Thank you Ernst-Georg a lot, great help. I am more aware now, and I code it.
Thanks a lot
Marianne
Le 16 déc. 2011 à 12:48, Ernst-Georg Schmid a
écrit :
> Hi,
>
> from the finger2.cpp source:
>
> For each of these fragments the atoms, bonding and whether
> they constitute a complete ring i
Ladies and gentlemen,
I would greatly appreciate any hint on the API for 2D coordinate
generation or 3D to 2D coordinate conversion, assuming those exist. That
can be done from the command line using the '--gen2d' option, which
makes me think there could be an API as well. I have not found one
Many thanks Chris, it is helpful. I see it
Best regards
Marianne
Le 16 déc. 2011 à 13:15, Chris Morley a écrit :
> On 16/12/2011 11:01, Marianne wrote:
>> Dear all,
>>
>> In order to have fingerprint of reactions, is it possible to make
>> fingerprint (FP2) difference between 2 (or more) comp
Dear Coordinator and users of obabel,
I want to use open babel to append properties to sdf file and also to filter a
sdf file with the properties like:
CAT_NO
PUBCHEM_CACTVS_HBOND_DONOR
PUBCHEM_CACTVS_HBOND_ACCEPTOR
PUBCHEM_MOLECULAR_WEIGHT
PUBCHEM_XLOGP3
but i got an error message like: not r
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
> 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
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
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
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
