├── .gitignore ├── LICENSE ├── README.md ├── checkpoints └── .gitignore ├── config ├── ablations │ ├── ablations_large.yml │ ├── ablations_large_pt.yml │ ├── ablations_large_pt_ln.yml │ ├── ablations_large_pt_tl.yml │ ├── ablations_large_pt_tl_ln.yml │ └── ablations_small.yml ├── all_prec_type │ ├── mona_inchikey_all_CFM.yml │ ├── mona_inchikey_all_FP.yml │ ├── mona_inchikey_all_MF.yml │ ├── mona_inchikey_all_WLN.yml │ ├── mona_scaffold_all_CFM.yml │ ├── mona_scaffold_all_FP.yml │ ├── mona_scaffold_all_MF.yml │ ├── mona_scaffold_all_WLN.yml │ ├── nist_inchikey_all_CFM.yml │ ├── nist_inchikey_all_FP.yml │ ├── nist_inchikey_all_MF.yml │ ├── nist_inchikey_all_WLN.yml │ ├── nist_scaffold_all_CFM.yml │ ├── nist_scaffold_all_FP.yml │ ├── nist_scaffold_all_MF.yml │ └── nist_scaffold_all_WLN.yml ├── casmi │ ├── casmi_CFM.yml │ ├── casmi_FP.yml │ ├── casmi_MF.yml │ └── casmi_WLN.yml ├── checkpoint_example │ └── checkpoint_example.yml ├── demo │ ├── demo_eval.yml │ └── demo_train.yml ├── mh_prec_type │ ├── mona_inchikey_mh_CFM.yml │ ├── mona_inchikey_mh_FP.yml │ ├── mona_inchikey_mh_MF.yml │ ├── mona_inchikey_mh_WLN.yml │ ├── mona_scaffold_mh_CFM.yml │ ├── mona_scaffold_mh_FP.yml │ ├── mona_scaffold_mh_MF.yml │ ├── mona_scaffold_mh_WLN.yml │ ├── nist_inchikey_mh_CFM.yml │ ├── nist_inchikey_mh_CFM_hr.yml │ ├── nist_inchikey_mh_ESP.yml │ ├── nist_inchikey_mh_ESP_og.yml │ ├── nist_inchikey_mh_FP.yml │ ├── nist_inchikey_mh_FP_hr.yml │ ├── nist_inchikey_mh_MF.yml │ ├── nist_inchikey_mh_MF_hr.yml │ ├── nist_inchikey_mh_WLN.yml │ ├── nist_inchikey_mh_WLN_hr.yml │ ├── nist_scaffold_mh_CFM.yml │ ├── nist_scaffold_mh_FP.yml │ ├── nist_scaffold_mh_MF.yml │ └── nist_scaffold_mh_WLN.yml ├── template.yml └── train_both │ ├── train_both_all_MF.yml │ ├── train_both_all_MF_hr.yml │ ├── train_both_mh_MF.yml │ └── train_both_mh_MF_hr.yml ├── data ├── cfm │ └── .gitignore ├── df │ └── .gitignore ├── proc │ └── .gitignore └── raw │ └── .gitignore ├── download_scripts ├── download_casmi_2016_proc.sh ├── download_casmi_2022_proc.sh ├── download_casmi_raw.sh ├── download_cfm_pred.sh ├── download_demo.sh ├── download_mona_raw.sh ├── download_nist20_outlier_proc.sh ├── download_nist_raw.txt └── download_public.sh ├── env ├── requirements-cpu.txt └── requirements-gpu.txt ├── img └── nist_export.png ├── licenses ├── CFM_LICENSE ├── GRAPHORMER_LICENSE ├── NEIMS_LICENSE └── RETROSIM_LICENSE ├── predictions ├── example_predictions.csv └── example_smiles.csv ├── preproc_scripts ├── mol_fix.py ├── parse_and_export.py ├── parse_cfm_output.py ├── prepare_casmi22_data.py ├── prepare_casmi_data.py ├── prepare_data.py └── prepare_pcasmi_data.py ├── scripts ├── compute_cfm_overlap.py ├── compute_ds_stats.py ├── compute_split_stats.py ├── compute_test_metrics.py ├── compute_test_ranks.py ├── plot_legends.py ├── plot_metrics.py ├── run_inference.py ├── run_train_eval.py └── viz_preds.py ├── setup.cfg ├── setup.py └── src └── massformer ├── __init__.py ├── algos1.pyx ├── algos2.pyx ├── casmi_utils.py ├── cfm_model.py ├── data_utils.py ├── dataset.py ├── gf_data_utils.py ├── gf_model.py ├── het_sep_utils.py ├── losses.py ├── lr.py ├── metric_table.py ├── misc_utils.py ├── model.py ├── plot_utils.py ├── runner.py └── spec_utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/README.md -------------------------------------------------------------------------------- /checkpoints/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /config/ablations/ablations_large.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/ablations/ablations_large.yml -------------------------------------------------------------------------------- /config/ablations/ablations_large_pt.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/ablations/ablations_large_pt.yml -------------------------------------------------------------------------------- /config/ablations/ablations_large_pt_ln.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/ablations/ablations_large_pt_ln.yml -------------------------------------------------------------------------------- /config/ablations/ablations_large_pt_tl.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/ablations/ablations_large_pt_tl.yml -------------------------------------------------------------------------------- /config/ablations/ablations_large_pt_tl_ln.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/ablations/ablations_large_pt_tl_ln.yml -------------------------------------------------------------------------------- /config/ablations/ablations_small.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/ablations/ablations_small.yml -------------------------------------------------------------------------------- /config/all_prec_type/mona_inchikey_all_CFM.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/mona_inchikey_all_CFM.yml -------------------------------------------------------------------------------- /config/all_prec_type/mona_inchikey_all_FP.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/mona_inchikey_all_FP.yml -------------------------------------------------------------------------------- /config/all_prec_type/mona_inchikey_all_MF.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/mona_inchikey_all_MF.yml -------------------------------------------------------------------------------- /config/all_prec_type/mona_inchikey_all_WLN.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/mona_inchikey_all_WLN.yml -------------------------------------------------------------------------------- /config/all_prec_type/mona_scaffold_all_CFM.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/mona_scaffold_all_CFM.yml -------------------------------------------------------------------------------- /config/all_prec_type/mona_scaffold_all_FP.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/mona_scaffold_all_FP.yml -------------------------------------------------------------------------------- /config/all_prec_type/mona_scaffold_all_MF.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/mona_scaffold_all_MF.yml -------------------------------------------------------------------------------- /config/all_prec_type/mona_scaffold_all_WLN.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/mona_scaffold_all_WLN.yml -------------------------------------------------------------------------------- /config/all_prec_type/nist_inchikey_all_CFM.