smiles
stringlengths 5
92
|
|---|
C=C(C)CN(CC)C(=O)CSc1n[nH]c(=O)n1C1CC1
|
CC[C@@H](C#N)S(=O)(=O)NCc1ccccc1F
|
N#C[C@@H]1C(=O)NC(=O)[C@@H](C#N)C1CCc1ccccc1
|
CC1CCC(NS(=O)(=O)N(C)CCC#N)CC1
|
C[C@H](O)CN1CCN(Cc2ccc(C#N)cc2)CC1
|
CS[C@@H]1C(C(=O)C(F)(F)F)=C(CC(=O)O)C(=O)N1C
|
Cc1nc(CN2CCCN(c3ncccc3C#N)CC2)no1
|
CCOc1ccc(NC(=O)NCC#CCN(C)C)cc1
|
COC[C@@](C)(CCO)NCc1cc(C#N)ccc1F
|
CCC[C@@H](C)S(=O)(=O)/N=C(\O)c1cccnc1
|
COc1cc(C#N)ccc1Cn1nc(C)c(CCO)c1C
|
C/C(=C\C(=O)N1CCO[C@@H](C#N)C1)c1cccc(F)c1
|
O/N=C1/CCc2nonc2/C1=N/Nc1ccccc1
|
Cn1ncc(/N=C/c2ccccc2[N+](=O)[O-])c1C(N)=O
|
C=CCCN1CCN(C2C[C@@H]3CC[C@@H](C2)N3C)CC1
|
CC1(C)OB(c2cc([N+](=O)[O-])c(N)cc2O)OC1(C)C
|
COc1ccc(C(=O)N2CCOC[C@@H]2C#N)c(OC)c1
|
CC[C@H](C)N/C(N)=N/CCNC(=O)c1ccccc1
|
CCc1nc2n(n1)CCC[C@@H]2/N=C(/O)CCc1cnc[nH]1
|
Cc1cccc2ncc(CN3CCN(C4CC4)[C@@H](C#N)C3)n12
|
C[C@H](CCN=c1nc[nH]cc1C#N)NC(=O)OC(C)(C)C
|
COCCN(CCOC)C(=O)c1cccc(C#N)c1
|
C#CCN(Cc1cccc(C)n1)Cc1cc(=O)c(O)co1
|
COC[C@]1(C(N)=O)CCCN1Cc1ccc(C#N)cc1F
|
C[C@H](C#N)NS(=O)(=O)c1cccc2ncccc12
|
O=C(NCC#C[C@H]1CCCCO1)c1cnc2nccn2c1
|
CC(C)(C)c1nnc(N/N=C/c2cccs2)[nH]c1=O
|
CO[C@H]1C[C@@H](CO)N(CCOc2cccc(C#N)c2)C1
|
C=C(Cl)COC(=O)[C@@H]1[C@@H](C(=O)O)[C@H]2C=C[C@H]1C2
|
C=C(Br)CN(C)C[C@H]1CCS(=O)(=O)C1
|
CC(C)[C@](C)(C#N)NC(=O)[C@H](C)N1CCO[C@H](C)C1
|
CCOc1cccc(/C=N/N2C(=O)CSC2=S)c1O
|
C#CCNC(=O)[C@H]1CCCC[C@H]1NC(=O)OC(C)(C)C
|
C[C@H]1CN=C(N2CCN(c3ccc(C#N)cn3)CC2)S1
|
N#C[C@@H](C(=O)NC1CCCC1)C(=O)C1CCOCC1
|
COC(=O)c1ccc2cccc(CNC(=O)[C@@H]3CO3)c2c1
|
C=CC(=O)NC1(c2ccc(C#N)cc2)CCOCC1
|
COC[C@@H]1CN(c2ccc(C#N)cn2)CC(C)(C)O1
|
COc1cc(C=C2C(=O)C=CC2=O)cc(OC)c1O
|
COC1(OC)CCC2=C(C)C(=O)CC[C@]2(CO)C1
|
N#Cc1cc([N+](=O)[O-])ccc1N1CCC[C@@H](CO)C1
|
Cn1c(N[C@H]2CCc3ccccc32)c(C#N)c(=O)n(C)c1=O
|
O=C(/C=C/c1ccc([N+](=O)[O-])o1)CCN1CCOCC1
|
Cc1nn(C)cc1C[C@H](C#N)C(=O)NCCc1ccccc1
|
C=C(Br)CSc1ncc(C#N)c(N)n1
|
C#CCN(CCC)S(=O)(=O)c1ccccc1C(=O)OC
|
C[C@H](C#N)CN(C)C(=O)c1ccc2c(c1)NC(=O)CN2C
