openbabel.cheminfo.org/v1/convert - Web API

Q

How to make a HTTP request to the Open Babel Web API at openbabel.cheminfo.org/v1/convert?

✍: FYIcenter.com

A

You can call the Open Babel Web API at https://openbabel.cheminfo.org/v1/convert with a HTTP POST request as shown below.

1. Use "curl" command to call the Web API to generate a 3D SDF file from a given SMILES string.

curl https://openbabel.cheminfo.org/v1/convert \
--form input='c1ccccc1' --form inputFormat='smiles -- SMILES format' \
--form outputFormat='sdf -- MDL MOL format' --form coordinates='3D' \
--form hydrogens='Delete'

{"result":"\n OpenBabel01122301573D\n\n
  6  6  0  0  0  0  0  0  0  0999 V2000\n
    1.3831   -0.2216    0.0059 C   0  0  0  0  0  0  0  0  0  0  0  0\n
    0.5071   -1.3070   -0.0080 C   0  0  0  0  0  0  0  0  0  0  0  0\n
   -0.8711   -1.0906   -0.0144 C   0  0  0  0  0  0  0  0  0  0  0  0\n
   -1.3727    0.2109   -0.0040 C   0  0  0  0  0  0  0  0  0  0  0  0\n
   -0.4966    1.2959    0.0106 C   0  0  0  0  0  0  0  0  0  0  0  0\n
    0.8813    1.0799    0.0144 C   0  0  0  0  0  0  0  0  0  0  0  0\n
...
}

Note that the "--form" options encode POST data as "multipart/form-data". If you use the "--data" option to encode POST data as "application/x-www-form-urlencoded", you will get an error:

curl https://openbabel.cheminfo.org/v1/convert \
--data 'input=c1ccccc1&inputFormat=smiles+--+SMILES+format&outputFormat=sdf+--+MDL+MOL+format&coordinates=3D&hydrogens=Delete'

{"statusCode":415,"code":"FST_ERR_CTP_INVALID_MEDIA_TYPE",
 "error":"Unsupported Media Type",
 "message":"Unsupported Media Type: application/x-www-form-urlencoded"}

2. Use PHP script to call the Web API to generate a 3D SDF file from a given SMILES string.

php > $post = [
php >     'input' => 'c1ccccc1',
php >     'inputFormat' => 'smiles -- SMILES format',
php >     'outputFormat' => 'sdf -- MDL MOL format',
php >     'coordinates' => '3D',
php >     'hydrogens' => 'Delete'
php > ];
php > 
php > $log = fopen('curl.log', 'w');
php > $ch = curl_init('https://openbabel.cheminfo.org/v1/convert');
php > curl_setopt($ch, CURLOPT_RETURNTRANSFER, true);
php > curl_setopt($ch, CURLOPT_POSTFIELDS, $post);
php > curl_setopt($ch, CURLOPT_VERBOSE, 1);
php > curl_setopt($ch, CURLOPT_STDERR, $log);
php > $response = curl_exec($ch);
php > curl_close($ch);
php > fclose($log);
php > 
php > print($response);

{"result":"\n OpenBabel01122301293D\n\n  6  6  0  0  0  0  0  0  0  0999 V2000\n    1.3831   -0.2215    0.0055 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.5068   -1.3068   -0.0081 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8712   -1.0907   -0.0144 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.3730    0.2107   -0.0047 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4968    1.2959    0.0101 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.8811    1.0798    0.0139 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  1  6  2  0  0  0  0\n  2  3  2  0  0  0  0\n  3  4  1  0  0  0  0\n  4  5  2  0  0  0  0\n  5  6  1  0  0  0  0\nM  END\n$$$$\n","log":"1 molecule converted\n"}

By default, CURLOPT_POSTFIELDS option will encode POST data as "multipart/form-data", not "application/x-www-form-urlencoded".

 

Open Babel Documentation and Resources

Open Babel Web Interface at cheminfo.org

Introduction to Open Babel

⇑⇑ Open Babel Tutorials

2023-01-24, 378🔥, 0💬