├── .flake8 ├── .gitignore ├── .gitmodules ├── .mypy.ini ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── assets └── animate.gif ├── bin └── .gitignore ├── chemprojector ├── __init__.py ├── chem │ ├── __init__.py │ ├── base.py │ ├── featurize.py │ ├── fpindex.py │ ├── matrix.py │ ├── mol.py │ ├── reaction.py │ ├── smiles_vocab.txt │ └── stack.py ├── data │ ├── __init__.py │ ├── collate.py │ ├── common.py │ ├── projection_dataset.py │ └── projection_dataset_old.py ├── models │ ├── __init__.py │ ├── chemprojector.py │ ├── decoder.py │ ├── encoder.py │ ├── old │ │ ├── __init__.py │ │ ├── projector.py │ │ └── projector_wrapper.py │ ├── output_head.py │ ├── transformer │ │ ├── __init__.py │ │ ├── graph_transformer.py │ │ ├── positional_encoding.py │ │ └── rotary_embedding.py │ └── wrapper.py ├── sampler │ ├── __init__.py │ ├── cli.py │ ├── old │ │ ├── __init__.py │ │ ├── cli.py │ │ ├── parallel.py │ │ └── state_pool.py │ ├── parallel.py │ └── state_pool.py ├── tools │ ├── __init__.py │ ├── crypt.py │ ├── docking.py │ ├── guacamol.py │ └── pocket2mol.py └── utils │ ├── __init__.py │ ├── image.py │ ├── misc.py │ ├── tqdm_joblib.py │ ├── train.py │ └── vc.py ├── configs ├── old │ ├── default.yml │ └── split.yml ├── original_default.yml └── original_split.yml ├── data ├── .gitignore ├── example.csv ├── goal_directed │ └── goal_hard_cwo.csv ├── hit_expansion │ └── hit.smi ├── processed.key ├── reaction_templates_hb.txt ├── sbdd │ ├── pocket2mol.csv │ └── receptors │ │ ├── ADRB2 │ │ ├── description.yaml │ │ └── receptor.pdbqt │ │ ├── ALDH1 │ │ ├── description.yaml │ │ └── receptor.pdbqt │ │ ├── ESR1_ago │ │ ├── description.yaml │ │ └── receptor.pdbqt │ │ ├── ESR1_ant │ │ ├── description.yaml │ │ └── receptor.pdbqt │ │ ├── FEN1 │ │ ├── description.yaml │ │ └── receptor.pdbqt │ │ ├── GBA │ │ ├── description.yaml │ │ └── receptor.pdbqt │ │ ├── IDH1 │ │ ├── description.yaml │ │ └── receptor.pdbqt │ │ ├── KAT2A │ │ ├── description.yaml │ │ └── receptor.pdbqt │ │ ├── MAPK1 │ │ ├── description.yaml │ │ └── receptor.pdbqt │ │ ├── MTORC1 │ │ ├── description.yaml │ │ └── receptor.pdbqt │ │ ├── OPRK1 │ │ ├── description.yaml │ │ └── receptor.pdbqt │ │ ├── PKM2 │ │ ├── description.yaml │ │ └── receptor.pdbqt │ │ ├── PPARG │ │ ├── description.yaml │ │ └── receptor.pdbqt │ │ ├── TP53 │ │ ├── description.yaml │ │ └── receptor.pdbqt │ │ └── VDR │ │ ├── description.yaml │ │ └── receptor.pdbqt ├── synthesis_planning │ ├── enamine_smiles_1k.csv │ ├── test_building_blocks.smi │ ├── test_chembl.csv │ └── test_synthesis.csv └── trained_weights │ └── .gitkeep ├── env.yml ├── pyproject.toml ├── sample.py ├── scripts ├── goal_directed │ ├── 00-run_chemprojector.sh │ └── 10-scoring.py ├── preprocess_data │ ├── archive_preprocessed_data.py │ ├── create_fingerprint_index.py │ ├── create_reaction_matrix.py │ ├── create_reaction_matrix_train_split.py │ └── encrypt_message.py ├── sbdd │ ├── 00-run_chemprojector.sh │ ├── 10-run_docking.py │ └── 20-summarize.py ├── synthesis_planning_chembl.sh ├── synthesis_planning_enamine.sh ├── synthesis_planning_test_split.sh ├── train_old.py └── upgrade_checkpoint.py ├── setup.py ├── third_party └── README.md ├── train.py └── unarchive_wizard.py /.flake8: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/.flake8 -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/.gitmodules -------------------------------------------------------------------------------- /.mypy.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/.mypy.ini -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/README.md -------------------------------------------------------------------------------- /assets/animate.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/assets/animate.gif -------------------------------------------------------------------------------- /bin/.gitignore: -------------------------------------------------------------------------------- 1 | * 2 | !.gitignore 3 | -------------------------------------------------------------------------------- /chemprojector/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /chemprojector/chem/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/chem/__init__.py -------------------------------------------------------------------------------- /chemprojector/chem/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/chem/base.py -------------------------------------------------------------------------------- /chemprojector/chem/featurize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/chem/featurize.py -------------------------------------------------------------------------------- /chemprojector/chem/fpindex.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/chem/fpindex.py -------------------------------------------------------------------------------- /chemprojector/chem/matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/chem/matrix.py -------------------------------------------------------------------------------- /chemprojector/chem/mol.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/chem/mol.py -------------------------------------------------------------------------------- /chemprojector/chem/reaction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/chem/reaction.py -------------------------------------------------------------------------------- /chemprojector/chem/smiles_vocab.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/chem/smiles_vocab.txt -------------------------------------------------------------------------------- /chemprojector/chem/stack.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/chem/stack.py -------------------------------------------------------------------------------- /chemprojector/data/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /chemprojector/data/collate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/data/collate.py -------------------------------------------------------------------------------- /chemprojector/data/common.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/data/common.py -------------------------------------------------------------------------------- /chemprojector/data/projection_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/data/projection_dataset.py -------------------------------------------------------------------------------- /chemprojector/data/projection_dataset_old.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/data/projection_dataset_old.py -------------------------------------------------------------------------------- /chemprojector/models/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /chemprojector/models/chemprojector.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/models/chemprojector.py -------------------------------------------------------------------------------- /chemprojector/models/decoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/models/decoder.py -------------------------------------------------------------------------------- /chemprojector/models/encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/models/encoder.py -------------------------------------------------------------------------------- /chemprojector/models/old/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /chemprojector/models/old/projector.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/models/old/projector.py -------------------------------------------------------------------------------- /chemprojector/models/old/projector_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/models/old/projector_wrapper.py -------------------------------------------------------------------------------- /chemprojector/models/output_head.