|
CC1=C2C(=CO[C@@H](C)[C@H]2C)C(=O)C(C(=O)O)=C1O
|
N#Cc1ccc2c(c1)N(C(=O)c1cnn3cccnc13)CC2
|
C=CCCC(=O)NCC#CCOc1ccccc1C(N)=O
|
COc1ccccc1N1CCC[C@H](N(C)CC#N)C1=O
|
N#Cc1c(Br)cccc1N1CCO[C@H](CN)C1
|
Cc1cc(NC(=O)COc2ccccc2C#N)n(C)n1
|
N#Cc1cnn(C(=O)[C@H]2CC[C@@H](c3ccccc3)O2)c1N
|
Cc1cc([C@@H]2CCCN2CC(=O)NCCC#N)no1
|
CC1(C)C[C@@]1(C#N)NS(=O)(=O)c1cccc2c1OCC2
|
CN(C)c1ccc(/C=N/Nc2ccc3nnnn3n2)cc1
|
C#CC[C@@H]1CCCN(c2nnnn2CC2CCOCC2)C1
|
C#CCN1CCC(C(=O)N=c2[nH]c3ccccc3[nH]2)CC1
|
COC(=O)CN(Cc1cc(F)ccc1C#N)C1CC1
|
CCCOc1ccc(C/N=C(/N)N2CCOCC2)cc1
|
CC#CC(=O)N(C)C[C@H]1OCCN(C)[C@H]1c1ccccc1
|
Cc1ccc([C@@H]2CNC(=NC[C@@H]3[C@H]4CCOC[C@H]43)N2)o1
|
CN(Cc1ccco1)c1ncnc2c1cnn2CCC#N
|
CC(C)[C@@](C)(C#N)NC(=O)COc1ccc(C#N)cc1
|
CCOCCN1CCN(Cc2cc(C#N)ccc2F)CC1
|
N#Cc1ccnc(N2CCC[C@H]2[C@@H]2CCCOC2)n1
|
N#C[C@]1(C(=O)N=c2cc(C(F)F)[nH][nH]2)C[C@H]1C(F)(F)F
|
Cn1nc2c(c1C/N=C(/O)c1cncnc1)CCCC2
|
CNCCOc1ccc(B2OC(C)(C)C(C)(C)O2)cc1
|
CSc1nc(SC)c2cnn(C[C@@H]3CO3)c2n1
|
O=C1c2cccc(Br)c2C(=O)[C@@H]1[N+](=O)[O-]
|
CN1CCN(c2cc(C#N)c(C#N)cc2[N+](=O)[O-])CC1
|
N#CCn1ccn(-c2ccccc2Cl)c(=O)c1=O
|
N#Cc1cccc(NC(=O)NCCCn2cccn2)c1
|
N#Cc1cc(Cl)ccc1N1CCS(=O)(=O)CC1
|
CC(C)C[C@@H](C#N)NC(=O)[C@H](C)NC(=O)c1ccoc1
|
O=C(NO)c1cccc(C(=O)NCCc2ccncc2)c1
|
C[C@H](NCCCNS(C)(=O)=O)c1ccc(C#N)s1
|
N#Cc1nc2[nH]c(-c3ccccc3)cc(=O)n2c1C#N
|
NC(=O)C(=O)[C@@H]1CCC2=C(Sc3ccccc3N2)C1=O
|
COCCCC/N=C(\N)Nc1ccc(OC)cc1
|
N#Cc1cccc([C@H]2CN(CCC3OCCO3)CCO2)c1
|
N#Cc1ccccc1CN1CCOC[C@@H]1[C@@H]1CCC[C@H]1O
|
CN1CCc2cccc(B3OC(C)(C)C(C)(C)O3)c21
|
CC(C)(C)[C@H]1OCC[C@@H]1C/N=C(/O)Cn1cncn1
|
CSCC/N=C(/O)NC[C@H]1CCO[C@@H]1C(C)C
|
CCN(CC(=O)O)C1CC(/N=C(/O)[C@H]2CCCCO2)C1
|
N#Cc1cc(C(=O)N2C[C@@H](O)C[C@H]2c2ccc(F)cc2)c[nH]1
|
C[C@H]1CN(C(=O)COc2ccc(C#N)cc2)CCO1
|
N#Cc1ccc(C(=O)NCCCN2CCOCC2)cc1
|
N#CCSc1nnc(CNC(=O)c2ccccc2)o1
|
C=C(C)[C@@H]1OCC[C@@H]1C(=O)Nc1ccn2nccc2n1
|
CCN(C/C(O)=N/C)S(=O)(=O)N1CCCCCC1
|
CCc1nnc(N/N=C\c2ccc(OC)cc2OC)n1N
|
