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cicd: update precommit (#443)
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* GenomicMedLab/software-templates#60
* GenomicMedLab/software-templates#61
* GenomicMedLab/software-templates#70
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@jsstevenson
jsstevenson authored Nov 20, 2024
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20 changes: 20 additions & 0 deletions .github/workflows/checks.yaml
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Expand Up @@ -55,3 +55,23 @@ jobs:

- name: Check style
run: python3 -m ruff check . && ruff format --check .

precommit_hooks:
runs-on: ubuntu-latest
strategy:
matrix:
hook:
- "end-of-file-fixer"
- "trailing-whitespace"
- "mixed-line-ending"
steps:
- uses: actions/checkout@v4

- name: Set up Python 3.12
uses: actions/setup-python@v5
with:
python-version: 3.12

- uses: pre-commit/action@v3.0.1
with:
extra_args: ${{ matrix.hook }} --all-files
2 changes: 2 additions & 0 deletions .pre-commit-config.yaml
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Expand Up @@ -9,6 +9,8 @@ repos:
- id: check-merge-conflict
- id: detect-aws-credentials
args: [ --allow-missing-credentials ]
- id: mixed-line-ending
args: [ --fix=lf ]
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.5.0 # ruff version
hooks:
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1 change: 0 additions & 1 deletion analysis/approval_status/approval_status_notes.md
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Expand Up @@ -61,4 +61,3 @@ def ApprovalStatus(Enum):
FDA_PRESCRIPTION = "fda_prescription"
FDA_DISCONTINUED = "fda_discontinued"
FDA_TENTATIVE = "fda_tentative"

16 changes: 8 additions & 8 deletions tests/data/drugbank/drugbank_5.1.10.csv
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@@ -1,8 +1,8 @@
DrugBank ID,Accession Numbers,Common name,CAS,UNII,Synonyms,Standard InChI Key
DB00515,APRD00359,Cisplatin,15663-27-1,Q20Q21Q62J,CDDP | Cis-DDP | cis-diamminedichloroplatinum(II) | Cisplatin | cisplatino,LXZZYRPGZAFOLE-UHFFFAOYSA-L
DB00522,APRD00818,Bentiromide,37106-97-1,239IF5W61J,Bentiromide | Bentiromido | Bentiromidum | BTPABA | PFT,SPPTWHFVYKCNNK-FQEVSTJZSA-N
DB01143,APRD00021,Amifostine,20537-88-6,ILA426L95O,Amifostina | Amifostine | Amifostine anhydrous | Amifostinum | Aminopropylaminoethyl thiophosphate | Ethiofos,JKOQGQFVAUAYPM-UHFFFAOYSA-N
