Saturation Checker seems to fail on the small molecule n12cncc1cccc2.
I know that multiple N polycyclic compounds always seem to be an issue.
From:
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To:
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Date:
05/14/2012 07:04 AM
Subject:
Cdk-user Digest, Vol 72, Issue 6
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Today's Topics:
1. Your feedback please: finding double bond locations
(Egon Willighagen)
2. Re: [Bioclipse-devel] Your feedback please: finding double
bond locations (Christoph Steinbeck)
3. Re: [Bioclipse-devel] Your feedback please: finding double
bond locations (Egon Willighagen)
4. Re: [Bioclipse-devel] Your feedback please: finding double
bond locations (Nina Jeliazkova)
----------------------------------------------------------------------
Message: 1
Date: Mon, 14 May 2012 10:15:02 +0200
From: Egon Willighagen <[email protected]>
Subject: [Cdk-user] Your feedback please: finding double bond
locations
To: [email protected], [email protected],
[email protected]
Message-ID:
<campqvy_e1pdea_jtpyxpr5tqb8ly6386mtee_g8enmj4p3v...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear CDK and Bioclipse users,
with this email I would like to ask 2 minutes of your time (no, I'm
not going to offer 1M euro via Mr. Williams :). One of the standing
issues in the CDK was the lack of a general-purpose implementation of
an algorithm to find the location of double bonds in delocalized
systems. Typical input where such localization information is missing
is SMILES and MDL molfiles that use the query bond order type 4 for
delocalized bond systems.
The CDK had two main algorithms up to CDK 1.4.9: the SaturationChecker
and the DeduceBondSystemTool. But both had know situations where they
did not work well, and independently from each other two teams set up
to work on improving the situation.
Kevin Lawson started from the direction of the DeduceBondSystemTool,
first focusing on speeding up the algorithm, later on other rewrites.
Klas J?nsson and me from the direction of the SaturationChecker,
improving it by having it use atom type knowledge. Patches for both
approaches are reaching a finalization phase, and while we already
tested our own tricky chemical structures, we seek your input. Please
follow these steps:
1. open the webpage Nina Jeliazkova has set up:
http://ambit.uni-plovdiv.bg:8080/dbst/depict/cdk
2. enter your favorite SMILES with lower case organic subset elements,
e.g. c1ccccc1.
3. check the double bond locations of these three algorithms:
- left is the old faithful DeduceBondSystemTool
- middle is Klas' AtomTypeAwareSaturationChecker
- right is Kevin's FixBondOrdersTool
4. if Klas' and Kevin's do not find the right location of the double
bonds, please reply that SMILES to this email (or in your blog)
5. optionally, report how many SMILES it did work properly for
Your input on this is very much appreciated!
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
------------------------------
Message: 2
Date: Mon, 14 May 2012 10:58:30 +0200
From: Christoph Steinbeck <[email protected]>
Subject: Re: [Cdk-user] [Bioclipse-devel] Your feedback please:
finding double bond locations
To: Egon Willighagen <[email protected]>
Cc: [email protected], [email protected],
[email protected]
Message-ID: <[email protected]>
Content-Type: text/plain; charset=iso-8859-1
Hi all,
Klas seems to have problems with Indoles (and derivatives) :-)
c1ccc(C[C@@H](C(N[C@H](Cc2c3ccccc3[nH]c2)C(N[C@@H](CCCN)C(N[C@@H](Cc2ccc(cc2)O)C(N[C@H](C(N[C@@H]
Cl.Cl.Oc1ccc2CC3[C@](Cc4c(-c5ccccc5)c(C)[nH0](Cc5ccccc5)c4[C@@H]([C@](CCN3CC3CC3)(c2c1O1)2)1)2(O)
Those are from my collection of CDK SDG layout nightmares :-)
Kind regards,
Chris
--
Dr. Christoph Steinbeck
Head of Cheminformatics and Metabolism
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640
What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..
On 14 May 2012, at 10:15, Egon Willighagen wrote:
> Dear CDK and Bioclipse users,
>
> with this email I would like to ask 2 minutes of your time (no, I'm
> not going to offer 1M euro via Mr. Williams :). One of the standing
> issues in the CDK was the lack of a general-purpose implementation of
> an algorithm to find the location of double bonds in delocalized
> systems. Typical input where such localization information is missing
> is SMILES and MDL molfiles that use the query bond order type 4 for
> delocalized bond systems.
