Olamide Isreal
f971fd0e21
- Nextflow pipeline using chai1 Docker image from Harbor - S3-based input/output paths (s3://omic/eureka/chai-lab/) - GPU-accelerated protein folding with MSA support Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
80 lines
2.5 KiB
Python
Executable File
80 lines
2.5 KiB
Python
Executable File
# Copyright (c) 2024 Chai Discovery, Inc.
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# Licensed under the Apache License, Version 2.0.
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# See the LICENSE file for details.
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from pathlib import Path
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from tempfile import TemporaryDirectory
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from chai_lab.data.parsing.fasta import read_fasta
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from chai_lab.data.parsing.input_validation import (
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constituents_of_modified_fasta,
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identify_potential_entity_types,
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)
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from chai_lab.data.parsing.structure.entity_type import EntityType
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from .example_inputs import example_dna, example_ligands, example_proteins, example_rna
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def test_simple_protein_fasta():
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parts = constituents_of_modified_fasta("RKDES")
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assert parts is not None
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assert all(x == y for x, y in zip(parts, ["R", "K", "D", "E", "S"]))
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def test_modified_protein_fasta():
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parts = constituents_of_modified_fasta("(KCJ)(SEP)(PPN)(B3S)(BAL)(PPN)KX(NH2)")
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assert parts is not None
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expected = ["KCJ", "SEP", "PPN", "B3S", "BAL", "PPN", "K", "X", "NH2"]
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assert all(x == y for x, y in zip(parts, expected))
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def test_rna_fasta():
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seq = "ACUGACG"
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parts = constituents_of_modified_fasta(seq)
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assert parts is not None
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assert all(x == y for x, y in zip(parts, seq))
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def test_dna_fasta():
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seq = "ACGACTAGCAT"
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parts = constituents_of_modified_fasta(seq)
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assert parts is not None
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assert all(x == y for x, y in zip(parts, seq))
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def test_parsing():
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for ligand in example_ligands:
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assert EntityType.LIGAND in identify_potential_entity_types(ligand)
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for protein in example_proteins:
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assert EntityType.PROTEIN in identify_potential_entity_types(protein)
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for dna in example_dna:
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assert EntityType.DNA in identify_potential_entity_types(dna)
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for rna in example_rna:
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assert EntityType.RNA in identify_potential_entity_types(rna)
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def test_fasta_parsing():
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test_string = """>foo\nRKDES\n>bar\nKEDESRRR"""
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with TemporaryDirectory() as tmpdir:
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fa_file = Path(tmpdir) / "test.fasta"
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fa_file.write_text(test_string)
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records = read_fasta(fa_file)
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assert len(records) == 2
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assert records[0].header == "foo"
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assert records[0].sequence == "RKDES"
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assert records[1].header == "bar"
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assert records[1].sequence == "KEDESRRR"
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def test_smiles_parsing():
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smiles = ">smiles\nCc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1C"
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with TemporaryDirectory() as tmpdir:
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fa_file = Path(tmpdir) / "test.fasta"
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fa_file.write_text(smiles)
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records = read_fasta(fa_file)
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assert len(records) == 1
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