DB01174,APRD00184,Phenobarbital,50-06-6,YQE403BP4D,"5-ethyl-5-phenyl-2,4,6(1H,3H,5H)-pyrimidinetrione | 5-Ethyl-5-phenyl-pyrimidine-2,4,6-trione | 5-Ethyl-5-phenylbarbituric acid | 5-ethyl-5-phenylpyrimidine-2,4,6(1H,3H,5H)-trione | 5-Phenyl-5-ethylbarbituric acid | Fenobarbital | Phenobarbital | Phenobarbitol | Phenobarbitone | Phenobarbituric Acid | Phenyläthylbarbitursäure | Phenylethylbarbiturate | Phenylethylbarbituric Acid | Phenylethylbarbitursäure | Phenylethylmalonylurea",DDBREPKUVSBGFI-UHFFFAOYSA-N
DB06145,,Spiramycin,24916-50-5,033ECH6IFG,Demycarosylturimycin H | Foromacidin A | Foromacidine A | Spiramycin 1 | Spiramycin A | Spiramycin I,ACTOXUHEUCPTEW-CEUOBAOPSA-N
DB12117,,Mitometh,107465-03-2,H8MTN7XVC2,DDP,MOTIYCLHZZLHHQ-UHFFFAOYSA-N
DB14257,,Aloe ferox leaf,,0D145J8EME,Aloe (Aloe Ferox) | Aloe Candelabrum Leaf | Aloe Capensis | Aloe Ferox Dry Leaf Juice | Aloe Ferox Juice | Aloe Ferox Leaf Extract | Aloe Ferox Leaf Exudate | Aloe Ferox Leaf Gel | Aloe Ferox Leaf Juice | Aloe Ferox Leaf Juice Extract | Aloe Ferox Leaf Juice Powder | Aloe Ferox Leaf Powder | Aloe Ferox Leaf Preparation | Aloe Folii Extractus (Aloe Ferox) | Aloe Folium (Aloe Ferox) | Aloe Galpinii Leaf | Aloe Herba (Aloe Ferox) | Aloe Horrida Leaf | Aloe Muricata Leaf | Aloe Pallancae Leaf | Aloe Pseudoferox Leaf | Aloe Subferox Leaf | Aloe Supralaevis Leaf | Aloes (Aloe Ferox) | Busipho Ferox Leaf | Cape Aloe Leaf | Cape Aloes | Lu Hui (Aloe Ferox) | Luhui (Aloe Ferox) | New Aloe | Pachidendron Ferox Leaf | Pachidendron Pseudoferox Leaf | Pachidendron Supralaeve Leaf,
DrugBank ID,Accession Numbers,Common name,CAS,UNII,Synonyms,Standard InChI Key
DB00515,APRD00359,Cisplatin,15663-27-1,Q20Q21Q62J,CDDP | Cis-DDP | cis-diamminedichloroplatinum(II) | Cisplatin | cisplatino,LXZZYRPGZAFOLE-UHFFFAOYSA-L
DB00522,APRD00818,Bentiromide,37106-97-1,239IF5W61J,Bentiromide | Bentiromido | Bentiromidum | BTPABA | PFT,SPPTWHFVYKCNNK-FQEVSTJZSA-N
DB01143,APRD00021,Amifostine,20537-88-6,ILA426L95O,Amifostina | Amifostine | Amifostine anhydrous | Amifostinum | Aminopropylaminoethyl thiophosphate | Ethiofos,JKOQGQFVAUAYPM-UHFFFAOYSA-N
DB01174,APRD00184,Phenobarbital,50-06-6,YQE403BP4D,"5-ethyl-5-phenyl-2,4,6(1H,3H,5H)-pyrimidinetrione | 5-Ethyl-5-phenyl-pyrimidine-2,4,6-trione | 5-Ethyl-5-phenylbarbituric acid | 5-ethyl-5-phenylpyrimidine-2,4,6(1H,3H,5H)-trione | 5-Phenyl-5-ethylbarbituric acid | Fenobarbital | Phenobarbital | Phenobarbitol | Phenobarbitone | Phenobarbituric Acid | Phenyläthylbarbitursäure | Phenylethylbarbiturate | Phenylethylbarbituric Acid | Phenylethylbarbitursäure | Phenylethylmalonylurea",DDBREPKUVSBGFI-UHFFFAOYSA-N
DB06145,,Spiramycin,24916-50-5,033ECH6IFG,Demycarosylturimycin H | Foromacidin A | Foromacidine A | Spiramycin 1 | Spiramycin A | Spiramycin I,ACTOXUHEUCPTEW-CEUOBAOPSA-N
