LICENSE
README.md
pyproject.toml
setup.py
src/MolecularDiffusion/__init__.py
src/MolecularDiffusion/_version.py
src/MolecularDiffusion/molcraftdiff.py
src/MolecularDiffusion/callbacks/__init__.py
src/MolecularDiffusion/callbacks/train_helper.py
src/MolecularDiffusion/cli/__init__.py
src/MolecularDiffusion/cli/_hydra.py
src/MolecularDiffusion/cli/analyze.py
src/MolecularDiffusion/cli/data.py
src/MolecularDiffusion/cli/eval_predict.py
src/MolecularDiffusion/cli/generate.py
src/MolecularDiffusion/cli/main.py
src/MolecularDiffusion/cli/predict.py
src/MolecularDiffusion/cli/train.py
src/MolecularDiffusion/configs/data/formed_data.yaml
src/MolecularDiffusion/configs/data/mol_dataset.yaml
src/MolecularDiffusion/configs/data/mol_dataset_extraf.yaml
src/MolecularDiffusion/configs/data/pharmacophore_dataset.yaml
src/MolecularDiffusion/configs/engine/original.yaml
src/MolecularDiffusion/configs/hydra/default.yaml
src/MolecularDiffusion/configs/interference/gen_cfg.yaml
src/MolecularDiffusion/configs/interference/gen_cfggg.yaml
src/MolecularDiffusion/configs/interference/gen_conditional.yaml
src/MolecularDiffusion/configs/interference/gen_gg.yaml
src/MolecularDiffusion/configs/interference/gen_hybrid.yaml
src/MolecularDiffusion/configs/interference/gen_inpaint.yaml
src/MolecularDiffusion/configs/interference/gen_outpaint.yaml
src/MolecularDiffusion/configs/interference/gen_outpaintft.yaml
src/MolecularDiffusion/configs/interference/gen_unconditional.yaml
src/MolecularDiffusion/configs/interference/pharm_condition.yaml
src/MolecularDiffusion/configs/interference/pharm_from_intermediate.yaml
src/MolecularDiffusion/configs/interference/pharm_inpaint.yaml
src/MolecularDiffusion/configs/interference/pharm_shape_conditioned.yaml
src/MolecularDiffusion/configs/interference/pharm_unconditional.yaml
src/MolecularDiffusion/configs/interference/prediction.yaml
src/MolecularDiffusion/configs/logger/default.yaml
src/MolecularDiffusion/configs/logger/wandb.yaml
src/MolecularDiffusion/configs/tasks/diffusion.yaml
src/MolecularDiffusion/configs/tasks/diffusion_adit.yaml
src/MolecularDiffusion/configs/tasks/diffusion_egt.yaml
src/MolecularDiffusion/configs/tasks/diffusion_extraf.yaml
src/MolecularDiffusion/configs/tasks/diffusion_pretrained.yaml
src/MolecularDiffusion/configs/tasks/diffusion_tabasco.yaml
src/MolecularDiffusion/configs/tasks/guidance.yaml
src/MolecularDiffusion/configs/tasks/pharmacophore.yaml
src/MolecularDiffusion/configs/tasks/regression.yaml
src/MolecularDiffusion/configs/tasks/vae_equiformer.yaml
src/MolecularDiffusion/configs/tasks/vae_transformer.yaml
src/MolecularDiffusion/configs/trainer/default.yaml
src/MolecularDiffusion/configs/trainer/regression.yaml
src/MolecularDiffusion/core/__init__.py
src/MolecularDiffusion/core/core.py
src/MolecularDiffusion/core/engine.py
src/MolecularDiffusion/core/logger.py
src/MolecularDiffusion/core/meter.py
src/MolecularDiffusion/data/__init__.py
src/MolecularDiffusion/data/dataloader.py
src/MolecularDiffusion/data/dataset.py
src/MolecularDiffusion/data/component/__init__.py
src/MolecularDiffusion/data/component/dataset.py
src/MolecularDiffusion/data/component/feature.py
src/MolecularDiffusion/data/component/pharmacophore.py
src/MolecularDiffusion/data/component/pointcloud.py
src/MolecularDiffusion/data/valency_tables/__init__.py
src/MolecularDiffusion/data/valency_tables/geom_drugs_h_tuple_valencies.json
src/MolecularDiffusion/data/valency_tables/legacy_valencies.json
src/MolecularDiffusion/data/valency_tables/legacy_valency_schema.json
src/MolecularDiffusion/data/valency_tables/valency_schema.json
src/MolecularDiffusion/modules/layers/common.py
src/MolecularDiffusion/modules/layers/conv.py
