[Open Babel] Silicos announces the release of ProfiLIB, a free compound library characterization tool
Silicos NV is pleased to announce the release of its open source online application tool called ProfiLIB, built on top of the Open Babel 2.3.0 C++ library and incorporating many of Silicos' open source programs. ProfiLIB is an online application tool that can be accessed from the Silicos website without any charges [http://www.silicos.com]. An example report is also available from this website. The profiLIB tool generates in an automated fashion a full report of the molecular characteristics of a user-provided compound library. The first part of the analysis is made in terms of molecular descriptors and physico-chemical properties. These properties are compared to Silicos' in-house vendor compound library Simosa™ to position the input set in relation to an average sample of these vendor compounds. Secondly, the library is mapped onto the vendor chemical space using Silicos' open source Spectrophores™. This mapping is overlaid with a set of diverse compound classes linked to specific drug targets. In the third and final part of the analysis, the library is characterized in terms of the molecular scaffolds represented by the set. Two distinct scaffold sets are statistically compared with the scaffolds from the vendor compounds from Simosa™. Silicos NV is a Belgian service-based company providing services and tools in the fields of chemoinformatics, chemogenomics and database characterisation. Several other chemoinformatics tools have been brought into the open source domain by Silicos, including SIEVE, PHARAO, PIRAMID, and OBSPECTROPHORE, the latter being part of Open Babel 2.3. For more information about ProfiLIB, or any other tools or services, please contact Silicos at i...@silicos.com. Kind regards, Hans De Winter Silicos NV -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Asking about SMARTS
Dear, My name is NGUYEN Thanh Binh. I am working about the SMARTS parsing. I have used the library OPENBABEL to do it. But i have a problem that needs your help. My following problem is : When i have constructed SMARTS Formulas in order to parse and to count the fonctional groups for the alpha alkene by using PYBEL, i can not count the number of groups CH2= of the Ethylene. The rests are good except for Ethylene. I have tried to correct the SMARTS but unsuccessfully yet. My SMARTS formula for CH2= is : [CX3H2]=[#6] I write to you for demande some advices about this problem. Many thanks in advance for your help, Best regards *NGUYEN Thanh Binh* P/S: please answer to me by this email adress: thanhbin...@gmail.com -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Asking about SMARTS
Did you try the SmartsViewer? http://smartsview.zbh.uni-hamburg.de/ Can you give an example molecule (SMILES) where you do not get the expected result? - Noel On 23 February 2011 10:16, NGUYEN Thanh Binh wrote: > Dear, > > My name is NGUYEN Thanh Binh. I am working about the SMARTS parsing. > I have used the library OPENBABEL to do it. > But i have a problem that needs your help. My following problem is : > > When i have constructed SMARTS Formulas in order to parse and to count the > fonctional groups for the alpha alkene by using PYBEL, i can not count the > number of groups CH2= of the Ethylene. The rests are good except for > Ethylene. I have tried to correct the SMARTS but unsuccessfully yet. > > My SMARTS formula for CH2= is : [CX3H2]=[#6] > > I write to you for demande some advices about this problem. > > Many thanks in advance for your help, > > Best regards > > NGUYEN Thanh Binh > > P/S: please answer to me by this email adress: thanhbin...@gmail.com > > > -- > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Asking about SMARTS
Hi again, Could you please send a small list of SMILES and the expected result along with your code so that we can see what's happening. Please also cc the list. Kind regards, Fredrik 24 feb 2011 kl. 10.45 skrev NGUYEN Thanh Binh: > Thank you very much Mr. Fredrik. It is exactly my problem. How can i solve > this problem ? > > Best regards, > > Thanh Binh > > > -- Forwarded message -- > From: NGUYEN Thanh Binh > Date: 2011/2/24 > Subject: Re: [Open Babel] Asking about SMARTS > To: Noel O'Boyle > > > Dear, > > I have not tried the SMARTSWiewer yet. Thank you very much for this useful > link. > > An example SMILES is C=C and C=CC. I want to parse and to regconize two > groups such as -CH= and =CH2. > > Many thanks in advance for your advices. > > Thanh Binh. > > > > > 2011/2/24 Noel O'Boyle > > Did you try the SmartsViewer? http://smartsview.zbh.uni-hamburg.de/ > > Can you give an example molecule (SMILES) where you do not get the > expected result? > > - Noel > > On 23 February 2011 10:16, NGUYEN Thanh Binh wrote: > > Dear, > > > > My name is NGUYEN Thanh Binh. I am working about the SMARTS parsing. > > I have used the library OPENBABEL to do it. > > But i have a problem that needs your help. My following problem is : > > > > When i have constructed SMARTS Formulas in order to parse and to count the > > fonctional groups for the alpha alkene by using PYBEL, i can not count the > > number of groups CH2= of the Ethylene. The rests are good except for > > Ethylene. I have tried to correct the SMARTS but unsuccessfully yet. > > > > My SMARTS formula for CH2= is : [CX3H2]=[#6] > > > > I write to you for demande some advices about this problem. > > > > Many thanks in advance for your help, > > > > Best regards > > > > NGUYEN Thanh Binh > > > > P/S: please answer to me by this email adress: thanhbin...