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‎apps/drug_target_interaction/moltrans_dti/README.md

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```txt
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dataset
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|-- classification
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| |-- BindingDB
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| | |-- test.csv
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| | |-- train.csv
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| | `-- val.csv
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| |-- BIOSNAP
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| | |-- full_data
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| | | |-- test.csv
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| | | |-- train.csv
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| | | `-- val.csv
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| | |-- missing_data
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| | | |-- 70
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| | | |-- 80
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| | | |-- 90
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| | | `-- 95
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| | |-- unseen_drug
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| | | |-- test.csv
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| | | |-- train.csv
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| | | `-- val.csv
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| | `-- unseen_protein
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| | |-- test.csv
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| | |-- train.csv
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| | `-- val.csv
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| `-- DAVIS
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| |-- test.csv
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| |-- train.csv
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| `-- val.csv
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`-- regression
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|-- benchmark
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| |-- DAVIStest
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| `-- KIBAtest
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|-- BindingDB
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| |-- bindingDB cleanup.R
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| |-- BindingDB_Kd.txt
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| |-- BindingDB_SMILES_new.txt
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| |-- BindingDB_SMILES.txt
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| |-- BindingDB_Target_Sequence_new.txt
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| `-- BindingDB_Target_Sequence.txt
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|-- ChEMBL
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| |-- Chem_Affinity.txt
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| |-- Chem_Kd_nM.txt
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| |-- Chem_SMILES_only.txt
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| |-- Chem_SMILES.txt
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| |-- ChEMBL cleanup.R
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| `-- ChEMBL_Target_Sequence.txt
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|-- DAVIS
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| |-- affinity.txt
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| |-- SMILES.txt
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| `-- target_seq.txt
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`-- KIBA
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|-- affinity.txt
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|-- SMILES.txt
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`-- target_seq.txt
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├── classification
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│ ├── BindingDB
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│ │ ├── test.csv
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│ │ ├── train.csv
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│ │ └── val.csv
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│ ├── BIOSNAP
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│ │ ├── full_data
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│ │ │ ├── test.csv
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│ │ │ ├── train.csv
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│ │ │ └── val.csv
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│ │ ├── missing_data
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│ │ │ ├── 70
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│ │ │ ├── 80
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│ │ │ ├── 90
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│ │ │ └── 95
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│ │ ├── unseen_drug
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│ │ │ ├── test.csv
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│ │ │ ├── train.csv
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│ │ │ └── val.csv
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│ │ └── unseen_protein
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│ │ ├── test.csv
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│ │ ├── train.csv
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│ │ └── val.csv
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│ └── DAVIS
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│ ├── test.csv
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│ ├── train.csv
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│ └── val.csv
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└── regression
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├── benchmark
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│ ├── DAVIStest
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│ └── KIBAtest
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├── BindingDB
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│ ├── bindingDB cleanup.R
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│ ├── BindingDB_Kd.txt
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│ ├── BindingDB_SMILES_new.txt
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│ ├── BindingDB_SMILES.txt
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│ ├── BindingDB_Target_Sequence_new.txt
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│ └── BindingDB_Target_Sequence.txt
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├── ChEMBL
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│ ├── Chem_Affinity.txt
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│ ├── Chem_Kd_nM.txt
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│ ├── Chem_SMILES_only.txt
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│ ├── Chem_SMILES.txt
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│ ├── ChEMBL cleanup.R
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│ └── ChEMBL_Target_Sequence.txt
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├── DAVIS
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│ ├── affinity.txt
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│ ├── SMILES.txt
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│ └── target_seq.txt
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└── KIBA
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├── affinity.txt
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├── SMILES.txt
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└── target_seq.txt
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```
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In the original work of MolTrans, it only contains classification task. Here we provide datasets for both classification and regression tasks of DTI.