src/MolecularDiffusion/modules/layers/functional.py
src/MolecularDiffusion/modules/layers/equiformer_v2/__init__.py
src/MolecularDiffusion/modules/layers/equiformer_v2/activation.py
src/MolecularDiffusion/modules/layers/equiformer_v2/drop.py
src/MolecularDiffusion/modules/layers/equiformer_v2/edge_rot_mat.py
src/MolecularDiffusion/modules/layers/equiformer_v2/equiformer_v2_oc20.py
src/MolecularDiffusion/modules/layers/equiformer_v2/gaussian_rbf.py
src/MolecularDiffusion/modules/layers/equiformer_v2/input_block.py
src/MolecularDiffusion/modules/layers/equiformer_v2/layer_norm.py
src/MolecularDiffusion/modules/layers/equiformer_v2/module_list.py
src/MolecularDiffusion/modules/layers/equiformer_v2/radial_function.py
src/MolecularDiffusion/modules/layers/equiformer_v2/so2_ops.py
src/MolecularDiffusion/modules/layers/equiformer_v2/so3.py
src/MolecularDiffusion/modules/layers/equiformer_v2/transformer_block.py
src/MolecularDiffusion/modules/layers/equiformer_v2/wigner.py
src/MolecularDiffusion/modules/layers/equiformer_v2_s/__init__.py
src/MolecularDiffusion/modules/layers/equiformer_v2_s/activation.py
src/MolecularDiffusion/modules/layers/equiformer_v2_s/drop.py
src/MolecularDiffusion/modules/layers/equiformer_v2_s/edge_rot_mat.py
src/MolecularDiffusion/modules/layers/equiformer_v2_s/equiformer_v2_oc20.py
src/MolecularDiffusion/modules/layers/equiformer_v2_s/gaussian_rbf.py
src/MolecularDiffusion/modules/layers/equiformer_v2_s/input_block.py
src/MolecularDiffusion/modules/layers/equiformer_v2_s/layer_norm.py
src/MolecularDiffusion/modules/layers/equiformer_v2_s/module_list.py
src/MolecularDiffusion/modules/layers/equiformer_v2_s/radial_function.py
src/MolecularDiffusion/modules/layers/equiformer_v2_s/so2_ops.py
src/MolecularDiffusion/modules/layers/equiformer_v2_s/so3.py
src/MolecularDiffusion/modules/layers/equiformer_v2_s/transformer_block.py
src/MolecularDiffusion/modules/layers/equiformer_v2_s/wigner.py
src/MolecularDiffusion/modules/layers/tabasco/__init__.py
src/MolecularDiffusion/modules/layers/tabasco/attention.py
src/MolecularDiffusion/modules/layers/tabasco/common.py
src/MolecularDiffusion/modules/layers/tabasco/losses.py
src/MolecularDiffusion/modules/layers/tabasco/positional_encoder.py
src/MolecularDiffusion/modules/layers/tabasco/transformer.py
src/MolecularDiffusion/modules/layers/tabasco/transformer_module.py
src/MolecularDiffusion/modules/layers/tabasco/transition.py
src/MolecularDiffusion/modules/models/__init__.py
src/MolecularDiffusion/modules/models/egcl.py
src/MolecularDiffusion/modules/models/egt.py
src/MolecularDiffusion/modules/models/en_diffusion.py
src/MolecularDiffusion/modules/models/noisemodel.py
src/MolecularDiffusion/modules/models/pharmacophore_dynamics.py
src/MolecularDiffusion/modules/models/ldm/__init__.py
src/MolecularDiffusion/modules/models/ldm/decoders/__init__.py
src/MolecularDiffusion/modules/models/ldm/decoders/equivariant_feedforward.py
src/MolecularDiffusion/modules/models/ldm/decoders/transformer.py
src/MolecularDiffusion/modules/models/ldm/denoisers/__init__.py
src/MolecularDiffusion/modules/models/ldm/denoisers/dit.py
src/MolecularDiffusion/modules/models/ldm/encoders/__init__.py
src/MolecularDiffusion/modules/models/ldm/encoders/equiformer.py
src/MolecularDiffusion/modules/models/ldm/encoders/transformer.py
src/MolecularDiffusion/modules/models/shepherd_arch/__init__.py
src/MolecularDiffusion/modules/models/shepherd_arch/egnn.py
src/MolecularDiffusion/modules/models/shepherd_arch/equiformer_operations.py
src/MolecularDiffusion/modules/models/shepherd_arch/equiformer_v2_encoder.py
src/MolecularDiffusion/modules/models/shepherd_arch/model.py
