mcs07/pubchempy

Python wrapper for the PubChem PUG REST API.

PubChemPy

PubChemPy provides a way to interact with PubChem in Python. It allows chemical searches by name, substructure and similarity, chemical standardization, conversion between chemical file formats, depiction and retrieval of chemical properties.

>>> from pubchempy import get_compounds, Compound
>>> comp = Compound.from_cid(1423)
>>> print(comp.isomeric_smiles)
CCCCCCCNC1CCCC1CCCCCCC(=O)O
>>> comps = get_compounds('Aspirin', 'name')
>>> print(comps[0].xlogp)
1.2

Installation

Install PubChemPy using:

pip install pubchempy

Alternatively, try one of the other installation options.

Documentation

Full documentation is available at http://pubchempy.readthedocs.io.

Contribute

• Feature ideas and bug reports are welcome on the Issue Tracker.
• Fork the source code on GitHub, make changes and file a pull request.

License

PubChemPy is licensed under the MIT license.

pubchempy's Issues

pubchempy missing results available on the pubchem web page

pubchempy.get_compounds('NSC231854', 'name')
results in an empty list, yet searching the same string on the pubchem web page gives

NSC231854; NSC-231854
Substance SID: 567558
Data Source: DTP/NCI External ID: 231854
Data Source Category: Governmental Organizations
Deposit Date: 2005-03-26 Last Modified Date: 2011-12-19

Get SDF coordinates

Dear all,

Is it possible to get the mol block coordinates of a query structure?

Bests

Search with InChI and InChI key not working

Search with InChI and InChI key not working with pubchempy.get_compounds() (tried with many different compounds copying the codes from PumChem.

Searching for InChI gives:

'PUGREST.BadRequest: error: '
2022-01-16 21:20:43.003 'PUGREST.NotFound: No CID found that matches the given InChI key'

Searching for InChI key gives:

'PUGREST.NotFound: No CID found that matches the given InChI key'

Unable to get 3D structures for some molecules using Pubchempy

Hi Folks:
I am trying to get 3D structures for compounds in a database. The issue is I was not able to get 3D structures for some of the compounds, but I am very condifent that 3D strucutres for these compounds do exist on Pubchem.
For instance, the molecule Bunamidine hydrochloride, whose Pubchem CID is 13985, does have a 3D strucutre on Pubchem (you can search manually to verify). Use the command below:
pcp.get_compounds('13985','cid',record_type = '3d')
would return an empty list [], meaning that Pubchempy thinks there is no 3D strucutre for this molecule;
However, when using
pcp.get_compounds('13985','cid')
I got the result [Compound(13985)], meaning that at least Pubchem is able to identify this molecule. This is happening to many of the compounds in the database I am using. Interestingly, Pubchempy is able to correctly acquire 3D structure for some (very few) of those moleucules, for instance, CID 10522.
Anyone can provide any insight on what is going on? Thanks in advance for any help!

Is there a way to get all the SMILES for an assay?

Right now I am downloading the smiles one by one, from a compound ID with

mycp = pcp.Compound.from_cid(myCid) canSmiles = mycp.canonical_smiles

After a while, however, I get

urllib2.URLError: <urlopen error [Errno 110] Connection timed out>

And I suspect that pubchem gets (rightfully) upset and blacklists me for a while.

Is there any other way to get all the smiles for an assay?

Returncode if the structure does not exist

Good afternoon,

I would like to ask a question because I'm not able to find it.

I send the name of the structure to PubChem, but I cannot recognize if the structure does not exist. For example, I have the wrong name of the structure. Does it have some return code in case of wrong input?

Thank you.

Broken services or IP ban

Hi I am trying to get pubchem id for about 3k smiles, I worked one by one but was very slow, so I programmed a simple multi threading loop to get them a little faster, but it did work very well and now the service seems to be down I am getting
PubChemHTTPError: 'Service Unavailable'

Generating Pubchem Binary Fingerprint

Hello, thank you for your nice package.

I want to generate PubChem fingerprint which is 881 length binary bit vector
(PubChem fingerprint description: https://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.pdf)

Looking at the folder below in git, I found a suitable example.
"PubChemPy/examples/Chemical fingerprints and similarity.ipynb."

import pubchempy as pcp

coumarin = pcp.Compound.from_cid(323)

bin(int(coumarin.fingerprint, 16))

But output of bin function is length 900 and it contains "b".

