Atom Label Assignment Tool using InChI String
Analyzed databases
NMRFAM Servers

  • 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:


It is easy to submit your structure file and get an ALATIS InChI string returned. Simply send a POST request to '' 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 = ''
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 =, data=data, files=files)

json_result = r.json()

print(json_result.keys(), json_result['inchi'])
  • 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,
  • Hesam Dashti , Jonathan R. Wedell , William M. Westler , John L. Markley, Hamid R. Eghbalnia, “Automated evaluation of consistency within the PubChem Compound database”, Scientific Data volume 6, Article number: 190023 (2019), doi:10.1038/sdata.2019.23,
  • 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.
    For any question or concern please contact Hesam Dashti (
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