schrodinger.seam.coders module

exception schrodinger.seam.coders.UnserializableMolError

Bases: Exception

class schrodinger.seam.coders.MolCoder

Bases: apache_beam.coders.coders.Coder

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

Encodes the given object into a byte string.

decode(mol_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.MolToSmilesCoder

Bases: schrodinger.seam.coders.MolCoder

Encodes and decodes Mol’s to and from SMILES strings similar, and 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).

NOTE: This is not as fast as MolCoder but will have a smaller binary size

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.

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