I want to get exact length of PubChem Fingerprint from CID.

Please describe me how to do this.

Thanks in advance,

Hyojin

How to get the PubChem similarities between two compounds?

Hi, nice to find this package.
Currently, I have multiple compounds (with SDF formats, in fact, they are from Zinc Database).
Is it possible that I use their SDF formats to get their PubChem similarities ?
Thanks ~
Songpeng

How to set proxy for this lib instead of global proxy？

I want to set a proxy for pubchempy.

But I just wang to set for pubchempy instead of global proxy.

What should I do?

Modify the pubchempy.py or is there another way?

Thanks for your help.

How to get the chemical_vendors

Hi,
your package helps me a lot~
Now I have a request that given a CID, return its chemical_vendors. The chemical_vendors information is like below :

I cannot find such a function in your package, is there a possible way to do that?
Thanks ~
Songpeng

Is it possible to get 3D coordinates of ligand using CID or SID?

Is it possible to get 3D coordinates of ligand using CID or SID?

Approach-1

import pubchempy as pcp
pcp.download('SDF', '4369521.sdf', 4369521, 'cid',overwrite=True)

Approach-2

c = pcp.Compound.from_cid(4369521)
coords = [(c.x, c.y, c.z) for c in c.atoms]
print(coords)

In both solutions above, they give the result in 2 dimensions (2D).

I get an error when I try a code like below

import pubchempy as pcp
pcp.download('SDF', '4369521.sdf', 4369521, 'cid',overwrite=True, record_type = '3d')

I'm sure this topic will be useful for this highly sought-after question on the internet.

substance SID is being returned as compound CID

get_compounds('CC(=CCCC(C)(C1CCC2(C1C(CC3C2(CCC4C3(CCC(C4(C)C)OC5C(C(C(CO5)O)O)OC6C(C(C(C(O6)CO)O)O)O)CO)C)O)C)O)C','smiles') returns [Compound(15590165)].

The equivalent web lookup shows one result w/ a substance SID of 15590165. The true compound CID is 10562613.

API down for SMILES Search?

Previously functioning code using get_compounds with the smiles argument is currently disfunctional.

For example:

get_compounds('C1=CC2=C(C3=C(C=CC=N3)C=C2)N=C1', 'smiles')

raises an pubchempy.BadRequestError. This does not happen when searching for name and also not for substructure searches.

Possible reason: A bug on pubchem side: The UI seems to have trouble standardizing SMILES atm: https://pubchem.ncbi.nlm.nih.gov/#query=C1=CC2=C(C3=C(C=CC=N3)C=C2)N=C1

What's going on here?

Feature suggest, documentation on readthedocs.io w/ pdf

If there is an easy option to toggle this one on, I would like to suggest to equally offer the documentation on readthedocs.io as an (offline) .pdf file for local download, storage, indexing as seen, e.g., for OpenBabel.

Textual Descriptions

Is it possible to extract the textual descriptions of compounds using PubChemPy?
They are featured on the site in the Compound Summary, but I am unsure if PubChemPy has this functionality.

Thanks

to_dic bugs on Substance

Some data in Pubchem does not provides compound value while other data source provides. In this case, to_dataframe or to_dict funtion generate error no "compound"

    """
    Some substances of pubchem data doesnot provide compound key
    for c in self.record['compound']:
        if c['id']['type'] == CompoundIdType.STANDARDIZED:
            return c['id']['id']['cid']

    """
    if 'compound' in self.record:
        for c in self.record['compound']:
            if c['id']['type'] == CompoundIdType.STANDARDIZED:
                return c['id']['id']['cid']

I think it can be fixed with checking whether Substances has a "compound" key in record

example case bug occurres:
pcp.get_substances("65983-31-5", "name")

It return almost 21 substance from pubchem server and 20th substance

Substance(342573178) has no "compound" key in record, therefore it generates errors when you use to_dataframe or to_dict

Discrepancy between the CACTVS fingerprint spec and Compound.fingerprint

The specifications for the compound fingerprints suggest different coding then the program reports.
For example:
CID 7844's fingerprint should be:

'AAADccBgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAACACAAAACAAAAAACAACBCAAAAAAAgAAAIAAAAAAgAAAAAAQAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA'

This is according to both the PubChem spec and the PubChem download page.
However the fingerprint collected from the program is:

'00000371C06000000000000000000000000000000000000000000000000000000000000000000018000000000008008000000200000000008000204200000000002000000800000000080000000001000000000000000000000000000000000000000000000000000000000000000000000000'

My guess is that this is a different encoding scheme. But this is different from the spec at ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.txt, which makes it hard to connect this fingerprint to the actual properties.

Fix warning: "is not" with a literal. Did you mean "!="?

/app/.heroku/python/lib/python3.8/site-packages/pubchempy.py:563: SyntaxWarning: "is not" with a literal. Did you mean "!="?

pubchempy.ServerError: 'PUGREST.ServerError'

The server appears to be down for about 24 hours now. How soon can we expect service to resume?

Thanks.

Is it possible to calculate the PMI of the compounds?

Dear team,

I am trying to calculate the principal moment of inertia (PMI) of a compound in PubChem. Is there a way to get this property directly from the script? If not, can you point me on how I can get the 3D conformer of the molecule that can be plugged into RDKit for further use with this - https://www.rdkit.org/docs/source/rdkit.Chem.Descriptors3D.html?

Thank you

Search by CAS #?

Hello. I am wondering if there is a way to use the PubChemPy to search by CAS #?

Thanks,

Stan

testing glucose example

Hi ,
I am trying to test the glucose example to retrieve compunds from pubchem - I am using a jupyter notebook with python 3:

import pubchempy as pcp
results = pcp.get_compounds('Glucose', 'name')
results

which only returns one of the

5793
C([C@@h]1C@HO)O

where I would expect the different forms of glc - the type is a list. has there been any changes to this lately ?

how to download several compounds at once?

Hello,
Thanks for this very useful library!
Is it possible to download at once
several (many?) compounds using their inchis?
I just know how to do one by one, but this is quite slow.
Thanks,
F.

Two substance tests out-of-date

The tests TestSubstance.test_synonyms and TestSubstance.test_source are out-of-date with respect to the Pubchem database making those tests fail.

get_compounds no longer returns multiple hits

On the getting started page there is this snippet:

results = pcp.get_compounds('Glucose', 'name')
print results
[Compound(79025), Compound(5793), Compound(64689), Compound(206)]

If I run that now, I only get one compound. Multiple compounds would be my preferred behavior. For example if I request '2-nonenal' I'd like to get both the isomers.

version 1.0.3

Extracting Dielectric constant

Hi,

How can we extract dielectric constant of of a solvent (say water) from the pubchem. I tried the code given in the manual for properties like MolecularWeight, HBondDonorCount etc and they worked. When I replace them with DielectricConstant it gives me the following error.

pubchempy.BadRequestError: 'PUGREST.BadRequest

Can someone please help me extract the DielectricConstant.

Thank you.

Xref-queries always 404

It's not possible to perform cross-reference queries (version 1.0.3, Python 3.6.1). For instance the query:
https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/xref/PatentID/US6187568B1/sids/JSON

Can be formulated as:

import pubchempy as pcp
response = pcp.request('US6187568B1', 'PatentID', 'substance', operation='sids', searchtype='xref')

However, this request 404:s since the ID is sent as payload data instead of inserted in the URL here.

SMILES string full of tungsten

4,4',4''-methanetriyltris(N,N-diethylaniline) (https://pubchem.ncbi.nlm.nih.gov/compound/Leucocrystal-Violet#section=MeSH-Entry-Terms) comes up with the following SMILES:
[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].CCN(CC)c1ccc(cc1)C+c3ccc(cc3)N(CC)CC'

I'm unsure if this is the right place to submit this info.

search by name function is not working for tetrabamate

Hi,
First of all, thanks for the nice package, it is very helpful for me.
I have a problem with the search function- get_compounds(Compound_Name, 'name') when I'm trying to fetch "tetrabamate" details and get no results, however, I had tried directly the pubchem API, and it finds the relevant cids I need.

the line code:
cs = get_compounds('tetrabamate', 'name') <- this line perfectly works for the other molecules.