COC(=O)COc1nc(C)c2c(c1C#N)CC(C)(C)OC2
|
CC1(c2cn(C[C@@H]3CCCN3C(=O)C#CC3CC3)nn2)CC1
|
C=CCNC(=O)CN1CCN(c2cccc(OC)c2)CC1
|
CCC[C@H](C#N)NC(=O)CNC(=O)CC(C)(C)C
|
N#CCCCCS(=O)(=O)N[C@H]1CCCSC1
|
End of preview. Expand
in Data Studio
From ZINC20 'In-stock, Goldilocks' tranche
Steps to prepare the database:
- Select the appropriate tranche from from ZINC20
- Select 'Purch' -> 'In-stock' + 'Exclusive'
- Select 'React' -> 'Standard' + 'Exclusive'
- Select 'Predefined Subsets' -> 'Goldilocks'
- Select 'Download Format' -> 'SMILES (*.smi)'
- Select 'Download Method' -> 'Raw URLs'
- Download and concatenate the SMILES
# Download all ZINC20 tranches from 'in-stock, goldilocks' subset
mkdir zinc
wget -i ZINC-downloader-2D-smi.uri -P zinc
# Remove first line of every file and save into txt file
for i in zinc/*; do tail -n +2 "$i" > "$i".txt; done
# Concatenate all created files into one (contains 185896 ligands)
cat zinc/*.txt > zinc_all.txt
- Parse the concatenated text file into a Huggingface dataset
from datasets import load_dataset
dataset = load_dataset('text', data_files='zinc_all.txt')
# Split SMILES from ZINC_id and store only SMILES
def split_text(dataset):
split_item = dataset["text"].split()
return {"smiles": split_item[0]}
dataset = dataset.map(split_text)
dataset = dataset.remove_columns("text")
- Compute ligand embeddings
from sentence_transformers import SentenceTransformer
import numpy as np
def calculate_embeddings(input, model_name, max_length):
model = SentenceTransformer(model_name, trust_remote_code=True)
model.max_seq_length = max_length
embeddings = model.encode(input, show_progress_bar=True)
keys = [k for k in input]
np.savez(f"{model_name.replace("/", "_")}_embeddings.npz", keys=np.array(keys), embs=np.asarray(embeddings, dtype=np.float32))
calculate_embeddings(dataset['train'].unique("smiles"), "ibm-research/MoLFormer-XL-both-10pct", 118)
- Downloads last month
- 57