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/nist_inchikey_all_CFM.yml -------------------------------------------------------------------------------- /config/all_prec_type/nist_inchikey_all_FP.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/nist_inchikey_all_FP.yml -------------------------------------------------------------------------------- /config/all_prec_type/nist_inchikey_all_MF.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/nist_inchikey_all_MF.yml -------------------------------------------------------------------------------- /config/all_prec_type/nist_inchikey_all_WLN.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/nist_inchikey_all_WLN.yml -------------------------------------------------------------------------------- /config/all_prec_type/nist_scaffold_all_CFM.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/nist_scaffold_all_CFM.yml -------------------------------------------------------------------------------- /config/all_prec_type/nist_scaffold_all_FP.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/nist_scaffold_all_FP.yml -------------------------------------------------------------------------------- /config/all_prec_type/nist_scaffold_all_MF.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/nist_scaffold_all_MF.yml -------------------------------------------------------------------------------- /config/all_prec_type/nist_scaffold_all_WLN.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/all_prec_type/nist_scaffold_all_WLN.yml -------------------------------------------------------------------------------- /config/casmi/casmi_CFM.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/casmi/casmi_CFM.yml -------------------------------------------------------------------------------- /config/casmi/casmi_FP.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/casmi/casmi_FP.yml -------------------------------------------------------------------------------- /config/casmi/casmi_MF.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/casmi/casmi_MF.yml -------------------------------------------------------------------------------- /config/casmi/casmi_WLN.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/casmi/casmi_WLN.yml -------------------------------------------------------------------------------- /config/checkpoint_example/checkpoint_example.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/checkpoint_example/checkpoint_example.yml -------------------------------------------------------------------------------- /config/demo/demo_eval.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/demo/demo_eval.yml -------------------------------------------------------------------------------- /config/demo/demo_train.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/demo/demo_train.yml -------------------------------------------------------------------------------- /config/mh_prec_type/mona_inchikey_mh_CFM.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/mona_inchikey_mh_CFM.yml -------------------------------------------------------------------------------- /config/mh_prec_type/mona_inchikey_mh_FP.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/mona_inchikey_mh_FP.yml -------------------------------------------------------------------------------- /config/mh_prec_type/mona_inchikey_mh_MF.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/mona_inchikey_mh_MF.yml -------------------------------------------------------------------------------- /config/mh_prec_type/mona_inchikey_mh_WLN.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/mona_inchikey_mh_WLN.yml -------------------------------------------------------------------------------- /config/mh_prec_type/mona_scaffold_mh_CFM.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/mona_scaffold_mh_CFM.yml -------------------------------------------------------------------------------- /config/mh_prec_type/mona_scaffold_mh_FP.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/mona_scaffold_mh_FP.yml -------------------------------------------------------------------------------- /config/mh_prec_type/mona_scaffold_mh_MF.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/mona_scaffold_mh_MF.yml -------------------------------------------------------------------------------- /config/mh_prec_type/mona_scaffold_mh_WLN.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/mona_scaffold_mh_WLN.yml -------------------------------------------------------------------------------- /config/mh_prec_type/nist_inchikey_mh_CFM.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/nist_inchikey_mh_CFM.yml -------------------------------------------------------------------------------- /config/mh_prec_type/nist_inchikey_mh_CFM_hr.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/nist_inchikey_mh_CFM_hr.yml -------------------------------------------------------------------------------- /config/mh_prec_type/nist_inchikey_mh_ESP.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/nist_inchikey_mh_ESP.yml -------------------------------------------------------------------------------- /config/mh_prec_type/nist_inchikey_mh_ESP_og.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/nist_inchikey_mh_ESP_og.yml -------------------------------------------------------------------------------- /config/mh_prec_type/nist_inchikey_mh_FP.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/nist_inchikey_mh_FP.yml -------------------------------------------------------------------------------- /config/mh_prec_type/nist_inchikey_mh_FP_hr.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/nist_inchikey_mh_FP_hr.yml -------------------------------------------------------------------------------- /config/mh_prec_type/nist_inchikey_mh_MF.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/nist_inchikey_mh_MF.yml -------------------------------------------------------------------------------- /config/mh_prec_type/nist_inchikey_mh_MF_hr.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/nist_inchikey_mh_MF_hr.yml -------------------------------------------------------------------------------- /config/mh_prec_type/nist_inchikey_mh_WLN.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/nist_inchikey_mh_WLN.yml -------------------------------------------------------------------------------- /config/mh_prec_type/nist_inchikey_mh_WLN_hr.