I will be happy if you can help me to solve this problem.

Thank you

How to use this code for generate input file form pubchem

for a Ml model i need to import pubchem data in order to make a data frame. The format id given bellow

Structure Smiles LogP MolWt IC50 value
CCCHOCC xxx xxxx xxxx
xxxxxx xxx xxxx xxxx

how to do that. I found following codes in your tutorial

from pubchempy import get_compounds, Compound
comp = Compound.from_cid(1423)
print(comp.isomeric_smiles)
CCCCCCCNC1CCCC1CCCCCCC(=O)O
comps = get_compounds('Aspirin', 'name')
print(comps[0].xlogp)

where i need to provide the structure identifier manually or i need to make a list.

any advice from your end.

Using pubchempy / urllib behind proxy

I'm using PubChem from behind a proxy (Research institute).
I ran into error Errno 65:

>>> import pubchempy as pug
>>> compound = pug.Compound.from_cid(1423)
...
URLError: <urlopen error [Errno 65] No route to host>

A relatively simple fix is to specify proxy information via urllib:

>>> import urllib
>>> import pubchempy as pug
>>> proxies = {'http': 'http://<proxy.address>:<port>',
...            'https': 'https://<proxy.address>:<port>'}
>>> proxy_support = urllib.request.ProxyHandler(proxies)
>>> opener = urllib.request.build_opener(proxy_support)
>>> urllib.request.install_opener(opener)
>>> compound = pug.Compound.from_cid(1423)
>>> compound
Compound(1423)

The issue is that there is no mention of specifying proxy information in the PubChem documentation.
Addressing this in your documentation (even just a link to the urllib docs) could save others a lot of time.

Dose

Hi,

Thank you for so useful library. One question, I am seeing as in request advance mode it's possible obtaing the doseresponse, I would like to obtain the therapeutic dose of drugs. Could you help me please?

Thanks!

How to retrieve compounds' physical property?

Is there any function in PubChemPy that can return compounds' physical properties?

On certain Compounds, the atoms() function fails

When I run the following (after importing Compound):

>>>c = Compound.from_cid(259)
>>>c.to_dict()

I get the following traceback:
http://pastebin.com/s0ReyQNG

I'm going to rewrite atoms() and see if I can stop this error from occuring. If I can, I'll make a pull request.

Conda installation problems

Hey there,

I tried to download your framework using "conda install -c mcs07 pubchempy" as suggested by the documentation. It's downloaded into the right folder (I can see all the other packages I've ever downloaded there as well), but when I try and install the package in my Anaconda Environment pubchempy is nowhere to be found.

Any ideas on how to fix this?

Thanks in advance.

ImportError: Failed to import test module: pubchempy_test

Hello,

I tried to run a test with setup.py test, but I encounter an error below, is this a problem?

Thanks.

python3 setup.py test
running test
WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox.
running egg_info
writing PubChemPy.egg-info/PKG-INFO
writing dependency_links to PubChemPy.egg-info/dependency_links.txt
writing requirements to PubChemPy.egg-info/requires.txt
writing top-level names to PubChemPy.egg-info/top_level.txt
reading manifest file 'PubChemPy.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'pubchempy_test.py'
no previously-included directories found matching 'docs/build'
writing manifest file 'PubChemPy.egg-info/SOURCES.txt'
running build_ext
pubchempy_test (unittest.loader._FailedTest) ... ERROR

======================================================================
ERROR: pubchempy_test (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: pubchempy_test
Traceback (most recent call last):
  File "/usr/lib64/python3.8/unittest/loader.py", line 154, in loadTestsFromName
    module = __import__(module_name)
ModuleNotFoundError: No module named 'pubchempy_test'


----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)
Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
error: Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>

Using the search bar

Hi, is there any way I could search for compounds like I do with the search bar?

That is, I input a string and the list of results would be that which I would get if I had inputted this string into PubChem's search bar.

PubChemPy stopped working today

Hi there,

I have been using PubChemPy for a while and it's been working great until today when commands that used to work don't anymore. For example, the simple command compounds = pcp.get_compounds('methane', 'name', record_type='3d') gives the error URLError:

<urlopen error [Errno 8] nodename nor servname provided, or not known>

I suspect there's been some changes to PubChem itself?

