PubChem_Similarity
Search for chemical structures in PubChem via a Fingerprint Tanimoto Similarity Search
% Vincent F. Scalfani, Serena C. Ralph, and Jason E. Bara
% The University of Alabama
% Tested with MATLAB R2020a, running Ubuntu 18.04 on March 30, 2020.
Define the PubChem API base URL
% PubChem API
api = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/';
% set MATLAB web options to a 30 second timeout
options = weboptions('Timeout', 30);
% Retrieve and display PNG Image of 1-Butyl-3-methyl-imidazolium; CID = 2734162
CID_SS_query = '2734162';
CID_url = [api 'cid/' CID_SS_query '/PNG'];
[CID_img,map] = imread(CID_url);
imshow(CID_img,map)
Replace the above CID value (CID_SS_query) with a different CID to customize.
Retrieve InChI and SMILES
% Retrieve InChI
inchi_url = [api 'cid/' CID_SS_query '/property/inchi/TXT'];
inchi = webread(inchi_url, options);
disp(inchi)
% Retrieve Isomeric SMILES
IS_url = [api 'cid/' CID_SS_query '/property/IsomericSMILES/TXT'];
IS = webread(IS_url, options);
disp(IS)
Perform a Similarity Search
% Search for chemical structures by Similarity Search (SS),
% (2D Tanimoto threshold 95% to 1-Butyl-3-methyl-imidazolium; CID = 2734162)
api = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/';
SS_url = [api 'fastsimilarity_2d/cid/' CID_SS_query '/cids/JSON?Threshold=95'];
SS_CIDs = webread(SS_url,options);
SS_CIDs = num2cell(SS_CIDs.IdentifierList.CID)
In the above SS_url value, you can adjust to the desired Tanimoto threshold (i.e., 97, 90, etc.)
% set a CID limit to 25 max
The CID limit of 25 was added as an initial testing safety for time consideration. This limit can be increased.
number_SS_CIDs = length(SS_CIDs)
number_SS_CIDs = 249
if number_SS_CIDs > 25
SS_CIDs = SS_CIDs(1:25)
else
disp('Number of SS_CIDs not changed')
end
Retrieve Identifier and Property Data
% Create an identifier/property dataset from Similarity Search results
% Retrieve the following data from CID hit results:
% InChI, Isomeric SMILES, MW, Heavy Atom Count, Rotable Bond Count, and
% Charge
% setup a for loop that processes each CID one-by-one
for r = 1:length(SS_CIDs)
CID = SS_CIDs{r};
% define api calls
api = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/';
CID_InChI_url = [api 'cid/' num2str(CID) '/property/InChI/TXT'];
CID_IsoSMI_url = [api 'cid/' num2str(CID) '/property/IsomericSMILES/TXT'];
CID_MW_url = [api 'cid/' num2str(CID) '/property/MolecularWeight/TXT'];
CID_HeavyAtomCount_url = [api 'cid/' num2str(CID) '/property/HeavyAtomCount/TXT'];
CID_RotatableBondCount_url = [api 'cid/' num2str(CID) '/property/RotatableBondCount/TXT'];
CID_Charge_url = [api 'cid/' num2str(CID) '/property/Charge/TXT'];
Additional property data can be collected by defining new api calls, for example, if you want TPSA data:
% CID_TPSA_url = [api 'cid/' num2str(CID) '/property/TPSA/TXT'];
% retrieve identifer and property data
try
CID_InChI = webread(CID_InChI_url,options);
catch ME
CID_InChI = 'not found'
end
% be polite to PubChem server
n = 0.5;
pause(n)
try
CID_IsoSMI = webread(CID_IsoSMI_url,options);
catch ME
CID_IsoSMI = 'not found'
end
n = 0.5;
pause(n)
try
CID_MW = webread(CID_MW_url,options);
catch ME
CID_MW = 'not found'
end
n = 0.5;
pause(n)
try
CID_HeavyAtomCount = webread(CID_HeavyAtomCount_url,options);
catch ME
CID_HeavyAtomCount = 'not found'
end
n = 0.5;
pause(n)
try
CID_RotatableBondCount = webread(CID_RotatableBondCount_url,options);
catch ME
CID_RotatableBondCount = 'not found'
end
n = 0.5;
pause(n)
try
CID_Charge = webread(CID_Charge_url,options);
catch ME
CID_Charge = 'not found'
end
n = 0.5;
pause(n)
% add property data to SS_CIDs data array
% column numbers indicate where the data will be stored.
% For example, the MW will be placed in column 4. r increases
% by 1 on each iteration, so the first CID_MW value gets stored in
% {1,4}, the second in {2,4}, the third in {3,4}, etc.
SS_CIDs{r,2} = CID_InChI;
SS_CIDs{r,3} = CID_IsoSMI;
SS_CIDs{r,4} = CID_MW;
SS_CIDs{r,5} = CID_HeavyAtomCount;
SS_CIDs{r,6} = CID_RotatableBondCount;
SS_CIDs{r,7} = CID_Charge;
% to add more data, simply index into the next column
% SS_CIDs{r,8} = CID_TPSA;
end
Compile Data into a Table
% convert cell array to string and remove leading and trailing white space
SS_CIDs_string = strtrim(string(SS_CIDs));
% convert to table
SSq_table = array2table(SS_CIDs_string, 'VariableNames',{'CID', 'InChI','IsoSMI','MW',...
'HeavyAtomCount','RotatableBondCount','Charge'})
% rearrange table
SSq_table2 = SSq_table(:, {'IsoSMI' 'CID' 'InChI' 'MW' 'HeavyAtomCount' 'RotatableBondCount' 'Charge'})
% data export as tabbed text file
% prompt user to select folder for data export
save_folder = uigetdir;
% change directory to selected folder
cd(save_folder)
writetable(SSq_table2,'MATLAB_Similarityq_results.txt','Delimiter','tab')
Retrieve Images of CID Compounds from Similarity Search
% loop through hit CIDs and show images
for r = 1:length(SS_CIDs)
CID = SS_CIDs{r};
api = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/';
CID_url = [api 'cid/' num2str(CID) '/PNG'];
try
% retrieve CID PNG image and display
[CID_img,map] = imread(CID_url);
figure;
imshow(CID_img,map)
drawnow;
title(num2str(CID));
% be polite to PubChem server
n = 0.5;
pause(n);
catch
disp('CID image not found')
disp('Execution will continue')
end
end
