From jji at cgl.ucsf.edu  Thu Sep 13 16:18:50 2007
From: jji at cgl.ucsf.edu (John J. Irwin)
Date: Thu, 13 Sep 2007 16:18:50 -0700
Subject: [Zinc-fans] [Dock-fans] more valences per nitrogen than they
	should be?
In-Reply-To: <Pine.SGI.4.51.0709131616000.1222638@pusar.scripps.edu>
References: <20070911083923.bnnr8udhc4kc0w4g@webmail.ualberta.ca>
	<Pine.SGI.4.51.0709131616000.1222638@pusar.scripps.edu>
Message-ID: <46E9C55A.6090406@cgl.ucsf.edu>

Hi -

Thanks for your email. We know there are some "broken" molecules in
ZINC. If you send me the list of molecules you found (to jji at
cgl.ucsf.edu) I will see what I can do to put it right.

John


Scott Brozell wrote:
> Hi,
>
> I am cc-ing Zinc-fans
> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
>
> Scott
>
> On Tue, 11 Sep 2007 burgosgu at ualberta.ca wrote:
>
>   
>> I'm just abour running a virtual screening and I just noticed that
>> most of the compounds I downloaded from the zinc database have 4
>> valences for nitrogen instead of 3, e.g. a nitrogen is bound to two
>> carbons and two hydrogens. Is this correct? I'm afraid that this
>> affect my dockings.
>>     
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>   

From baoilleach at gmail.com  Fri Sep 14 02:23:36 2007
From: baoilleach at gmail.com (Noel O'Boyle)
Date: Fri, 14 Sep 2007 10:23:36 +0100
Subject: [Zinc-fans] [Dock-fans] more valences per nitrogen than they
	should be?
In-Reply-To: <46E9C55A.6090406@cgl.ucsf.edu>
References: <20070911083923.bnnr8udhc4kc0w4g@webmail.ualberta.ca>
	<Pine.SGI.4.51.0709131616000.1222638@pusar.scripps.edu>
	<46E9C55A.6090406@cgl.ucsf.edu>
Message-ID: <a882e48b0709140223r1852ba0dn9af5b6acde3e8655@mail.gmail.com>

Hello all,

I came across this problem some time ago (see email below from Jul
18). I've placed the list of molecules at
http://www.redbrick.dcu.ie/~noel/dodgyNs.txt.

I am an OpenBabel developer, and if you need any help using OpenBabel
to sort out problems in ZINC, I'd only be too happy to volunteer some
time. We have some nice canonicalisation code donated by eMolecules,
etc., etc.

Noel

==== original email =====
Dear John,

I mentioned in passing some problems with some of the structures in
the MOL2 files. I've now followed this up. The main problem seems to
be that there are molecules containing nitrogen atoms of type N.3
(this is specified in the file) but which have four bonds.

This must be an error (right?). Either these are of type N.4 (and have
a positive charge), or they are of type N.3 and have at most three
bonds. I think that it is the latter, and that there has been some
mistake by a structure generation program at an earlier stage in your
pipeline.

I looked for all examples of this in ZINC and have attached the
result. There are 97211 molecules with atoms of type N.3 but with 4
bonds. That's almost 5% (Out of 2021041).

Regards,
  Noel

For the record, here's the Python code to create the attached file:

import glob

import pybel
import openbabel as ob

outputfile = open("dodgyNs.txt", "w")
for filename in glob.glob("gzipfiles/*.mol2"):
   for mol in pybel.readfile("mol2", filename):
       for atom in mol:
           if atom.type == "N3": # Internal OB atom type (equivalent to N.3)
               numbonds = len([1 for x in ob.OBAtomBondIter(atom.OBAtom)])
               if numbonds == 4:
                   print >> outputfile, mol.title
                   break
outputfile.close()

==== end of original email =====

On 14/09/2007, John J. Irwin <jji at cgl.ucsf.edu> wrote:
> Hi -
>
> Thanks for your email. We know there are some "broken" molecules in
> ZINC. If you send me the list of molecules you found (to jji at
> cgl.ucsf.edu) I will see what I can do to put it right.
>
> John
>
>
> Scott Brozell wrote:
> > Hi,
> >
> > I am cc-ing Zinc-fans
> > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
> >
> > Scott
> >
> > On Tue, 11 Sep 2007 burgosgu at ualberta.ca wrote:
> >
> >
> >> I'm just abour running a virtual screening and I just noticed that
> >> most of the compounds I downloaded from the zinc database have 4
> >> valences for nitrogen instead of 3, e.g. a nitrogen is bound to two
> >> carbons and two hydrogens. Is this correct? I'm afraid that this
> >> affect my dockings.
> >>
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >
> _______________________________________________
> Zinc-fans mailing list
> Zinc-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
>

From jji at cgl.ucsf.edu  Fri Sep 14 12:19:32 2007
From: jji at cgl.ucsf.edu (John J. Irwin)
Date: Fri, 14 Sep 2007 12:19:32 -0700
Subject: [Zinc-fans] [Dock-fans] more valences per nitrogen than they
 should be?
In-Reply-To: <a882e48b0709140223r1852ba0dn9af5b6acde3e8655@mail.gmail.com>
References: <20070911083923.bnnr8udhc4kc0w4g@webmail.ualberta.ca>	
	<Pine.SGI.4.51.0709131616000.1222638@pusar.scripps.edu>	
	<46E9C55A.6090406@cgl.ucsf.edu>
	<a882e48b0709140223r1852ba0dn9af5b6acde3e8655@mail.gmail.com>
Message-ID: <46EADEC4.1040104@cgl.ucsf.edu>

Noel

Thank you for your kind offer of assistance. I would like to move
towards some kind of community-based system whereby helpful and
enterprising people like you could "fix" problems in ZINC, even without
contacting me (wikizincia?). Unfortunately, we don't have a mechanism
for that yet. For now, I gratefully accept notification of problems, and
will redouble my effort to fix errors.