Errors in the encoding of some bits

Hi,
I was checking the code behind the PubChem fingerprint generation.
I did some comparisons between fingerprints calculated with your code and those calculated with PyFingerprint which uses the cdk library and noticed some differences.
I noticed that for bits in the range 0-98, smarts are not used and therefore when carbons are counted for example, only aliphatic carbons are considered since the corresponding key is C.
As a result the counting and encoding are incorrect.
The second point concerns the bits in the range 115-231: in this case there are two conditions to be met such as bits 116 and 117 mention ">= 1 saturated or aromatic carbon-only ring size 3 " and ">= 1 saturated or aromatic nitrogen-containing ring size 3" respectively. In this case a cyclopropane ring should be detected by bit 116 but not by bit 117. Instead with your code it is encoded for both bits.

I hope the bugs I reported are corrected otherwise I would be glad to have an explanation of my mistake

Thank you for your helpfulness
Salvatore

the sdf record approach recommend

I have study the pubchem api for a while, and found that the best api approach from cheminformatics view, maybe the best api approach is not the general json approach method which is popularity in the web.

I reccomend the sdf approach , the temp pysdf project .

It is really ease to parse the sdf content , and we will get the molfile_content and other property.

Please check here my work: chem .

we get the original property from the sdf file, and only need do some rename trick and we will get out property name directly.

Get full assays data

Is there a way to get a full assay data without having to do a manual request?

Getting 3D coordinates

Hello, I'm trying to get xyz coordinates from Compound class. In _setup_atoms function (line 689) it looks like you are assigning the coordinates to _atoms dict with set_coordinates function. Where is this set_coordinates? There is one in Atom class sure but it's not in Compound class. I get no coordinates when I run this:

import pubchempy as pcp
cid = pcp.get_cids('methane', 'name')[0]
m = pcp.Compound.from_cid(cid, record_type='3d')
m._atom

Am I doing something wrong?

Retrieving MoA (mechanism of action)

I'm looking for a method to give me the MoA (mechanism of action) of compounds. I could not find such a method in your API. I also downloaded the XML files of compounds both using your download method and directly from the FTP server and couldn't find the MoA information (I haven't looked at the ASN1 files yet though.)

I wonder if there's any method in pubchempy which can give me the MoA of compounds, if available.

[UPDATE] I just realized I can programmatically get the MoA information by sending a request like: https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/2519/JSON?heading=Mechanism+of+Action for a compound with cid 2519. But still wondering if I can get such information using the PubChemPy?

Fetch Solubility data

I want to get Solubility data (4.2.7) for a list of compounds.
get_properties fetches 4.1 Computed Properties but I am not sure how to get 4.2 Experimental Properties.

Please let me know what would be the best way to fetch this field.
Thanks in advance.

BadRequestError

Running this code from the documentation:

pcp.get_compounds('CC', searchtype='superstructure', listkey_count=3)

Generates the following error:

Traceback (most recent call last):
File "", line 1, in
File "c:\Python27\lib\site-packages\pubchempy.py", line 124, in get_compounds
results = get_json(identifier, namespace, searchtype=searchtype, **kwargs)
File "c:\Python27\lib\site-packages\pubchempy.py", line 109, in get_json
return json.loads(get(identifier, namespace, domain, operation, 'JSON', sear
chtype, **kwargs).decode())
File "c:\Python27\lib\site-packages\pubchempy.py", line 90, in get
response = request(identifier, namespace, domain, None, 'JSON', searchtype,
**kwargs).read()
File "c:\Python27\lib\site-packages\pubchempy.py", line 84, in request
raise PubChemHTTPError(e)
File "c:\Python27\lib\site-packages\pubchempy.py", line 1089, in init
raise BadRequestError(self.msg)
pubchempy.BadRequestError: 'Bad Request'

This preceding example from the same page works without error:

>>> pcp.get_compounds('Aspirin', 'name', record_type='3d')
[Compound(2244)]
>>>

JSON Decode Error when using similarity search

Hey,

I am trying to search pubchem for similar compounds with this call:

similars = pcp.get_compounds(smile, 'smiles', searchtype='similarity', threshold=0.7, as_dataframe=True)

