elements in that PCollection.

The default implementation encodes the given value and returns its byte size. If a coder can provide a fast estimate of the encoded size of a value (e.g., if the encoding has a fixed size), it can provide its estimate here to improve performance.

Arguments:

value: the value whose encoded size is to be estimated.

Returns:

The estimated encoded size of the given value.

to_type_hint() → type

class schrodinger.seam.coders.SafeMolToSmilesCoder

Bases: schrodinger.seam.coders.MolToSmilesCoder

Encodes and decodes Mol’s to and from SMILES strings similar to MolToSmilesCoder. However, this coder will raise an exception if the molecule is not sanitizable.

“Sanitizable” in this context is defined as a smiles that will return None when passed to Chem.MolFromSmiles (which by default attempts to sanitize the molecule). This is not as fast as MolToSmilesCoder because of the additional check, but will

encode(mol: rdkit.Chem.rdchem.Mol) → bytes

Encodes the given object into a byte string.

class schrodinger.seam.coders.StructureCoder

Bases: apache_beam.coders.coders.Coder

encode(st: schrodinger.structure._structure.Structure) → bytes

Encodes the given object into a byte string.

decode(mae_bytes: bytes) → schrodinger.structure._structure.Structure

Decodes the given byte string into the corresponding object.

is_deterministic()

Whether this coder is guaranteed to encode values deterministically.

A deterministic coder is required for key coders in GroupByKey operations to produce consistent results.

For example, note that the default coder, the PickleCoder, is not deterministic: the ordering of picked entries in maps may vary across executions since there is no defined order, and such a coder is not in general suitable for usage as a key coder in GroupByKey operations, since each instance of the same key may be encoded differently.

Returns:

Whether coder is deterministic.

to_type_hint() → type

class schrodinger.seam.coders.RouteNodeCoder

Bases: apache_beam.coders.coders.Coder

encode(route_node: schrodinger.application.pathfinder.route.RouteNode) → bytes

Encodes the given object into a byte string.

decode(route_node_bytes: bytes) → schrodinger.application.pathfinder.route.RouteNode

Decodes the given byte string into the corresponding object.

is_deterministic()

Whether this coder is guaranteed to encode values deterministically.

A deterministic coder is required for key coders in GroupByKey operations to produce consistent results.

For example, note that the default coder, the PickleCoder, is not deterministic: the ordering of picked entries in maps may vary across executions since there is no defined order, and such a coder is not in general suitable for usage as a key coder in GroupByKey operations, since each instance of the same key may be encoded differently.

Returns:

Whether coder is deterministic.

to_type_hint() → type