‎apps/drug_target_interaction/moltrans_dti/README_cn.md

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```txt
3535
dataset
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|-- classification
37-
| |-- BindingDB
38-
| | |-- test.csv
39-
| | |-- train.csv
40-
| | `-- val.csv
41-
| |-- BIOSNAP
42-
| | |-- full_data
43-
| | | |-- test.csv
44-
| | | |-- train.csv
45-
| | | `-- val.csv
46-
| | |-- missing_data
47-
| | | |-- 70
48-
| | | |-- 80
49-
| | | |-- 90
50-
| | | `-- 95
51-
| | |-- unseen_drug
52-
| | | |-- test.csv
53-
| | | |-- train.csv
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| | | `-- val.csv
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| | `-- unseen_protein
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| | |-- test.csv
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| | |-- train.csv
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| | `-- val.csv
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| `-- DAVIS
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| |-- test.csv
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| |-- train.csv
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| `-- val.csv
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`-- regression
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|-- benchmark
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| |-- DAVIStest
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| `-- KIBAtest
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|-- BindingDB
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| |-- bindingDB cleanup.R
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| |-- BindingDB_Kd.txt
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| |-- BindingDB_SMILES_new.txt
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| |-- BindingDB_SMILES.txt
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| |-- BindingDB_Target_Sequence_new.txt
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| `-- BindingDB_Target_Sequence.txt
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|-- ChEMBL
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| |-- Chem_Affinity.txt
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| |-- Chem_Kd_nM.txt
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| |-- Chem_SMILES_only.txt
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| |-- Chem_SMILES.txt
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| |-- ChEMBL cleanup.R
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| `-- ChEMBL_Target_Sequence.txt
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|-- DAVIS
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| |-- affinity.txt
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| |-- SMILES.txt
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| `-- target_seq.txt
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`-- KIBA
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|-- affinity.txt
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|-- SMILES.txt
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`-- target_seq.txt
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├── classification
37+
│ ├── BindingDB
38+
│ │ ├── test.csv
39+
│ │ ├── train.csv
40+
│ │ └── val.csv
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│ ├── BIOSNAP
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│ │ ├── full_data
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│ │ │ ├── test.csv
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│ │ │ ├── train.csv
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│ │ │ └── val.csv
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│ │ ├── missing_data
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│ │ │ ├── 70
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│ │ │ ├── 80
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│ │ │ ├── 90
50+
│ │ │ └── 95
51+
│ │ ├── unseen_drug
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│ │ │ ├── test.csv
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│ │ │ ├── train.csv
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│ │ │ └── val.csv
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│ │ └── unseen_protein
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│ │ ├── test.csv
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│ │ ├── train.csv
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│ │ └── val.csv
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│ └── DAVIS
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│ ├── test.csv
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│ ├── train.csv
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│ └── val.csv
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└── regression
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├── benchmark
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│ ├── DAVIStest
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│ └── KIBAtest
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├── BindingDB
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│ ├── bindingDB cleanup.R
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│ ├── BindingDB_Kd.txt
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│ ├── BindingDB_SMILES_new.txt
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│ ├── BindingDB_SMILES.txt
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│ ├── BindingDB_Target_Sequence_new.txt
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│ └── BindingDB_Target_Sequence.txt
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├── ChEMBL
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│ ├── Chem_Affinity.txt
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│ ├── Chem_Kd_nM.txt
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│ ├── Chem_SMILES_only.txt
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│ ├── Chem_SMILES.txt
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│ ├── ChEMBL cleanup.R
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│ └── ChEMBL_Target_Sequence.txt
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├── DAVIS
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│ ├── affinity.txt
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│ ├── SMILES.txt
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│ └── target_seq.txt
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└── KIBA
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├── affinity.txt
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├── SMILES.txt
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└── target_seq.txt
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```
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在MolTrans原工作中，只包含了分类任务。我们提供了DTI分类和回归任务的数据集与代码。