@gmail.com > > > > > > -- > > Free Software Download: Index, Search & Analyze Logs and other IT data in > > Real-Time with Splunk. Collect, index and harness all the fast moving IT > > data > > generated by your applications, servers and devices whether physical, > > virtual > > or in the cloud. Deliver compliance at lower cost and gain new business > > insights. http://p.sf.net/sfu/splunk-dev2dev > > ___ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > > > -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Asking about SMARTS
What was your expected result for Ethylene? And how did you do the search. I'm guessing that you want Ethylene to report two CH2= groups, but since your SMARTS matches both atoms in Ethylene, you will only get one result from findall(), namely [(1, 2)]. The other hit would be identical and is therefor not reported I believe. /Fredrik 24 feb 2011 kl. 10.33 skrev Noel O'Boyle: > Did you try the SmartsViewer? http://smartsview.zbh.uni-hamburg.de/ > > Can you give an example molecule (SMILES) where you do not get the > expected result? > > - Noel > > On 23 February 2011 10:16, NGUYEN Thanh Binh wrote: >> Dear, >> >> My name is NGUYEN Thanh Binh. I am working about the SMARTS parsing. >> I have used the library OPENBABEL to do it. >> But i have a problem that needs your help. My following problem is : >> >> When i have constructed SMARTS Formulas in order to parse and to count the >> fonctional groups for the alpha alkene by using PYBEL, i can not count the >> number of groups CH2= of the Ethylene. The rests are good except for >> Ethylene. I have tried to correct the SMARTS but unsuccessfully yet. >> >> My SMARTS formula for CH2= is : [CX3H2]=[#6] >> >> I write to you for demande some advices about this problem. >> >> Many thanks in advance for your help, >> >> Best regards >> >> NGUYEN Thanh Binh >> >> P/S: please answer to me by this email adress: thanhbin...@gmail.com >> >> >> -- >> Free Software Download: Index, Search & Analyze Logs and other IT data in >> Real-Time with Splunk. Collect, index and harness all the fast moving IT >> data >> generated by your applications, servers and devices whether physical, >> virtual >> or in the cloud. Deliver compliance at lower cost and gain new business >> insights. http://p.sf.net/sfu/splunk-dev2dev >> ___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> >> > > -- > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT data > generated by your applications, servers and devices whether physical, virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Asking about SMARTS
Hi again,
On looking at the Pybel code for findall I thought that what you probably want
is to use the openbabel backbone and call GetMapList instead of GetUMapList as
findall() does. However, that didn't work either for me (the result was still
only 1 set of atoms). I also tried MatchesSMARTS as in:
[x.OBAtom.MatchesSMARTS("C=C") for x in mol.atoms] (mol being C=C) but that
gave [True, False] and not [True, True] as I would have expected. So,
unfortunately, I don't have any idea how to solve this at the moment...
Kind regards,
Fredrik
24 feb 2011 kl. 10.52 skrev Fredrik Wallner:
> Hi again,
>
> Could you please send a small list of SMILES and the expected result along
> with your code so that we can see what's happening. Please also cc the list.
>
> Kind regards,
> Fredrik
>
> 24 feb 2011 kl. 10.45 skrev NGUYEN Thanh Binh:
>
>> Thank you very much Mr. Fredrik. It is exactly my problem. How can i solve
>> this problem ?
>>
>> Best regards,
>>
>> Thanh Binh
>>
>>
>> -- Forwarded message --
>> From: NGUYEN Thanh Binh
>> Date: 2011/2/24
>> Subject: Re: [Open Babel] Asking about SMARTS
>> To: Noel O'Boyle
>>
>>
>> Dear,
>>
>> I have not tried the SMARTSWiewer yet. Thank you very much for this useful
>> link.
>>
>> An example SMILES is C=C and C=CC. I want to parse and to regconize two
>> groups such as -CH= and =CH2.
>>
>> Many thanks in advance for your advices.
>>
>> Thanh Binh.
>>
>>
>>
>>
>> 2011/2/24 Noel O'Boyle
>>
>> Did you try the SmartsViewer? http://smartsview.zbh.uni-hamburg.de/
>>
>> Can you give an example molecule (SMILES) where you do not get the
>> expected result?
>>
>> - Noel
>>
>> On 23 February 2011 10:16, NGUYEN Thanh Binh wrote:
>> > Dear,
>> >
>> > My name is NGUYEN Thanh Binh. I am working about the SMARTS parsing.
>> > I have used the library OPENBABEL to do it.
>> > But i have a problem that needs your help. My following problem is :
>> >
>> > When i have constructed SMARTS Formulas in order to parse and to count the
>> > fonctional groups for the alpha alkene by using PYBEL, i can not count the
>> > number of groups CH2= of the Ethylene. The rests are good except for
>> > Ethylene. I have tried to correct the SMARTS but unsuccessfully yet.
>> >
>> > My SMARTS formula for CH2= is : [CX3H2]=[#6]
>> >
>> > I write to you for demande some advices about this problem.
