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Atom Label Assignment Tool using InChI String
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News:
  • Aug 2018: We deployed ALATIS application programming interface (API) here
  • May 2018: More than 91M PubChem entries have been processed and are available via the search engine.
  • April 2018: ALATIS naming system adopted by NMReData: https://doi.org/10.1002/mrc.4737.

ALATIS API

It is easy to submit your structure file and get an ALATIS InChI string returned. Simply send a POST request to 'http://alatis.nmrfam.wisc.edu/upload' with a JSON body with the following parameters:

  1. 'format_': The format of the uploaded structure file. Allowed values: 'sdf', 'mol', 'pdb', 'cdx'
  2. 'project_2_to_3': 'on' to project the 2D structure into a 3D one. Omit or set to any other value to not project.
  3. 'add_hydrogens': 'on' to add hydrogens. Omit or set to any other value to not project.
  4. 'response_type': 'json' - This tells the server to return the InChI in JSON format rather than returning a HTML web page.
  5. 'file': A file included in the body according to the standard HTTP POST file upload format.

Below is sample python code that you can use to query the API:

URL = 'http://alatis.nmrfam.wisc.edu/upload'
input_file_path = 'PATH_TO_YOUR_SDF_FILE'
format_ = 'sdf'
project_2_to_3 = 'off'
add_hydrogens = 'off'

files = {'infile': open(input_file_path, 'r')}
data = {'format': format_,
        'response_type': 'json',
        'project_2_to_3': project_2_to_3, # This can be omitted if the value is not 'on'
        'add_hydrogens': add_hydrogens # This can be omitted if the value is not 'on'
       }

r = requests.post(URL, data=data, files=files)

json_result = r.json()

print(json_result.keys(), json_result['inchi'])
            
Citation:
  • Hesam Dashti, William M. Westler, John L. Markley, Hamid R. Eghbalnia, "Unique identifiers for small molecules enable rigorous labeling of their atoms", Scientific Data 4, Article number: 170073 (2017), doi:10.1038/sdata.2017.73, https://www.nature.com/articles/sdata201773
Disclaimer:
  • ALATIS is available to the public as a web-service via our web-server, and also through the NMRBox virtual machine. The custom source code, developed using the academic license of MATLAB® in the Linux environment (MATLAB® 2016a for CentOS 6.5). This work is copyrighted under the terms of GPL. The web-service and the source codes are provided on an “as is” basis without warranty of any kind, either expressed or implied. Any usage of the web-server, or modification and application of the source codes are free for academic use when ALATIS publication is cited.
  • The input/output file formats to ALATIS are Mol V2000 and its corresponding SDF. Other acceptable input/output file formats of this website are provided by utilizing the Open Babel (The Open Source Chemistry Toolbox) software package, please comply with the Open Babel license agreements.
Contact:
    For any question or concern please contact Hesam Dashti (dashti@wisc.edu).
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