John


Noel O'Boyle wrote:
> Hello all,
>
> I came across this problem some time ago (see email below from Jul
> 18). I've placed the list of molecules at
> http://www.redbrick.dcu.ie/~noel/dodgyNs.txt.
>
> I am an OpenBabel developer, and if you need any help using OpenBabel
> to sort out problems in ZINC, I'd only be too happy to volunteer some
> time. We have some nice canonicalisation code donated by eMolecules,
> etc., etc.
>
> Noel
>
> ==== original email =====
> Dear John,
>
> I mentioned in passing some problems with some of the structures in
> the MOL2 files. I've now followed this up. The main problem seems to
> be that there are molecules containing nitrogen atoms of type N.3
> (this is specified in the file) but which have four bonds.
>
> This must be an error (right?). Either these are of type N.4 (and have
> a positive charge), or they are of type N.3 and have at most three
> bonds. I think that it is the latter, and that there has been some
> mistake by a structure generation program at an earlier stage in your
> pipeline.
>
> I looked for all examples of this in ZINC and have attached the
> result. There are 97211 molecules with atoms of type N.3 but with 4
> bonds. That's almost 5% (Out of 2021041).
>
> Regards,
>   Noel
>
> For the record, here's the Python code to create the attached file:
>
> import glob
>
> import pybel
> import openbabel as ob
>
> outputfile = open("dodgyNs.txt", "w")
> for filename in glob.glob("gzipfiles/*.mol2"):
>    for mol in pybel.readfile("mol2", filename):
>        for atom in mol:
>            if atom.type == "N3": # Internal OB atom type (equivalent to N.3)
>                numbonds = len([1 for x in ob.OBAtomBondIter(atom.OBAtom)])
>                if numbonds == 4:
>                    print >> outputfile, mol.title
>                    break
> outputfile.close()
>
> ==== end of original email =====
>
> On 14/09/2007, John J. Irwin <jji at cgl.ucsf.edu> wrote:
>   
>> Hi -
>>
>> Thanks for your email. We know there are some "broken" molecules in
>> ZINC. If you send me the list of molecules you found (to jji at
>> cgl.ucsf.edu) I will see what I can do to put it right.
>>
>> John
>>
>>
>> Scott Brozell wrote:
>>     
>>> Hi,
>>>
>>> I am cc-ing Zinc-fans
>>> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
>>>
>>> Scott
>>>
>>> On Tue, 11 Sep 2007 burgosgu at ualberta.ca wrote:
>>>
>>>
>>>       
>>>> I'm just abour running a virtual screening and I just noticed that
>>>> most of the compounds I downloaded from the zinc database have 4
>>>> valences for nitrogen instead of 3, e.g. a nitrogen is bound to two
>>>> carbons and two hydrogens. Is this correct? I'm afraid that this
>>>> affect my dockings.
>>>>
>>>>         
>>> _______________________________________________
>>> Dock-fans mailing list
>>> Dock-fans at docking.org
>>> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>>>
>>>       
>> _______________________________________________
>> Zinc-fans mailing list
>> Zinc-fans at docking.org
>> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
>>
>>     

From lucioric at ibt.unam.mx  Thu Sep 27 13:56:22 2007
From: lucioric at ibt.unam.mx (Lucio Montero)
Date: Thu, 27 Sep 2007 15:56:22 -0500
Subject: [Zinc-fans] ZINC database updates
Message-ID: <001601c80148$df746740$f520f884@x>

Hi. When the ZINC database is updated, can I retrieve only the new records
insetad of having to re-download all records?. Can the ZINC_ID change for
the old records?

 

 

Lucio Montero

Laboratorio de Federico S?nchez

Ext. 27666

Instituto de Biotecnolog?a, UNAM

Cuernavaca, Morelos, M?xico

 

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From jji at cgl.ucsf.edu  Thu Sep 27 14:14:52 2007
From: jji at cgl.ucsf.edu (John J. Irwin)
Date: Thu, 27 Sep 2007 14:14:52 -0700
Subject: [Zinc-fans] ZINC database updates
In-Reply-To: <001601c80148$df746740$f520f884@x>
References: <001601c80148$df746740$f520f884@x>
Message-ID: <46FC1D4C.3010307@cgl.ucsf.edu>

Hi Lucio

Thanks for your email and your interest in ZINC.

I'll take your second question first. ZINC IDs are never re-used for
other molecules. ZINC IDs do disappear in new versions, for example by
becoming unavailable ("depleted") or being "retired" when we realize
they are the same as another molecule. But we will never re-use a ZINC ID.

Back to your first question. It would be nice to be able to download
just a delta of what is new instead of the entire database. We did
consider offering this, and it does seem to be feasible. I have the
information on hand, and I may see about offering it at some point.

At the moment, like the Red Queen to Alice, I find I myself breathless
just to stay in the same place. So we ask you to download everything you
need again.

Here is the good news: you can run one of our handy c-shell scripts that
invoke wget last thing in the evening, and ZINC should be on your disk
the next morning, if not before.

John


Lucio Montero wrote:
>
> Hi. When the ZINC database is updated, can I retrieve only the new
> records insetad of having to re-download all records?. Can the ZINC_ID
> change for the old records?
>
>  
>
>  
>
> Lucio Montero
>
> Laboratorio de Federico S?nchez
>
> Ext. 27666
>
> Instituto de Biotecnolog?a, UNAM
>
> Cuernavaca, Morelos, M?xico
>
>  
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Zinc-fans mailing list
> Zinc-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
>