‎docs/api_doc/datasets.rst

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:members: get_default_clintox_task_names, load_clintox_dataset
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:inherited-members:
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davis_dataset
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===============
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.. automodule:: pahelix.datasets.davis_dataset
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:members: load_davis_dataset
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:inherited-members:
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ddi_dataset
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===============
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.. automodule:: pahelix.datasets.ddi_dataset
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:members: get_default_ddi_task_names, load_ddi_dataset
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:inherited-members:
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dti_dataset
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===============
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.. automodule:: pahelix.datasets.dti_dataset
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:members: get_default_dti_task_names, load_dti_dataset
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:inherited-members:
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esol_dataset
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============
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.. automodule:: pahelix.datasets.esol_dataset
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:members: get_default_esol_task_names, load_esol_dataset
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:members: get_default_esol_task_names, get_default_esol_range, load_esol_dataset
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:inherited-members:
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freesolv_dataset
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================
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.. automodule:: pahelix.datasets.freesolv_dataset
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:members: get_default_freesolv_task_names, load_freesolv_dataset
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:members: get_default_freesolv_task_names, get_default_freesolv_range, load_freesolv_dataset
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:inherited-members:
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hiv_dataset
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:members: InMemoryDataset
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:inherited-members:
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lipophilicity_dataset
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=====================
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kiba_dataset
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===============
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.. automodule:: pahelix.datasets.lipophilicity_dataset
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:members: get_default_lipophilicity_task_names, load_lipophilicity_dataset
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.. automodule:: pahelix.datasets.kiba_dataset
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:members: load_kiba_dataset
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:inherited-members:
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mutag_dataset
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=============
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lipophilicity_dataset
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=====================
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.. automodule:: pahelix.datasets.mutag_dataset
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:members: load_mutag_dataset
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.. automodule:: pahelix.datasets.lipophilicity_dataset
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:members: get_default_lipophilicity_task_names, get_default_lipophilicity_range, load_lipophilicity_dataset
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:inherited-members:
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muv_dataset
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:members: get_default_muv_task_names, load_muv_dataset
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:inherited-members:
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ptc_mr_dataset
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==============
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pdbbind_dataset
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===============
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.. automodule:: pahelix.datasets.pdbbind_dataset
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:members: load_pdbbind_dataset
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:inherited-members:
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ppi_dataset
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===========
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.. automodule:: pahelix.datasets.ptc_mr_dataset
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:members: load_ptc_mr_dataset
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.. automodule:: pahelix.datasets.ppi_dataset
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:members: get_default_ppi_task_names, load_ppi_dataset
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:inherited-members:
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sider_dataset

‎docs/api_doc/featurizers.rst

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featurizer
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==========
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.. automodule:: pahelix.featurizers.featurizer
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:members: Featurizer
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.. automodule:: pahelix.featurizers.het_gnn_featurizer
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:members: DDiFeaturizer, num_nodes_stat, nx_graph_build
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:inherited-members:
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pretrain_gnn_featurizer
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=======================
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.. automodule:: pahelix.featurizers.pretrain_gnn_featurizer
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:members: PreGNNAttrMaskFeaturizer, PreGNNSupervisedFeaturizer, reset_idxes, graph_data_obj_to_nx_simple, nx_to_graph_data_obj_simple, transform_contextpred, PreGNNContextPredFeaturizer
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:members: AttrmaskTransformFn, AttrmaskCollateFn, SupervisedTransformFn, SupervisedCollateFn
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:inherited-members:
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Helpful Link
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============

‎docs/api_doc/model_zoo.rst

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===================
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.. automodule:: pahelix.model_zoo.pretrain_gnns_model
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:members: PretrainGNNModel, PreGNNAttrmaskModel, PreGNNContextpredModel, PreGNNSupervisedModel
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:members: PretrainGNNModel, AttrmaskModel, SupervisedModel
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protein_sequence_model
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======================
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.. autoclass:: pahelix.model_zoo.protein_sequence_model.ProteinSequenceModel
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:members: _prepare_emb, _transformer, _lstm, _resnet, forward
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.. autoclass:: pahelix.model_zoo.protein_sequence_model
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:members: LstmEncoderModel, ResnetEncoderModel, TransformerEncoderModel, PretrainTaskModel, SeqClassificationTaskModel, ClassificationTaskModel, RegressionTaskModel, ProteinEncoderModel, ProteinModel, ProteinCriterion
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:inherited-members:
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sd_vae_model
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============
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.. autoclass:: pahelix.model_zoo.sd_vae_model
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:members: StateDecoder, PerpCalculator, MyPerpLoss, CNNEncoder, MolVAE
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:inherited-members:
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seq_vae_model
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============
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.. autoclass:: pahelix.model_zoo.seq_vae_model
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:members: VAE
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:inherited-members:
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Helpful Link

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