model_utils.drug

class pytrial.model_utils.drug.DrugTransformer[source]

Bases: object

Provide a series of drug-related functions for

  1. drug name to atc / atc to drug name

  2. drug name to ndc-11 / ndc-11 to drug name

  3. drug name to smiles (molecule structure)

  4. atc to smiles

  5. ndc-11 to smiles

  6. ndc-11 to atc / atc to ndc

To convert ndc-10 ditis to ndc-11, use convert_ndc10_ndc11.

atc2name(code)[source]
Parameters

code (str or list[str]) – ATC4 codes.

Returns

names – Drug names.

Return type

list[str] or list[list[str,None]]

atc2ndc(code)[source]
Parameters

code (str or list[str]) – ATC-4 codes.

Returns

NDC-11 codes

Return type

list[str] or list[list[str,None]]

atc2smiles(code)[source]
Parameters

code (str or list[str]) – ATC4 codes.

Returns

smiles – Drug molecule structures represented by SMILES.

Return type

list[str] or list[list[str,None]]

name2atc(name)[source]
Parameters

name (str or list[str]) – Drug names.

Returns

codes – ATC4 codes.

Return type

list[str] or list[list[str,None]]

name2ndc(name)[source]
Parameters

name (str or list[str]) – Drug names.

Returns

ndc codes

Return type

list[str] or list[list[str,None]]

name2smiles(name)[source]
Parameters

name (str or list[str]) – Drug names.

Returns

smiles – Drug molecule structures represented by SMILES.

Return type

list[str] or list[list[str,None]]

ndc2atc(code)[source]
Parameters

code (str or list[str]) – NDC-11 codes.

Returns

atc codes

Return type

list[str] or list[list[str,None]]

ndc2name(code)[source]
Parameters

code (str or list[str]) – NDC-11 codes.

Returns

name – Drug names.

Return type

list[str] or list[list[str,None]]

ndc2smiles(code)[source]
Parameters

name (str or list[str]) – Drug names.

Returns

smiles – Drug molecule structures represented by SMILES.

Return type

list[str] or list[list[str,None]]

class pytrial.model_utils.drug.DrugGraph(input_dir='./resources')[source]

Bases: object

Provide tools to get hierarchy of drug by ACT codes.

From ATC2 - ATC4 (dont include ATC5)

preprocess(dir='./resources')[source]

Process raw data and deposit the graph data to the local disk. Search ndc_atc.csv under the given directory dir. If not, download the raw files to the disk and unzip.