This works well for some SMILES, for example for "Cc1noc(C)c1Br".
But for others, e.g. "Cn1c(=O)c2nc(Cl)[nH]c2n(C)c1=O", I get the following error:

Traceback (most recent call last):
  File "/home/caro/leval/.snakemake/scripts/tmpqq4csqb1.find_pubchem_hits.py", line 37, in <module>
    similars = pcp.get_compounds("Cn1c(=O)c2nc(Cl)[nH]c2n(C)c1=O", 'smiles', searchtype='similarity', threshold=similarity_threshold, as_dataframe=True)
  File "/home/caro/leval/.snakemake/conda/db9d54b7c1d0500c41e4539e39469ab2/lib/python3.9/site-packages/pubchempy.py", line 321, in get_compounds
    results = get_json(identifier, namespace, searchtype=searchtype, **kwargs)
  File "/home/caro/leval/.snakemake/conda/db9d54b7c1d0500c41e4539e39469ab2/lib/python3.9/site-packages/pubchempy.py", line 299, in get_json
    return json.loads(get(identifier, namespace, domain, operation, 'JSON', searchtype, **kwargs).decode())
  File "/home/caro/leval/.snakemake/conda/db9d54b7c1d0500c41e4539e39469ab2/lib/python3.9/site-packages/pubchempy.py", line 288, in get
    status = json.loads(response.decode())
  File "/home/caro/leval/.snakemake/conda/db9d54b7c1d0500c41e4539e39469ab2/lib/python3.9/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/home/caro/leval/.snakemake/conda/db9d54b7c1d0500c41e4539e39469ab2/lib/python3.9/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/caro/leval/.snakemake/conda/db9d54b7c1d0500c41e4539e39469ab2/lib/python3.9/json/decoder.py", line 353, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 322816 column 7 (char 7196244)

If I turn the double quotation marks around the SMILES into single ones, I get

json.decoder.JSONDecodeError: Expecting property name enclosed in double quotes: line 215438 column 3 (char 4812373)

I would be glad if you could help me here!

Cheers,
Caro

TypeError when trying to download a compund with None as cid

I was doing a search with get_compounds with smiles string and I got a compound with None as cid.
I know it could not make sense to ask for a compound with a cid as None, but we could do a check on the cid formats.
I will analyse why get_compounds returned a Compound object with None as cid later.
I can provide a fix to this issue and to get_compunds if there is a bug there also (I will open other ticket in that case)

This was the error:

Traceback (most recent call last):
  File "convert_old_ligand_to_pubchem.py", line 29, in <module>
    pcp.download('sdf', temp_filename, pubchem_ligand.cid, 'cid')
  File "/home/leonardo/workspace/PubChemPy/pubchempy.py", line 450, in download
    response = get(identifier, namespace, domain, operation, outformat, searchtype, **kwargs)
  File "/home/leonardo/workspace/PubChemPy/pubchempy.py", line 287, in get
    response = request(identifier, namespace, domain, operation, output, searchtype, **kwargs).read()
  File "/home/leonardo/workspace/PubChemPy/pubchempy.py", line 247, in request
    identifier = ','.join(str(x) for x in identifier)
TypeError: 'NoneType' object is not iterable

SSL error

getting a SSL error and an urllib error. I'm just following the examples in the documentation so I'm not sure how to fix it. I've tried using the API on two different networks and I am still getting this error. Does it have something to do with the pubchem servers or is this on my end?

thanks

Search by canonical SMILES to retrieve all stereoisomers

Is it possible to perform a PUG REST synchronous (fastidentity) search to retrieve all related isomers for a canonical SMILES string (unspecified sterochemistry)? get_cids() returns a list with a single CID.

For example, the following request returns the desired information as JSON.
CC(C)(C)NCC(C1=CC(=C(C=C1)O)CO)O is the canonical SMILES for albuterol (CID = 2083).

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/smiles/CC(C)(C)NCC(C1=CC(=C(C=C1)O)CO)O/cids/JSON?identity_type=same_isotope

Returns:

{
  "IdentifierList": {
    "CID": [
      2083,
      123600,
      182176
    ]
  }
}