sdf file problem

Hi,

 

I have a database of compounds in sdf format and I’m trying to generate a corresponding fingerprint database. Some compounds don’t get processes by generatemd and can’t be opened by JChem viewer – I’ve attached an example. This will open with other molecular viewing software. I can’t see any problem with the bond topology (is this the only data read to generate the fingerprint?).

 

Any suggestions greatly appreciated.

Gareth

Hello,

Your SDF file is not correct. In the Bond Block in your file the third column is for the bond type.
Legal values are between 1 and 8. There is a 0 in the third column, which causes the error.
See the specification of the Bond Block in this document:
http://www.mdli.com/downloads/public/ctfile/ctfile.jsp />
Regards,
Erika

Thanks for the help.

So, generatemd requires bond type information. Is the minimal data then atom type connectivity and bond type? I ask this because the bond lengths are often wrong in sdf files.

My colleague, who can answer this, is on holiday, he will answer to you soon.

 

Best regards,

Erika.

Hi,

bond length is not needed, as our fingerprints (including the chemical fingerprint and the pharmacophore fingerprint) are topological (ie. connectivity based v.s. geometry based). But exact bond information, i.e. connectivity plus bond type are needed.

Some of our applications, like molconverter (and apparently our library of developers tool) have the capability to perceive bond and bond type. However, at present this feature is limited to those structure file types that cannot represent bond types (like PDB, for instance). Bear in mind though, that this bond/bond type recognition works for 3D structures.

HTH

Miklos