[ghemical-devel] Molecule Comparison

[Geoffrey Hutchison]

On Apr 11, 2006, at 5:07 PM, Donald Ephraim Curtis wrote:

> information, along with requiring the code to find molecules that  
> are the same.  For example, selecting one molecule and finding all  
> similar molecules (finding all water molecules).  I was just  
> wondering what facilities are already included in the ghemical code  
> that would help do this, or any algorithms that would help.  One  
> idea was to convert the molecules using openbabel to the SMILE  
> format and then doing a string comparison.  Any suggestions would  
> be helpful.

You don't need to even do that. Besides, it's generally a bad idea to  
do straight string comparisons with SMILES. There's no guarantee that  
equivalent molecules necessarily have equivalent SMILES strings.

* Inside Open Babel, you can easily do SMARTS matching (e.g., if this  
set of atoms matches SMARTS of [OD2]).
* There isn't support for "equivalence" (e.g. mol1 == mol2) but  
that's certainly a reasonable feature request.
* Open Babel 2 also supports similarity searching using molecular  
fingerprints.

So to answer your question, using code like project::HtoMethyl() you  
can sync to an OBMol and write code to search for water molecules.

Cheers,
-Geoff