Re: [Open Babel] pdf export

2016-01-22 Thread Geoffrey Hutchison 
> Apologies the title should be sdf export.

But there is sdf.. do you mean csv (i.e., spreadsheet)?

> It would be useful to have options for the delimiter. It is possible the 
> content may contain commas, so options for tab or pipe might be useful and/or 
> putting quotes around text.
> Not every record in a sdf will have all fields so the usual strategy is to 
> first scan the sdf file to identify all fields and then go back to the start 
> to do the export.

If you give some examples, it shouldn't be too hard to cook up another export 
format.

-Geoff
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Re: [Open Babel] pdf export

2016-01-22 Thread Maciek Wójcikowski 
If you need this badly there is na option to write CSV file in ODDT's
virtual screening module. You can choose a delimiter and quotation signs,
but unfortunately it does not write smiles to CSV. If you need it badly i
can add parameter to include smiles in CSV. Sorry for off-OpenBabel mail.

from oddt.virtualscreening import virtualscreening as vs
pipeline = vs()
pipeline.load_ligands('sdf', 'ampc/actives_final.sdf.gz')
pipeline.write_csv('ampc_docked.csv')



Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-01-22 14:17 GMT+01:00 Chris Swain :

> Apologies the title should be sdf export.
>
> A couple of additional comments.
>
> It would be useful to have options for the delimiter. It is possible the
> content may contain commas, so options for tab or pipe might be useful
> and/or putting quotes around text.
>
> Not every record in a sdf will have all fields so the usual strategy is to
> first scan the sdf file to identify all fields and then go back to the
> start to do the export.
>
> Cheers,
>
> Chris
>
> --
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Re: [Open Babel] pdf export

2016-01-22 Thread Chris Swain 
Hi,

Thanks for this very kind offer.

I actually have tools to do this, I use Vortex or MOE. However I am asked about 
this occasionally and I just thought it might be a useful addition to have an 
Open-Source tool available. Usually people just want to import the data into a 
spreadsheet application.

Cheers,

Chris
> On 22 Jan 2016, at 13:33, Maciek Wójcikowski  wrote:
> 
> If you need this badly there is na option to write CSV file in ODDT's virtual 
> screening module. You can choose a delimiter and quotation signs, but 
> unfortunately it does not write smiles to CSV. If you need it badly i can add 
> parameter to include smiles in CSV. Sorry for off-OpenBabel mail.
> 
> from oddt.virtualscreening import virtualscreening as vs
> pipeline = vs()
> pipeline.load_ligands('sdf', 'ampc/actives_final.sdf.gz')
> pipeline.write_csv('ampc_docked.csv')
> 
> 
> 
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl 
> 
> 2016-01-22 14:17 GMT+01:00 Chris Swain >:
> Apologies the title should be sdf export.
> 
> A couple of additional comments.
> 
> It would be useful to have options for the delimiter. It is possible the 
> content may contain commas, so options for tab or pipe might be useful and/or 
> putting quotes around text.
> 
> Not every record in a sdf will have all fields so the usual strategy is to 
> first scan the sdf file to identify all fields and then go back to the start 
> to do the export.
> 
> Cheers,
> 
> Chris
> --
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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> 
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> 
> 

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Re: [Open Babel] pdf export

2016-01-22 Thread Chris Swain 
Apologies the title should be sdf export.

A couple of additional comments.

It would be useful to have options for the delimiter. It is possible the 
content may contain commas, so options for tab or pipe might be useful and/or 
putting quotes around text.

Not every record in a sdf will have all fields so the usual strategy is to 
first scan the sdf file to identify all fields and then go back to the start to 
do the export.

Cheers,

Chris
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