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/nist_inchikey_mh_WLN_hr.yml -------------------------------------------------------------------------------- /config/mh_prec_type/nist_scaffold_mh_CFM.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/nist_scaffold_mh_CFM.yml -------------------------------------------------------------------------------- /config/mh_prec_type/nist_scaffold_mh_FP.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/nist_scaffold_mh_FP.yml -------------------------------------------------------------------------------- /config/mh_prec_type/nist_scaffold_mh_MF.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/nist_scaffold_mh_MF.yml -------------------------------------------------------------------------------- /config/mh_prec_type/nist_scaffold_mh_WLN.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/mh_prec_type/nist_scaffold_mh_WLN.yml -------------------------------------------------------------------------------- /config/template.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/template.yml -------------------------------------------------------------------------------- /config/train_both/train_both_all_MF.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/train_both/train_both_all_MF.yml -------------------------------------------------------------------------------- /config/train_both/train_both_all_MF_hr.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/train_both/train_both_all_MF_hr.yml -------------------------------------------------------------------------------- /config/train_both/train_both_mh_MF.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/train_both/train_both_mh_MF.yml -------------------------------------------------------------------------------- /config/train_both/train_both_mh_MF_hr.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/config/train_both/train_both_mh_MF_hr.yml -------------------------------------------------------------------------------- /data/cfm/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/df/.gitignore: -------------------------------------------------------------------------------- 1 | !.gitignore -------------------------------------------------------------------------------- /data/proc/.gitignore: -------------------------------------------------------------------------------- 1 | !.gitignore -------------------------------------------------------------------------------- /data/raw/.gitignore: -------------------------------------------------------------------------------- 1 | !.gitignore -------------------------------------------------------------------------------- /download_scripts/download_casmi_2016_proc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/download_scripts/download_casmi_2016_proc.sh -------------------------------------------------------------------------------- /download_scripts/download_casmi_2022_proc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/download_scripts/download_casmi_2022_proc.sh -------------------------------------------------------------------------------- /download_scripts/download_casmi_raw.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/download_scripts/download_casmi_raw.sh -------------------------------------------------------------------------------- /download_scripts/download_cfm_pred.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/download_scripts/download_cfm_pred.sh -------------------------------------------------------------------------------- /download_scripts/download_demo.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/download_scripts/download_demo.sh -------------------------------------------------------------------------------- /download_scripts/download_mona_raw.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/download_scripts/download_mona_raw.sh -------------------------------------------------------------------------------- /download_scripts/download_nist20_outlier_proc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/download_scripts/download_nist20_outlier_proc.sh -------------------------------------------------------------------------------- /download_scripts/download_nist_raw.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/download_scripts/download_nist_raw.txt -------------------------------------------------------------------------------- /download_scripts/download_public.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/download_scripts/download_public.sh -------------------------------------------------------------------------------- /env/requirements-cpu.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/env/requirements-cpu.txt -------------------------------------------------------------------------------- /env/requirements-gpu.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/env/requirements-gpu.txt -------------------------------------------------------------------------------- /img/nist_export.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/img/nist_export.png -------------------------------------------------------------------------------- /licenses/CFM_LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/licenses/CFM_LICENSE -------------------------------------------------------------------------------- /licenses/GRAPHORMER_LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/licenses/GRAPHORMER_LICENSE -------------------------------------------------------------------------------- /licenses/NEIMS_LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/licenses/NEIMS_LICENSE -------------------------------------------------------------------------------- /licenses/RETROSIM_LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/licenses/RETROSIM_LICENSE -------------------------------------------------------------------------------- /predictions/example_predictions.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/predictions/example_predictions.csv -------------------------------------------------------------------------------- /predictions/example_smiles.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/predictions/example_smiles.csv -------------------------------------------------------------------------------- /preproc_scripts/mol_fix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/preproc_scripts/mol_fix.py -------------------------------------------------------------------------------- /preproc_scripts/parse_and_export.