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Add examples

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  1. examples/conditional_generation/bfd_uniclust_hits.a3m +0 -0
  2. examples/conditional_generation/conditional_generation_relaxed_colabfold.pdb +0 -0
  3. examples/conditional_generation/example_output.json +3 -0
  4. examples/inpainted_idr/example_output.json +6 -0
  5. examples/inpainted_idr/generated_relaxed_colabfold.pdb +0 -0
  6. examples/inpainted_idr/original_relaxed_colabfold.pdb +0 -0
  7. examples/scaffolding_functional_motifs/example_output.json +8 -0
  8. examples/scaffolding_functional_motifs/scaffold_relaxed_colabfold.pdb +0 -0
  9. examples/unconditional_generation/example_output.json +3 -0
  10. examples/unconditional_generation/unconditional_generation_relaxed_colabfold.pdb +0 -0
examples/conditional_generation/bfd_uniclust_hits.a3m ADDED
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examples/conditional_generation/conditional_generation_relaxed_colabfold.pdb ADDED
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examples/conditional_generation/example_output.json ADDED
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+ {
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+ "generated_sequence" : "MDLRSSLVEHEGLRWKVYNNAEYVPTIGLGQIHNRPSQYWDYPVPLPEQYAEKDQISWSLETIQAVFDERYTKAKSEMVNLETIGKNFDDLPSEHTNAVTDMMFQLGTDHLSEFHKMITALKNNTYEEACREMKSSFWTRQMGNRCTRYLNDALEENYFFFNHH"
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+ }
examples/inpainted_idr/example_output.json ADDED
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+ {
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+ "original_sequence":"DQTERTVRSFEGRRTAPYLDSRNVLTIGYGHLLNRPGANKSWEGRLTSALPREFKQRLTELAASQLHETDVRLATARAQALYGSGAYFESVPVSLNDLWFDSVFNLGERKLLNWSGLRTKLESRDWGAAAKDLGRHTFGREPVSRRMAESMRMRRGIDLNHYNI",
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+ "generated_sequence":"DQTERTVRSFEGRRTAPYLDPASGAILADQWHTLAATGRMVSPLSTTFWTPREFKQRLTELAASQLHETDVRLATARAQALYGSGAYFESVPVSLNDLWFDSVFNLGERKLLNWSGLRTKLESRDWGAAAKDLGRHTFGREPVSRRMAESMRMRRGIDLNHYNI",
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+ "original_region":"SRNVLTIGYGHLLNRPGANKSWEGRLTSAL",
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+ "generated_region":"PASGAILADQWHTLAATGRMVSPLSTTFWT"
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+ }
examples/inpainted_idr/generated_relaxed_colabfold.pdb ADDED
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examples/inpainted_idr/original_relaxed_colabfold.pdb ADDED
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examples/scaffolding_functional_motifs/example_output.json ADDED
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+ {
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+ "sequence_from_pdb": "ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGELTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK",
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+ "motif_extracted_from_pdb": "FSLFDKDGDGTITTKELGTV",
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+ "motif_start_indices": [4, 40],
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+ "motif_end_indices": [23, 59],
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+ "generated_motif": "FKEAFSLFDKDGDGTITTKELGTVMRSLGQNPLEAELQDMINEVDADGNGTIDFPEFLTMMAHKMKDTDSKEEIREAFRVFDRDGNGTILKEELRRTFREMRDSLSEFEQIDKDKDGAIWIEEYQSTPKKS",
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+ "generated_sequence": "ADQLTEEQIAEFKEAFSLFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPLEAELQDMINEVDADGNGTIDFPEFLTMMAHKMKDTDSKEEIREAFRVFDRDGNGTILKEELRRTFREMRDSLSEFEQIDKDKDGAIWIEEYQSTPKKSMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGELTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK"
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+ }
examples/scaffolding_functional_motifs/scaffold_relaxed_colabfold.pdb ADDED
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examples/unconditional_generation/example_output.json ADDED
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+ {
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+ "generated_sequence": "MNILKQIAFFAIALTSNDVNRTEDYVQCVIPEYQYQQFDLYASTERIIELSSFSPPHVIIGGYDFLRNDKDIVYIRFCNNINRDIHNYVSTQYMTCRHYF"
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+ }
examples/unconditional_generation/unconditional_generation_relaxed_colabfold.pdb ADDED
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