I think you give a very good suggestion. I should define my own atom type.
There are much more work if if match the atom type between openbabel and
opls-aa. I only need to define the atom type in
http://towhee.sourceforge.net/forcefields/oplsaa.html and then use SMARTS to
match more atom.
Very tha
Thank you for your reply.
You are right. The atoms type in open babel are not match exactly with
opls-aa. Like your suggestion, first I want to approximately match the atom
type using openbabel, and then using SMARTS to define more exact atom type
in a table.
Parden for my poor English.
Recards
> for example, C3 may mean [#6^3]. So how do I know what's mean of the extra
> atoms; is there a list to explain them. I want to use them to match the
> atom type in opls-aa forcefield.
I don't think the atom types defined by Open Babel are anywhere precise enough
for OPLS-AA, which has speciali
Dear:
In types.txt file which is used by data.cpp:OBTypeTable, there are a lot of
atom type. How do I know what's mean of atom type?
for example, C3 may mean [#6^3]. So how do I know what's mean of the extra
atoms; is there a list to explain them. I want to use them to match the
atom type in opl
Hi Noel,
Thanks for the update, and also for the slides! Great presentation! Also I
appreciate you mentioned our study, as you pointed out this is a win-win
situation for both cheminformatic tool developers and database maintainers.
We will probably get back with more test results very soon.
Rega
Hi Robert,
I've gotten the figure down to 120.
69 of the remaining problems (as far as I can tell) are due to
differences between how the InChI code and Open Babel handle the
situation where you have a tetrahedral center where two of the three
non-stereo bonds are very close (in angle) to each ot
> 1) there are structures that have information in labels. So sometimes the
> stereochemistry at a particular center is is given by a dummy atom nearby
> with a label 'R' or 'S'.
I think this is a perfect example of how "standard formats" quickly become
complicated by "in practice usage." If y
On Aug 29, 2011, at 4:51 AM, Noel O'Boyle wrote:
> Hi all,
>
> Some of you may be interested in a talk I presented last week at the
> 5th Meeting on U.S. Government Chemical Databases and Open Chemistry
> (in Frederick, MD). The talk, entitled "Improving the quality of
> chemical databases with
Hi all,
Some of you may be interested in a talk I presented last week at the
5th Meeting on U.S. Government Chemical Databases and Open Chemistry
(in Frederick, MD). The talk, entitled "Improving the quality of
chemical databases with community-developed tools (and vice versa)",
described improvem