src/MolecularDiffusion/modules/models/shepherd_arch/ocp_compat.py
src/MolecularDiffusion/modules/models/shepherd_arch/utils.py
src/MolecularDiffusion/modules/models/shepherd_arch/inference/__init__.py
src/MolecularDiffusion/modules/models/shepherd_arch/inference/initialization.py
src/MolecularDiffusion/modules/models/shepherd_arch/inference/noise.py
src/MolecularDiffusion/modules/models/shepherd_arch/inference/sampler.py
src/MolecularDiffusion/modules/models/shepherd_arch/inference/steps.py
src/MolecularDiffusion/modules/models/tabasco/__init__.py
src/MolecularDiffusion/modules/models/tabasco/flow_model.py
src/MolecularDiffusion/modules/models/tabasco/lightning_tabasco.py
src/MolecularDiffusion/modules/models/tabasco/callbacks/__init__.py
src/MolecularDiffusion/modules/models/tabasco/callbacks/dataset_stats.py
src/MolecularDiffusion/modules/models/tabasco/callbacks/ema.py
src/MolecularDiffusion/modules/models/tabasco/callbacks/molecule_metrics.py
src/MolecularDiffusion/modules/models/tabasco/callbacks/posebusters.py
src/MolecularDiffusion/modules/models/tabasco/callbacks/save_molecules.py
src/MolecularDiffusion/modules/models/tabasco/chem/__init__.py
src/MolecularDiffusion/modules/models/tabasco/chem/constants.py
src/MolecularDiffusion/modules/models/tabasco/chem/convert.py
src/MolecularDiffusion/modules/models/tabasco/chem/utils.py
src/MolecularDiffusion/modules/models/tabasco/data/__init__.py
src/MolecularDiffusion/modules/models/tabasco/data/lmdb_datamodule.py
src/MolecularDiffusion/modules/models/tabasco/data/transforms.py
src/MolecularDiffusion/modules/models/tabasco/data/utils.py
src/MolecularDiffusion/modules/models/tabasco/data/components/__init__.py
src/MolecularDiffusion/modules/models/tabasco/data/components/lmdb_base.py
src/MolecularDiffusion/modules/models/tabasco/data/components/lmdb_unconditional.py
src/MolecularDiffusion/modules/models/tabasco/flow/__init__.py
src/MolecularDiffusion/modules/models/tabasco/flow/interpolate.py
src/MolecularDiffusion/modules/models/tabasco/flow/path.py
src/MolecularDiffusion/modules/models/tabasco/flow/time_factor.py
src/MolecularDiffusion/modules/models/tabasco/flow/utils.py
src/MolecularDiffusion/modules/models/tabasco/sample/__init__.py
src/MolecularDiffusion/modules/models/tabasco/sample/guided_sampling.py
src/MolecularDiffusion/modules/models/tabasco/sample/interpolant_guidance.py
src/MolecularDiffusion/modules/models/tabasco/sample/noise_schedule.py
src/MolecularDiffusion/modules/models/tabasco/utils/__init__.py
src/MolecularDiffusion/modules/models/tabasco/utils/artifacts.py
src/MolecularDiffusion/modules/models/tabasco/utils/instantiators.py
src/MolecularDiffusion/modules/models/tabasco/utils/metric_utils.py
src/MolecularDiffusion/modules/models/tabasco/utils/metrics.py
src/MolecularDiffusion/modules/models/tabasco/utils/pylogger.py
src/MolecularDiffusion/modules/models/tabasco/utils/rich_utils.py
src/MolecularDiffusion/modules/models/tabasco/utils/tensor_ops.py
src/MolecularDiffusion/modules/models/tabasco/utils/utils.py
src/MolecularDiffusion/modules/tasks/__init__.py
src/MolecularDiffusion/modules/tasks/diffusion.py
src/MolecularDiffusion/modules/tasks/diffusion_ldm.py
src/MolecularDiffusion/modules/tasks/diffusion_tabasco.py
src/MolecularDiffusion/modules/tasks/metrics.py
src/MolecularDiffusion/modules/tasks/pharmacophore.py
src/MolecularDiffusion/modules/tasks/regression.py
src/MolecularDiffusion/modules/tasks/task.py
src/MolecularDiffusion/runmodes/__init__.py
src/MolecularDiffusion/runmodes/analyze/__init__.py
src/MolecularDiffusion/runmodes/analyze/compare_to_optimized.py
src/MolecularDiffusion/runmodes/analyze/compute_metrics.py
src/MolecularDiffusion/runmodes/analyze/xtb_electronic.py
