CCL: Pipeline Pilot Question
- From: "Richard Compton"
<rcompton###accelrys.com>
- Subject: CCL: Pipeline Pilot Question
- Date: Fri, 8 Feb 2008 14:41:40 +0000
Hi Jeremy,
Just to let you know that PipelinePilot is available to
Academics for free.
You can find more information on our Academic program at
http://www.accelrys.com/products/scitegic/pp-student/
Kind
regards,
Richard.
_______________________
Mr Richard
Compton
Senior Director, EMEA
Accelrys Ltd.
334 Cambridge Science
Park
Cambridge
CB4 0WN
"Jeremy Besnard
j10b84%%hotmail.com" ---06/02/2008 20:24:40---Sent to CCL by: "Jeremy
Besnard" [j10b84[]hotmail.com]
From: |
"Jeremy Besnard j10b84%%hotmail.com"
<owner-chemistry]![ccl.net> |
To: |
"Compton,
Richard " <rcompton]![accelrys.com> |
Date: |
06/02/2008
20:24 |
Subject: |
CCL: Pipeline
Pilot Question |
Sent to CCL by: "Jeremy
Besnard" [j10b84[]hotmail.com]
Hi Richard,
I used Pipeline
Pilot last year (internship) and I managed to do it.
Now that I'm back to
school, I don't have access to PP, so Ill try to remind (there could be some
errors, and I apologize for it).
You can use the group component to group by
number (for example 5000).
Then you add a counter, with (~)counter.
Then
you create a subprotocol with inside:
-a component to define the name of the
file, you can use the (~)counter
(~)file:="c:\blabla\file_".(~)counter."sdf";
-an
ungroup component
-a sdf writer, and for the destination: $(file)
And
for the subprotocol you enable the option : "run to completion"
(true)
And now you will have a new file for each 5000
molecules.
Note: 1. to reduce the size of a file, you can write a gz
file, Pipeline does it, for the destination you write c:\blabla\file.sdf.gz, and
it works.
2. For the number of molecule to group, you can use a global
variable, which you can defined at the beginning.
I hope you will
understand what I said.
Jrmy
--------------------------------------------------------------------------------
>
Sent to CCL by: "Richard L. Wood" [woodx278:-:umn.edu]
> Hi
all,
>
> I've written a protocol in Pipeline Pilot that reads in a
database in smiles
> format, coonverts it to 3D coordinates, then adds
hydrogens and minimizes the
> structures. After this, I have it write the
structures to an SDF file.
>
> The problem is that if there are a
lot of molecules in the original database, this file will be very large. I've
generated one that is 34 GB. I would like to be able to do something with this
file, so I was wondering how or what I can do in Pipeline Pilot so that I can
write out the molecules into multiple files that have fewer molecules per file?
I'd like to be able to create something that I can use over and over, as opposed
to just going in and having it write out x output files by having x output
statements. I'm thinking that it has to be some kind of For Next loop, but I'm
not sure how to write that in Pipeline Pilot.
>
> TIA,
>
> Richard
>
> Richard L. Wood, Ph. D.
> University of
Minnesota
> Dept. of Medicinal Chemistry,
> College of
Pharmacy
> 717 Delaware St. SE
> Minneapolis, MN 55414-2959
>
woodx278^umn.edu
>
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