Avoiding TimeoutError

If there are too many results for a request, you will receive a TimeoutError. There are different ways to avoid this, depending on what type of request you are doing.

If retrieving full compound or substance records, instead request a list of cids or sids for your input, and then request the full records for those identifiers individually or in small groups. For example:

sids = get_sids('Aspirin', 'name')
for sid in sids:
    s = Substance.from_sid(sid)

When using the formula namespace or a searchtype, you can also alternatively use the listkey_count and listkey_start keyword arguments to specify pagination. The listkey_count value specifies the number of results per page, and the listkey_start value specifies which page to return. For example:

get_compounds('CC', 'smiles', searchtype='substructure', listkey_count=5)
get('C10H21N', 'formula', listkey_count=3, listkey_start=6)


PubChemPy can generate logging statements if required. Just set the desired logging level:

import logging

The logger is named ‘pubchempy’. There is more information on logging in the Python logging documentation.

Using behind a proxy

When using PubChemPy behind a proxy, you may receive a URLError:

URLError: <urlopen error [Errno 65] No route to host>

A simple fix is to specify the proxy information via urllib. For Python 3:

import urllib
proxy_support = urllib.request.ProxyHandler({
    'http': 'http://<proxy.address>:<port>',
    'https': 'https://<proxy.address>:<port>'
opener = urllib.request.build_opener(proxy_support)

For Python 2:

import urllib2
proxy_support = urllib2.ProxyHandler({
    'http': 'http://<proxy.address>:<port>',
    'https': 'https://<proxy.address>:<port>'
opener = urllib2.build_opener(proxy_support)

Custom requests

If you wish to perform more complicated requests, you can use the request function. This is an extremely simple wrapper around the REST API that allows you to construct any sort of request from a few parameters. The PUG REST Specification has all the information you will need to formulate your requests.

The request function simply returns the exact response from the PubChem server as a string. This can be parsed in different ways depending on the output format you choose. See the Python json, xml and csv packages for more information. Additionally, cheminformatics toolkits such as Open Babel and RDKit offer tools for handling SDF files in Python.

The get function is very similar to the request function, except it handles listkey type responses automatically for you. This makes things simpler, however it means you can’t take advantage of using the same listkey repeatedly to obtain different types of information. See the PUG REST specification for more information on how listkey responses work.

Summary of possible inputs

<identifier> = list of cid, sid, aid, source, inchikey, listkey; string of name, smiles, xref, inchi, sdf;
<domain> = substance | compound | assay

compound domain
<namespace> = cid | name | smiles | inchi | sdf | inchikey | <structure search> | <xref> | listkey | formula
<operation> = record | property/[comma-separated list of property tags] | synonyms | sids | cids | aids | assaysummary | classification

substance domain
<namespace> = sid | sourceid/<source name> | sourceall/<source name> | name | <xref> | listkey
<operation> = record | synonyms | sids | cids | aids | assaysummary | classification

assay domain
<namespace> = aid | listkey | type/<assay type> | sourceall/<source name>
<assay type> = all | confirmatory | doseresponse | onhold | panel | rnai | screening | summary
<operation> = record | aids | sids | cids | description | targets/{ProteinGI, ProteinName, GeneID, GeneSymbol} | doseresponse/sid

<structure search> = {substructure | superstructure | similarity | identity}/{smiles | inchi | sdf | cid}
<xref> = xref/{RegistryID | RN | PubMedID | MMDBID | ProteinGI | NucleotideGI | TaxonomyID | MIMID | GeneID | ProbeID | PatentID}
<output> = XML | ASNT | ASNB | JSON | JSONP [ ?callback=<callback name> ] | SDF | CSV | PNG | TXT