DB12117,,Mitometh,107465-03-2,H8MTN7XVC2,DDP,MOTIYCLHZZLHHQ-UHFFFAOYSA-N
DB14257,,Aloe ferox leaf,,0D145J8EME,Aloe (Aloe Ferox) | Aloe Candelabrum Leaf | Aloe Capensis | Aloe Ferox Dry Leaf Juice | Aloe Ferox Juice | Aloe Ferox Leaf Extract | Aloe Ferox Leaf Exudate | Aloe Ferox Leaf Gel | Aloe Ferox Leaf Juice | Aloe Ferox Leaf Juice Extract | Aloe Ferox Leaf Juice Powder | Aloe Ferox Leaf Powder | Aloe Ferox Leaf Preparation | Aloe Folii Extractus (Aloe Ferox) | Aloe Folium (Aloe Ferox) | Aloe Galpinii Leaf | Aloe Herba (Aloe Ferox) | Aloe Horrida Leaf | Aloe Muricata Leaf | Aloe Pallancae Leaf | Aloe Pseudoferox Leaf | Aloe Subferox Leaf | Aloe Supralaevis Leaf | Aloes (Aloe Ferox) | Busipho Ferox Leaf | Cape Aloe Leaf | Cape Aloes | Lu Hui (Aloe Ferox) | Luhui (Aloe Ferox) | New Aloe | Pachidendron Ferox Leaf | Pachidendron Pseudoferox Leaf | Pachidendron Supralaeve Leaf,
16 changes: 8 additions & 8 deletions tests/data/guidetopharmacology/gtop_ligand_id_mapping_2024.3.tsv
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"# GtoPdb Version: 2024.3 - published: 2024-10-03"
"Ligand id" "Name" "Species" "Type" "PubChem SID" "PubChem CID" "ChEMBl ID" "Chebi ID" "UniProt id" "Ensembl ID" "IUPAC name" "INN" "CAS" "DrugBank ID" "Drug Central ID"
"2169" "arginine vasotocin" "" "Peptide" "135652004" "68649" "" "" "" "" "L-cysteinyl-L-tyrosyl-(3S)-DL-isoleucyl-L-glutaminyl-L-asparagyl-L-cysteinyl-DL-prolyl-L-arginyl-glycinamide (1->6)-disulfide" "argiprestocin" "113-80-4" "" ""
"240" "cisapride" "" "Synthetic organic" "135650104" "2769" "CHEMBL1729" "CHEBI:151790" "" "" "4-amino-5-chloro-N-[1-[3-(4-fluorophenoxy)propyl]-3-methoxypiperidin-4-yl]-2-methoxybenzamide" "cisapride" "81098-60-4" "DB00604" "660"
"5343" "cisplatin" "" "Inorganic" "178102005" "441203" "CHEMBL11359" "CHEBI:27899" "" "" "" "cisplatin" "15663-27-1" "DB00515" ""
"3303" "L745870" "" "Synthetic organic" "178100340" "5311200" "CHEMBL267014" "" "" "" "3-[[4-(4-chlorophenyl)piperazin-1-yl]methyl]-1H-pyrrolo[2,3-b]pyridine" "" "158985-00-3" "" ""
"2804" "phenobarbital" "" "Synthetic organic" "135650817" "4763" "CHEMBL40" "CHEBI:8069" "" "" "5-ethyl-5-phenyl-1,3-diazinane-2,4,6-trione" "phenobarbital" "50-06-6" "DB01174" "2134"
"5260" "rolipram" "" "Synthetic organic" "178101944" "5092" "CHEMBL63" "CHEBI:104872" "" "" "4-[3-(cyclopentyloxy)-4-methoxyphenyl]pyrrolidin-2-one" "rolipram" "61413-54-5" "DB04149|DB03606" ""
"# GtoPdb Version: 2024.3 - published: 2024-10-03"
"Ligand id" "Name" "Species" "Type" "PubChem SID" "PubChem CID" "ChEMBl ID" "Chebi ID" "UniProt id" "Ensembl ID" "IUPAC name" "INN" "CAS" "DrugBank ID" "Drug Central ID"
