Hello All,
I am using OBMol->GetMapList to get the occurrences of fragments in
molecules. I'm not to sure that everything works correctly, though.
OpenBabel(-2.2.3) apparently tells me that N matches only twice in
C10H19N5O:
code:
[[[
OBMol * mol = new OBMol();
OBConversion obconversion;
obconver
On Wed, Jul 14, 2010 at 3:59 PM, Geoffrey Hutchison
wrote:
>> I am using OBMol->GetMapList to get the occurrences of fragments in
>> molecules. I'm not to sure that everything works correctly, though.
> ...
>> obconversion.ReadString(mol, "C1(N=C(NC(C)C)N=C(N=1)OC)NC(C)C");
> ...
>> smartsPattern.
Hello All,
I came across an example that causes OBBuilder to produce a
segmentation fault (g++ version is 4.4.3, openbabel-2.2.3). See code
below.
Best regards,
Martin
#include
#include
#include
#include
using namespace std;
using namespace OpenBabel;
int main(int argc,char **argv)
{
Hello all,
when converting a aromatic smiles to sdf, it does only contain single and
double bonds (kekule notation).
how can I have aromatic bonds in my sdf?
(I tried openbabel-2.3.0, via command line and c++ api)
Best regards,
Martin
--
Dipl-Inf. Martin Gütlein
Phone:
+49 (0)761 203 7633 (of
On Mon, Jun 20, 2011 at 2:28 PM, Martin Guetlein <
martin.guetl...@googlemail.com> wrote:
> Hello all,
>
> when converting a aromatic smiles to sdf, it does only contain single and
> double bonds (kekule notation).
>
> how can I have aromatic bonds in my sdf?
>
>
On Wed, Jun 22, 2011 at 4:28 PM, Nina Jeliazkova
wrote:
> Hello Martin,
>
> On 22 June 2011 17:19, Noel O'Boyle wrote:
>
>> On 22 June 2011 13:35, Martin Guetlein
>> wrote:
>> >
>> > On Mon, Jun 20, 2011 at 2:28 PM, Martin Guetlein
>> > w
Hi,
I would like to have the corresponding fragment for each bit of the fp2
fingerprint.
Using the -s param (as described by Noel here:
http://forums.openbabel.org/Need-help-in-calculationg-tanimoto-coefficient-td3233604.html)
is not very practical for what I want to do, I would prefer a list of 1
On Thu, Sep 15, 2011 at 12:33 PM, Fredrik Wallner wrote:
> Hi again,
> (I realized i forgot to cc the list in my last reply)
> 15 sep 2011 kl. 12:29 skrev Martin Guetlein:
>
> On Thu, Sep 15, 2011 at 12:21 PM, Fredrik Wallner wrote:
>
>> Hi,
>>
>> Since the fp
On Fri, Sep 16, 2011 at 8:33 AM, Nina Jeliazkova
wrote:
>
>
> On 16 September 2011 09:29, Martin Guetlein <
> martin.guetl...@googlemail.com> wrote:
>
>>
>>
>> On Thu, Sep 15, 2011 at 12:33 PM, Fredrik Wallner wrote:
>>
>>> Hi again,
&g
On Fri, Sep 16, 2011 at 8:39 AM, Martin Guetlein <
martin.guetl...@googlemail.com> wrote:
>
>
> On Fri, Sep 16, 2011 at 8:33 AM, Nina Jeliazkova <
> jeliazkova.n...@gmail.com> wrote:
>
>>
>>
>> On 16 September 2011 09:29, Martin Guetle
On Sat, Sep 17, 2011 at 1:58 PM, Noel O'Boyle wrote:
> > I went with the -xs and am currently working on the to-smarts conversion.
> >
> > First question:
> >
> > I got those lines:
> > 0 16 5 6 5 7 5 6 1 6 2 7 1 8 <7>
> > 0 16 5 6 5 7 5 6 5 6 <668>
> > 1 7 1 6 1 6 1 6 <544>
> > 1 16 1 6 1 7 1 6
Hi,
I would like to do smarts matching with OpenBabel, and for some
reasons I am restricted to use the command line interface.
Is there an efficient way to match a range of smarts strings against a dataset?
What I found out is that I could use the "-s" option, but I would have
to call babel once
On Mon, Sep 19, 2011 at 11:04 AM, Chris Morley wrote:
> On 19/09/2011 09:32, Martin Guetlein wrote:
>> Hi,
>>
>> I would like to do smarts matching with OpenBabel, and for some
>> reasons I am restricted to use the command line interface.
>> Is there an efficie
On Mon, Sep 19, 2011 at 11:23 AM, Martin Guetlein <
martin.guetl...@googlemail.com> wrote:
> On Mon, Sep 19, 2011 at 11:04 AM, Chris Morley
> wrote:
> > On 19/09/2011 09:32, Martin Guetlein wrote:
> >> Hi,
> >>
> >> I would like to do smarts matchin
On Tue, Sep 27, 2011 at 3:37 PM, Chris Morley wrote:
> On 26/09/2011 11:50, Martin Guetlein wrote:
> > On Mon, Sep 19, 2011 at 11:23 AM, Martin Guetlein<
> > martin.guetl...@googlemail.com> wrote:
> >
> >> On Mon, Sep 19, 2011 at 11:04 AM, Chris Morley
&
Hi All,
is there a more accurate description on how openbabel detects
aromaticity then this page?
http://openbabel.org/wiki/Aromaticity
Im asking because I am using CDK and OpenBabel, and I am suffering of
interoperability problems, because both tools have different ways of
defining aromaticity.
Hi All,
this is how I use openbabel to compute descriptors, L5 is not working,
though (openbabel version is 2.3.1).
$obabel -:CCC -otxt --append MW -osmi
CCC 44.0956
1 molecule converted
$obabel -:CCC -otxt --append L5 -osmi
CCC nan
1 molecule converted
Thanks for your help, with best re
Hi,
I just noticed that the OpenBabel 3D builder gives different results
on each run (see example below). Can I set a seed somehow?
Kind regards,
Martin
$ echo "CCC" > in.smi
$ babel --gen3d -d -ismi in.smi -osdf out1.sdf
$ babel --gen3d -d -ismi in.smi -osdf out2.sdf
$ diff out1.sdf out2.sdf
5
Sorry, the second example command is missing the ".Cl":
obabel -:"CNC[C@@H](c1ccc(c(c1)O)O)O.Cl" -d --gen3d -osdf
On Thu, Dec 5, 2013 at 12:10 PM, Martin Guetlein
wrote:
> Hi,
>
> apparently the --gen3D option takes ages and does not work for
> mixtures in mo
Hi,
apparently the --gen3D option takes ages and does not work for
mixtures in most cases.
Does anyone know the reason and/or a workaround?
An Example:
obabel -:"CNC[C@@H](c1ccc(c(c1)O)O)O" -d --gen3d -osdf
works fine and takes about 8 seconds on my machine.
obabel -:"CNC[C@@H](c1ccc(c(c1)O)O)O"
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