Thanks Geoff,
I took some time to really examine the SMARTS language today and it's not
so bad - I panicked when I saw things like aliphatic/aromatic.
Instead of writing a parser, I am going to try and use a bunch of if/else
clauses. Would it be logically sound to proceed from bottom of the list
You don't have to use SMARTS -- you could program the atom types with a set of
if/else clauses. Essentially all of MMFF94 atom typing is done this way in Open
Babel. It's probably more tedious, though.
> Sorry, but my question remains as to how can element is assigned its atom
> type based sole
Hi Geoff,
Don't get me wrong, I think that Babel is the best. But I am unable to use
Babel for various reasons (I am intending to implement a web-based docking
experiment, that is one of them). I've been using Babel to verify my
calculations. I'm so close to finishing, and I have everything nearly
On Dec 19, 2011, at 7:48 PM, Eric Jang wrote:
> 1. Is the assignment of atom types somehow based on the SMARTS string of a
> molecule? It would make sense that each atom has some SMARTS string property
> that is compared to the gaff.prm file.
SMARTS is essentially a programming language. So a
Thanks for pointing out parsmart.cpp!
Sorry, let me rephrase my question (or separate my many related questions):
I have a very basic atomic structure (not part of OpenBabel) that I am
implementing and I would like to assign GAFF atom types to it. All I know
are the element names and the types of
> So I guess the question becomes: how do I obtain the SMARTS string for each
> atom in GAFF? Again, all I know is which atoms are connected to each other
> and the bond type (single, double).
I'm not sure I understand your question. SMARTS is a pattern matching system.
So the Open Babel code
Hello,
I am trying to figure out how the forcefieldgaff.cpp file reads the
gaff.prm file to assign atom types. Given a molecular model where I know
the bonds connected between atoms (and I know their basic element name
C,N,O,H, etc.), how can I deduce their atom type? (e.g. n2,n1,cp,cd, etc.)
wit