"2169" "arginine vasotocin" "" "Peptide" "135652004" "68649" "" "" "" "" "L-cysteinyl-L-tyrosyl-(3S)-DL-isoleucyl-L-glutaminyl-L-asparagyl-L-cysteinyl-DL-prolyl-L-arginyl-glycinamide (1->6)-disulfide" "argiprestocin" "113-80-4" "" ""
"240" "cisapride" "" "Synthetic organic" "135650104" "2769" "CHEMBL1729" "CHEBI:151790" "" "" "4-amino-5-chloro-N-[1-[3-(4-fluorophenoxy)propyl]-3-methoxypiperidin-4-yl]-2-methoxybenzamide" "cisapride" "81098-60-4" "DB00604" "660"
"5343" "cisplatin" "" "Inorganic" "178102005" "441203" "CHEMBL11359" "CHEBI:27899" "" "" "" "cisplatin" "15663-27-1" "DB00515" ""
"3303" "L745870" "" "Synthetic organic" "178100340" "5311200" "CHEMBL267014" "" "" "" "3-[[4-(4-chlorophenyl)piperazin-1-yl]methyl]-1H-pyrrolo[2,3-b]pyridine" "" "158985-00-3" "" ""
"2804" "phenobarbital" "" "Synthetic organic" "135650817" "4763" "CHEMBL40" "CHEBI:8069" "" "" "5-ethyl-5-phenyl-1,3-diazinane-2,4,6-trione" "phenobarbital" "50-06-6" "DB01174" "2134"
"5260" "rolipram" "" "Synthetic organic" "178101944" "5092" "CHEMBL63" "CHEBI:104872" "" "" "4-[3-(cyclopentyloxy)-4-methoxyphenyl]pyrrolidin-2-one" "rolipram" "61413-54-5" "DB04149|DB03606" ""
16 changes: 8 additions & 8 deletions tests/data/guidetopharmacology/gtop_ligands_2024.3.tsv
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"# GtoPdb Version: 2024.3 - published: 2024-10-03"
"Ligand ID" "Name" "Species" "Type" "Approved" "Withdrawn" "Labelled" "Radioactive" "PubChem SID" "PubChem CID" "UniProt ID" "Ensembl ID" "ChEMBL ID" "Ligand Subunit IDs" "Ligand Subunit Name" "Ligand Subunit UniProt IDs" "Ligand Subunit Ensembl IDs" "IUPAC name" "INN" "Synonyms" "SMILES" "InChIKey" "InChI" "GtoImmuPdb" "GtoMPdb" "Antibacterial"
"2169" "arginine vasotocin" "" "Peptide" "" "" "" "" "135652004" "68649" "" "" "" "" "" "" "" "L-cysteinyl-L-tyrosyl-(3S)-DL-isoleucyl-L-glutaminyl-L-asparagyl-L-cysteinyl-DL-prolyl-L-arginyl-glycinamide (1->6)-disulfide" "argiprestocin" "[Arg<sup>8</sup>]vasotocin|AVT" "CC[C@@H](C1NC(=O)[C@H](Cc2ccc(cc2)O)NC(=O)[C@@H](N)CSSC[C@H](NC(=O)[C@@H](NC(=O)[C@@H](NC1=O)CCC(=O)N)CC(=O)N)C(=O)N1CCCC1C(=O)N[C@H](C(=O)NCC(=O)N)CCCN=C(N)N)C" "OXDZADMCOWPSOC-ICBIOJHSSA-N" "InChI=1S/C43H67N15O12S2/c1-3-21(2)34-41(69)53-26(12-13-31(45)60)37(65)55-28(17-32(46)61)38(66)56-29(20-72-71-19-24(44)35(63)54-27(39(67)57-34)16-22-8-10-23(59)11-9-22)42(70)58-15-5-7-30(58)40(68)52-25(6-4-14-50-43(48)49)36(64)51-18-33(47)62/h8-11,21,24-30,34,59H,3-7,12-20,44H2,1-2H3,(H2,45,60)(H2,46,61)(H2,47,62)(H,51,64)(H,52,68)(H,53,69)(H,54,63)(H,55,65)(H,56,66)(H,57,67)(H4,48,49,50)/t21-,24-,25-,26-,27-,28-,29-,30?,34?/m0/s1" "" "" ""