>> >
>> > Many thanks in advance for your help,
>> >
>> > Best regards
>> >
>> > NGUYEN Thanh Binh
>> >
>> > P/S: please answer to me by this email adress: thanhbin...@gmail.com
>> >
>> >
>> > --
>> > Free Software Download: Index, Search & Analyze Logs and other IT data in
>> > Real-Time with Splunk. Collect, index and harness all the fast moving IT
>> > data
>> > generated by your applications, servers and devices whether physical,
>> > virtual
>> > or in the cloud. Deliver compliance at lower cost and gain new business
>> > insights. http://p.sf.net/sfu/splunk-dev2dev
>> > ___
>> > OpenBabel-discuss mailing list
>> > OpenBabel-discuss@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >
>> >
>>
>>
>
> --
> Free Software Download: Index, Search & Analyze Logs and other IT data in
> Real-Time with Splunk. Collect, index and harness all the fast moving IT data
> generated by your applications, servers and devices whether physical, virtual
> or in the cloud. Deliver compliance at lower cost and gain new business
> insights. http://p.sf.net/sfu/splunk-dev2dev
> ___
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> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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Re: [Open Babel] Asking about SMARTS
Hi again,
I am preparing a file for you , but now it is not important. Indeed, i have
used Findall() but unsuccessfully yet. Anyway, thank you very much.
Best regards,
T-B
2011/2/24 Fredrik Wallner
> Hi again,
>
> On looking at the Pybel code for findall I thought that what you probably
> want is to use the openbabel backbone and call GetMapList instead of
> GetUMapList as findall() does. However, that didn't work either for me (the
> result was still only 1 set of atoms). I also tried MatchesSMARTS as
> in: [x.OBAtom.MatchesSMARTS("C=C") for x in mol.atoms] (mol being C=C) but
> that gave [True, False] and not [True, True] as I would have expected. So,
> unfortunately, I don't have any idea how to solve this at the moment...
>
> Kind regards,
> Fredrik
> 24 feb 2011 kl. 10.52 skrev Fredrik Wallner:
>
> Hi again,
>
> Could you please send a small list of SMILES and the expected result along
> with your code so that we can see what's happening. Please also cc the list.
>
> Kind regards,
> Fredrik
>
> 24 feb 2011 kl. 10.45 skrev NGUYEN Thanh Binh:
>
> Thank you very much Mr. Fredrik. It is exactly my problem. How can i solve
> this problem ?
>
> Best regards,
>
> Thanh Binh
>
>
> -- Forwarded message --
> From: NGUYEN Thanh Binh
> Date: 2011/2/24
> Subject: Re: [Open Babel] Asking about SMARTS
> To: Noel O'Boyle
>
>
> Dear,
>
> I have not tried the SMARTSWiewer yet. Thank you very much for this useful
> link.
>
> An example SMILES is C=C and C=CC. I want to parse and to regconize two
> groups such as -CH= and =CH2.
>
> Many thanks in advance for your advices.
>
> Thanh Binh.
>
>
>
>
> 2011/2/24 Noel O'Boyle
>
> Did you try the SmartsViewer? http://smartsview.zbh.uni-hamburg.de/
>>
>> Can you give an example molecule (SMILES) where you do not get the
>> expected result?
>>
>> - Noel
>>
>> On 23 February 2011 10:16, NGUYEN Thanh Binh
>> wrote:
>> > Dear,
>> >
>> > My name is NGUYEN Thanh Binh. I am working about the SMARTS parsing.
>> > I have used the library OPENBABEL to do it.
>> > But i have a problem that needs your help. My following problem is :
>> >
>> > When i have constructed SMARTS Formulas in order to parse and to count
>> the
>> > fonctional groups for the alpha alkene by using PYBEL, i can not count
>> the
>> > number of groups CH2= of the Ethylene. The rests are good except for
>> > Ethylene. I have tried to correct the SMARTS but unsuccessfully yet.
>> >
>> > My SMARTS formula for CH2= is : [CX3H2]=[#6]
>> >
>> > I write to you for demande some advices about this problem.
>> >
>> > Many thanks in advance for your help,
>> >
>> > Best regards
>> >
>> > NGUYEN Thanh Binh
>> >
>> > P/S: please answer to me by this email adress: thanhbin...@gmail.com
>> >
>> >
>> >
>> --
>> > Free Software Download: Index, Search & Analyze Logs and other IT data
>> in
>> > Real-Time with Splunk. Collect, index and harness all the fast moving IT
>> > data
>> > generated by your applications, servers and devices whether physical,
>> > virtual
>> > or in the cloud. Deliver compliance at lower cost and gain new business
>> > insights. http://p.sf.net/sfu/splunk-dev2dev
>> > ___
>> > OpenBabel-discuss mailing list
>> > OpenBabel-discuss@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >
>> >
>>
>
>
>
>
> --
> Free Software Download: Index, Search & Analyze Logs and other IT data in
> Real-Time with Splunk. Collect, index and harness all the fast moving IT
> data
> generated by your applications, servers and devices whether physical,
> virtual
> or in the cloud. Deliver compliance at lower cost and gain new business
> insights.
> http://p.sf.net/sfu/splunk-dev2dev___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
>
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