sendoff
The minimal SDF metadata parser.
Often, SDFs have lots of useful metadata on them in the title and record fields/values. However, reading a molecule (via rdkit, OpenEye toolkits, etc) can be slow because those libraries also construct the molecules. Modifying the metadata, or filtering/sorting based on the metadata also can induce non-idempotent differences in the file based on opinionated approaches in chemical libraries.
This library strives to be able to handle SDF files even with malformed chemistry or metadata. Since much debugging of our files and data deals with such files, having access to simple fast tools to interrogate the files while not modifying the file is crucial.
This package also tries to document the “canonical” ways metadata is handled by the larger packages. To wit, there are tests to monitor how, for example, rdkit deals with molecules that have multiline record values, or a “$$$$” molecule title.
In time per operation, sendoff is 31–79× faster than RDKit, 7.1–30× faster than OEChem, and 8.8–59× faster than the pure-Python sendoff 0.1.6 (geomeans by dataset; see the benchmarks).
Usage
from collections import Counter
from rdkit import Chem
from sendoff import SDBlock, parse_sdf, sdf_writer, write_sdf
for block in parse_sdf("compounds.sdf"):
block.title
block["ID"]
block.get("ID")
block.to_dict()
block.records()
block.iter_records()
"ID" in block, len(block), list(block)
"V3000" in block.mdl
mol = Chem.MolFromMolBlock(block.molblock)
Counter(name for block in parse_sdf("compounds.sdf") for name in block)
def tag(block):
block["Source"] = "vendor"
block.remove_record("Internal note")
return block
write_sdf("out.sdf", (tag(block) for block in parse_sdf("in.sdf")))
with sdf_writer("active.sdf") as active, sdf_writer("rest.sdf") as rest:
for block in parse_sdf("in.sdf"):
(active if block.get("Active") == "1" else rest).write(block)
block = SDBlock(Chem.MolToMolBlock(mol), {"ID": "X-1"})
str(block)
SDBlock.from_sdf(sdf_text)parse_sdf memory-maps local files, so write to a new path: truncating a file while it is parsed crashes the process. parse_sdf(path, borrow=True) also skips copying each block: blocks read the file in place until edited, so the same holds for as long as they live.
New headers are > <name>; header="padded" writes > <name>, as RDKit does, and header="copy" follows the block’s first header.
Non-UTF-8 files
str paths decode UTF-8. Open other encodings yourself, or stay in bytes:
with open("vendor.sdf", encoding="gbk") as f:
names = {block["CAS"]: block["Product name"] for block in parse_sdf(f)}
in_stock = (
block
for block in parse_sdf(os.fsencode("vendor.sdf"))
if block.get(b"Availability") == b"In-stock"
)
write_sdf("in-stock.sdf", in_stock)Shell pipelines
python -m sendoff.cli.count my.sdf
zcat chembl.sdf.gz | python -m sendoff.cli.count
python -m sendoff.cli.head -n 100 my.sdf > sample.sdf
python -m sendoff.cli.tail -n +2 my.sdf > without-first.sdf
python -m sendoff.cli.get Supplier my.sdf | sort | uniq -c
paste <(python -m sendoff.cli.get -t my.sdf) <(python -m sendoff.cli.get CAS my.sdf)
python -m sendoff.cli.get ID my.sdf | sed 's/^/TL-/' |
python -m sendoff.cli.title --from - my.sdf > titled.sdf
python -m sendoff.cli.filter --eq Availability In-stock vendor.sdf |
python -m sendoff.cli.set Batch --value B7 -o batch.sdf
python -m sendoff.cli.filter --unique InChIKey my.sdf > unique.sdfThe count, head, tail, get, set, title, and filter commands read FILE or -i FILE, else stdin, as bytes and write -o FILE, else stdout; -o cannot name an input. get prints one line per block, empty where a record is missing, and --from reads one line per block; -z uses NUL instead. Run any with -h.
In Python, read compressed files with parse_sdf(gzip.open(path)), and write a pipe with write_sdf(sys.stdout, blocks), or sys.stdout.buffer for bytes blocks.
1 maintainer
Metadata
1 maintainer
Release files for sendoff 1.0.0
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