"240" "cisapride" "" "Synthetic organic" "yes" "yes" "" "" "135650104" "2769" "" "" "CHEMBL1729" "" "" "" "" "4-amino-5-chloro-N-[1-[3-(4-fluorophenoxy)propyl]-3-methoxypiperidin-4-yl]-2-methoxybenzamide" "cisapride" "Prepulsid&reg;|Propulsid&reg;" "COC1CN(CCCOc2ccc(cc2)F)CCC1NC(=O)c1cc(Cl)c(cc1OC)N" "DCSUBABJRXZOMT-UHFFFAOYSA-N" "InChI=1S/C23H29ClFN3O4/c1-30-21-13-19(26)18(24)12-17(21)23(29)27-20-8-10-28(14-22(20)31-2)9-3-11-32-16-6-4-15(25)5-7-16/h4-7,12-13,20,22H,3,8-11,14,26H2,1-2H3,(H,27,29)" "" "" ""
"5343" "cisplatin" "" "Inorganic" "yes" "" "" "" "178102005" "441203" "" "" "CHEMBL11359" "" "" "" "" "" "cisplatin" "Platinol&reg;" "" "" "" "" "" ""
"3303" "L745870" "" "Synthetic organic" "" "" "" "" "178100340" "5311200" "" "" "CHEMBL267014" "" "" "" "" "3-[[4-(4-chlorophenyl)piperazin-1-yl]methyl]-1H-pyrrolo[2,3-b]pyridine" "" "L 745870|L-745,870" "Clc1ccc(cc1)N1CCN(CC1)Cc1c[nH]c2c1cccn2" "OGJGQVFWEPNYSB-UHFFFAOYSA-N" "InChI=1S/C18H19ClN4/c19-15-3-5-16(6-4-15)23-10-8-22(9-11-23)13-14-12-21-18-17(14)2-1-7-20-18/h1-7,12H,8-11,13H2,(H,20,21)" "" "" ""
"2804" "phenobarbital" "" "Synthetic organic" "yes" "" "" "" "135650817" "4763" "" "" "CHEMBL40" "" "" "" "" "5-ethyl-5-phenyl-1,3-diazinane-2,4,6-trione" "phenobarbital" "fenobarbital|Luminal&reg;|phenobarb|phenobarbital sodium|phenobarbitone|phenylethylbarbiturate" "CCC1(C(=O)NC(=O)NC1=O)c1ccccc1" "DDBREPKUVSBGFI-UHFFFAOYSA-N" "InChI=1S/C12H12N2O3/c1-2-12(8-6-4-3-5-7-8)9(15)13-11(17)14-10(12)16/h3-7H,2H2,1H3,(H2,13,14,15,16,17)" "" "" ""
"5260" "rolipram" "" "Synthetic organic" "" "" "" "" "178101944" "5092" "" "" "CHEMBL63" "" "" "" "" "4-[3-(cyclopentyloxy)-4-methoxyphenyl]pyrrolidin-2-one" "rolipram" "(&plusmn;)-rolipram|(R,S)-rolipram" "COc1ccc(cc1OC1CCCC1)C1CNC(=O)C1" "HJORMJIFDVBMOB-UHFFFAOYSA-N" "InChI=1S/C16H21NO3/c1-19-14-7-6-11(12-9-16(18)17-10-12)8-15(14)20-13-4-2-3-5-13/h6-8,12-13H,2-5,9-10H2,1H3,(H,17,18)" "yes" "" ""
"# GtoPdb Version: 2024.3 - published: 2024-10-03"
"Ligand ID" "Name" "Species" "Type" "Approved" "Withdrawn" "Labelled" "Radioactive" "PubChem SID" "PubChem CID" "UniProt ID" "Ensembl ID" "ChEMBL ID" "Ligand Subunit IDs" "Ligand Subunit Name" "Ligand Subunit UniProt IDs" "Ligand Subunit Ensembl IDs" "IUPAC name" "INN" "Synonyms" "SMILES" "InChIKey" "InChI" "GtoImmuPdb" "GtoMPdb" "Antibacterial"
