├── .gitignore ├── LICENSE.txt ├── README.md ├── analysis └── model_comparison.py ├── baselines ├── diffdock.py └── vina_gnina.py ├── common ├── __init__.py ├── cache.py ├── cfg_utils.py ├── old_routine.py ├── plot_metrics.py ├── plotting_utils.py ├── pose_transform.py ├── torsion.py ├── utils.py └── wandb_utils.py ├── configs └── icml.yaml ├── create_env.sh ├── data ├── cur_best.pt ├── dummy_rec.pdb ├── plantain_ff.pt └── plantain_final.pt ├── data_formats ├── graphs │ ├── __init__.py │ ├── dist_edge.py │ ├── graph3d.py │ ├── interaction_graph.py │ ├── knn.py │ ├── mol_graph.py │ ├── plot_graph.py │ └── prot_graph.py ├── tasks.py └── transforms.py ├── datasets ├── base_datasets.py ├── combo_dataloader.py ├── crossdocked.py ├── inference_dataset.py ├── make_dataset.py ├── samplers.py └── utils.py ├── dev_requirements.txt ├── inference.py ├── models ├── attention_gnn.py ├── cat_scal_embedding.py ├── diffdock.py ├── force_field.py ├── gnina.py ├── gnina_combo.py ├── graph_embedding.py ├── make_model.py ├── model.py ├── plantain.py ├── pretrained_plantain.py ├── twister.py └── vina.py ├── outputs └── .gitkeep ├── prior_work └── gnina │ ├── completelig │ ├── completerec │ ├── default2018.model │ ├── it2_cd_retrain_DEF2018_s0.0_iter_1354000.caffemodel │ ├── it2_cd_retrain_DEF2018_s0.1_iter_1532000.caffemodel │ ├── it2_cd_retrain_DEF2018_s1.0_iter_2149000.caffemodel │ ├── it2_cd_retrain_DEF2018_s1.1_iter_1518000.caffemodel │ ├── it2_cd_retrain_DEF2018_s2.0_iter_1085000.caffemodel │ ├── it2_cd_retrain_DEF2018_s2.1_iter_1278000.caffemodel │ ├── it2_cd_retrain_DEF2018_s3.0_iter_1728000.caffemodel │ ├── it2_cd_retrain_DEF2018_s3.1_iter_1856000.caffemodel │ ├── it2_cd_retrain_DEF2018_s4.0_iter_1096000.caffemodel │ └── it2_cd_retrain_DEF2018_s4.1_iter_1875000.caffemodel ├── requirements.txt ├── scripts ├── benchmark.py ├── bug.py ├── dock_crossdocked.py ├── ff_bigbind_struct.py ├── make_animation.py ├── profile.py ├── test_diff_v3.py ├── twist_block_test.py └── view.py ├── train.py ├── training ├── loss.py └── trainer.py └── validation ├── metrics.py ├── screen.py ├── val_plots.py └── validate.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/README.md -------------------------------------------------------------------------------- /analysis/model_comparison.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/analysis/model_comparison.py -------------------------------------------------------------------------------- /baselines/diffdock.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/baselines/diffdock.py -------------------------------------------------------------------------------- /baselines/vina_gnina.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/baselines/vina_gnina.py -------------------------------------------------------------------------------- /common/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /common/cache.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/common/cache.py -------------------------------------------------------------------------------- /common/cfg_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/common/cfg_utils.py -------------------------------------------------------------------------------- /common/old_routine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/common/old_routine.py -------------------------------------------------------------------------------- /common/plot_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/common/plot_metrics.py -------------------------------------------------------------------------------- /common/plotting_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/common/plotting_utils.py -------------------------------------------------------------------------------- /common/pose_transform.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/common/pose_transform.py -------------------------------------------------------------------------------- /common/torsion.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/common/torsion.py -------------------------------------------------------------------------------- /common/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/common/utils.py -------------------------------------------------------------------------------- /common/wandb_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/common/wandb_utils.py -------------------------------------------------------------------------------- /configs/icml.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/configs/icml.yaml -------------------------------------------------------------------------------- /create_env.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/create_env.sh -------------------------------------------------------------------------------- /data/cur_best.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/data/cur_best.pt -------------------------------------------------------------------------------- /data/dummy_rec.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/data/dummy_rec.pdb -------------------------------------------------------------------------------- /data/plantain_ff.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/data/plantain_ff.pt -------------------------------------------------------------------------------- /data/plantain_final.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/data/plantain_final.pt -------------------------------------------------------------------------------- /data_formats/graphs/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data_formats/graphs/dist_edge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/data_formats/graphs/dist_edge.py -------------------------------------------------------------------------------- /data_formats/graphs/graph3d.