Create README.md

generation/README.md

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+# Molecule Generation
+
+This fold contains the molecule generation script. The polymer generation experiment in the paper can be reproduced through the following steps:
+
+## Motif Extraction
+Extract substructure vocabulary from a given set of molecules:
+```
+python get_vocab.py --min_frequency 100 --ncpu 8 < data/polymers/all.txt > vocab.txt
+```
+Please replace `data/polymers/all.txt` with your molecules data file. 
+The `--min_frequency` means to discard any large motifs with lower than 100 occurances in the dataset. The discarded motifs will be decomposed into simple rings and bonds. Change `--ncpu` to specify the number of jobs for multiprocessing.
+
+## Data Preprocessing
+Preprocess the dataset using the vocabulary extracted from the first step: 
+```
+python preprocess.py --train data/polymers/train.txt --vocab data/polymers/inter_vocab.txt --ncpu 8 
+mkdir train_processed
+mv tensor* train_processed/
+```
+
+## Training
+```
+mkdir ckpt/
+python gnn_train.py --train train_processed/ --vocab data/polymers/inter_vocab.txt --save_dir ckpt/ 
+```
+
+## Sample Molecules
+```
+python sample.py --vocab ../data/polymers/inter_vocab.txt --model ckpt/inter-h250z24b0.1/model.19
+```