"2169" "arginine vasotocin" "" "Peptide" "" "" "" "" "135652004" "68649" "" "" "" "" "" "" "" "L-cysteinyl-L-tyrosyl-(3S)-DL-isoleucyl-L-glutaminyl-L-asparagyl-L-cysteinyl-DL-prolyl-L-arginyl-glycinamide (1->6)-disulfide" "argiprestocin" "[Arg<sup>8</sup>]vasotocin|AVT" "CC[C@@H](C1NC(=O)[C@H](Cc2ccc(cc2)O)NC(=O)[C@@H](N)CSSC[C@H](NC(=O)[C@@H](NC(=O)[C@@H](NC1=O)CCC(=O)N)CC(=O)N)C(=O)N1CCCC1C(=O)N[C@H](C(=O)NCC(=O)N)CCCN=C(N)N)C" "OXDZADMCOWPSOC-ICBIOJHSSA-N" "InChI=1S/C43H67N15O12S2/c1-3-21(2)34-41(69)53-26(12-13-31(45)60)37(65)55-28(17-32(46)61)38(66)56-29(20-72-71-19-24(44)35(63)54-27(39(67)57-34)16-22-8-10-23(59)11-9-22)42(70)58-15-5-7-30(58)40(68)52-25(6-4-14-50-43(48)49)36(64)51-18-33(47)62/h8-11,21,24-30,34,59H,3-7,12-20,44H2,1-2H3,(H2,45,60)(H2,46,61)(H2,47,62)(H,51,64)(H,52,68)(H,53,69)(H,54,63)(H,55,65)(H,56,66)(H,57,67)(H4,48,49,50)/t21-,24-,25-,26-,27-,28-,29-,30?,34?/m0/s1" "" "" ""
"240" "cisapride" "" "Synthetic organic" "yes" "yes" "" "" "135650104" "2769" "" "" "CHEMBL1729" "" "" "" "" "4-amino-5-chloro-N-[1-[3-(4-fluorophenoxy)propyl]-3-methoxypiperidin-4-yl]-2-methoxybenzamide" "cisapride" "Prepulsid&reg;|Propulsid&reg;" "COC1CN(CCCOc2ccc(cc2)F)CCC1NC(=O)c1cc(Cl)c(cc1OC)N" "DCSUBABJRXZOMT-UHFFFAOYSA-N" "InChI=1S/C23H29ClFN3O4/c1-30-21-13-19(26)18(24)12-17(21)23(29)27-20-8-10-28(14-22(20)31-2)9-3-11-32-16-6-4-15(25)5-7-16/h4-7,12-13,20,22H,3,8-11,14,26H2,1-2H3,(H,27,29)" "" "" ""
"5343" "cisplatin" "" "Inorganic" "yes" "" "" "" "178102005" "441203" "" "" "CHEMBL11359" "" "" "" "" "" "cisplatin" "Platinol&reg;" "" "" "" "" "" ""
"3303" "L745870" "" "Synthetic organic" "" "" "" "" "178100340" "5311200" "" "" "CHEMBL267014" "" "" "" "" "3-[[4-(4-chlorophenyl)piperazin-1-yl]methyl]-1H-pyrrolo[2,3-b]pyridine" "" "L 745870|L-745,870" "Clc1ccc(cc1)N1CCN(CC1)Cc1c[nH]c2c1cccn2" "OGJGQVFWEPNYSB-UHFFFAOYSA-N" "InChI=1S/C18H19ClN4/c19-15-3-5-16(6-4-15)23-10-8-22(9-11-23)13-14-12-21-18-17(14)2-1-7-20-18/h1-7,12H,8-11,13H2,(H,20,21)" "" "" ""
"2804" "phenobarbital" "" "Synthetic organic" "yes" "" "" "" "135650817" "4763" "" "" "CHEMBL40" "" "" "" "" "5-ethyl-5-phenyl-1,3-diazinane-2,4,6-trione" "phenobarbital" "fenobarbital|Luminal&reg;|phenobarb|phenobarbital sodium|phenobarbitone|phenylethylbarbiturate" "CCC1(C(=O)NC(=O)NC1=O)c1ccccc1" "DDBREPKUVSBGFI-UHFFFAOYSA-N" "InChI=1S/C12H12N2O3/c1-2-12(8-6-4-3-5-7-8)9(15)13-11(17)14-10(12)16/h3-7H,2H2,1H3,(H2,13,14,15,16,17)" "" "" ""
"5260" "rolipram" "" "Synthetic organic" "" "" "" "" "178101944" "5092" "" "" "CHEMBL63" "" "" "" "" "4-[3-(cyclopentyloxy)-4-methoxyphenyl]pyrrolidin-2-one" "rolipram" "(&plusmn;)-rolipram|(R,S)-rolipram" "COc1ccc(cc1OC1CCCC1)C1CNC(=O)C1" "HJORMJIFDVBMOB-UHFFFAOYSA-N" "InChI=1S/C16H21NO3/c1-19-14-7-6-11(12-9-16(18)17-10-12)8-15(14)20-13-4-2-3-5-13/h6-8,12-13H,2-5,9-10H2,1H3,(H,17,18)" "yes" "" ""
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