[Rdkit-discuss] Error reading SDF dataset from BindingDB

[Rafael L <raf...@al...>]

Hi, I'm just creating this thread to get the problem and the solution
indexed by Google

I downloaded several SDF datasets from BindingDB and got errors like this
one when using Chem.SDMolSupplier:

ERROR: Cannot convert 1. to unsigned int

After some digging I found [
https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/CAB3Bi0AYKAYOzMUumk6BscipsujkmG_-uuho3%3Dsf9mNyfoBAwA%40mail.gmail.com/#msg32641808],
and it turns out the headers (before every mol) should have three lines.
The BindingDB files only had two.

In these files, each mol+properties block was separated by four dollar sign
symbols. My solution was to add a blank line after each $$$$ by using
Notepad++ Find and replace: $$$$ by $$$$ + (new line).

--
*Rafael da Fonseca Lameiro*
PhD Student - Medicinal and Biological Chemistry Group (NEQUIMED)
São Carlos Institute of Chemistry - University of São Paulo - Brazil
[image: orcid logo 16px] https://orcid.org/0000-0003-4466-2682