wadi.api_utils module

wadi.api_utils.translate_strings(strings, src_lang, dst_lang, max_attempts)

This method attempts to translate a list of strings from src_lang to dst_lang using Google Translate.

Parameters:

  • src_lang (str) – String that specifies the language to translate from. Default: “NL”.

  • dst_lang (str) – String that specifies the language to translate to. Default: “EN”.

  • max_attempts (int) – The maximum number of attempts to connect to the Google Translate API. Default: 10.

wadi.api_utils.get_pubchem_json(url)

This method interacts with the PubChem REST API by sending a URL and, when successful, returns a json dict.

Parameters:

url (str) – The URL containing the query/request.

Returns:

result – Returns the json dictonary returned by the PubChem API, or None if an error occurred.

Return type:

dict or None

wadi.api_utils.query_pubchem_fuzzy(s)

This method uses the PubChem REST auto-complete API service that supports fuzzy matching of input strings.

Parameters:

s (str) – The string to look up

Returns:

result – A two-element list. The first element is the first compound name returned if the request was successful, the second the first synonym returned by calling query_pubchem_synonyms. Returns [None, None] if any error occurred.

Return type:

list

wadi.api_utils.query_pubchem_synonyms(s, namespace='name')

This method uses the PubChem REST API service to look up synonyms of a PubChem compound based on its name or other allowed namespace. See https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest#section=Input.

Parameters:

  • s (str) – The string to look up

  • namespace (str, optional) – The namespace to seach for (for example, ‘name’, ‘cid’, ‘smiles’, …). Default: ‘name’

Returns:

result – The return value is the list that is stored in the ‘Information’ item of the json dict. This list contains a dict (or perhaps more?) with the CID and a list of synonyms. Returns None if an error occurred.

Return type:

list

wadi.api_utils.query_pubchem_cas(s, namespace='name', allow_multiple=False)

This method uses the PubChem REST API service to look up the CAS of a PubChem compound based on its name or other allowed namespace. See https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest#section=Input. The CAS number returned is the first number matched by a regular expression in the list of synonyms for the compound.

Parameters:

  • s (str) – The string to look up

  • namespace (str, optional) – The namespace to seach for (for example, ‘name’, ‘cid’, ‘smiles’, …). Default: ‘name’

  • allow_multiple (bool, optional) – When False only the first CAS that was identified is returned. When True all CAS numbers in the synonym list are returned. Default: False.

Returns:

result – The return value is the list that is stored in the ‘Information’ item of the json dict. This list contains a dict (or perhaps more?) with the CID and a list of synonyms. Returns None if an error occurred.

Return type:

list

wadi.api_utils.get_pubchem_molecular_weight(s, namespace='name')

This method uses the PubChem REST API service to look up the molecular weight of a PubChem compound based on its name or other allowed namespace. See https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest#section=Input.

Parameters:

  • s (str) – The string to look up

  • namespace (str, optional) – The namespace to seach for (for example, ‘name’, ‘cid’, ‘smiles’, …). Default: ‘name’

Returns:

result – The return value is the ‘MolecularWeight’ item of the json dict returned by PubChem or None if an error occurred.

Return type:

float

wadi.api_utils.get_pubchem_properties(cids, props)

This method uses the PubChem REST API service to retrieve a table of compound properties for one or more compounds based on their cid(s).

Parameters:
Returns:

result – A list with the requested properties, or None if the request was unsuccessful.

Return type:

list