Thanks everyone for your valuable inputs.
Chem.SDMolSupplier('lig.sdf', sanitize=False)
worked well at the moment for my compounds. I am not sure if I will have
problem in calculating descriptors or further in my calculations.
I will also try to turn off the strict property checking.
Thanks,
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 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 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
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.
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