Re: [Open Babel] Suggestions

[Geoffrey H. <ge...@ge...>]

Hi Chris,

> might be useful to compile them into a list and share them.

Great. Could you (or someone) please enter these into the feature  
request tracker. I'm not sure if we'll necessarily implement all of  
them, but it's nice to have them in the tracker, so they don't get  
lost amid all the e-mail traffic. :-)

(I think a few of them are duplicates of existing suggestions.)
http://sourceforge.net/tracker/?atid=428743&group_id=40728&func=browse

> 1. Conversion from SMILES to sdf etc.

I'm not sure what this means. I'm guessing this (like #2) means  
coordinate generation?

> 2. Generate "reasonable" 3D structures from 2D.
> 10. Generate multiple "reasonable" conformations of a structure

All of these are really going to require access to a force field or  
MOPAC or somesuch. Like Michael, I've thought about accessing  
libghemical where available. I think this may make some sense, but  
maybe someone will contribute a force field. (We have donated code  
for a tripos-like field, but the included parameters weren't copyleft.)

> 6. Calculate properties, number of HBond donors, acceptors, cLogP,  
> PSA etc.
> 9. Pharmacophore based searching, e.g. HBond acceptor 3 bonds away  
> from aromatic ring.

A number of these already exist as function calls in the library --  
there just aren't command-line tools. Perhaps someone would be  
interested in adding to obprop?

As for the searching, I can think of possible SMARTS patterns for  
such queries -- perhaps a better question is a tool to help build  
proper SMARTS patterns for chemical questions. :-) After all, someone  
might want HBond acceptor 4 bonds away, or a pyridine ring instead of  
any old aromatic ring.

Cheers,
-Geoff