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/data_formats/graphs/graph3d.py -------------------------------------------------------------------------------- /data_formats/graphs/interaction_graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/data_formats/graphs/interaction_graph.py -------------------------------------------------------------------------------- /data_formats/graphs/knn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/data_formats/graphs/knn.py -------------------------------------------------------------------------------- /data_formats/graphs/mol_graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/data_formats/graphs/mol_graph.py -------------------------------------------------------------------------------- /data_formats/graphs/plot_graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/data_formats/graphs/plot_graph.py -------------------------------------------------------------------------------- /data_formats/graphs/prot_graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/data_formats/graphs/prot_graph.py -------------------------------------------------------------------------------- /data_formats/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/data_formats/tasks.py -------------------------------------------------------------------------------- /data_formats/transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/data_formats/transforms.py -------------------------------------------------------------------------------- /datasets/base_datasets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/datasets/base_datasets.py -------------------------------------------------------------------------------- /datasets/combo_dataloader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/datasets/combo_dataloader.py -------------------------------------------------------------------------------- /datasets/crossdocked.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/datasets/crossdocked.py -------------------------------------------------------------------------------- /datasets/inference_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/datasets/inference_dataset.py -------------------------------------------------------------------------------- /datasets/make_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/datasets/make_dataset.py -------------------------------------------------------------------------------- /datasets/samplers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/datasets/samplers.py -------------------------------------------------------------------------------- /datasets/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/datasets/utils.py -------------------------------------------------------------------------------- /dev_requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/dev_requirements.txt -------------------------------------------------------------------------------- /inference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/inference.py -------------------------------------------------------------------------------- /models/attention_gnn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/models/attention_gnn.py -------------------------------------------------------------------------------- /models/cat_scal_embedding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/models/cat_scal_embedding.py -------------------------------------------------------------------------------- /models/diffdock.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/models/diffdock.py -------------------------------------------------------------------------------- /models/force_field.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/models/force_field.py -------------------------------------------------------------------------------- /models/gnina.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/models/gnina.py -------------------------------------------------------------------------------- /models/gnina_combo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/models/gnina_combo.py -------------------------------------------------------------------------------- /models/graph_embedding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/models/graph_embedding.py -------------------------------------------------------------------------------- /models/make_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/models/make_model.py -------------------------------------------------------------------------------- /models/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/models/model.py -------------------------------------------------------------------------------- /models/plantain.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/models/plantain.py -------------------------------------------------------------------------------- /models/pretrained_plantain.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/models/pretrained_plantain.py -------------------------------------------------------------------------------- /models/twister.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/models/twister.py -------------------------------------------------------------------------------- /models/vina.