Re: [Rdkit-discuss] Sanitizing SD file

2017-12-16 Thread Sundar
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,

Re: [Rdkit-discuss] Sanitizing SD file

2017-12-13 Thread Greg Landrum
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: > > > >

Re: [Rdkit-discuss] Sanitizing SD file

2017-12-13 Thread Francois BERENGER
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

Re: [Rdkit-discuss] Sanitizing SD file

2017-12-13 Thread Greg Landrum
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

Re: [Rdkit-discuss] Sanitizing SD file

2017-12-13 Thread Francois BERENGER
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

Re: [Rdkit-discuss] Sanitizing SD file

2017-12-13 Thread Ling Chan
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.