Re: [Rdkit-discuss] Error reading SDF dataset from BindingDB

[Ling C. <lin...@gm...>]

Interesting. Thanks Rafael. So it's a bug of BindingDB. Perhaps you should
let them know too.

Ling


Rafael L via Rdkit-discuss <rdk...@li...> 於
2023年7月25日週二 上午12:53寫道：

> 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
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