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/models/vina.py -------------------------------------------------------------------------------- /outputs/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /prior_work/gnina/completelig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/prior_work/gnina/completelig -------------------------------------------------------------------------------- /prior_work/gnina/completerec: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/prior_work/gnina/completerec -------------------------------------------------------------------------------- /prior_work/gnina/default2018.model: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/prior_work/gnina/default2018.model -------------------------------------------------------------------------------- /prior_work/gnina/it2_cd_retrain_DEF2018_s0.0_iter_1354000.caffemodel: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/prior_work/gnina/it2_cd_retrain_DEF2018_s0.0_iter_1354000.caffemodel -------------------------------------------------------------------------------- /prior_work/gnina/it2_cd_retrain_DEF2018_s0.1_iter_1532000.caffemodel: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/prior_work/gnina/it2_cd_retrain_DEF2018_s0.1_iter_1532000.caffemodel -------------------------------------------------------------------------------- /prior_work/gnina/it2_cd_retrain_DEF2018_s1.0_iter_2149000.caffemodel: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/prior_work/gnina/it2_cd_retrain_DEF2018_s1.0_iter_2149000.caffemodel -------------------------------------------------------------------------------- /prior_work/gnina/it2_cd_retrain_DEF2018_s1.1_iter_1518000.caffemodel: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/prior_work/gnina/it2_cd_retrain_DEF2018_s1.1_iter_1518000.caffemodel -------------------------------------------------------------------------------- /prior_work/gnina/it2_cd_retrain_DEF2018_s2.0_iter_1085000.caffemodel: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/prior_work/gnina/it2_cd_retrain_DEF2018_s2.0_iter_1085000.caffemodel -------------------------------------------------------------------------------- /prior_work/gnina/it2_cd_retrain_DEF2018_s2.1_iter_1278000.caffemodel: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/prior_work/gnina/it2_cd_retrain_DEF2018_s2.1_iter_1278000.caffemodel -------------------------------------------------------------------------------- /prior_work/gnina/it2_cd_retrain_DEF2018_s3.0_iter_1728000.caffemodel: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/prior_work/gnina/it2_cd_retrain_DEF2018_s3.0_iter_1728000.caffemodel -------------------------------------------------------------------------------- /prior_work/gnina/it2_cd_retrain_DEF2018_s3.1_iter_1856000.caffemodel: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/prior_work/gnina/it2_cd_retrain_DEF2018_s3.1_iter_1856000.caffemodel -------------------------------------------------------------------------------- /prior_work/gnina/it2_cd_retrain_DEF2018_s4.0_iter_1096000.caffemodel: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/prior_work/gnina/it2_cd_retrain_DEF2018_s4.0_iter_1096000.caffemodel -------------------------------------------------------------------------------- /prior_work/gnina/it2_cd_retrain_DEF2018_s4.1_iter_1875000.caffemodel: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/prior_work/gnina/it2_cd_retrain_DEF2018_s4.1_iter_1875000.caffemodel -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/requirements.txt -------------------------------------------------------------------------------- /scripts/benchmark.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/scripts/benchmark.py -------------------------------------------------------------------------------- /scripts/bug.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/scripts/bug.py -------------------------------------------------------------------------------- /scripts/dock_crossdocked.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/scripts/dock_crossdocked.py -------------------------------------------------------------------------------- /scripts/ff_bigbind_struct.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/scripts/ff_bigbind_struct.py -------------------------------------------------------------------------------- /scripts/make_animation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/scripts/make_animation.py -------------------------------------------------------------------------------- /scripts/profile.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/scripts/profile.py -------------------------------------------------------------------------------- /scripts/test_diff_v3.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/scripts/test_diff_v3.py -------------------------------------------------------------------------------- /scripts/twist_block_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/scripts/twist_block_test.py -------------------------------------------------------------------------------- /scripts/view.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/scripts/view.py -------------------------------------------------------------------------------- /train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/train.py -------------------------------------------------------------------------------- /training/loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/training/loss.py -------------------------------------------------------------------------------- /training/trainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/training/trainer.py -------------------------------------------------------------------------------- /validation/metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/validation/metrics.py -------------------------------------------------------------------------------- /validation/screen.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/validation/screen.py -------------------------------------------------------------------------------- /validation/val_plots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/validation/val_plots.py -------------------------------------------------------------------------------- /validation/validate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molecularmodelinglab/plantain/HEAD/validation/validate.py --------------------------------------------------------------------------------