Drug database

Simple command line interface for getting scaling factors for different drugs

• Documentation: https://ComputationalPhysiology.github.io/drug-database/
• Source code: https://github.com/ComputationalPhysiology/drug-database

Install

$ python -m pip install drug-database

Once installed you will get access to the drug-db command.

Usage

Get help using

$ drug-db --help

List all available drugs

$ drug-db list-drugs
    Drugs
┏━━━━━━━━━━━━━━━━┓
┃           Name ┃
┡━━━━━━━━━━━━━━━━┩
│        Sotalol │
│      Azimilide │
│      Ibutilide │
│    Risperidone │
│ Clarithromycin │
│    Terfenadine │
│       Bepridil │
│       Pimozide │
│     Dofetilide │
│   Disopyramide │
│      Cisapride │
│      Tamoxifen │
│     Vandetanib │
│     Metropolol │
│     Droperidol │
│     Loratadine │
│     Ranolazine │
│      Quinidine │
│      Diltiazem │
│     Astemizole │
│   Nitrendipine │
│ Chlorpromazine │
│      Clozapine │
│        Control │
│     Nifedipine │
│      Verapamil │
│    Domperidone │
│    Ondansetron │
│     Mexiletine │
└────────────────┘

Showing information about specific drug

$ drug-db show-drug Verapamil
   Scaling factors for drug
     Verapamil and FPC 1
┏━━━━━━━━━━━━━━━━━━━┳━━━━━━━━┓
┃              Name ┃ Value  ┃
┡━━━━━━━━━━━━━━━━━━━╇━━━━━━━━┩
│    scale_drug_INa │ 1.0    │
│   scale_drug_INaL │ 1.0    │
│    scale_drug_Ito │ 1.0    │
│   scale_drug_ICaL │ 0.7342 │
│    scale_drug_IKr │ 0.8815 │
│    scale_drug_IKs │ 1.0    │
│    scale_drug_IK1 │ 1.0    │
│    scale_drug_IKb │ 1.0    │
│   scale_drug_INab │ 1.0    │
│   scale_drug_ICab │ 1.0    │
│   scale_drug_IpCa │ 1.0    │
│ scale_drug_Isacns │ 1.0    │
│  scale_drug_Isack │ 1.0    │
└───────────────────┴────────┘

Note that this is showing the values that are 1 times FPC (FIXME: explain what this means). If you want to get the values for 5 times FPC the you can do

$ drug-db show-drug Verapamil --fpc 5
   Scaling factors for drug
     Verapamil and FPC 5
┏━━━━━━━━━━━━━━━━━━━┳━━━━━━━━┓
┃              Name ┃ Value  ┃
┡━━━━━━━━━━━━━━━━━━━╇━━━━━━━━┩
│    scale_drug_INa │ 1.0    │
│   scale_drug_INaL │ 0.9997 │
│    scale_drug_Ito │ 1.0    │
│   scale_drug_ICaL │ 0.3199 │
│    scale_drug_IKr │ 0.5588 │
│    scale_drug_IKs │ 1.0    │
│    scale_drug_IK1 │ 1.0    │
│    scale_drug_IKb │ 1.0    │
│   scale_drug_INab │ 1.0    │
│   scale_drug_ICab │ 1.0    │
│   scale_drug_IpCa │ 1.0    │
│ scale_drug_Isacns │ 1.0    │
│  scale_drug_Isack │ 1.0    │
└───────────────────┴────────┘

json support

By default the tables are displayed in a Rich table, however sometimes you might want to use these values in another program in which you can convert the values to json by using the --json flag, e.g

$ drug-db show-drug Verapamil --fpc 5 --json
{"scale_drug_INa": 1.0, "scale_drug_INaL": 0.9997, "scale_drug_Ito": 1.0, "scale_drug_ICaL": 0.3199, "scale_drug_IKr": 0.5588, "scale_drug_IKs": 1.0, "scale_drug_IK1": 1.0, "scale_drug_IKb": 1.0,
"scale_drug_INab": 1.0, "scale_drug_ICab": 1.0, "scale_drug_IpCa": 1.0, "scale_drug_Isacns": 1.0, "scale_drug_Isack": 1.0}

You can also save this to a file using e.g

$ drug-db show-drug Verapamil --fpc 5 --json > verapamil_5.json

License

MIT

Author

Henrik Finsberg (henriknf@simula.no)