mirror of
https://github.com/KosinskiLab/AlphaPulldown.git
synced 2026-06-04 22:34:26 +08:00
4d802be7d6
* symmetrical refactoring to support both af2 and af3 data pipelines * Clean tests * Keep GPU tests in place * Reverted accidentally deleted templates * Add AlphaFold3 feature creation pipeline and per-chain input generation - Implement `create_pipeline_af3` to construct the AlphaFold3 data pipeline with correct database and binary paths. - Add `create_af3_individual_features` to generate AlphaFold3 input features for each chain in a FASTA, handling protein, RNA, and DNA sequences. - Integrate new AF3 logic into the main entry point, dispatching to AF2 or AF3 as appropriate. - Ensure output directory creation and error handling for missing dependencies or invalid sequences. * Convert template dates to datetime for af3 * First check for nucleotides, then for amino-acids * Skip existing features json if --skip_existing=true * Check if DNA before RNA * Bump 2.1.0 * Git ignore build/ dir
30 lines
1.4 KiB
Python
30 lines
1.4 KiB
Python
from absl.testing import absltest
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from alphapulldown.objects import MultimericObject
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import pickle
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import numpy as np
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class TestCreateMultimericObject(absltest.TestCase):
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"""A class that test major functions of creating feature_dict of a MultimericObject object"""
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def setUp(self) -> None:
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self.monomer1 = pickle.load(open("./test/test_data/features/3L4Q_A.3L4Q.cif.A.pkl", "rb"))
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self.monomer2 = pickle.load(open("./test/test_data/features/3L4Q_C.3L4Q.pdb.C.pkl", "rb"))
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def test_1_initiate_default_multimericobject(self) -> MultimericObject:
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multimer_obj = MultimericObject([self.monomer1, self.monomer2])
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return multimer_obj
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def test_1_initiate_multimericobject_without_msa_pairing(self) -> MultimericObject:
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multimer_obj = MultimericObject([self.monomer1, self.monomer2],pair_msa=False)
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return multimer_obj
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def test_2_check_residue_indexes(self):
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multimer_obj = self.test_1_initiate_default_multimericobject()
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seq_1_length = self.monomer1.feature_dict['seq_length'][0]
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seq_2_length = self.monomer2.feature_dict['seq_length'][0]
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expected_residue_index=np.array(list(range(seq_1_length)) + list(range(seq_2_length)))
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self.assertTrue(np.array_equal(multimer_obj.feature_dict['residue_index'],expected_residue_index))
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if __name__=="__main__":
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absltest.main() |