src/MolecularDiffusion/runmodes/analyze/xtb_optimization.py
src/MolecularDiffusion/runmodes/analyze/xyz2mol.py
src/MolecularDiffusion/runmodes/data/ase_ops.py
src/MolecularDiffusion/runmodes/data/augmentation.py
src/MolecularDiffusion/runmodes/data/featurization.py
src/MolecularDiffusion/runmodes/data/preparation.py
src/MolecularDiffusion/runmodes/generate/__init__.py
src/MolecularDiffusion/runmodes/generate/tasks_generate.py
src/MolecularDiffusion/runmodes/train/__init__.py
src/MolecularDiffusion/runmodes/train/data.py
src/MolecularDiffusion/runmodes/train/eval.py
src/MolecularDiffusion/runmodes/train/logger.py
src/MolecularDiffusion/runmodes/train/tasks_egcl.py
src/MolecularDiffusion/runmodes/train/tasks_egt.py
src/MolecularDiffusion/runmodes/train/trainer.py
src/MolecularDiffusion/utils/__init__.py
src/MolecularDiffusion/utils/comm.py
src/MolecularDiffusion/utils/diffusion_utils.py
src/MolecularDiffusion/utils/file.py
src/MolecularDiffusion/utils/geom_analyzer.py
src/MolecularDiffusion/utils/geom_constant.py
src/MolecularDiffusion/utils/geom_constraint.py
src/MolecularDiffusion/utils/geom_metrics.py
src/MolecularDiffusion/utils/geom_stability.py
src/MolecularDiffusion/utils/geom_utils.py
src/MolecularDiffusion/utils/io.py
src/MolecularDiffusion/utils/molgraph_utils.py
src/MolecularDiffusion/utils/plot_function.py
src/MolecularDiffusion/utils/pretty.py
src/MolecularDiffusion/utils/sascore.py
src/MolecularDiffusion/utils/shepherd_utils.py
src/MolecularDiffusion/utils/smilify.py
src/MolecularDiffusion/utils/torch.py
src/MolecularDiffusion/utils/shepherd_score/__init__.py
src/MolecularDiffusion/utils/shepherd_score/extract_profiles.py
src/MolecularDiffusion/utils/shepherd_score/generate_point_cloud.py
src/MolecularDiffusion/utils/shepherd_score/alignment/__init__.py
src/MolecularDiffusion/utils/shepherd_score/alignment/_torch.py
src/MolecularDiffusion/utils/shepherd_score/alignment/_torch_analytical.py
src/MolecularDiffusion/utils/shepherd_score/alignment/utils/__init__.py
src/MolecularDiffusion/utils/shepherd_score/alignment/utils/pca.py
src/MolecularDiffusion/utils/shepherd_score/alignment/utils/pca_np.py
src/MolecularDiffusion/utils/shepherd_score/alignment/utils/se3.py
src/MolecularDiffusion/utils/shepherd_score/alignment/utils/se3_np.py
src/MolecularDiffusion/utils/shepherd_score/pharm_utils/__init__.py
src/MolecularDiffusion/utils/shepherd_score/pharm_utils/pharmacophore.py
src/MolecularDiffusion/utils/shepherd_score/pharm_utils/pharmvec.py
src/MolecularDiffusion/utils/shepherd_score/score/__init__.py
src/MolecularDiffusion/utils/shepherd_score/score/constants.py
src/MolecularDiffusion/utils/shepherd_score/score/electrostatic_scoring.py
src/MolecularDiffusion/utils/shepherd_score/score/electrostatic_scoring_np.py
src/MolecularDiffusion/utils/shepherd_score/score/gaussian_overlap.py
src/MolecularDiffusion/utils/shepherd_score/score/gaussian_overlap_np.py
src/MolecularDiffusion/utils/shepherd_score/score/pharmacophore_scoring.py
src/MolecularDiffusion/utils/shepherd_score/score/pharmacophore_scoring_np.py
src/MolecularDiffusion/utils/shepherd_score/score/analytical_gradients/__init__.py
src/MolecularDiffusion/utils/shepherd_score/score/analytical_gradients/_torch.py
src/MolecularDiffusion/utils/xyz2mol/__init__.py
src/MolecularDiffusion/utils/xyz2mol/converter.py
src/MolecularDiffusion/utils/xyz2mol/elements.py
src/molcraftdiffusion.egg-info/PKG-INFO
src/molcraftdiffusion.egg-info/SOURCES.txt
src/molcraftdiffusion.egg-info/dependency_links.txt
src/molcraftdiffusion.egg-info/entry_points.txt
src/molcraftdiffusion.egg-info/requires.txt
src/molcraftdiffusion.egg-info/top_level.txt
tests/test_import.py