Hi,
Getting the similarity maps for multiple structures should be straightforward,
just add the function call in your loop.
Concerning the export of the generated images to a web service, I did the
following:
(assuming the figure returned by the SimilarityMaps.GetSimilarityMapForModel()
Hi Marina,
I assume you are using this SDF file:
http://zinc11.docking.org/fget.pl?l=0=57393683=d
which contains 3D coordinates and no wedge bond information. If this is
the case, you will need to call MolOps::assignStereochemistryFrom3D()
Hi Marina,
If you wish to assign stereochemistry from the atom block parity flag
rather than from 3D coordinates you might try the following:
#include
#include
#include
#include
#include
int main(int argc, char **argv) {
std::string in_file_name = "zinc_3833800.sdf";
Ok thank you for the help!
Marina
> El 13 dic 2017, a las 11:22, Greg Landrum escribió:
>
>
> On Wed, Dec 13, 2017 at 10:39 AM, Marina Garcia de Lomana
> > wrote:
> Thanks for your answer Paolo!
> But I
On Thu, Dec 14, 2017 at 4:22 AM, Francois BERENGER <
beren...@bioreg.kyushu-u.ac.jp> wrote:
> On 12/14/2017 05:15 AM, Sundar wrote:
> > Hi RDkit users,
> >
> > I encounter following sanitize issue while I was trying to load an SD
> > file using
> > Chem.SDMolSupplier('lig.sdf')
> >
> > Explicit
Hi Jason,
This is a nice one.
Here's what's going on:
The depiction code (the piece that generates 2D coordinates) attempts to
generate "canonical" coordinates : it tries to generate the same
coordinates for a molecule no matter what the input atom ordering is.
In order to do that it needs a
On 12/14/2017 02:10 PM, Greg Landrum wrote:
>
> On Thu, Dec 14, 2017 at 4:22 AM, Francois BERENGER
> >
> wrote:
>
> On 12/14/2017 05:15 AM, Sundar wrote:
> > Hi RDkit users,
> >
> > I encounter following
On Thu, Dec 14, 2017 at 6:35 AM, Francois BERENGER <
beren...@bioreg.kyushu-u.ac.jp> wrote:
> On 12/14/2017 02:10 PM, Greg Landrum wrote:
> >
> > On Thu, Dec 14, 2017 at 4:22 AM, Francois BERENGER
> > >
> > wrote:
> >
> >
On 12/14/2017 05:15 AM, Sundar wrote:
> Hi RDkit users,
>
> I encounter following sanitize issue while I was trying to load an SD
> file using
> Chem.SDMolSupplier('lig.sdf')
>
> Explicit valence for atom # 16 N, 4, is greater than permitted
> ERROR: Could not sanitize molecule ending on line
Hello Sundar,
Without access to your sd file I cannot be sure. But it is likely that you
have a nitrogen with a valence exceeding 4. You may need to, e.g., change
the N=O form into [N+][O-]. You may take a look at some of the following
threads.
using the recent release,
m = Chem.MolFromSmiles("N[C@@H](C)C(=O)O")
m2 = Chem.MolFromSmiles("N[C@@H](C)C(=O)O")
Chem.rdmolops.SanitizeMol(m2)
The two molecules above seem identical - MolFromSmiles already performs a
sanitization so why wouldn't they be? They produce the same pickle,
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