using
OPOb, but I can't seem to call that class. I have Chemistry::OpenBabel
installed, latest version. Any help would be greatly appreciated.
--
Wallace Chan
Zhang Lab
Department of Biological Chemistry
University of Michigan
wal
Any
help woudl be greatly appreciated!
On Fri, Nov 8, 2013 at 2:25 PM, Noel O'Boyle wrote:
> I don't have the exact code to hand, but it's something like the
> following in Python:
>
> myop = OBOp.FindType("gen3d")
> success = myop.Do(myOBMol)
>
On Wed, Nov 13, 2013 at 2:37 PM, Noel O'Boyle wrote:
> OBOp should be in Chemistry::OpenBabel just like OBConversion. If not,
> there's a problem at our end.
>
> - Noel
>
> On 13 November 2013 17:18, Wallace Chan wrote:
> > Thanks for the reply, Noel. I apologiz
module. Any help would be greatly appreciated!
>
> That’s not actually how you load an OBOp. But incidentally, what version
> of Open Babel are you using?
>
> As Noel mentioned, you want something like this (sorry, my Perl is rusty):
>
> my $genOp = Chemistry::OpenBabel::OBOp::FindTyp
in the
> Perl wrapper for that version. It's now over 4 years old.
>
> The latest version is 2.3.2:
> http://openbabel.org/wiki/Install
>
> Hope that helps,
> -Geoff
--
Wallace Chan
Zhang Lab
Department of Biological Chemistry
University of Michigan
walla...@umich.
on (in bold), it
seems to have gotten rid of the "segmentation fault" message and started
generating data with 3D coordinates. Hope this helps others having the same
problem!
Wallace
On Thu, Nov 21, 2013 at 3:13 PM, Wallace Chan wrote:
> I finally figured out how to call the the OB
nAndOutFormats("sdf", "sdf");
Here are some of the reasons why I think it doesn't work:
1.) It isn't possible to convert 2D SDF to 3D SDF
2.) I was successful using this converting InChI to 3D SDF, but maybe I
need to call a different class
Thanks
out whether something works in your code, you can
> test if it works from the command-line tools. So yes, converting from 2D to
> 3D should work just fine. If not, that’s our bug. Can you send an example
> 2D SDF file?
>
> Thanks,
> -Geoff
--
Wallace Chan
Zhang Lab
Departme
it. Thanks!
--
Wallace Chan
PhD Candidate
Zhang Lab
Department of Biological Chemistry
University of Michigan
walla...@umich.edu
--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of
atch
> themselves as SMARTS.
>
> Hope that helps,
> -Geoff
--
Wallace Chan
PhD Candidate
Zhang Lab
Department of Biological Chemistry
University of Michigan
walla...@umich.edu
--
Want fast and easy a
no universal SMILES canonicalization
> algorithm. Different toolkits will result in different canonical SMILES
> (which are canonical only when using the same toolkit). InChI on the hand
> has a single reference implementation.
>
> Tim
>
>
> On Wed, Jul 23, 2014 at 12:03 AM, Wallace
Chris,
Many thanks! This did the trick. =)
Wallace
On Sat, Jul 26, 2014 at 11:02 AM, Chris Morley wrote:
> On 24/07/2014 17:06, Wallace Chan wrote:
> > Tim,
> >
> > Thanks for your reply. Yes, we have the canonical SMILES strings stored
> > as properties in our
er to one thing? The reason why I ask is because
I am afraid that there is a possibility I may not be able to use this for
fingerprint profile construction because the bits will not be comparable
one-to-one.
Any help would be greatly appreciated. Thanks!
--
Wallace Chan
PhD Candidate
Zhan
seems fine.
This has been driving me crazy and any help given will be much appreciated.
Thanks!
--
Wallace Chan
PhD Candidate
Zhang Lab
Department of Biological Chemistry
University of Michigan
walla...@umich.edu
*
*0 molecules converted*
*1 errors 2 audit log messages *
Seems to be a problem with the molecule being a radical.
Wallace
On Wed, Oct 28, 2015 at 3:16 PM, Noel O'Boyle wrote:
> Convert to smi and figure out which molecules are missing.
>
> - Noel
>
> On 28 October 2015 at
1 0 0 0
> 27 42 1 0 0 0
> 28 29 2 0 0 0
> 28 32 1 0 0 0
> 29 30 1 0 0 0
> 29 43 1 0 0 0
> 30 31 2 0 0 0
> 31 32 1 0 0 0
> 31 44 1 0 0 0
> 32 45 1 0 0 0
> M RAD 8 1 2 3 2 5
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