search

wenhao-gao / SynNet

MIT License
84 stars 21 forks source link

No output in Synthesis Planning #21

Closed sjchasel closed 1 year ago

sjchasel commented 1 year ago

I have trained models and data ready, then follow steps 0-2 from the INSTRUCTIONS.md.

python /data/users/xx/projects/SynNet/src/00-extract-smiles-from-sdf.py \
    --input-file="/data/users/xx/data/enamine_us/Enamine_Rush-Delivery_Building_Blocks-US_222337cmpd_20230801.sdf" \
    --output-file="/data/users/xx/projects/SynNet/data/assets/building-blocks/enamine-us-smiles.csv.gz"
python /data/users/xx/projects/SynNet/src/01-filter-building-blocks.py \
    --building-blocks-file "/data/users/xx/projects/SynNet/data/assets/building-blocks/enamine-us-smiles.csv.gz" \
    --rxn-templates-file "/data/users/xx/projects/SynNet/data/assets/reaction-templates/hb.txt" \
    --output-bblock-file "/data/users/xx/projects/SynNet/data/pre-process/building-blocks-rxns/bblocks-enamine-us.csv.gz" \
    --output-rxns-collection-file "/data/users/xx/projects/SynNet/data/pre-process/building-blocks-rxns/rxns-hb-enamine-us.json.gz" --verbose
python /data/users/xx/projects/SynNet/src/02-compute-embeddings.py \
    --building-blocks-file "/data/users/xx/projects/SynNet/data/pre-process/building-blocks-rxns/bblocks-enamine-us.csv.gz" \
    --output-file "/data/users/xx/projects/SynNet/data/pre-process/embeddings/hb-enamine-embeddings.npy" \
    --featurization-fct "fp_256"

but after running the script of synthesis planning

BUILDING_BLOCKS_FILE=/data/users/xx/projects/SynNet/data/pre-process/building-blocks-rxns/bblocks-enamine-us.csv.gz
RXN_COLLECTION_FILE=/data/users/xx/projects/SynNet/data/pre-process/building-blocks-rxns/rxns-hb-enamine-us.json.gz
EMBEDDINGS_KNN_FILE=/data/users/xx/projects/SynNet/data/pre-process/embeddings/hb-enamine-embeddings.npy
python /data/users/xx/projects/SynNet/src/20-predict-targets.py \
    --building-blocks-file $BUILDING_BLOCKS_FILE \
    --rxns-collection-file $RXN_COLLECTION_FILE \
    --embeddings-knn-file $EMBEDDINGS_KNN_FILE \
    --data "/data/users/xx/projects/SynNet/data/assets/molecules/sample-targets.txt" \
    --ckpt-dir "/data/users/xx/projects/SynNet/checkpoints/" \
    --output-dir "/data/users/xx/projects/SynNet/results/demo-inference/"

I get the result as

targets,decoded,similarity
COc1cc(Cn2c(C)c(Cc3ccccc3)c3c2CCCC3)ccc1OCC(=O)N(C)C,,0
CCC1CCCC(Nc2cc(C(F)(F)F)c(Cl)cc2SC)CC1,,0
Clc1cc(Cl)c(C2=NC(c3cccc4c(Br)cccc34)=NN2)nn1,,0
COc1ccc(S(=O)(=O)c2ccc(-c3nc(-c4cc(B(O)O)ccc4O)no3)cn2)cc1,,0
CNS(=O)(=O)c1ccc(-c2cc3c4c(ccc3[nH]2)CCCN4C(N)=O)cc1,,0
CC(NC(=O)C1Cn2c(O)nnc2CN1)c1cc(F)ccc1N1CCC(n2nnn(-c3ccc(Br)cc3)c2=S)CC1,,0
COc1cc(-c2nc(-c3ccccc3)c(-c3ccccc3)s2)ccn1,,0
CCCn1c(C)nnc1CC(C)(O)C(=C(C)C)c1nccnc1S(=O)(=O)F,,0
CN(c1ccccc1)c1ccc(-c2nc3ncccc3s2)cn1,,0
COc1cc(-c2nc(-c3ccc(F)cc3)c(-c3ccc(F)cc3)n2c2cc(Cl)ccc2Cl)ccc1Oc1ccc(S(=O)(=O)N2CCCCC2)cc1[N+](=O)[O-],,0

It seems there is no output. Can you help me with this? Thank you!