schrodinger.seam.io.chemio module¶
Transforms for reading and writing structures and molecules.
- class schrodinger.seam.io.chemio.ReadStructuresFromFile(file_pattern: Union[str, pathlib.Path], **kwargs)¶
Bases:
schrodinger.seam.transforms._resources._LocalOnlyPTransform
,schrodinger.seam.io.chemio.ReadStructuresFromFile
Read a file (or files) containing a structure or a list of structures and return a PCollection of schrodinger.structure.Structure objects.
Example:
>>> from schrodinger.test import mmshare_data_file >>> with beam.Pipeline() as p: ... _ = (p ... | ReadStructuresFromFile(mmshare_data_file('cookbook/stereoisomers-form-1.maegz')) ... | beam.Map(lambda st: st.title) ... | textio.WriteToText('titles.txt')) >>> with open('titles.txt') as f: ... titles = sorted(set(line.strip() for line in f)) >>> titles ['stereoisomers-1-form-1', 'stereoisomers-2-form-1', ...]
- class schrodinger.seam.io.chemio.ReadAllStructuresFromFile(label: Optional[str] = None)¶
Bases:
schrodinger.seam.transforms._resources._LocalOnlyPTransform
,schrodinger.seam.io.chemio.ReadAllStructuresFromFile
A
PTransform
for reading aPCollection
of structure files.Example:
>>> from schrodinger.test import mmshare_data_file >>> with beam.Pipeline() as p: ... _ = (p ... | beam.Create([mmshare_data_file('cookbook/stereoisomers-form-1.maegz')]) ... | ReadAllStructuresFromFile() ... | beam.Map(lambda st: st.title) ... | textio.WriteToText('titles.txt')) >>> with open('titles.txt') as f: ... titles = sorted(set(line.strip() for line in f)) >>> titles ['stereoisomers-1-form-1', 'stereoisomers-2-form-1', ...]
- class schrodinger.seam.io.chemio.WriteStructuresToFile(file_name: Union[str, pathlib.Path], *, sort_key: Optional[Callable[[schrodinger.structure._structure.Structure], Any]] = None, **kwargs)¶
Bases:
schrodinger.seam.transforms._resources._LocalOnlyPTransform
,schrodinger.seam.io.chemio.WriteStructuresToFile
Write a PCollection of schrodinger.structure.Structure objects to a file.
The file format is determined by the file extension. See schrodinger.structure.StructureWriter for more details.
Example:
>>> from schrodinger import structure >>> from pathlib import Path >>> outfile = Path('out.maegz') >>> outfile.unlink(missing_ok=True) >>> with beam.Pipeline() as p: ... sts = [structure.create_new_structure(num_atoms=i) for i in range(1, 11)] ... _ = (p | beam.Create(sts) | WriteStructuresToFile(outfile)) >>> sts = list(structure.StructureReader(outfile)) >>> len(sts) 10
- Parameters
file_name – the output file name
sort_key – a function of one argument that is used to extract a comparison key from each element.
- Raises
ValueError – if the file already exists
- class schrodinger.seam.io.chemio.ReadMolsFromFile(file_pattern: Union[str, pathlib.Path], silent=False, **kwargs)¶
Bases:
schrodinger.seam.transforms._resources._LocalOnlyPTransform
,schrodinger.seam.io.chemio.ReadMolsFromFile
Read a file containing a newline separated list of SMILES strings and return a PCollection of RDKit molecules.
Invalid SMILES strings are skipped. A warning is printed if silent is set to False.
Example:
>>> from pathlib import Path >>> infile = Path('test.smi') >>> _ = infile.write_text("C\nCC\nCCC") >>> Path('num_atoms.txt').unlink(missing_ok=True) >>> with beam.Pipeline() as p: ... _ = (p ... | ReadMolsFromFile(infile) ... | beam.Map(lambda m: m.GetNumHeavyAtoms()) ... | textio.WriteToText('num_atoms.txt')) >>> with open('num_atoms.txt') as f: ... num_atoms = sorted(int(line.strip()) for line in f) >>> num_atoms [1, 2, 3]
- class schrodinger.seam.io.chemio.WriteMolsToFile(file_name: str, **kwargs)¶
Bases:
schrodinger.seam.transforms._resources._LocalOnlyPTransform
,schrodinger.seam.io.chemio.WriteMolsToFile
Write a PCollection of RDKit molecules to a file as a newline separated list of SMILES strings.
Example:
>>> from rdkit import Chem >>> from pathlib import Path >>> outfile = Path('test.smi') >>> outfile.unlink(missing_ok=True) >>> with beam.Pipeline() as p: ... mols = [Chem.MolFromSmiles('C' * i) for i in range(1, 4)] ... _ = (p | beam.Create(mols) | WriteMolsToFile(outfile)) >>> with open(outfile) as f: ... smiles = sorted(line.strip() for line in f) >>> smiles ['C', 'CC', 'CCC']
- Raises
ValueError – if the file already exists