>
> The CDK had two main algorithms up to CDK 1.4.9: the SaturationChecker
> and the DeduceBondSystemTool. But both had know situations where they
> did not work well, and independently from each other two teams set up
> to work on improving the situation.
>
> Kevin Lawson started from the direction of the DeduceBondSystemTool,
> first focusing on speeding up the algorithm, later on other rewrites.
> Klas J?nsson and me from the direction of the SaturationChecker,
> improving it by having it use atom type knowledge. Patches for both
> approaches are reaching a finalization phase, and while we already
> tested our own tricky chemical structures, we seek your input. Please
> follow these steps:
>
> 1. open the webpage Nina Jeliazkova has set up:
> http://ambit.uni-plovdiv.bg:8080/dbst/depict/cdk
> 2. enter your favorite SMILES with lower case organic subset elements,
> e.g. c1ccccc1.
> 3. check the double bond locations of these three algorithms:
> - left is the old faithful DeduceBondSystemTool
> - middle is Klas' AtomTypeAwareSaturationChecker
> - right is Kevin's FixBondOrdersTool
> 4. if Klas' and Kevin's do not find the right location of the double
> bonds, please reply that SMILES to this email (or in your blog)
> 5. optionally, report how many SMILES it did work properly for
>
> Your input on this is very much appreciated!
>
> Egon
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
>
------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond.
Discussions
> will include endpoint security, mobile security and the latest in
malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Bioclipse-devel mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/bioclipse-devel
------------------------------
Message: 3
Date: Mon, 14 May 2012 12:18:29 +0200
From: Egon Willighagen <[email protected]>
Subject: Re: [Cdk-user] [Bioclipse-devel] Your feedback please:
finding double bond locations
To: Christoph Steinbeck <[email protected]>
Cc: [email protected], [email protected],
[email protected]
Message-ID:
<CAMPqvY-onqUD0WL_nk9JQ6rYuL81gVj=vsxjqc9lpijtjcr...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Mon, May 14, 2012 at 10:58 AM, Christoph Steinbeck
<[email protected]> wrote:
>
c1ccc(C[C@@H](C(N[C@H](Cc2c3ccccc3[nH]c2)C(N[C@@H](CCCN)C(N[C@@H](Cc2ccc(cc2)O)C(N[C@H](C(N[C@@H]
Mmm... if I try the indole bit, it seems to work fine:
Cc2c3ccccc3[nH]c2
I also note that Daylight fails on the long SMILES too....
>
Cl.Cl.Oc1ccc2CC3[C@](Cc4c(-c5ccccc5)c(C)[nH0](Cc5ccccc5)c4[C@@H]([C@](CCN3CC3CC3)(c2c1O1)2)1)2(O)
Thanx for checking!
We'll have to look at these...
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
------------------------------
Message: 4
Date: Mon, 14 May 2012 13:25:52 +0300
From: Nina Jeliazkova <[email protected]>
Subject: Re: [Cdk-user] [Bioclipse-devel] Your feedback please:
finding double bond locations
To: Egon Willighagen <[email protected]>
Cc: [email protected], [email protected],
[email protected]
Message-ID:
<CAE5qDd1iorJyqd-cprSvFnndCPj-PGtX98xW0YofY=wpnfy...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
On 14 May 2012 13:18, Egon Willighagen <[email protected]> wrote:
> On Mon, May 14, 2012 at 10:58 AM, Christoph Steinbeck
> <[email protected]> wrote:
> > c1ccc(C[C@@H](C(N[C@H](Cc2c3ccccc3[nH]c2)C(N[C@@H](CCCN)C(N[C@
> @H](Cc2ccc(cc2)O)C(N[C@H](C(N[C@@H]
>
> Mmm... if I try the indole bit, it seems to work fine:
>
> Cc2c3ccccc3[nH]c2
>
>
Try CCc2c3ccccc3[nH]c2
http://ambit.uni-plovdiv.bg:8080/dbst/depict/cdk?search=CCc2c3ccccc3%5BnH%5Dc2
Regards,
Nina
> I also note that Daylight fails on the long SMILES too....
>
> > Cl.Cl.Oc1ccc2CC3[C@](Cc4c(-c5ccccc5)c(C)[nH0](Cc5ccccc5)c4[C@@H]([C@
> ](CCN3CC3CC3)(c2c1O1)2)1)2(O)
>
> Thanx for checking!
>
> We'll have to look at these...
>
> Egon
>
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
>
>
------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond.
Discussions
> will include endpoint security, mobile security and the latest in
malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Cdk-user mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
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