seqchem

Python client for the free SeqChem chemistry and bioinformatics API — convert between 190+ chemical formats, compute molecular descriptors, draw structures, generate 3D conformers, search substructures and process FASTA/FASTQ sequences.

No API key, no account, no dependencies (standard library only).

pip install seqchem

Quick start

from seqchem import Client

c = Client()

# SMILES -> InChI
print(c.convert("CC(=O)Oc1ccccc1C(=O)O", to="inchi")["result"])

# Descriptors (MW, logP, TPSA, HBD, HBA, rotatable bonds, InChIKey, ...)
props = c.properties("CC(=O)Oc1ccccc1C(=O)O")[0]["props"]
print(props["MW"], props["logP"], props["InChIKey"])

# 2D structure as SVG, ready to embed in a notebook or a web page
svg = c.depict("CC(=O)Oc1ccccc1C(=O)O")

# 3D conformer as an SDF block
sdf = c.gen3d("CC(=O)Oc1ccccc1C(=O)O")

# Tanimoto similarity
print(c.similarity("CCO", "CCCO", fp="MACCS"))

# IUPAC name -> structure
print(c.iupac("2-acetoxybenzoic acid")["smiles"])

# FASTA/FASTQ: fasta2fastq, fastq2fasta, revcomp, translate, stats
print(c.bio("revcomp", "ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG")["result"])

Command line

The package installs a seqchem command:

seqchem convert "CC(=O)Oc1ccccc1C(=O)O" --to inchi
seqchem properties "CCO" --json
seqchem depict "CCO" > ethanol.svg
seqchem similarity CCO CCCO
seqchem bio revcomp ATGGCC
seqchem formula C9H8O4
cat molecules.sdf | seqchem convert - --from sdf --to smiles

Errors

Everything raises SeqChemError, which carries the HTTP status and any detail the service sent:

from seqchem import Client, SeqChemError

try:
    Client().convert("not a molecule", to="inchi")
except SeqChemError as exc:
    print(exc.status, exc.message)

429 means either the fair-use rate limit (120 requests/minute per client) or that a heavy job is already running — 3D generation is serialised across the whole service.

Limits

Links

• Website: https://seqandchem.com
• API reference: https://seqandchem.com/api
• OpenAPI spec: https://seqandchem.com/api/openapi.json
• Source: https://github.com/MR820/seqandchem

Licensed under Apache-2.0.