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/models/output_head.py -------------------------------------------------------------------------------- /chemprojector/models/transformer/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /chemprojector/models/transformer/graph_transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/models/transformer/graph_transformer.py -------------------------------------------------------------------------------- /chemprojector/models/transformer/positional_encoding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/models/transformer/positional_encoding.py -------------------------------------------------------------------------------- /chemprojector/models/transformer/rotary_embedding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/models/transformer/rotary_embedding.py -------------------------------------------------------------------------------- /chemprojector/models/wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/models/wrapper.py -------------------------------------------------------------------------------- /chemprojector/sampler/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /chemprojector/sampler/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/sampler/cli.py -------------------------------------------------------------------------------- /chemprojector/sampler/old/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /chemprojector/sampler/old/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/sampler/old/cli.py -------------------------------------------------------------------------------- /chemprojector/sampler/old/parallel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/sampler/old/parallel.py -------------------------------------------------------------------------------- /chemprojector/sampler/old/state_pool.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/sampler/old/state_pool.py -------------------------------------------------------------------------------- /chemprojector/sampler/parallel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/sampler/parallel.py -------------------------------------------------------------------------------- /chemprojector/sampler/state_pool.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/sampler/state_pool.py -------------------------------------------------------------------------------- /chemprojector/tools/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /chemprojector/tools/crypt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/tools/crypt.py -------------------------------------------------------------------------------- /chemprojector/tools/docking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/tools/docking.py -------------------------------------------------------------------------------- /chemprojector/tools/guacamol.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/tools/guacamol.py -------------------------------------------------------------------------------- /chemprojector/tools/pocket2mol.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/tools/pocket2mol.py -------------------------------------------------------------------------------- /chemprojector/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /chemprojector/utils/image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/utils/image.py -------------------------------------------------------------------------------- /chemprojector/utils/misc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/utils/misc.py -------------------------------------------------------------------------------- /chemprojector/utils/tqdm_joblib.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/utils/tqdm_joblib.py -------------------------------------------------------------------------------- /chemprojector/utils/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/utils/train.py -------------------------------------------------------------------------------- /chemprojector/utils/vc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/chemprojector/utils/vc.py -------------------------------------------------------------------------------- /configs/old/default.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/configs/old/default.yml -------------------------------------------------------------------------------- /configs/old/split.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/configs/old/split.yml -------------------------------------------------------------------------------- /configs/original_default.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/configs/original_default.yml -------------------------------------------------------------------------------- /configs/original_split.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/configs/original_split.yml -------------------------------------------------------------------------------- /data/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/.gitignore -------------------------------------------------------------------------------- /data/example.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/example.csv -------------------------------------------------------------------------------- /data/goal_directed/goal_hard_cwo.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/goal_directed/goal_hard_cwo.csv -------------------------------------------------------------------------------- /data/hit_expansion/hit.smi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/hit_expansion/hit.smi -------------------------------------------------------------------------------- /data/processed.key: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/processed.key -------------------------------------------------------------------------------- /data/reaction_templates_hb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/reaction_templates_hb.txt -------------------------------------------------------------------------------- /data/sbdd/pocket2mol.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/pocket2mol.csv -------------------------------------------------------------------------------- /data/sbdd/receptors/ADRB2/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/ADRB2/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/ADRB2/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/ADRB2/receptor.pdbqt -------------------------------------------------------------------------------- /data/sbdd/receptors/ALDH1/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/ALDH1/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/ALDH1/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/ALDH1/receptor.pdbqt -------------------------------------------------------------------------------- /data/sbdd/receptors/ESR1_ago/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/ESR1_ago/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/ESR1_ago/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/ESR1_ago/receptor.pdbqt -------------------------------------------------------------------------------- /data/sbdd/receptors/ESR1_ant/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/ESR1_ant/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/ESR1_ant/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/ESR1_ant/receptor.pdbqt -------------------------------------------------------------------------------- /data/sbdd/receptors/FEN1/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/FEN1/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/FEN1/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/FEN1/receptor.pdbqt -------------------------------------------------------------------------------- /data/sbdd/receptors/GBA/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/GBA/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/GBA/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/GBA/receptor.pdbqt -------------------------------------------------------------------------------- /data/sbdd/receptors/IDH1/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/IDH1/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/IDH1/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/IDH1/receptor.pdbqt -------------------------------------------------------------------------------- /data/sbdd/receptors/KAT2A/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/KAT2A/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/KAT2A/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/KAT2A/receptor.pdbqt -------------------------------------------------------------------------------- /data/sbdd/receptors/MAPK1/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/MAPK1/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/MAPK1/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/MAPK1/receptor.pdbqt -------------------------------------------------------------------------------- /data/sbdd/receptors/MTORC1/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/MTORC1/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/MTORC1/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/MTORC1/receptor.pdbqt -------------------------------------------------------------------------------- /data/sbdd/receptors/OPRK1/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/OPRK1/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/OPRK1/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/OPRK1/receptor.pdbqt -------------------------------------------------------------------------------- /data/sbdd/receptors/PKM2/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/PKM2/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/PKM2/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/PKM2/receptor.pdbqt -------------------------------------------------------------------------------- /data/sbdd/receptors/PPARG/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/PPARG/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/PPARG/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/PPARG/receptor.pdbqt -------------------------------------------------------------------------------- /data/sbdd/receptors/TP53/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/TP53/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/TP53/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/TP53/receptor.pdbqt -------------------------------------------------------------------------------- /data/sbdd/receptors/VDR/description.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/VDR/description.yaml -------------------------------------------------------------------------------- /data/sbdd/receptors/VDR/receptor.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/sbdd/receptors/VDR/receptor.pdbqt -------------------------------------------------------------------------------- /data/synthesis_planning/enamine_smiles_1k.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/synthesis_planning/enamine_smiles_1k.csv -------------------------------------------------------------------------------- /data/synthesis_planning/test_building_blocks.smi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/synthesis_planning/test_building_blocks.smi -------------------------------------------------------------------------------- /data/synthesis_planning/test_chembl.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/synthesis_planning/test_chembl.csv -------------------------------------------------------------------------------- /data/synthesis_planning/test_synthesis.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/data/synthesis_planning/test_synthesis.csv -------------------------------------------------------------------------------- /data/trained_weights/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /env.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/env.yml -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/pyproject.toml -------------------------------------------------------------------------------- /sample.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/sample.py -------------------------------------------------------------------------------- /scripts/goal_directed/00-run_chemprojector.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/goal_directed/00-run_chemprojector.sh -------------------------------------------------------------------------------- /scripts/goal_directed/10-scoring.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/goal_directed/10-scoring.py -------------------------------------------------------------------------------- /scripts/preprocess_data/archive_preprocessed_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/preprocess_data/archive_preprocessed_data.py -------------------------------------------------------------------------------- /scripts/preprocess_data/create_fingerprint_index.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/preprocess_data/create_fingerprint_index.py -------------------------------------------------------------------------------- /scripts/preprocess_data/create_reaction_matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/preprocess_data/create_reaction_matrix.py -------------------------------------------------------------------------------- /scripts/preprocess_data/create_reaction_matrix_train_split.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/preprocess_data/create_reaction_matrix_train_split.py -------------------------------------------------------------------------------- /scripts/preprocess_data/encrypt_message.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/preprocess_data/encrypt_message.py -------------------------------------------------------------------------------- /scripts/sbdd/00-run_chemprojector.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/sbdd/00-run_chemprojector.sh -------------------------------------------------------------------------------- /scripts/sbdd/10-run_docking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/sbdd/10-run_docking.py -------------------------------------------------------------------------------- /scripts/sbdd/20-summarize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/sbdd/20-summarize.py -------------------------------------------------------------------------------- /scripts/synthesis_planning_chembl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/synthesis_planning_chembl.sh -------------------------------------------------------------------------------- /scripts/synthesis_planning_enamine.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/synthesis_planning_enamine.sh -------------------------------------------------------------------------------- /scripts/synthesis_planning_test_split.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/synthesis_planning_test_split.sh -------------------------------------------------------------------------------- /scripts/train_old.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/train_old.py -------------------------------------------------------------------------------- /scripts/upgrade_checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/scripts/upgrade_checkpoint.py -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/setup.py -------------------------------------------------------------------------------- /third_party/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/third_party/README.md -------------------------------------------------------------------------------- /train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/train.py -------------------------------------------------------------------------------- /unarchive_wizard.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luost26/ChemProjector/HEAD/unarchive_wizard.py --------------------------------------------------------------------------------