I/O

Source and sink blocks handle reading and writing molecules in various file formats.

Supported Formats

Extension	Format
.sdf	SD file
.sdf.gz	Gzipped SD file
.mol2	Mol2 file
.smi	SMILES file
.smi.gz	Gzipped SMILES file
.csv	CSV with SMILES column
.parquet	Parquet with SMILES column

Sources

cmxflow.sources.reader.MoleculeSourceBlock(wrap: bool = True)

Bases: SourceBlock

Source block for reading molecules from various file formats.

Supports .sdf, .sdf.gz, .mol2, .smi, .smi.gz, .csv, and .parquet files. File format is automatically detected based on extension.

Example

workflow.add(
    MoleculeSourceBlock(),
    MoleculeSinkBlock(),
)

Initialize the molecule source block.

Parameters:

Name	Type	Description	Default
wrap	bool	If True (default), wrap molecules in Mol for property preservation through pickling.	True

Sinks

cmxflow.sinks.writer.MoleculeSinkBlock()

Bases: SinkBlock

Sink block for writing molecules to various file formats.

Supports .sdf, .sdf.gz, .mol2, .smi, .smi.gz, .csv, and .parquet files. File format is automatically detected based on extension.

Example

workflow.add(
    MoleculeSourceBlock(),
    MoleculeSinkBlock(),
)

Initialize the molecule sink block.