APCyc
Autonomous cyclization and property-aware design for cyclic peptides.
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- pages.yml
- PULL_REQUEST_TEMPLATE.md
- SECURITY.md
- __init__.py
- apcyc_dpm.py
- eval_default.yaml
- md_default.yaml
- md_report.yaml
- __init__.py
- aggregate.py
- pdb_utils.py
- report.py
- seq_utils.py
- __init__.py
- metric_rosetta_interface_dg.py
- metric_rosetta_total_score.py
- metric_vina_score.py
- __init__.py
- metric_aggregate_per_sample.py
- metric_succ_cyclization.py
- metric_succ_energy_cyclization.py
- metric_success_rows.py
- metric_valid_rate.py
- __init__.py
- metric_cramers_v.py
- __init__.py
- metric_co_diversity.py
- metric_tm_mean.py
- metric_tm_median.py
- __init__.py
- metric_rama_allowed.py
- metric_rama_favored.py
- __init__.py
- metric_diversity_shared.py
- metric_failure_counts.py
- metric_helpers.py
- metric_rama_shared.py
- metric_tm_shared.py
- __init__.py
- metric_bond_length_validity.py
- metric_cyclization_success.py
- metric_energy_success.py
- __init__.py
- cpcomposer_kl.py
- cpsea_geom.py
- foldx.py
- md_sim.py
- pepglad_divcons.py
- ppflow_validity.py
- rosetta_score.py
- tm_score.py
- vina_score.py
- __init__.py
- eval_runner.py
- md_report.py
- md_runner.py
- README.md
- __init__.py
- constants.py
- cyc_enhance.py
- cyclic_injection.py
- cyclization_heads.py
- dataset.py
- guidance.py
- model.py
- pair_init.py
- pocket_cross_attn.py
- property_predictor.py
- train_property.py
- version.py
- detect_pocket.py
- run.py
- 1ssc_A_B.pdb
- 1ssc_A_pocket.json
- cover.png
- teaser.png
- sample_codesign.sh
- sample_struct_pred.sh
- train_apcyc.sh
- .gitkeep
- property_anchor.yaml
- property_base.yaml
- property_vocab.yaml
- property_vocab_anchor.yaml
- apcyc_ae.yaml
- apcyc_ae_anchor.yaml
- apcyc_ae_vocab.yaml
- apcyc_ae_vocab_anchor.yaml
- apcyc_balance_ldm.yaml
- apcyc_ldm.yaml
- apcyc_ldm_sample.yaml
- apcyc_ldm_sample_anchor.yaml
- apcyc_ldm_sample_vocab.yaml
- apcyc_ldm_sample_vocab_cg.yaml
- apcyc_ldm_vocab.yaml
- pepglad_ldm_sample.yaml
- train_codesign.yaml
- train_fixseq.yaml
- setup_latent_guidance.yaml
- train_codesign.yaml
- train_fixseq.yaml
- test_codesign.yaml
- test_fixseq.yaml
- train_codesign.yaml
- train_fixseq.yaml
- setup_latent_guidance.yaml
- train_codesign.yaml
- train_fixseq.yaml
- test_codesign.yaml
- test_fixseq.yaml
- joint.yaml
- stage12.yaml
- stage123.yaml
- blocks_interface.py
- blocks_to_data.py
- list_blocks_to_pdb.py
- pdb_to_list_blocks.py
- __init__.py
- codesign.py
- dataset_wrapper.py
- format.py
- mmap_dataset.py
- resample.py
- quickstart.md
- reproduction.md
- base.py
- energy.py
- openmm_relaxer.py
- RosettaFastRelaxUtil.xml
- run.py
- __init__.py
- diversity.py
- dockq.py
- rmsd.py
- seq_metric.py
- README.md
- api.py
- backbone.py
- __init__.py
- geometry.py
- sequence.py
- geometry.py
- api.py
- sidechain.py
- model.py
- am_egnn.py
- am_enc.py
- radial_basis.py
- model.py
- nn_utils.py
- dpm_full.py
- transition.py
- dist.py
- ldm.py
- __init__.py
- dev.txt
- framework.txt
- install_all.sh
- __init__.py
- build_router_mmap.py
- check_ids_in_pdb.py
- count_valid_cstar.py
- data.py
- model.py
- pairs.py
- README.md
- aug_from_monomer.py
- cpcore_mmap.py
- monomer.py
- pepbdb.py
- process.py
- split.py
- build_pharm_csv.py
- apcyc_energy_postprocess.py
- apcyc_extract_pockets.py
- apcyc_postprocess.py
- apcyc_prepare_lnr_sampling.py
- check_chirality_mirror.py
- check_chirality_residues.py
- check_ckpt_compat.py
- check_gtpair_range.py
- compare_vae_latent.py
- group_by_receptor.py
- rename_chain_ab_to_lr.py
- run_exp_pipe.sh
- train.sh
- check_syntax.py
- test_repository_layout.py
- __init__.py
- abs_trainer.py
- autoencoder_trainer.py
- ldm_trainer.py
- config_utils.py
- const.py
- decorators.py
- file_utils.py
- logger.py
- network.py
- nn_utils.py
- oom_decorator.py
- random_seed.py
- register.py
- APCyc_final_1t4f.png
- APCyc_final_2np0.png
- APCyc_final_2qos.png
- denoising_1t4f.mp4
- denoising_2xyi.mp4
- denoising_5y59.mp4
- injection.png
- overview.png
- paper.pdf
- radar.png
- teaser.png
- favicon.svg
- accordion.tsx
- alert-dialog.tsx
- alert.tsx
- aspect-ratio.tsx
- avatar.tsx
- badge.tsx
- breadcrumb.tsx
- button.tsx
- calendar.tsx
- card.tsx
- carousel.tsx
- chart.tsx
- checkbox.tsx
- collapsible.tsx
- command.tsx
- context-menu.tsx
- dialog.tsx
- drawer.tsx
- dropdown-menu.tsx
- form.tsx
- hover-card.tsx
- input-otp.tsx
- input.tsx
- label.tsx
- menubar.tsx
- navigation-menu.tsx
- pagination.tsx
- popover.tsx
- progress.tsx
- radio-group.tsx
- resizable.tsx
- scroll-area.tsx
- select.tsx
- separator.tsx
- sheet.tsx
- sidebar.tsx
- skeleton.tsx
- slider.tsx
- sonner.tsx
- switch.tsx
- table.tsx
- tabs.tsx
- textarea.tsx
- toggle-group.tsx
- toggle.tsx
- tooltip.tsx
- use-mobile.tsx
- error-capture.ts
- error-page.ts
- lovable-error-reporting.ts
- utils.ts
- __root.tsx
- index.tsx
- router.tsx
- routeTree.gen.ts
- server.ts
- start.ts
- static-main.tsx
- styles.css
- .gitignore
- .prettierignore
- .prettierrc
- components.json
- eslint.config.js
- index.html
- package-lock.json
- package.json
- tsconfig.json
- vite.config.ts
- vite.pages.config.ts
- .gitignore
- .pre-commit-config.yaml
- apcyc_sample.py
- apcyc_train.py
- cal_metrics.py
- data_check.py
- env.yaml
- generate.py
- globals.py
- LICENSE
- Makefile
- MANIFEST.in
- README.md
- requirements.txt
- setup.cfg
- setup.py
- setup_latent_guidance.py
- train.py
- train_router.py
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