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/preproc_scripts/parse_and_export.py -------------------------------------------------------------------------------- /preproc_scripts/parse_cfm_output.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/preproc_scripts/parse_cfm_output.py -------------------------------------------------------------------------------- /preproc_scripts/prepare_casmi22_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/preproc_scripts/prepare_casmi22_data.py -------------------------------------------------------------------------------- /preproc_scripts/prepare_casmi_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/preproc_scripts/prepare_casmi_data.py -------------------------------------------------------------------------------- /preproc_scripts/prepare_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/preproc_scripts/prepare_data.py -------------------------------------------------------------------------------- /preproc_scripts/prepare_pcasmi_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/preproc_scripts/prepare_pcasmi_data.py -------------------------------------------------------------------------------- /scripts/compute_cfm_overlap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/scripts/compute_cfm_overlap.py -------------------------------------------------------------------------------- /scripts/compute_ds_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/scripts/compute_ds_stats.py -------------------------------------------------------------------------------- /scripts/compute_split_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/scripts/compute_split_stats.py -------------------------------------------------------------------------------- /scripts/compute_test_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/scripts/compute_test_metrics.py -------------------------------------------------------------------------------- /scripts/compute_test_ranks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/scripts/compute_test_ranks.py -------------------------------------------------------------------------------- /scripts/plot_legends.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/scripts/plot_legends.py -------------------------------------------------------------------------------- /scripts/plot_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/scripts/plot_metrics.py -------------------------------------------------------------------------------- /scripts/run_inference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/scripts/run_inference.py -------------------------------------------------------------------------------- /scripts/run_train_eval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/scripts/run_train_eval.py -------------------------------------------------------------------------------- /scripts/viz_preds.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/scripts/viz_preds.py -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/setup.cfg -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/setup.py -------------------------------------------------------------------------------- /src/massformer/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/__init__.py -------------------------------------------------------------------------------- /src/massformer/algos1.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/algos1.pyx -------------------------------------------------------------------------------- /src/massformer/algos2.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/algos2.pyx -------------------------------------------------------------------------------- /src/massformer/casmi_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/casmi_utils.py -------------------------------------------------------------------------------- /src/massformer/cfm_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/cfm_model.py -------------------------------------------------------------------------------- /src/massformer/data_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/data_utils.py -------------------------------------------------------------------------------- /src/massformer/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/dataset.py -------------------------------------------------------------------------------- /src/massformer/gf_data_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/gf_data_utils.py -------------------------------------------------------------------------------- /src/massformer/gf_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/gf_model.py -------------------------------------------------------------------------------- /src/massformer/het_sep_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/het_sep_utils.py -------------------------------------------------------------------------------- /src/massformer/losses.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/losses.py -------------------------------------------------------------------------------- /src/massformer/lr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/lr.py -------------------------------------------------------------------------------- /src/massformer/metric_table.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/metric_table.py -------------------------------------------------------------------------------- /src/massformer/misc_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/misc_utils.py -------------------------------------------------------------------------------- /src/massformer/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/model.py -------------------------------------------------------------------------------- /src/massformer/plot_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/plot_utils.py -------------------------------------------------------------------------------- /src/massformer/runner.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/runner.py -------------------------------------------------------------------------------- /src/massformer/spec_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Roestlab/massformer/HEAD/src/massformer/spec_utils.py --------------------------------------------------------------------------------