2.3 Creating a Molecule from SMILES

A common method of creating a molecule in OEChem is via the SMILES representation. SMILES notation is commonly used in chemical information systems, as it provides a convenient string representation of a molecule. An introduction to SMILES syntax is provided later in this manual. For examples, below we'll use the SMILES ``c1ccccc1'' which describes the molecule benzene.

A molecule can be created from a SMILES string using the function OEParseSmiles

 1 #include "openeye.h"
 2 #include "oechem.h"
 3
 4 using namespace OEChem;
 5
 6 int main()
 7 {
 8   OEGraphMol mol;
 9
10   OEParseSmiles(mol,"c1ccccc1");
11   return 0;
12 }

Listing:2.4 Creating a molecule from SMILES

The OEParseSmiles function returns a boolean value indicating whether the input string was a valid SMILES string. It is good programming practice to check the return value and report an error message if anything went wrong. The following example uses C++'s iostream library to report the error.

 1 #include "openeye.h"
 2 #include "oechem.h"
 3 #include <iostream>
 4
 5 using namespace OEChem;
 6 using namespace std;
 7
 8 int main()
 9 {
10   OEGraphMol mol;
11
12   if (OEParseSmiles(mol,"c1ccccc1"))
13   {
14     // Do something with the molecule!
15   }
16   else cerr << "SMILES string was invalid!" << endl;
17   return 0;
18 }

Listing:2.5 Checking the return from OEParseSmiles

The molecule returned by OEParseSmiles preserves the aromaticity present in the input SMILES string. For example, if benzene is expressed as ``c1ccccc1,'' all atoms and bonds are marked as aromatic, but if it is expressed as a Kekulé form, ``C1=CC=CC=C1,'' all atoms and bonds are kept aliphatic. A common task after creating a molecule from SMILES is to normalize its aromaticity with OEAssignAromaticFlags

 1 #include "openeye.h"
 2 #include "oechem.h"
 3 #include <iostream>
 4
 5 using namespace OEChem;
 6 using namespace std;
 7
 8 int main()
 9 {
10   OEGraphMol mol;
11
12   if (OEParseSmiles(mol,"c1ccccc1"))
13   {
14     OEAssignAromaticFlags(mol);
15     // Do something with the molecule!
16   }
17   else cerr << "SMILES string was invalid!" << endl;
18   return 0;
19 }

Listing:2.6 Assigning aromatic flags

				OEChem - C++ Theory Manual

				OEChem - C++ Theory Manual