File size: 5,345 Bytes
a74f603 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 | """Export matched experimental data and ESMFold structures; never substitute sequences."""
import csv
import hashlib
import json
import shutil
from pathlib import Path
ROOT=Path(__file__).resolve().parents[1]
AUDIT=ROOT.parent/'Ouroboros_Showcase_Research/wetlab_20260927'
PUBLIC=ROOT/'public'
AA=dict(zip('ALA ARG ASN ASP CYS GLN GLU GLY HIS ILE LEU LYS MET PHE PRO SER THR TRP TYR VAL UNK'.split(),'ARNDCQEGHILKMFPSTWYVX'))
def digest(path):return hashlib.sha256(path.read_bytes()).hexdigest()
def save(path,data):path.write_text(json.dumps(data,ensure_ascii=False,indent=2)+'\n')
def main():
import xlrd
original=AUDIT/'PETde实验情况20260927.xls'
sheet=xlrd.open_workbook(original,use_mmap=False).sheet_by_index(0)
sequences=json.loads((AUDIT/'sequence_mapping.json').read_text())
generation=json.loads((AUDIT/'de2_generation.json').read_text())
manifest=json.loads((AUDIT/'fold_results/manifest.json').read_text())
ids=['de2','rcsb_5XG0_IsPETase','rcsb_4EB0_LCC','rcsb_7EOA_BhrPETase']
assert len(manifest)==len(ids)
names={'rcsb_5XG0_IsPETase':('IsPETase','Y1','5XG0'),'rcsb_4EB0_LCC':('LCC','Y2','4EB0'),'rcsb_7EOA_BhrPETase':('BhrPETase','Y3','7EOA')}
cases=[]
for index,fid in enumerate(ids):
row=next(r for r in sequences if r['id']==fid)
fold=next(r for r in manifest if r['sequence_id']==f'{index:04d}')
seq=row['sequence'];assert hashlib.sha256(seq.encode()).hexdigest()==fold['source_pred_seq_sha256']
pdb=AUDIT/'fold_results'/fold['pdb_file']
atoms=[line for line in pdb.read_text().splitlines() if line.startswith('ATOM') and line[12:16].strip()=='CA']
assert ''.join(AA[s[17:20]] for s in atoms)==seq
residues=[dict(index=int(s[22:26]),chain=s[21].strip(),code=AA[s[17:20]],confidence=float(s[60:66])) for s in atoms]
design=fid=='de2'
name,sample,pdb_id=('de2','de2',None) if design else names[fid]
if design:assert generation['sequence'].replace(' ','')==seq
provenance=(f"Exact sequence match: submitted de2 FASTA → group_02.part_1530 → petase_lora_2891 → lora_petase_3epoch/test/test_result.json, prediction index {generation['predictionIndex0']} (zero-based). Original prompt recovered from the same generation record." if design else f"Supplied wild-type reference FASTA: {fid}.fasta, labeled {pdb_id}. Matched by name to assay sample {sample}. This view is a new ESMFold prediction of the supplied sequence.")
case=dict(id=name,assetId='wetlab-'+fid,title=name,kind='design' if design else 'wildtype',modelLabel='LoRA-generated' if design else 'WT reference',assaySample=sample,cohort='PETase wet-lab report · 2026-09-27',rank=1 if design else 0,cohortSize=4,sequence=seq,length=len(seq),residues=residues,prompt=generation['prompt'] if design else '',plddt=sum(r['confidence'] for r in residues)/len(residues),pae=fold['mean_pae'],pdbUrl=f'/structures/wetlab-{fid}.pdb',fastaUrl=f'/structures/wetlab-{fid}.fasta',selection='Selected by highest reported TPA + MHET among the four measured designs.' if design else f'Wild-type reference {name}, assay sample {sample}.',structureStatus='ESMFold-v1 prediction of submitted FASTA',experimentalStatus='Reported TPA and MHET concentrations are available in the 2026-09-27 workbook. Assay conditions and replication are awaiting confirmation.',provenance=provenance,pdbSha256=digest(pdb),sequenceSha256=row['sha256'],foldJob='ouroboros-wetlab-de2-1009b',foldMethod='ESMFold-v1',residueConfidenceDefinition='Mean of CA B factors in the exported ESMFold PDB')
shutil.copyfile(pdb,PUBLIC/'structures'/f'wetlab-{fid}.pdb')
cases.append(case)
audit=json.loads((AUDIT/'assay_audit.json').read_text())
for row in audit['rows']:
i=row['sourceRow']-1
assert sheet.cell_value(i,1)==row['id']
for col,key in [(3,'tpa'),(4,'mhet'),(5,'total')]:assert sheet.cell_value(i,col)==row[key]
assert abs(row['tpa']+row['mhet']-row['total'])<1e-7
for row in sequences:shutil.copyfile(AUDIT/(row['id']+'.fasta'),PUBLIC/'structures'/('wetlab-'+row['id']+'.fasta'))
audit['generation']={k:v for k,v in generation.items() if k not in ['referenceSequence','sequence']}
audit['structurePrediction']={'method':'ESMFold-v1','job':'ouroboros-wetlab-de2-1009b','manifestSha256':digest(AUDIT/'fold_results/manifest.json'),'date':'2026-10-09','experimentalStructure':False}
save(PUBLIC/'data/wetlab.json',audit)
save(PUBLIC/'data/petase-wetlab-structures.json',cases)
save(PUBLIC/'data/petase.json',[c for c in cases if c['id'] in ['de2','IsPETase']])
provenance=json.loads((PUBLIC/'data/provenance.json').read_text())
provenance['petase']='de2 from the LoRA 3-epoch generation archive; featured by reported wet-lab product concentration. Three provided WT reference sequences are included. Earlier confidence-ranked candidates remain in petase-archive.json.'
provenance['wetlab']={'report':audit['source'],'sequenceMatches':[{'id':r['id'],'sha256':r['sha256'],'generationMatches':r.get('exactMatches',[])} for r in sequences],'structurePrediction':audit['structurePrediction']}
save(PUBLIC/'data/provenance.json',provenance)
print(json.dumps([{'id':r['id'],'length':r['length'],'plddt':r['plddt']} for r in cases],indent=2))
if __name__=='__main__':main()
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